Intelligent Design

Double debunking: Glenn Williamson on human-chimp DNA similarity and genes unique to human beings

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Computer programmer Glenn Williamson now claims that ICR geneticist Jeff Tomkins made an elementary error when using the nucmer program to show that human and chimp DNA are only 88% similar. Williamson also asserts that 60 de novo protein coding genes said to be unique to human beings have very similar counterparts in apes, contrary to claims made last year by Dr. Cornelius Hunter, who is an adjunct professor of biophysics at Biola University.

What Dr. Tomkins allegedly got wrong

As readers of my recent post, Human and chimp DNA: They really are about 98% similar, will recall, Glenn Williamson demolished Dr. Tomkins’s original claim, made back in 2013, that human and chimp DNA are only about 70% similar. Williamson’s detailed takedown of Dr. Tomkins’s 70% similarity figure can be accessed here. In short: the version of the BLAST computer algorithm used by Tomkins contained a bug which invalidated his results. Dr. Tomkins responded by performing a new study which came up with a similarity figure of 88% – still far below the 98% similarity figure commonly claimed in textbooks for human and chimp DNA. Tomkins arrived at that figure by using a version of the BLAST algorithm which did not contain the bug, and in my last post, I pointed out the errors identified by Glenn Williamson in Dr. Tomkins’ new paper, relating to BLAST.

But to give credit where credit is due, Dr. Tomkins didn’t rely on just one computer program to come up with his 88% figure; he relied on three. In addition to BLAST, Dr. Tomkins made use of two other programs: nucmer and LASTZ. Creation scientist Jay Wile described these programs in a recent post discussing Dr. Tomkins’ work:

The nucmer program’s results agreed with the unbugged BLAST results: on average the human and chimpanzee genomes are 88% similar. The LASTZ program produced a lower average similarity (73%), which indicates that perhaps LASTZ has a bug or is not optimized for such comparisons, since its results are very close to the results Dr. Tomkins got with the bugged version of BLAST.

In today’s post, I’ll discuss the flaws identified by Glenn Williamson in Dr. Tomkins’s comparisons that were made using the nucmer program.

Basic methodological errors?

As we saw in yesterday’s post on Uncommon Descent, Glenn Williamson claims that Dr. Tomkins’s new study makes some fundamental errors in the way it performs the BLASTN analysis. Now, however, Williamson has gone further, and identified some very basic errors in the way Dr. Tomkins obtained his results from the nucmer program. What Williamson has shown is that even when human chromosome 20 is compared with itself, the calculation method used by Dr. Tomkins when running the “nucmer” program would imply (absurdly) that it is less than 90% similar to itself!

I have been in email correspondence with Glenn Williamson over the past 24 hours, and he kindly allowed me to publish his responses, as well as some emails he sent to Dr. Tomkins. Here’s an excerpt from his first email to me.

Hi Vincent,

I’ve only just seen your post on UD, and I thought I’d fill you in on where we are at with one of the other comparisons (“nucmer”) Jeff did in his recent paper. Basically what he is doing in this comparison is taking every single alignment for each query sequence (as opposed to taking just the best alignment) and taking the average of all those. Obviously all the repeat motifs will find many matches across each chromosome, but only one of those will be (putatively) homologous. If you can follow the email thread from the bottom, hopefully you can understand the issue.

I’m currently running a nucmer job with human chromosome 20 being compared to itself, just to show the absurdity of his calculation method. I should have the results by tomorrow.

I subsequently emailed him, and asked if he could tell me about the results:

I would greatly appreciate it if you would let me know about your results, after you finish running your nucmer job. I was also wondering if you would allow me to quote excepts from your correspondence in a forthcoming post on UD.

Glenn Williamson replied:

Hey,

Yup, no problems quoting any of the emails…

The first nucmer job I ran took 37 hours (human 20 to chimp 20), and this current “control” job (human 20 to human 20) has taken 37 hours as of right now, so it should finish soon. It will take a couple of hours to put all the results together, so should have something by tonight.

It wasn’t long before I heard from Glenn Williamson again:

It’s done!

And human chromosome 20 is only 88.86% identical to human chromosome 20! 🙂

Unix commands, if you care:

awk ‘NR>5 { print $7″\t”$8″\t”$10 }’ control.coords > control.tab
awk ‘{ sum += ($1 + $2) / 2; prod += ($1 + $2) / 2 * $3 } END { print prod; print sum; print prod / sum }’ control.tab

Output:

1.71549e+09
1.52439e+11
88.8601

So basically the alignments covered 1.715Gb for a chromosome that is only 64Mb long (27x coverage). There were 4.8 million individual alignments …

So there we have it. If Dr. Tomkins is right, then not only is chimpanzee DNA only 88% similar to our own, but human DNA is only 89% similar to itself!

Do human beings really have 60 de novo protein-coding genes with no counterparts in apes?

But there was more – much more. In my original email to Glenn Williamson, I had expressed curiosity over a comment he made on a January 2014 post titled, Chinese Researchers Demolish Evolutionary Pseudo-Science, over at Dr. Cornelius Hunter’s Website, Darwin’s God, in which Williamson expressed skepticism over Dr. Hunter’s claim that no less than 60 protein-coding orphan genes had been identified in human DNA which had no counterpart in chimpanzees. To support his claim, Dr. Hunter cited a 2011 PLOS study by Dong-Dong Wu, David M. Irwin and Ya-Ping Zhang, titled De Novo Origin of Human Protein-Coding Genes. Here is the authors’ summary of their paper (emphases mine – VJT):

The origin of genes can involve mechanisms such as gene duplication, exon shuffling, retroposition, mobile elements, lateral gene transfer, gene fusion/fission, and de novo origination. However, de novo origin, which means genes originate from a non-coding DNA region, is considered to be a very rare occurrence. Here we identify 60 new protein-coding genes that originated de novo on the human lineage since divergence from the chimpanzee, supported by both transcriptional and proteomic evidence. It is inconsistent with the traditional view that the de novo origin of new genes is rare. RNA–seq data indicate that these de novo originated genes have their highest expression in the cerebral cortex and testes, suggesting these genes may contribute to phenotypic traits that are unique to humans, such as development of cognitive ability. Therefore, the importance of de novo origination needs greater appreciation.

Commenting on the paper, Dr. Hunter remarked (bold emphases mine – VJT):

A 2011 paper out of China and Canada, for example, found 60 protein-coding genes in humans that are not in the chimp. And that was an extremely conservative estimate. They actually found evidence for far more such genes, but used conservative filters to arrive at 60 unique genes. Not surprisingly, the research also found evidence of function, for these genes, that may be unique to humans.

If the proteins encoded by these genes are anything like most proteins, then this finding would be another major problem for evolutionary theory. Aside from rebuking the evolutionist’s view that the human-chimp genome differences must be minor, 6 million years simply would not be enough time to evolve these genes.

In fact, 6 billion years would not be enough time. The evolution of a single new protein, even by evolutionists’ incredibly optimistic assumptions, is astronomically unlikely, even given the entire age of the universe to work on the problem.

Note the claim that Dr. Hunter is making here: “60 protein-coding genes in humans that are not in the chimp.” But as we’ll see, these genes do have virtually identical counterparts in chimps, even if they are noncoding.

So, how many ORFan genes do humans really have?

In his comment, Glenn Williamson responded to Dr. Hunter’s claim that humans have 60 protein-coding genes that are “not in the chimp” by pointing out that the first of these 60-odd genes actually has a counterpart in chimpanzee DNA which is 98% identical to the human gene (emphasis mine – VJT):

“So how many ORFan genes are actually in humans???”

Depends what you call an ORFan gene. I looked at the paper that Cornelius cites as having 60 de novo protein coding genes.

Now, granted that I only looked at the very first one (“ZNF843”), it was quite easy to find the corresponding DNA on the chimpanzee chromosome, with approximately 98.5% identity.

So whether it is protein-coding in humans and non-coding in everything else doesn’t really concern me. What concerns me is whether it has an evolutionary history: clearly this one does.

Like I said, I’ve only done one. I’d happily take bets on the majority of these de novo genes having an evolutionary history (chimpanzee > 95% and/or gorilla > 90%).

Any takers?

I had only come across this exchange in the last couple of days, while surfing the Net, and my curiosity was piqued. So I wrote back to Williamson:

By the way, I was intrigued with your work on orphan genes, and I thought I’d have a look at the 60 genes mentioned by Cornelius Hunter in a post he wrote last year. However, I don’t have any experience in this area. Can you tell me how to go about running these comparisons?

Orphan genes – did Dr. Hunter get his facts wrong?

Glenn Williamson’s reply was very helpful – and it pulled no punches. He accused Dr. Hunter of getting his facts wrong about ORFan genes (emphasis mine – VJT):

As for Orphan genes, I assume you mean this comment? http://darwins-god.blogspot.com.au/2014/01/chinese-researchers-demolish.html?showComment=1421299517820#c1105680265537141676

There are a couple of points to be made here. First is that Cornelius fundamentally misunderstands what an orphan gene is and what an ORF(an) is – they are not equivalent terms. A true orphan gene should be called a “taxonomically restricted gene” (TRG), and no trace of its evolutionary history can be found outside a particular taxonomic group. These would be examples of de novo evolution. With respect to humans and chimpanzees, I don’t know of any TRGs that exist in either genome (with respect to the other), and if there were, I would then check the other great apes to see if it was likely that this gene was deleted in one of the genomes (rather than evolved out of nothing in 6mn years!).

Good point. Williamson continued:

An ORFan gene usually refers to a putative protein coding gene. “Putative” because these are generally the result of a computer program trying to find long open reading frames, and if it finds something over a certain length (300bp? 400bp?) then, since a long open reading frame is quite unlikely, the program thinks that this open reading frame is evolutionarily conserved, and it might be conserved because it codes for an important protein. Have a read of Eric Lander’s paper – http://www.ncbi.nlm.nih.gov/pubmed/18040051 – where he says we should be removing these ORFs from the gene database unless and until we can actually find their corresponding proteins.

Glad we got that point cleared up. So, what about those 60 protein-coding genes in humans which Dr. Hunter claimed are not found in the chimp? Here’s what Williamson wrote back to me:

So, these 60-odd genes that Cornelius brings up, he is claiming that they must have evolved de novo:

“In fact, 6 billion years would not be enough time. The evolution of a single new protein, even by evolutionists’ incredibly optimistic assumptions, is astronomically unlikely, even given the entire age of the universe to work on the problem.”

And that’s why I checked the first one on the list, just to demonstrate that it was in the chimpanzee genome (at 98.5% identity). So if this gene codes for a protein in humans, maybe we just haven’t found the protein in chimps. Maybe it codes for a protein in humans, and there was a single mutation that caused it not to be translated in chimps. Maybe it doesn’t actually code for a protein in humans at all? (Although I think we can check that). In any case, it’s not an example of de novo evolution – it’s not an orphan gene in the sense of being taxonomically restricted.

As to how to do the work yourself .. let me send this one off first and I’ll start another email 🙂

For my part, I am somewhat skeptical about Williamson’s speculation that these genes got switched off in the lin leading to chimpanzees – especially in view of the discovery of three undoubted cases of de novo genes in human beings where the ancestral sequence in apes was noncoding. But given the striking 98% similarities between these genes and their non-coding counterparts in apes, I would also urge caution about Dr. Hunter’s claim that even billions of years would not have been long enough for these protein-coding genes to have evolved. If they were evolving from scratch, yes; but if they were evolving from 98% identical counterparts, I wouldn’t be so sure about that.

I learn how to do a BLAST comparison

In his next email, Glenn Williamson kindly informed me how to do a BLAST comparison, and how he obtained his results for ZNF843, which was the first of the 60 de novo protein coding genes cited by Dr. Hunter in his 2014 post. In his response to Dr. Hunter, Williamson had reported that “it was quite easy to find the corresponding DNA on the chimpanzee chromosome, with approximately 98.5% identity.” Here’s what he wrote to me:

Alright, I’ll run you through a simple BLAST search on the Ensembl website. Although, if you want to do some serious BLASTing, then you probably should install the software on your own machine, and download the genomes onto your hard drive.

Anyway, go to:

http://www.ensembl.org/index.html

and stick the name of the gene: ZNF843 into the search box. That should get you to here:

http://asia.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000176723;r=16:31432593-31443160

On the left hand side, there should be an “Export Data” tab. Click it. Deselect all the checkboxes (we just want the raw DNA) and hit “Next”. Hit the “Text” button, and then just Copy the whole output, starting with the “>blah blah blah”. Now, at the top left of the page is the “BLAST/BLAT” tool. Click it.

Paste the copied DNA into the box, make sure you search against the chimpanzee genome (i.e. uncheck the human genome) and then run the search – using the default parameters should be fine for now.

The results can be found here:

http://www.ensembl.org/Homo_sapiens/Tools/Blast/Ticket?tl=mQCTv8YnFRQKB0Kx

Unfortunately the results are given in chunks, and if you want to get an exact number, stick them in Excel and work it out. But if you just want to look at it on the website, click on the “Genomic Location” header to sort them in that order, scroll down to chromosome 16, and you’ll see that it covers the vast majority of the 10.5kb of query DNA, and the matches are around 98.5%-99.5%. Rough guess for the overall identity (including some small indels) is about 98.5%.

If you need help just email me back and I’ll see what I can do. I gotta run now tho 🙂

And here’s what Williamson got when he ran the BLAST comparison on his computer:

I ran it on my local machine:

#!/bin/sh

QRY=”ZNF843.fa”
SBJ=”${HOME}/Data/Ensembl/chimp/Pan_troglodytes.CHIMP2.1.4.dna.chromosome.16.fa”

blastn -query ${QRY} -subject ${SBJ} -max_hsps 1 -outfmt ’10 qseqid qstart qend sstart send nident pident qlen length’

Output:

16,1,10568,31611859,31601307,10375,97.62,10568,10628

So, only 97.62% identity for that one … 0.57% of the alignment is indels. Boooooooooooooo.

So, for the first of the alleged 60 “de novo” protein coding genes cited by Dr. Hunter (“ZNF843″), Glenn Williamson managed to locate some corresponding DNA on the chimpanzee chromosome, which was approximately 98% identical. Are these genes without an evolutionary history? I hardly think so!

More good news – the results for all the other genes are already in!

In his most recent email, Glenn Williamson shared further good tidings: comparisons for the other 59 genes have already been done!

Just looking into that 2011 paper a little further – they’ve already done all the work for us!

http://journals.plos.org/plosgenetics/article/asset?unique&id=info:doi/10.1371/journal.pgen.1002379.s009
http://journals.plos.org/plosgenetics/article/asset?unique&id=info:doi/10.1371/journal.pgen.1002379.s011

These are the 60 “de novo” genes, and their alignments with chimpanzee and orang-utan 🙂

I’ve had a look at the output, and even to my untutored eye, it’s obvious that any claims that these “de novo” genes are not found in the DNA of chimps and other apes are flat-out wrong. They have virtually identical counterparts on the chimpanzee and orang-utan genomes, even if these are non-protein coding.

Some cautionary remarks about the 2011 paper cited by Dr. Hunter

The 2011 paper by Wu et al. which was cited by Dr. Hunter was critiqued in another article in PLOS Genetics (7(11): e1002381. doi:10.1371/journal.pgen.1002381, published 10 November 2011), titled,
De Novo Origins of Human Genes by Daniele Guerzoni and Aoife McLysaght. The authors felt that the estimate of 60 de novo human-specific genes in the paper by Wu et al. was based on rather lax criteria. What’s more, they seemed confident that the genes could have evolved:

In this issue of PLoS Genetics, Wu et al. [15] report 60 putative de novo human-specific genes. This is a lot higher than a previous, admittedly conservative, estimate of 18 such genes [13], [16]. The genes identified share broad characteristics with other reported de novo genes [13]: they are short, and all but one consist of a single exon. In other words, the genes are simple, and their evolution de novo seems plausible. The potential evolution of complex features such as intron splicing and protein domains within de novo genes remains somewhat puzzling. However, features such as proto-splice sites may pre-date novel genes [9], [17], and the appearance of protein domains by convergent evolution may be more likely than previously thought [2].

The operational definition of a de novo gene used by Wu et al. [15] means that there may be an ORF (and thus potentially a protein-coding gene) in the chimpanzee genome that is up to 80% of the length of the human gene (for about a third of the genes the chimpanzee ORF is at least 50% of the length of the human gene). This is a more lenient criterion than employed by other studies, and this may partly explain the comparatively high number of de novo genes identified. Some of these cases may be human-specific extensions of pre-existing genes, rather than entirely de novo genes — an interesting, but distinct, phenomenon.

In a 2009 paper titled Recent de novo origin of human protein-coding genes (Genome Research 2009, 19: 1752-1759), David Knowles and Aoife McLysaght presented evidence for the de novo origin of at least three human protein-coding genes since the divergence with chimp, and estimated that there may be 18 such genes in the human genome, altogether. Here’s what they said about the three genes they identified:

Each of these genes has no protein-coding homologs in any other genome, but is supported by evidence from expression and, importantly, proteomics data. The absence of these genes in chimp and macaque cannot be explained by sequencing gaps or annotation error. High-quality sequence data indicate that these loci are noncoding DNA in other primates. Furthermore, chimp, gorilla, gibbon, and macaque share the same disabling sequence difference, supporting the inference that the ancestral sequence was noncoding over the alternative possibility of parallel gene inactivation in multiple primate lineages.

Note the wording: “Each of these genes has no protein-coding homologs in any other genome.” Nevertheless, the genes have non-coding counterparts in the DNA of apes: “High-quality sequence data indicate that these loci are noncoding DNA in other primates.”

Whether these genes could have evolved naturally from their ape counterparts is a question I’ll leave for the experts to sort out. One thing I do know, however: they are not “new” in the sense that layfolk would construe that term – that is, functioning genes which have no counterparts in the DNA of apes. Clearly, they do have very similar counterparts in apes, even if those counterparts are non-coding.

Conclusion

Well, I think that’s about enough new revelations for one day, so I shall stop there. It seems to me that any claims that humans have a large number of “de novo” genes with no counterparts in the DNA of chimpanzees and other apes should be treated with extreme caution. In fact, I wouldn’t bet on our having any de novo protein-coding genes having no counterparts in apes, after that takedown.

We already have very good arguments demonstrating the impossibility of proteins having evolved via an undirected process, thanks to the excellent work of Dr. Douglas Axe – see, for instance, his excellent article, The Case Against a Darwinian Origin of Protein Folds. It seems to me that arguments based on de novo genes alleged to exist in human beings, with no counterparts in apes, have much weaker evidential support, and that Intelligent Design proponents would be better off not using them.

But perhaps those who are feeling adventurous might like to take up Glenn Williamson on his 2014 wager:

I’d happily take bets on the majority of these de novo genes having an evolutionary history (chimpanzee > 95% and/or gorilla > 90%).

Any takers?

Well? Is anyone feeling lucky?

POSTSCRIPT: Readers may be interested to know that Dr. Ann Gauger has written a very balanced post titled, Orphan Genes—A Guide for the Perplexed. In her post, Dr. Gauger defines orphan genes as ” those open reading frames that lack identifiable sequence similarity to other protein-coding genes.” Note the word “protein-coding.” She raises the possibility that “they are uniquely designed for species- and clade-specific functions” but draws no firm conclusions.

625 Replies to “Double debunking: Glenn Williamson on human-chimp DNA similarity and genes unique to human beings

  1. 1
    ThickPython says:

    Hi, there are a couple of things that I need to add to this:

    1. In order to get the “less than 90% similar to itself!” result, I was using the same parameters that Tomkins used in his study:

    nucmer -maxmatch -c 100 -p blah human-20.fa chimp-20.fa

    The problem here is the maxmatch parameter which “Use[s] all anchor matches regardless of their uniqueness”. This means that if there is a part of the query sequence that is found multiple times on the target sequence, it will return all those multiple hits. And as everyone knows, there are many repeat motifs spread across all of our chromosomes. This maxmatch parameter means it will return hits for all of those matches, rather than just the best match.

    Tomkins then takes the average of all of these matches, and applying that same logic leads to the absurd result that the human chromosome is only 88.86% identical to itself.

  2. 2
    ThickPython says:

    2. I don’t think anyone will be taking me up on that bet anytime soon given that we’ve found the alignments in the original paper 😀 I should note that these appear to be alignments of the exons only. The 97.62% result I gave is for the full length of the gene – introns included (~10kbp).

  3. 3
    bornagain says:

    Dr. Torley, ORFans are not so easily dismissed as you seem to believe:

    ,,”Typical bacterial species. The smallest part of the pie are the genes that all bacteria share. 8% roughly. This second and largest slice (of the pie, 64%) are the genes that are specialized to some particular environment. They call them character genes. By far the biggest number of genes are the ones that are unique. This big green ball here (on the right of the illustration). These are genes found only in one species or its near relatives. Those are the ORFans (i.e. Genes with no ancestry). They said, on the basis of our analysis the genetic diversity of bacteria is of infinite size.”
    Paul Nelson – quoted from 103:48 minute mark of the following video
    Widespread ORFan Genes Challenge Common Descent – Paul Nelson – video
    https://youtu.be/9UTrZX47e00?t=3820

    You can see the pie chart that Dr. Nelson used in his talk here on page 108 (figure 2) of this following article:

    Estimating the size of the bacterial pan-genome
    Excerpt Figure 2 pg. 108: At the genomic level, a typical bacterial genome is composed of _8% of core genes, 64% of character genes and 28% of accessory genes,,,
    http://www.paulyu.org/wp-conte.....genome.pdf

    Estimating the size of the bacterial pan-genome – Pascal Lapierre and J. Peter Gogarten – 2008
    Excerpt: We have found greater than 139 000 rare (ORFan) gene families scattered throughout the bacterial genomes included in this study. The finding that the fitted exponential function approaches a plateau indicates an open pan-genome (i.e. the bacterial protein universe is of infinite size); a finding supported through extrapolation using a Kezdy-Swinbourne plot (Figure S3). This does not exclude the possibility that, with many more sampled genomes, the number of novel genes per additional genome might ultimately decline; however, our analyses and those presented in Ref. [11] do not provide any indication for such a decline and confirm earlier observations that many new protein families with few members remain to be discovered.
    http://www.paulyu.org/wp-conte.....genome.pdf

    Can new genes arise from junk DNA? – August 24, 2015
    Excerpt: The first evidence that a strict duplication model might not suffice came in the 1990s, when DNA sequencing technologies took hold. Researchers analyzing the yeast genome found that a third of the organism’s genes had no similarity to known genes in other organisms. At the time, many scientists assumed that these orphans belonged to families that just hadn’t been discovered yet. But that assumption hasn’t proven true. Over the last decade, scientists sequenced DNA from thousands of diverse organisms, yet many orphan genes still defy classification. Their origins remain a mystery.
    http://www.uncommondescent.com.....ent-577361

    Can new genes arise from junk DNA? – August 24, 2015
    Excerpt: Scientists also want to understand how de novo genes get incorporated into the complex network of reactions that drive the cell, a particularly puzzling problem. It’s as if a bicycle spontaneously grew a new part and rapidly incorporated it into its machinery, even though the bike was working fine without it. “The question is fascinating but completely unknown,” Begun said.
    BA77: Moreover, the essential genes were somehow incorporated into the ‘bicycle’ while the bicycle was being peddled, i.e. while the cell was busy being alive.
    “How does novel gene become functional? How does it get incorporated into actual cellular processes?” McLysaght said. “To me, that’s the most important question at the moment.”
    http://www.uncommondescent.com.....ent-577484

    Age doesn’t matter: New genes are as essential as ancient ones – December 2010
    Excerpt: “A new gene is as essential as any other gene; the importance of a gene is independent of its age,” said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. “New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked.”
    http://www.sciencedaily.com/re.....142523.htm

    New Genes Are Essential 6-13-2015 by Paul Giem – video
    https://www.youtube.com/watch?v=6qgGPV1AO1E

    Is the Origin of New Genes “Basically a Solved Problem”? – Cornelius Hunter – Sept. 11, 2014
    Excerpt: If you read the headlines, you would have the impression that the problem is well in hand. For instance, super-star science writer Carl Zimmer wrote in the New York Times earlier this year that “researchers have documented the step-by-step process by which a new gene can come into existence.”

    Case closed right?

    Well not quite. In fact, not even close. What Zimmer tells his readers is a “step-by-step process” is what scientists affectionately refer to as a cartoon. In fact, here it is:,,,
    ,,,This evolutionary narrative is certainly not “basically a solved problem.” In fact, what evolutionists have are high claims of the spontaneous evolution of incredibly complex structures, not because of the evidence, but in spite of the evidence. So what gives evolutionist’s their confidence? It is not that they understand how such genes could have evolved, but that the genes must have evolved because solo genes are observed over and over:
    “Several studies have by now also shown that de novo emerged transcripts and proteins can assume a function within the organism. All of this provided solid evidence that de novo gene birth was indeed possible.”,,,
    Does any of this mean that the de novo genes evolved from random mutations as the evolutionists claim? Of course not.,,,
    Only a few years ago they agreed that such evolution of new genes would be impossible. Now they have been forced to adopt it because the evidence unambiguously reveals solo genes, and evolutionists dogmatically insist that everything must have spontaneously evolved.,,
    http://darwins-god.blogspot.co.....olved.html

    Moreover, there is a disconnect between protein sequences and gene sequences:

    A survey of orphan enzyme activities – 2007
    Abstract: We demonstrate that for ~80% of sampled orphans, the absence of sequence data is bona fide. Our analyses further substantiate the notion that many of these (orfan) enzyme activities play biologically important roles.
    http://www.biomedcentral.com/1471-2105/8/244

  4. 4
    bornagain says:

    Does the ‘ThickPython’ handle refer to the fact that you have swallowed Dr. Torley so completely into believing you have the ORFan problem well in hand??

  5. 5
    Mung says:

    In short: the version of the BLAST computer algorithm used by Tomkins contained a bug which invalidated his results.

    Other than those of Tomkins, which other results were invalidated? Surely Tomkins was not singled out.

  6. 6
    ThickPython says:

    I’ve just run nucmer again – without maxmatch – against chimpanzee chromosome 20 just to show the difference in behaviour:

    1. Run time of about 10 minutes (as opposed to 37 hours!)
    2. 36,000 alignments, not 4.8 million
    3. Coverage of 81Mbp (as opposed to more than 1bn base pairs)
    4. Identity of 96.10%*

    Now, I put asterisks on that result because even without maxmatch there is still a decent amount of overlap (although nowhere near as much: 36,000 vs 4.8mn alignments!). So I ran these matches through a filter whereby a match is discarded if there exists another match which “wholly encloses” the previous match. So for example, in the results there is a match that spans ~37,000 base pairs, between the loci 93,165 and 129,957 and has a 98.28% identity. Immediately following that are about twenty other matches where the loci fall entirely within the larger match (for example, 98,763 to 99,517; 645bp with 88.67% identity) so these are discarded.

    After filtering these out, there are ~10,300 alignments, and the overall result comes out the be 97.54%**.

    Another asterisk??? WHAT? Well, what I’ve noticed in these filtered results is that the non-syntenic hits tend to be fairly short and low identity ~85%-90%. What I figured out is that these hits correspond rather well to sequencing gaps in the chimpanzee chromosome (which are usually repeat motifs). It would be quite the job to match these up, and I doubt that it would make a material difference to the end result – I dont think anyone would care if if the result was 97.80% (???) instead of 97.54%.

    In summary, there are quite a few different methods of calculating an overall number, and the details of these methods is up for debate – some methods are more defensible than others. What is not up for debate though is that the end result (regardless of which method) is around 97%, and possibly as high as 98%. This includes ALL of the genome, not just protein coding regions. Conservative methods will get you a slightly lower result; other methods, while certainly defensible, might get you above 98%. If you are just looking at the nucleotide divergence you should get a figure of around 98.8%. If you are looking at coding regions only, you should get over 99%.

  7. 7
    Mung says:

    Latest findings indicate Chimps are only 82.3% Chimpanzee!

  8. 8
    Box says:

    Okay, we are a 101% match with Chimps. Now what?

  9. 9
    ThickPython says:

    Does the ‘ThickPython’ handle refer to the fact that you have swallowed Dr. Torley so completely into believing you have the ORFan problem well in hand??

    If you are attempting to use orphan genes as evidence that chimpanzees and humans do not share a common ancestor, then yes, I think it’s pretty much under control. What percentage of genes are two organisms allowed to have as orphans to declare that they could still have shared a common ancestor? At what point (as a percentage of genes) would you say two organisms cannot be related? Not asking for hard numbers, just ballpark.

    @Mung:

    Other than those of Tomkins, which other results were invalidated? Surely Tomkins was not singled out.

    I’m not aware of any other creationists that have done this kind of stuff. I know that Tomkins paired up with Jerry Bergman to do a review of the secular literature, so I guess that’s invalidated. Tomkins cites two studies that he thinks supports his position – Buggs 2008 (and I use the word “study” loosely here), and Progetto Cosmo 2012. So those are invalidated as well. Progetto Cosmo because he was using a silly calculation method to obtain his 63%-66% result (“How frequently does a 30bp sequence have a 100% identity?”) and Buggs I guess because it just looks like something he did on the back of a napkin 🙂

    Sometimes I feel sorry for the guy because much of his work over the past few years is for nought, but then I start to question just how honest he has been in his research (and it doesn’t help that he has rubbed me the wrong way a couple of times!).

  10. 10
    bornagain says:

    ThickPython, my argument that chimps and humans do not share a common ancestor is based on the fact that you can mutate DNA until the cows come home and it does not matter because you are not going to create new body plans by mutating DNA alone.

    Body plans, contrary to neo-Darwinian presuppositions, simply are not reducible to DNA, period! That finding pretty much renders any Darwinian argument for common ancestry based on DNA alone moot and void:

    http://www.uncommondescent.com.....ent-584045
    http://www.uncommondescent.com.....ent-584055
    http://www.uncommondescent.com.....ent-584106

    Moreover, as to genetic similarity being supposed irrefutable evidence for common descent, that argument is not nearly as strong as you presuppose because some creatures are, DNA wise, far more similar to humans than Darwinists ever expected they would be.
    http://www.uncommondescent.com.....ent-584064

    Moreover, anatomy wise, we are more similar to pigs than we are to monkeys:

    Human hybrids: a closer look at the theory and evidence – July 25, 2013
    Excerpt: There was considerable fallout, both positive and negative, from our first story covering the radical pig-chimp hybrid theory put forth by Dr. Eugene McCarthy,,,By and large, those coming out against the theory had surprisingly little science to offer in their sometimes personal attacks against McCarthy.
    ,,,Under the alternative hypothesis (humans are not pig-chimp hybrids), the assumption is that humans and chimpanzees are equally distant from pigs. You would therefore expect chimp traits not seen in humans to be present in pigs at about the same rate as are human traits not found in chimps. However, when he searched the literature for traits that distinguish humans and chimps, and compiled a lengthy list of such traits, he found that it was always humans who were similar to pigs with respect to these traits. This finding is inconsistent with the possibility that humans are not pig-chimp hybrids, that is, it rejects that hypothesis.,,,
    http://phys.org/news/2013-07-h.....dence.html

    Of supplemental note:

    The severe bias of Darwinists in regards to interpreting the fossil record is gone over here
    http://www.uncommondescent.com.....ent-584303

  11. 11
    Mapou says:

    Glenn Williamson:

    So whether it is protein-coding in humans and non-coding in everything else doesn’t really concern me. What concerns me is whether it has an evolutionary history: clearly this one does.

    It’s obvious that some ID supporters have painted themselves in a corner most likely for religious reasons. But the question is, why is this result a plus for Darwinian evolution and not a plus for design evolution? Why could not the designers reuse whatever genes they already had in their giant gene database and modify some of them for different purposes? Indeed this is at the heart of modern intelligent software design. It’s called adding functionality through class inheritance and modification.

  12. 12
    bornagain says:

    Mapou, the evidence for ORFan genes did not come from ID proponents to begin with, but came from mainstream biologists. Moreover, the evidence for ORFan genes, from many different studies mind you, is found throughout life, bacteria to multicelluluar creatures, i.e. not just in the human genome. Thus it is far too early to take a computer programmer’s word that he has overthrown all those previous studies for ORFan genes throughout life, with a few afternoons of sequence comparisons on his computer between chimps and humans.

    In fact, I’m shocked that Dr. Torley was not more careful in his disavowal of ORFan genes before he posted his OP.
    This could come back and bite him big time when more information comes in from more knowledgeable commenters

  13. 13
    Mapou says:

    bornagain, I agree that ORFan genes also falsify Darwinian evolution regardless of the spin they try to put on it. This being said, I don’t understand why some in the ID camp are so adamant that the genomes or humans and chimps could not be so similar. I also don’t understand why Darwinists are so adamant that it supports their pseudoscience.

    I am an ID supporter and I am not in the least bothered by it. In fact, I fully embrace it. It is a perfect example of beautiful intelligent design in action. In design and engineering circles, it’s called “don’t reinvent the wheel” or “if it works, don’t fix it”.

  14. 14
    bornagain says:

    Mapou, I’m certainly not wedded to ORFan genes myself (seeing as DNA does not determine body plans anyway), but, as I said earlier, with all the different studies finding ORFan genes throughout life, not just in humans mind you, it is far too early to rely on evidence generated on a atheistic blog to throw the ORFan genes out in the street just yet.

    Something about this refutation definitely does not smell right.

    Now if it gets peer reviewed and passes muster, that will be a different story. And definitely noteworthy, and will indeed turn quite a few heads, since it is a far bigger anomaly, and problem, than either Torley or Python seem to realize at the present time.

    a few more notes:

    Genes from nowhere: Orphans with a surprising story – 16 January 2013 – Helen Pilcher
    Excerpt: When biologists began sequencing genomes they discovered up to a third of genes in each species seemed to have no parents or family of any kind. Nevertheless, some of these “orphan genes” are high achievers (are just as essential as ‘old’ genes),,,
    But where do they come from? With no obvious ancestry, it was as if these genes appeared out of nowhere, but that couldn’t be true. Everyone assumed that as we learned more, we would discover what had happened to their families. But we haven’t-quite the opposite, in fact.,,,
    The upshot is that the chances of random mutations turning a bit of junk DNA into a new gene seem infinitesmally small. As the French biologist Francois Jacob wrote 35 years ago, “the probability that a functional protein would appear de novo by random association of amino acids is practically zero”.,,,
    Orphan genes have since been found in every genome sequenced to date, from mosquito to man, roundworm to rat, and their numbers are still growing.
    http://ccsb.dfci.harvard.edu/w.....n_2013.pdf

    Darwin’s (Failed Predictions) – Similar species share similar genes – Cornelius Hunter PhD.
    Excerpt: As much as a third of the genes in a given species may be unique, and even different variants within the same species have large numbers of genes unique to each variant. Different variants of the Escherichia coli bacteria, for instance, each have hundreds of unique genes. (Daubin and Ochman)
     
    Significant genetic differences were also found between different fruit fly species. Thousands of genes showed up missing in many of the species, and some genes showed up in only a single species. (Levine et. al.) As one science writer put it, “an astonishing 12 per cent of recently evolved genes in fruit flies appear to have evolved from scratch.” (Le Page) These novel genes must have evolved over a few million years, a time period previously considered to allow only for minor genetic changes. (Begun et. al.; Chen et. al., 2007)
     
    Initially some evolutionists thought these surprising results would be resolved when more genomes were analyzed. They predicted that similar copies of these genes would be found in other species. But instead each new genome has revealed yet more novel genes. (Curtis et. al.; Marsden et. al.; Pilcher)
     
    Next evolutionists thought that these rapidly-evolving unique genes must not code for functional or important proteins. But again, many of the unique proteins were in fact found to play essential roles. (Chen, Zhang and Long 1010; Daubin and Ochman; Pilcher) As one researcher explained, “This goes against the textbooks, which say the genes encoding essential functions were created in ancient times.” (Pilcher)
    https://sites.google.com/site/darwinspredictions/similar-species-share-similar-genes

    Bigelowiella natans: Evolution Damage Control is Frantic – December 5, 2012
    Excerpt: (Extremely complex) Alternative splicing is not the only contradiction (to Darwinism) offered up by this humble (single celled) organism. B. natans also surprised evolutionists with unique, novel genes. In fact it has, err, about ten thousand unique genes.
    When unique genes first starting appearing in the genomic data, evolutionists figured their evolutionary cousins would be discovered in the genomes of other species. The problem was that we did not yet have sufficient genome data in hand. Surely once the genome data from more species were obtained, the cousins of those pesky unique genes would be found. Unique genes would become a thing of the past. But once again evolutionary theory pointed in the wrong direction. In fact, as the genomic data have increased, so have the unique genes. Now we can throw another 10,000 onto the heap.
    http://darwins-god.blogspot.co.....amage.html

    Octopus genome study reveals “alien” results – Aug. 13, 2015
    Excerpt: “The late British zoologist Martin Wells said the octopus is an alien. In this sense, then, our study describes the first sequenced genome from an alien,”,,,
    “The octopus appears to be utterly different from all other animals, even other molluscs,,,
    In fact, many of these genes are brand new, according to Daniel Rokhsar who co-led the study. “We’ve found hundreds of novel genes that don’t have counterparts in other animals and may be involved in this unique camouflage process.”
    http://www.alphr.com/science/1.....en-results

  15. 15
    Mung says:

    Mung: Other than those of Tomkins, which other results were invalidated? Surely Tomkins was not singled out.

    ThickPython: I’m not aware of any other creationists that have done this kind of stuff.

    The claim is that “the BLAST computer algorithm used by Tomkins contained a bug which invalidated his results.”

    It is simply not believable that Tomkins was the only creationist to use BLAST.

    It is simply not believable that Tomkins was the only person to use BLAST.

    Surely Tomkins was not the only person to use the BLAST computer algorithm that you claim is defective.

    What other frauds have you exposed?

  16. 16
    Mung says:

    Apparently, only Creationists have used this particular defective BLAST algorithm. But not just Creationists, of all Creationists, only Tomkins has used this particular defective BLAST algorithm.

    It took a ThickPython to pick out that one Creationist from all other Creationists selected from all other users.

    A Miracle.

  17. 17
    vjtorley says:

    Hi bornagain,

    Thanks very much for your comments and your valuable links. I certainly don’t think scientists have solved the problem of how orphan genes arose, and I’m not saying they could have arisen via an unguided process.

    What I am saying is that:

    (i) the strong sequence similarities between these genes and the non-coding DNA of chimpanzees and other apes is difficult to account for except on a hypothesis of common descent;

    (ii) it would be premature for ID proponents to argue that these genes were designed. We need to do some calculations of what kinds of changes would have been required to transform 98% similar non-coding DNA into a functional gene., and how probable (or improbable) those changes would have been, before we can make a design inference.

    I welcome any evidence that you wish to present, arguing that orphan genes were designed.

  18. 18
    vjtorley says:

    Hi bornagain,

    You write:

    Mapou, the evidence for ORFan genes did not come from ID proponents to begin with, but came from mainstream biologists. Moreover, the evidence for ORFan genes, from many different studies mind you, is found throughout life, bacteria to multicelluluar creatures, i.e. not just in the human genome. Thus it is far too early to take a computer programmer’s word that he has overthrown all those previous studies for ORFan genes throughout life, with a few afternoons of sequence comparisons on his computer between chimps and humans.

    As I understand it, Glenn Williamson was not questioning the existence of ORFan genes. What he is questioning is the assumption (made by some creationists) that these genes have no counterpart in apes. As he stated in his response to Dr. Hunter:

    So whether it is protein-coding in humans and non-coding in everything else doesn’t really concern me. What concerns me is whether it has an evolutionary history: clearly this one does.

    ORFan genes are quite real.

  19. 19
    Mung says:

    vjt, thank you for your recent posts. Heck, thank you for all your posts.

    The idea that the universe and the earth is only 6000 years old is not something that ought to be associated with the claims of Intelligent Design.

  20. 20
    bFast says:

    VJ, on de novos I think you missed the boat. I think it reasonable to assume that de novos grew in the “junk” until they were ready to be implemented. But why the heck would a gene that has meaning grow in junk that has no guidance.

    I think this does say something important, however, about how the designer goes about making de novo genes. This evidence shows that they are not “poofed” into existence, but that they do grow, mutation by mutation. Yet, if they are growing in unused DNA, or even in DNA used for some purpose other than protein coding (as protein coding has a specific vocabulary, unlike any other code within DNA) the chance calculations remain the same — ridiculous.

    It may be demonstrated that a gene exists in say gorilla and human, but has been disabled in chimp. If so, no de novo has been found. But if the first time the thing was “turned on, and produces a useful product” was in humans, it still uses the same chance calculations.

  21. 21
    butifnot says:

    “What concerns me is whether it has an evolutionary history: clearly this one does.”

    At best, it is consistent with a posited evolutionary history, under assumed evolutionary history.

  22. 22
    ThickPython says:

    @BornAgain:

    Body plans, contrary to neo-Darwinian presuppositions, simply are not reducible to DNA, period!

    I’m not quite sure I follow. Are you saying that there is some other method of inheriting traits that is not passed on via DNA? Sure there is plenty going on epigenetically, but of that I ask the same question – are epigenetics inherited by means other than DNA?

    I see you quote Stephen Meyer making a point on the basis of a lower figure for human-chimp DNA similarity, but I’m not sure why you would quote that when the entire point of the post is that these lower figures are wrong. These “vast chasms” between human and chimp DNA just don’t exist, so whatever the differences are between us, those differences are (ultimately) explainable by the differences in our DNA.

    Moreover, as to genetic similarity being supposed irrefutable evidence for common descent …

    Just to be clear, I do not consider genetic similarity between humans and chimpanzees – in and of itself – to be evidence of common descent. It’s a necessary condition, but not sufficient.

    I’ve heard of that pig-chimp hybrid thing before, and while I haven’t looked into it that much, it does pose a conundrum for creationists: if two animals can successfully interbreed, then they are necessarily of the same Biblical “kind” (according to AiG, CMI, ICR and probably others). Let’s call that the “pimp” kind. It follows then that both humans and chimps are in the “pimp” kind, and therefore humans and chimps are related by common descent. So BornAgain, I suspect you’re a YEC (?) – do you think humans and chimpanzees are of the same Biblical kind? Or do you reject the fairly solid positions of those creationist organisations?

  23. 23
    ThickPython says:

    @BornAgain:

    “Thus it is far too early to take a computer programmer’s word … “

    As Vincent has already kindly pointed out, I am not taking issue with the paper itself, I take issue with Cornelius Hunter’s treatment of the topic. Cornelius suggested quite strongly that these proteins evolved basically out of nothing, but if the paper is understood correctly, it is clear that these genes are only considered “de novo protein-coding genes” in the sense that there was a point mutation (or three!) in each gene that caused the sequence to be transcribed in humans but not in chimpanzees or orang-utans. Please see the links to the supplementary material in the OP.

    “Orphan genes have since been found in every genome sequenced to date, from mosquito to man …”

    Give me your top five. I know you’ve linked to a paper here, but I’m asking YOU to do the work. You seem to be throwing your hands up in the air as if this is just one guy’s opinion over another, which is always a good opportunity to investigate things for yourself. So yeah, if you can find a list of these human genes that are orphans relative to chimpanzees, then I will take it from there.

    “But where do they come from? With no obvious ancestry …” and “As much as a third of the genes in a given species may be unique …”

    And again I ask you the question – if one third of the genes in a given species would be good evidence of separate creation, then what percentage of orphan genes would be acceptable between two species such that you would consider common descent a possibility?

  24. 24
    ThickPython says:

    @Mung:

    “Apparently, only Creationists have used this particular defective BLAST algorithm. But not just Creationists, of all Creationists, only Tomkins has used this particular defective BLAST algorithm.”

    My sarcasm detector is beeping at me, but I’m still not quite sure what you’re trying to get at.

    Jeff Tomkins is the only creationist I know of that has used this particular defective BLAST algorithm. I know that Todd Wood also used BLAST, but he seemed to have come to the correct result, so it looks unlikely that he was affected by this bug.

    Are you suggesting that only creationists have been affected by this bug? Well, creationists could well be the only ones that were affected by the bug and not know it. If you look at the release notes for BLAST (http://www.ncbi.nlm.nih.gov/books/NBK131777/) and scroll down to version 2.2.29, you’ll see that the developers fixed an issue concerning “missing hits when running blastn with multiple queries, word size 7, large evalue, and no low complexity filtering.” (Although if Tomkins’ new paper can be trusted on this point, it appears they didn’t fix it properly).

    So what seems to have happened is that another researcher (presumably from the secular scientific community) has noticed this bug, reported it to the developers, and they have attempted to fix it. Why didn’t Jeff report the bug? Well, I’m not feeling particularly charitable at the moment … basically I think it gave him the result he wanted, so he didn’t look any further.

  25. 25
    ThickPython says:

    @Mung:

    “What other frauds have you exposed?”

    Ha! Don’t get me started on Tomkins’ work on the fusion in chromosome 2 …

  26. 26
    ThickPython says:

    @Mung:

    ” … basically I think it gave him the result he wanted, so he didn’t look any further.”

    Just to give a little context to that statement, please have a read of my paper (linked in the OP), and in particular read the section that discusses the mathematical impossibility of Tomkins getting the results he did. This should have been a blazing neon sign that there was something wrong with the software, but Tomkins didn’t investigate.

  27. 27
    bornagain says:

    Python you ask:

    “Are you saying that there is some other method of inheriting traits that is not passed on via DNA?”

    In Embryo Development, Non-DNA Information Is at Least as Important as DNA – Jonathan Wells – May 2012
    Excerpt: Evidence shows that non-DNA developmental information can be inherited in several ways. For example, it can be inherited through chromatin modifications, which affect gene expression without altering underlying DNA sequences. Another example is cytoplasmic inheritance, which involves cytoskeletal patterns and localization of intracellular molecules. Still another example is cortical inheritance, which involves membrane patterns.
    http://www.evolutionnews.org/2.....60031.html

    Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA – 2014 – Jonathan Wells
    http://bio-complexity.org/ojs/.....O-C.2014.2

    “Live memory” of the cell, the other hereditary memory of living systems – 2005
    Excerpt: To understand this notion of “live memory”, its role and interactions with DNA must be resituated; indeed, operational information belongs as much to the cell body and to its cytoplasmic regulatory protein components and other endogenous or exogenous ligands as it does to the DNA database. We will see in Section 2, using examples from recent experiments in biology, the principal roles of “live memory” in relation to the four aspects of cellular identity, memory of form, hereditary transmission and also working memory.
    http://www.ncbi.nlm.nih.gov/pubmed/15888340

    “But Darwinism is based on what I call the Genetic Reductionist Model of organisms. It is (based) on the assumption that DNA is the sole carrier of information and heredity and development. And all the characteristics of an organism are encoded in its DNA (DNA as blueprint or recipe).
    DNA is god and RNA is prophet is how my Biology lecturer at Birmingham University put it.,,,
    (Darwinism also holds) Mutations in the DNA lead to new organisms and explain the evolutionary descent of all living things.,,,
    And yet, an unknown secret here, that neo-Darwinian paradigm has been known to be false, unquestionably false, irrefutably false, for over 50 years.
    I say that the year that the scientific evidence became overwhelming was 1954.,,,
    It is all to do with what is often called cortical inheritance. Cortex is just the name given to the cell membrane and past the cytoplasmic structure underneath.,,,
    In fact, until the 1930’s it was commonly believe by biologists that the genes do not determine the fundamental features of an organism”s body plan.
    Many developmental biologist still agree (that genes do not).
    And the evidence comes from lots of animals but the key organism on which all the key research was done was Ciliates. (Microscopic single celled animals).,,,
    By the 1950’s it was proven beyond doubt that the ciliate cell surface structures and their patterns were inherited independently of genes and DNA. How was this done? Quiet easily. You could perform just a little surgical operation on these animals and remove some structures or replace them, or alter them in some way, carefully remove some cilia and put it in backwards,,, and they would heal very quickly, and then that defect was just reproduced indefinitely. The next generation would produce exactly the same defect. Even though you could show genetically that the DNA had not been changed one iota.,,
    At first many dismissed this as a quirk of ciliates with their elaborate cell surface structures. (Darwinists called them) a ‘rare example’ etc..,,, (They claimed) that this is just a unique thing to do with ciliates.,,,
    But it is clearly universal:
    1. Cilate cortex is an elaboration of the cell membrane and cytoskeleton that are universal features of animal and plant cells.,,,
    2. Developmental processes are the same,,
    3. Some cilates form cysts and then lose all visible surface structures, but cortical inheritance still occurs.,,,
    So however that cell surface is coded, it is not coded at the molecular, i.e. visible, level. There is clearly another system of heredity operating in cells.
    And in fact there is plenty of evidence for a wide variety of animals and plants that say this system is there, exists and operates, and is in fact responsible for the main features of the body plan. not the genes (DNA).
    So the definitive papers were produced back in the 1950s. So we have known since then that genetic paradigm is dead and therefore so is neo-Darwinism.,,, That there is more to heredity than DNA. And yet stubbornly, biologists carry on as if that was not the case.
    A historian of science has written a history of the whole affair. In fact, his PhD thesis, which was written in the 1980s, and he produced a book about it all in 1987. And in 1987 he concluded this, “Throughout the 1960s and 1970s the evolutionary significance of cortical inheritance was largely ignored by Darwinian evolutionists. Indeed for the most part, it still is. And in 2005 he wrote, “After 20 years it is still ignored and not answered”.
    – Dr. Arthur Jones as quoted at the 56:08 minute mark of the following video
    Fish, Fossils and Evolution – Dr. Arthur Jones – video
    https://youtu.be/PtqdZKeyY1Y?t=3368

    “Additional evidence of this kind comes from ciliates, large single-celled eukaryotic organisms. Biologists have shown that microsurgery on the cell membranes of ciliates can produce heritable changes in membrane patterns without altering the DNA.34 This suggests that membrane patterns (as opposed to membrane constituents) are impressed directly on daughter cells. In both cases—in membrane patterns and centrosomes—form is transmitted from parent three-dimensional structures to daughter three-dimensional structures directly. It is not entirely contained in DNA sequences or the proteins for which these sequences code.35
    Instead, in each new generation, the form and structure of the cell arises as the result of both gene products and the preexisting three-dimensional structure and organization inherent in cells, cell membranes, and cyto-skeletons. Many cellular structures are built from proteins, but proteins find their way to correct locations in part because of preexisting three-dimensional patterns and organization inherent in cellular structures. Neither structural proteins nor the genes that code for them can alone determine the three-dimensional shape and structure of the entities they build. Gene products provide necessary, but not sufficient, conditions for the development of three-dimensional structure within cells, organs, and body plans.36 If this is so, then natural selection acting on genetic variation and mutations alone cannot produce the new forms that arise in the history of life.”
    Stephen Meyer [Darwin’s Doubt, ch.14]

    podcast – Jonathan Wells: Is There Biological Information Outside of the DNA?, pt. 3 – Bioelectric code
    http://intelligentdesign.podom.....5_52-07_00

    Not in the Genes: Embryonic Electric Fields – Jonathan Wells – December 2011
    Excerpt: although the molecular components of individual sodium-potassium channels may be encoded in DNA sequences, the three-dimensional arrangement of those channels — which determines the form of the endogenous electric field — constitutes an independent source of information in the developing embryo.
    http://www.evolutionnews.org/2.....54071.html

    “Experiments have shown that electromagnetic fields have “morphogenetic” effects—in other words, effects that influence the form of a developing organism. In particular, some experiments have shown that the targeted disturbance of these electric fields disrupts normal development in ways that suggest the fields are controlling morphogenesis.22 Artificially applied electric fields can induce and guide cell migration. There is also evidence that direct current can affect gene expression, meaning internally generated electric fields can provide spatial coordinates that guide embryogenesis.23 Although the ion channels that generate the fields consist of proteins that may be encoded by DNA (just as microtubules consist of subunits encoded by DNA), their pattern in the membrane is not. Thus, in addition to the information in DNA that encodes morphogenetic proteins, the spatial arrangement and distribution of these ion channels influences the development of the animal.”
    Stephen Meyer on electromagnetic fields; “Darwin’s Doubt”, ch.14, ‘Epigenetic Revolution’, ‘Beyond Genes’, ‘Ion Channels and Electromagnetic Fields’.

    Timelapse Video Reveals Electric Face in Embryonic Tadpole – July 2011
    Excerpt: “When a frog embryo is just developing, before it gets a face, a pattern for that face lights up on the surface of the embryo. We believe this is the first time such patterning has been reported for an entire structure, not just for a single organ. I would never have predicted anything like it. It’s a jaw dropper.”
    http://www.sciencespacerobots......ole-718111

  28. 28
    vjtorley says:

    Hi bFast,

    I was intrigued by your comment:

    I think it reasonable to assume that de novos grew in the “junk” until they were ready to be implemented. But why the heck would a gene that has meaning grow in junk that has no guidance.

    Yes, I had been wondering that, too. On the other hand, I was also wondering why a designer would make a new gene from non-coding DNA rather than “poofing” it into existence.

    You suggest that de novo genes “are not ‘poofed’ into existence, but that they do grow, mutation by mutation,” and you propose that they may be growing in “DNA used for some purpose other than protein coding.” Now that’s an interesting suggestion, which I hadn’t considered. If true, it would explain why these genes need to be built up step by step.

    Thanks again for your post.

  29. 29
    bornagain says:

    As well Python, to repeat, the following experiments clearly show that the ‘form’ of a organism is not reducible to any conceivable ‘bottom up’ material explanation, i.e. to reductive materialism:

    http://www.uncommondescent.com.....ent-584055

    Moreover, we have the enigma of intrinsically disordered proteins (IDPs) in which proteins take on different shapes depending on what ‘context’ they find themselves in:

    “It was long believed that a protein molecule’s three-dimensional shape, on which its function depends, is uniquely determined by its amino acid sequence. But we now know that this is not always true – the rate at which a protein is synthesized, which depends on factors internal and external to the cell, affects the order in which its different portions fold. So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape, (intrinsically disoredered proteins), taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous (very weak or slight) influence over their functions.
    ,,,,So, to reiterate, the genes do not uniquely determine what is in the cell, but what is in the cell determines how the genes get used. Only if the pie were to rise up, take hold of the recipe book and rewrite the instructions for its own production, would this popular analogy for the role of genes be pertinent.
    Stuart A. Newman, Ph.D. – Professor of Cell Biology and Anatomy

    Biology’s Quiet Revolution – Jonathan Wells – September 8, 2014
    Excerpt: In 1996, biologists discovered a protein that does not fold into a unique shape but can assume different shapes when it interacts with other molecules. Since then, many such proteins have been found; they are called “intrinsically disordered proteins,” or IDPs. IDPs are surprisingly common, and their disordered regions play important functional roles.,,,
    So it is not true that biologists know all the basic features of living cells and are merely filling in the details. Nor is it true that Darwinian evolution is a settled scientific “fact,” as its defenders claim. Huge unanswered questions remain, and they will only be answered by going beyond the discredited myth that “DNA makes RNA makes protein makes us.”
    http://www.evolutionnews.org/2.....89651.html

    podcast – Dr. Jonathan Wells: Biology’s Quiet Revolution – September 17, 2014
    “We are talking about 1/3 of the proteins in our body, (could be Intrinsically Disordered Proteins)” – Jonathan Wells
    http://www.discovery.org/multi.....evolution/
    On this episode of ID the Future, Dr. Jonathan Wells discusses a popular claim, which he describes as “DNA makes RNA makes protein makes us”—or, every organism contains a program for itself in its DNA. Though this view fits neatly with the perspective of Darwinian evolution, it has been shown to be incorrect at every step. Listen in as Dr. Wells explains.

    As well, the fact that the ‘form’ of a organism is not reducible to DNA is also shown when just considering the problem of protein folding.

    It is now known that proteins do not find their final folded form by random processes as would be held in the neo-Darwinian view of things:

    The Humpty-Dumpty Effect: A Revolutionary Paper with Far-Reaching Implications – Paul Nelson – October 23, 2012
    Excerpt: Anyone who has studied the protein folding problem will have met the famous Levinthal paradox, formulated in 1969 by the molecular biologist Cyrus Levinthal. Put simply, the Levinthal paradox states that when one calculates the number of possible topological (rotational) configurations for the amino acids in even a small (say, 100 residue) unfolded protein, random search could never find the final folded conformation of that same protein during the lifetime of the physical universe. Therefore, concluded Levinthal, given that proteins obviously do fold, they are doing so, not by random search, but by following favored pathways. The challenge of the protein folding problem is to learn what those pathways are.
    http://www.evolutionnews.org/2.....65521.html

    Confronting Science’s Logical Limits – John L. Casti – 1996
    Excerpt: It has been estimated that a supercomputer applying plausible rules for protein folding would need 10^127 years to find the final folded form for even a very short sequence consisting of just 100 amino acids. (The universe is 13.7 x 10^9 years old). In fact, in 1993 Aviezri S. Fraenkel of the University of Pennsylvania showed that the mathematical formulation of the protein-folding problem is computationally “hard” in the same way that the traveling-salesman problem is hard.
    http://www.cs.virginia.edu/~ro.....Limits.pdf

    The reason why finding the final form of a folded protein is so hard for supercomputers is that it is like the ‘traveling salesman’ puzzle, which are ‘Just about the meanest problems you can set a computer (on) ‘.

    DNA computer helps traveling salesman – Philip Ball – 2000
    Excerpt: Just about the meanest problems you can set a computer belong to the class called ‘NP-complete’. The number of possible answers to these conundrums, and so the time required to find the correct solution, increases exponentially as the problem is scaled up in size. A famous example is the ‘travelling salesman’ puzzle, which involves finding the shortest route connecting all of a certain number of cities.,,,
    Solving the traveling-salesman problem is a little like finding the most stable folded shape of a protein’s chain-like molecular structure — in which the number of ‘cities’ can run to hundreds or even thousands.
    http://www.nature.com/news/200.....13-10.html

    And protein folding is found to be ‘NP-complete’

    Combinatorial Algorithms for Protein Folding in Lattice
    Models: A Survey of Mathematical Results – 2009
    Excerpt: Protein Folding: Computational Complexity
    4.1
    NP-completeness: from 10^300 to 2 Amino Acid Types
    4.2
    NP-completeness: Protein Folding in Ad-Hoc Models
    4.3
    NP-completeness: Protein Folding in the HP-Model
    http://www.cs.brown.edu/~sorin.....survey.pdf

    Yet it is exactly this type of ‘traveling salesman problem’ that quantum computers excel at:

    Speed Test of Quantum Versus Conventional Computing: Quantum Computer Wins – May 8, 2013
    Excerpt: quantum computing is, “in some cases, really, really fast.”
    McGeoch says the calculations the D-Wave excels at involve a specific combinatorial optimization problem, comparable in difficulty to the more famous “travelling salesperson” problem that’s been a foundation of theoretical computing for decades.,,,
    “This type of computer is not intended for surfing the internet, but it does solve this narrow but important type of problem really, really fast,” McGeoch says. “There are degrees of what it can do. If you want it to solve the exact problem it’s built to solve, at the problem sizes I tested, it’s thousands of times faster than anything I’m aware of. If you want it to solve more general problems of that size, I would say it competes — it does as well as some of the best things I’ve looked at. At this point it’s merely above average but shows a promising scaling trajectory.”
    http://www.sciencedaily.com/re.....122828.htm

    And proteins, like DNA, are found to have Quantum Information within them so as to be able to perform quantum computation

    Quantum Entanglement and Information
    Quantum entanglement is a physical resource, like energy, associated with the peculiar nonclassical correlations that are possible between separated quantum systems. Entanglement can be measured, transformed, and purified. A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems. The general study of the information-processing capabilities of quantum systems is the subject of quantum information theory.
    http://plato.stanford.edu/entries/qt-entangle/

  30. 30
    bornagain says:

    Classical and Quantum Information in DNA – Elisabeth Rieper – video (Longitudinal Quantum Information along the entire length of DNA discussed at the 19:30 minute mark; at 24:00 minute mark Dr Rieper remarks that practically the whole DNA molecule can be viewed as quantum information with classical information embedded within it)
    https://youtu.be/2nqHOnVTxJE?t=1176

    Classical and Quantum Information Channels in Protein Chain – Dj. Koruga, A. Tomi?, Z. Ratkaj, L. Matija – 2006
    Abstract: Investigation of the properties of peptide plane in protein chain from both classical and quantum approach is presented. We calculated interatomic force constants for peptide plane and hydrogen bonds between peptide planes in protein chain. On the basis of force constants, displacements of each atom in peptide plane, and time of action we found that the value of the peptide plane action is close to the Planck constant. This indicates that peptide plane from the energy viewpoint possesses synergetic classical/quantum properties. Consideration of peptide planes in protein chain from information viewpoint also shows that protein chain possesses classical and quantum properties. So, it appears that protein chain behaves as a triple dual system: (1) structural – amino acids and peptide planes, (2) energy – classical and quantum state, and (3) information – classical and quantum coding. Based on experimental facts of protein chain, we proposed from the structure-energy-information viewpoint its synergetic code system.
    http://www.scientific.net/MSF.518.491

    Quantum coherent-like state observed in a biological protein for the first time – October 13, 2015
    Excerpt: If you take certain atoms and make them almost as cold as they possibly can be, the atoms will fuse into a collective low-energy quantum state called a Bose-Einstein condensate. In 1968 physicist Herbert Fröhlich predicted that a similar process at a much higher temperature could concentrate all of the vibrational energy in a biological protein into its lowest-frequency vibrational mode. Now scientists in Sweden and Germany have the first experimental evidence of such so-called Fröhlich condensation (in proteins).,,,
    The real-world support for Fröhlich’s theory (for proteins) took so long to obtain because of the technical challenges of the experiment, Katona said.
    http://phys.org/news/2015-10-q.....otein.html

    Of note, quantum coherence, like quantum entanglement, is a ‘non-local’, beyond space and time, effect. (Also of note, Schrodinger would be very happy with the preceding finding, i.e. see “What is Life?’)

    Coherence and nonlocality
    Usually quantum nonlocality is discussed in terms of correlated multiparticle systems such as those discussed by John Bell in his famous 1964 theorem and then later clarified by GHZ, David Mermin and others.
    But more striking and significant is the qualitative nonlocal phenomena associated with coherent states,,,,
    In fact, theoretically these two kinds of nonlocality have precisely the same basis: the unmeasured singlet state uncovered by EPR is a coherent ‘pure state’ despite its spacial extension, and when the parts are realized in a measurement (a la Bell) this coherence is harvested or cashed in.
    Whereas the “EPR” connections are ephemeral and fragile, some forms of nonlocal coherence are robust.
    http://www.nonlocal.com/hbar/n.....rence.html

    Here is a paper that proved that protein folding belongs to the physics of the quantum world and that protein folding does not belong to the physics of the classical world as is presupposed in the reductive materialism of neo-Darwinism:

    Physicists Discover Quantum Law of Protein Folding – February 22, 2011
    Quantum mechanics finally explains why protein folding depends on temperature in such a strange way.
    Excerpt: To put this in perspective, a relatively small protein of only 100 amino acids can take some 10^100 different configurations. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Just how these molecules do the job in nanoseconds, nobody knows.,,,
    Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins.
    That’s a significant breakthrough. Luo and Lo’s equations amount to the first universal laws of protein folding. That’s the equivalent in biology to something like the thermodynamic laws in physics.
    http://www.technologyreview.co.....f-protein/

    That ‘non-local’ quantum entanglement/coherence, which conclusively demonstrates that ‘information’ in its ‘quantum form’ is completely transcendent of any time and space constraints (Bell, Aspect, Leggett, Zeilinger, etc..), should be found in molecular biology on such a massive scale, in every DNA and protein molecule, is a direct empirical falsification of Darwinian claims, for how can the ‘non-local’ quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy) cause when the quantum entanglement effect falsified material particles as its own causation in the first place? Appealing to the probability of various ‘random’ configurations of material particles, as Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the material particles themselves to supply!

    Looking beyond space and time to cope with quantum theory – 29 October 2012
    Excerpt: “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,”
    http://www.quantumlah.org/high.....uences.php

    Closing the last Bell-test loophole for photons – Jun 11, 2013
    Excerpt:– requiring no assumptions or correction of count rates – that confirmed quantum entanglement to nearly 70 standard deviations.,,,
    http://phys.org/news/2013-06-b.....otons.html

    etc.. etc..

    In other words, to give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time and space! i.e. Put more simply, you cannot explain an effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘special’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place!

    And although Naturalists have proposed various, far fetched, naturalistic scenarios to try to get around the Theistic implications of quantum non-locality, none of the ‘far fetched’ naturalistic solutions, in themselves, are compatible with the reductive materialism that undergirds neo-Darwinian thought.

    “[while a number of philosophical ideas] may be logically consistent with present quantum mechanics, …materialism is not.”
    Eugene Wigner
    Quantum Physics Debunks Materialism – video playlist
    https://www.youtube.com/watch?list=PL1mr9ZTZb3TViAqtowpvZy5PZpn-MoSK_&v=4C5pq7W5yRM

    Why Quantum Theory Does Not Support Materialism By Bruce L Gordon, Ph.D
    Excerpt: The underlying problem is this: there are correlations in nature that require a causal explanation but for which no physical explanation is in principle possible. Furthermore, the nonlocalizability of field quanta entails that these entities, whatever they are, fail the criterion of material individuality. So, paradoxically and ironically, the most fundamental constituents and relations of the material world cannot, in principle, be understood in terms of material substances. Since there must be some explanation for these things, the correct explanation will have to be one which is non-physical – and this is plainly incompatible with any and all varieties of materialism.
    http://www.4truth.net/fourtrut.....8589952939

  31. 31
    bornagain says:

    Thus, as far as empirical science itself is concerned, Neo-Darwinism is falsified in its claim that information is ‘emergent’ from a reductive materialist basis.

    Moreover, in quantum mechanics it is information that is conserved, not matter or energy:

    Quantum no-hiding theorem experimentally confirmed for first time
    Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment.
    http://www.physorg.com/news/20.....tally.html

    etc.. etc..

    Besides providing direct empirical falsification of neo-Darwinian claims as to the generation of information from a material basis, the implication of finding ‘non-local’, (i.e. beyond space and time), and ‘conserved’, quantum information in molecular biology on a massive scale is fairly, and pleasantly, obvious:

    Does Quantum Biology Support A Quantum Soul? – Stuart Hameroff – video
    https://www.youtube.com/watch?v=iIyEjh6ef_8

    The Unbearable Wholeness of Beings – Stephen L. Talbott – 2010
    Excerpt: Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary.
    ,,, the question, rather, is why things don’t fall completely apart — as they do, in fact, at the moment of death. What power holds off that moment — precisely for a lifetime, and not a moment longer?
    Despite the countless processes going on in the cell, and despite the fact that each process might be expected to “go its own way” according to the myriad factors impinging on it from all directions, the actual result is quite different. Rather than becoming progressively disordered in their mutual relations (as indeed happens after death, when the whole dissolves into separate fragments), the processes hold together in a larger unity.
    http://www.thenewatlantis.com/.....-of-beings

    picture – What power holds off that moment — precisely for a lifetime, and not a moment longer?
    http://cdn-4.spiritscienceandm.....ardd-2.jpg

    Verse and Music:

    Luke 23: 42-43
    And he was saying, “Jesus, remember me when You come in Your kingdom!” And He said to him, “Truly I say to you, today you shall be with Me in Paradise.”

    Moriah Peters – You Carry Me – music
    https://www.youtube.com/watch?v=x2H-zQjgurQ

  32. 32
    butifnot says:

    Sure there is plenty going on epigenetically

    This is the type of breezy, flippant, arrogant, unfounded nonsense that marks those who espouse such things as possibly hopelessly stuck outside of reality. Epigenetics was unknown a short while ago. The DNA was it, man. And just the parts we had uncovered doing something we were aware of.

    but of that I ask the same question – are epigenetics inherited by means other than DNA?

    As if ‘epigenetics’ are all discovered now. All evidence points to we don’t even know, what we don’t know. The ‘epigenetics’ that are known to us so far?

    These “vast chasms” between human and chimp DNA just don’t exist, so whatever the differences are between us, those differences are (ultimately) explainable by the differences in our DNA.

    That’s some ‘ultimate’ assertion! Clearly there are controls and communications we are not aware of yet. BA at 27, those are fascinating! It should be obvious that the mechanisms identified thus far are woefully incomplete and inadequate to explain the observed – life.

  33. 33
    ThickPython says:

    @BornAgain:

    tl;dr.

    That’s over 4,000 words, and 30 links to even more material that I presume I’m being asked to read.

    I have better things to do with my time.

  34. 34
    Larry Moran says:

    Be careful when talking about ORFan “genes.” Most of them are just regions of DNA that contain an open reading frame (ORF) of about 300 base pairs. These can occur by chance in large genomes.

    Very few of these ORFan “genes” have proven to be actual functioning genes.

  35. 35
    bornagain says:

    Python, don’t read it. I don’t care. You are certainly not the first atheist on UD to refuse to deal honestly with the evidence that refutes your position. In fact, I have given up on atheists ever being honest towards the evidence.
    I posted the links primarily for people who want to see why neo-Darwinism is falsified from a empirical point of view. Seeing as I have been through this same dance countless times with atheists, I did not post the links primarily for you anyway.

    Of note, I still can’t get over the feeling that there is something very fishy with your results.

    I have a question, was the chimp genome that you used to compare the human genome to assembled and oriented based on a map/framework built for chimpanzee and not for humans?

    From your page we find that you used the earlier 2006 Chimp genome that was biased towards mapping to the human genome.

    “This meant using human genome assemblies from February 2009 (ftp://hgdownload.cse.ucsc.edu/.....romosomes/)and chimpanzee genome assemblies from March 2006 (ftp://hgdownload.cse.ucsc.edu/.....romosomes/
    per your cite:
    https://www.dropbox.com/sh/dm2lgg0l93sjayv/AACQasd3Z0zLvGn8HTOPM8uQa/Tomkins-BLAST.pdf?dl=0

    The reason I ask, is because, as pointed out earlier, earlier Chimp genomes were assembled and oriented based on a map of the human genome, not assembled and oriented based on the Chimp genome. i.e. the presupposition of common descent was hidden within the construction of the earlier Chimp genomes.

    New Chromosome Research Undermines Human-Chimp Similarity Claims – Tomkins – 2010
    Excerpt: In the 2005 chimpanzee genome project and resulting Nature journal publication, the sequence contigs4 were not assembled and oriented based on a map of the chimpanzee genome, but rather on a map of the human genome. Given the fact that the chimpanzee genome is at least 10 percent larger5 overall than the human genome, this method of assembly was not only biased toward an evolutionary presupposition of human-chimp similarity, but was also inherently flawed.

    The title of the recent journal article accurately sums up the research findings: “Chimpanzee and Human Y Chromosomes are Remarkably Divergent in Structure and Gene Content.” Before getting into the details of their results, it is important to understand that for the first time, the chimpanzee DNA sequence for a chromosome was assembled and oriented based on a Y chromosome map/framework built for chimpanzee and not human. As a result, the chimpanzee DNA sequence could then be more accurately compared to the human Y chromosome because it was standing on its own merit.
    http://www.icr.org/article/new.....ndermines/

    Hughes, J.F. et al. 2010. Chimpanzee and human Y chromosomes are remarkably divergent in structure gene content. Nature. 463 (7280): 536-539.

    Statistics on sequencing and mapping of the chimp genome are difficult to pin down even though the mapping and sequencing were largely completed by 2006. A report describing the massive effort to produce a more accurate view of the chimpanzee genome has not yet been published.

    Frankly, I think the whole set up that you used is rigged to give Darwinists the answers they want. But seeing as this is the only evidence that you can appeal to, I guess you are stuck beating this dead horse! 🙂

    It is interesting to note some of the comments that came out when comparisons were done with a Chimp sequence that was assembled properly, i.e. ‘on its own merits’

    Recent Genetic Research Shows Chimps More Distant From Humans,,, – Jan. 2010
    Excerpt: A Nature paper from January, 2010 titled, “Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content,” found that Y chromosomes in humans and chimps “differ radically in sequence structure and gene content,” showing “extraordinary divergence” where “wholesale renovation is the paramount theme.”,,, “Even more striking than the gene loss is the rearrangement of large portions of the chromosome. More than 30% of the chimp Y chromosome lacks an alignable counterpart on the human Y chromosome, and vice versa,,,”
    http://www.evolutionnews.org/2.....shows.html

    A False Trichotomy
    Excerpt: The common chimp (Pan troglodytes) and human Y chromosomes are “horrendously different from each other”, says David Page,,, “It looks like there’s been a dramatic renovation or reinvention of the Y chromosome in the chimpanzee and human lineages.”
    http://www.uncommondescent.com.....richotomy/

  36. 36
    Virgil Cain says:

    Earth to Larry Moran- Your position cannot account for DNA nor biological reproduction. That is why you need to leave ID alone and focus on your lame position- it needs help, badly.

  37. 37
    bornagain says:

    as to:

    “Very few of these ORFan “genes” have proven to be actual functioning genes.”

    and yet:

    Age doesn’t matter: New genes are as essential as ancient ones – December 2010
    Excerpt: “A new gene is as essential as any other gene; the importance of a gene is independent of its age,” said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. “New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked.”
    http://www.sciencedaily.com/re.....142523.htm

    New Genes Are Essential 6-13-2015 by Paul Giem – video
    https://www.youtube.com/watch?v=6qgGPV1AO1E

    It must be hard to stay up with current evidence when you are stuck defending a 19th century dinosaur of a theory! 🙂

  38. 38
    Larry Moran says:

    butifnot said,

    Epigenetics was unknown a short while ago.

    The word “epigenetics” is notoriously difficult to define. If it means any kind of heritable effect that’s not directly due to DNA sequence then we’ve known about it since the early 1960s (<50 years).

    If it's restricted to just modifications of DNA base pairs then we only known about that since the mid 1970s (~40 years).

    Since I'm older than 50, I'm willing to concede that knowing something for 50 years is a relatively "short while ago" but I wonder if that's what butifnot meant?

  39. 39
    Virgil Cain says:

    but of that I ask the same question – are epigenetics inherited by means other than DNA?

    Yes- for example, experiments of microsurgery on Paramecium. A piece of the cortex was cut out, rotated 180 degrees and reinserted. The offspring inherited the change. Lamarck 101.- Source “Evolution in Four Dimensions” page 122

  40. 40
    jeffblue102 says:

    So there we have it. If Dr. Tomkins is right, then not only is chimpanzee DNA only 88% similar to our own, but human DNA is only 89% similar to itself!

    a single query is not a valid debunking or criticism of Tomkins work. According to his own paper on chromosome 20 using Numcer he received results ranging from 61% to 100% from multiple queries when comparing chimpanzee to human dna,

    Resulting data for the returned nucmer identities and length of alignments is given in Tables 4 and 5, respectively. Individual alignments within chromosomes varied in their percent identity between a low of 57% and a high of 100%. The average percent identity across chromosome was 88%

    IMO, Williamson needs to perform the same amount of queries comparing human to human using Numcer too see whether or not there is a trend near 100% before debunking Tompkins use of the average between human and ape.

  41. 41
    Virgil Cain says:

    And Larry, why do you delete comments from your blog that expose your ignorance and bias? Oops, I know why…

  42. 42
    Larry Moran says:

    bornagain posts a link to a press release about a 2010 paper then gloats …

    It must be hard to stay up with current evidence when you are stuck defending a 19th century dinosaur of a theory!

    Yes, it IS hard to keep up with the scientific literature. That’s why I spend hours reading it every day and that’s why I try to limit my comments to areas where I feel competent.

    In this case, there are many recent papers on ORFans pointing out that what’s missing from the hype is any substantive evidence that they are functional as opposed to simply noise or accidental reading frames. In the vast majority of cases, there’s no evidence that the predicted protein is actually synthesized in cells.

    I was simply pointing out to readers of Uncommon Descent that you shouldn’t jump to unwarranted conclusions.

    Here’s a link to a recent paper (April 2015) that discusses the problems with nomenclature and recommends that we use the term “de novo” genes to identify new genes. The paper discusses four ways that these genes can evolve from pre-existing sequences.

    All of you can read this paper for yourselves because it’s open access. Nevertheless, I’ll quote a paragraph to show you what’s being discussed in the scientific literature.

    Schlötterer, C. (2015) Genes from scratch–the evolutionary fate of de novo genes. TRENDS in Genetics, 31:215-219. [doi: 10.1016/j.tig.2015.02.007]

    Are de novo genes real?

    De novo genes arise from previously noncoding DNA, are short, and are expressed at low levels [10–12]. These features frequently raise doubts about the biological significance of de novo genes. In light of these concerns, several approaches have been used to distinguish true de novo genes from random noise.”

    The approaches are; (1) Neutrality tests, (2) Gene expression: RNA and protein, (3) Regulation of gene expression, and (4) Reverse genetics.

  43. 43
    Virgil Cain says:

    Larry Moran:

    The paper discusses four ways that these genes can evolve from pre-existing sequences.

    Which of those four are blind watchmaker mechanisms and how was the determined?

  44. 44
    Larry Moran says:

    Virgil Cain (is that really his name?) says,

    And Larry, why do you delete comments from your blog that expose your ignorance and bias? Oops, I know why…

    I’ve recently begun deleting comments that don’t contribute to an intelligent discussion. I’m not happy about this because I’m a strong supporter of freedom of expression. However, the problem was getting severe when some readers (mostly ID supporters) began spamming my blog.

    You are still more than welcome to comment on Sandwalk even if you disagree with me … ESPECIALLY if you disagree with me. All I ask is that you engage in an intelligent discussion of the issues.

    I could have just banned comments altogether like the main ID blog Evolution News & Views but I don’t think that’s how we should encourage debate and discussion.

    I could just ban everyone who disagrees with me, as Barry Arrington usually does here on Uncommon Descent, but I don’t think that’s healthy either.

    If I were running this blog I would definitely delete some of the comments by ID supporters because they don’t contribute to the discussion; for example, your comment #36, which has nothing to do with the point I was making.

  45. 45
    Larry Moran says:

    Virgil Cain asks,

    Which of those four are blind watchmaker mechanisms and how was the determined?

    Did you have trouble reading the paper? Which words didn’t you understand?

  46. 46
    Virgil Cain says:

    Larry Moran:

    I’ve recently begun deleting comments that don’t contribute to an intelligent discussion.

    Then you should be deleting your posts and comments.

    your comment #36, which has nothing to do with the point I was making.

    My comment in 36 shows that your “point” is moot.

  47. 47
    bornagain says:

    LM, Actually, despite what you may believe to the contrary, you have no actual empirical evidence that genes can ‘randomly’ arise from non-coding regions. The claim that they can arise from non-coding regions is a ‘just so story’, like the myriad of other evidence free ‘just so stories’ from Darwinists. A story that was created to cover up the embarrassing empirical shortcoming for neo-Darwinian evolution that held genes can not suddenly pop into essential functionality.

    Is the Origin of New Genes “Basically a Solved Problem”? – Cornelius Hunter – Sept. 11, 2014
    Excerpt: If you read the headlines, you would have the impression that the problem is well in hand. For instance, super-star science writer Carl Zimmer wrote in the New York Times earlier this year that “researchers have documented the step-by-step process by which a new gene can come into existence.”

    Case closed right?

    Well not quite. In fact, not even close. What Zimmer tells his readers is a “step-by-step process” is what scientists affectionately refer to as a cartoon. In fact, here it is:,,,
    ,,,This evolutionary narrative is certainly not “basically a solved problem.” In fact, what evolutionists have are high claims of the spontaneous evolution of incredibly complex structures, not because of the evidence, but in spite of the evidence. So what gives evolutionist’s their confidence? It is not that they understand how such genes could have evolved, but that the genes must have evolved because solo genes are observed over and over:
    “Several studies have by now also shown that de novo emerged transcripts and proteins can assume a function within the organism. All of this provided solid evidence that de novo gene birth was indeed possible.”,,,
    Does any of this mean that the de novo genes evolved from random mutations as the evolutionists claim? Of course not.,,,
    Only a few years ago they agreed that such evolution of new genes would be impossible. Now they have been forced to adopt it because the evidence unambiguously reveals solo genes, and evolutionists dogmatically insist that everything must have spontaneously evolved.,,
    http://darwins-god.blogspot.co.....olved.html

    Moreover, there was this recent telling admission

    Can new genes arise from junk DNA? – August 2015
    Excerpt: Researchers are beginning to understand that de novo genes seem to make up a significant part of the genome, yet scientists have little idea of how many there are or what they do. What’s more, mutations in these genes can trigger catastrophic failures. “It seems like these novel genes are often the most important ones,” said Erich Bornberg-Bauer, a bioinformatician at the University of Münster in Germany.,,,
    “How does novel gene become functional? How does it get incorporated into actual cellular processes?” McLysaght said. “To me, that’s the most important question at the moment.”
    http://www.uncommondescent.com.....-junk-dna/

    That ‘new’ genes would have essential function early in embryonic development should, if Darwinism were a normal science, falsify Darwinism. But alas, Darwinian evolution is not really a science but is instead a faith based religion. A belief system held with such fervor by atheists that it would put the faith that many Christians have to shame.

  48. 48
    Virgil Cain says:

    Larry Moran:

    Did you have trouble reading the paper? Which words didn’t you understand?

    So you can’t answer the question. Figures…

  49. 49
    Virgil Cain says:

    And Larry, please read the following UD post:

    “Intelligent Design is NOT Anti-Evolution” — a guest post– my bet is that you are not intelligent enough to understand it.

    Post that on your blog and watch the implosion!

  50. 50
    vjtorley says:

    Hi Professor Moran,

    While you’re over here, I have a quick question about orphan genes in cichlid fish. Have any orphan genes been discovered to code for proteins in some species of cichlid fish but not others? I ask this because I think everyone (including creationists) would agree that all cichlids are descended from a common stock.

  51. 51
    Andre says:

    Let is ask Prof Moran then.

    Prof Moran can your position account for how DNA came about? Do you have any testable results?

  52. 52
    vjtorley says:

    While Professor Moran is here, I’d also like to politely ask him to put up a short post on Sandwalk summarizing his take on a recent article by Dr. Jonathan Wells, titled, Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA. It’s very meaty, and the implications for the theory of evolution (whether “neutralist” or neo-Darwinian) are substantial. I think it warrants a serious response from evolutionary biologists.

  53. 53
    EvilSnack says:

    So, will Darwinists now respond to every report of an orphan gene by citing earlier, disproven reports, and rejecting the newest report out-of-hand?

  54. 54
    juwilker says:

    Just a quick observation. It seems that Dr Moran is being polite with his recent comments and discussion. He actually referred to people as “readers of Uncommon Decent” instead of the usual IDiots or other derogatory terms. This is a nice change. Thank you Dr Moran for being civil; I will read your posts with more consideration as a result.

  55. 55
    gpuccio says:

    VJ:

    I have really appreciated your sincere efforts to clarify some important issues about the chimp human comparison and related problems.

    I would like to briefly offer some personal thoughts.

    1) As far as I can understand, it is perfectly reasonable that the difference at genome level between humans and chimps is about 2%.

    2) It remains absolutely true, on the other hand, that humans and chimps are greatly different. Therefore, either the difference can be explained at other, non genomic, levels, or it should be explained by the 2% differences. Or both.

    3) If the difference must be explained mainly as neutral mutations which become fixed, as suggested by some, it seems really unlikely that they can help explain the differences existing between humans and chimps. If only a minor part of the genomic differences is non neutral and functional, it becomes very difficult to believe that such a small genomic variation can explain the features in humans. If, instead, most of the observed variation is functional, then it’s another story, but in that case intelligent design is the only possible explanation for such an outcome.

    4) On the other hand, a lot of non strictly genomic differences could be of help, let’s say at all possible epigenetic levels. Our deep ignorance at this level makes any convincing evaluation of that scenario still impossible.

    5) Regarding new protein coding genes or orphan genes in humans, I don’t know how many there can be in the human genome. That remains probably a point which needs more investigation.

    6) In the case on new protein coding genes which are protein coding only in humans, but which have large homologies with non coding sequences in primates, that is exactly my idea of one modality about how new protein coding genes may come into existence: by the gradual engineering of non coding sequences into a coding sequence. Some examples have been described, and transposons could have an important role in the process. Which can only be interpreted, obviously, as an intelligent design process.

    7) Finally, as I have always said, common descent remains IMO the most valid scientific explanation for most of the facts we can observe in existing genomes and proteomes. I am firmly convinced of that, as much as I am firmly convinced that Intelligent Design remains the most valid scientific explanation, indeed the only credible one, for the functional information observed in genomes and proteomes.

  56. 56
    EugeneS says:

    GP,

    Welcome back.

  57. 57
    Larry Moran says:

    vjtorley says,

    While Professor Moran is here, I’d also like to politely ask him to put up a short post on Sandwalk summarizing his take on a recent article by Dr. Jonathan Wells, titled, Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA. It’s very meaty, and the implications for the theory of evolution (whether “neutralist” or neo-Darwinian) are substantial. I think it warrants a serious response from evolutionary biologists.

    I scanned the article. It’s a lengthy review of some observations in developmental biology. Wells builds a case for the transmission of membrane functions from cell to cell and concludes …

    As we have seen, however, the idea that embryo development is controlled by a genetic program is inconsistent with the biological evidence. Embryo development requires far more ontogenetic information than is carried by DNA sequences.

    Thus Neo-Darwinism is false.

    It’s just another attack on evolution by an ID proponent who puts his own spin on what evolutionary biologists are saying. There’s not a single word on proving that gods an intelligent designer is behind developmental biology.

    It’s the same-old, same-old that we’ve been hearing for decades. Attack evolution and hope that your followers will draw the correct conclusions based on a false dichotomy.

  58. 58
    Larry Moran says:

    EvilSnark (really?) asks,

    So, will Darwinists now respond to every report of an orphan gene by citing earlier, disproven reports, and rejecting the newest report out-of-hand?

    I don’t know what “Darwinists” will do but real scientists will ask for evidence that the ORFan sequence is actually a functional gene.

    You do know about the importance of evidence, don’t you?

    What will ID proponents do? Will they continue to proclaim that every new putative ORFan genes destroys evolution?

  59. 59
    Larry Moran says:

    Andre asks,

    Prof Moran can your position account for how DNA came about? Do you have any testable results?

    I don’t know how DNA (or RNA) first arose over 3.5 billion years ago.

    Now let me ask YOU some questions. Do you believe that life on Earth is billions of years old and that all life shares a common ancestor?

    I need to know the answer to those questions before trying to explain some things to you.

  60. 60
    Virgil Cain says:

    Larry Moran- Do you think the genetic code is a real code (like Morse Code is a real code)?

    If you do what would you say to people who claim the genetic code isn’t a real code? Get a real life?

  61. 61
    Virgil Cain says:

    Larry Moran:

    Do you believe that life on Earth is billions of years old and that all life shares a common ancestor?

    I think that in order to know how old the earth is you have to know how it formed. Otherwise you are just getting the age of the materials used. As for a common ancestor, I wanted to believe but then actually to a look at the evidence and found there isn’t any way to objectively test the claim.

    That means that universal common descent is a religious claim. I am looking for science, thank you.

  62. 62
    Virgil Cain says:

    gpuccio and VJT-

    Have you considered a common design to account for the genetic similarities and the appearance of the fossil succession is due to terraforming?

  63. 63
    Andre says:

    Prof Moran

    I think the best evidence we have suggest a 4.5 billion year earth and I have no problem with that. Common ancestry does have some circumstantial evidence but I am in no way convinced yet that it is a fact.

  64. 64
    Virgil Cain says:

    Andre- FYI: A 4.5x billion year old earth relies on the assumption that the proto-earth was molten and at least 20,000 degrees Kelvin. That way all the crystals from all of the cosmic debris were melted and there was homogeneity. Then when new crystals formed they trapped the isotopes and decay began then.

    If not the actual decay started when the element was formed and the age of the crystals date back to when they were formed in the comet, meteor or asteroid.

  65. 65
    Andre says:

    Virgil

    I hear you, and in no way do I believe it I just accept it as the current best explanation. Science however is always open to correction and I’m not attached to an outcome I’m open to it.

  66. 66
    Larry Moran says:

    Virgil Cain (who I suspect also posts under different pseudonyms) says,

    And Larry, please read the following UD post:

    “Intelligent Design is NOT Anti-Evolution” — a guest post– my bet is that you are not intelligent enough to understand it.

    Post that on your blog and watch the implosion!

    So, you maintain that ID is not mostly about anti-evolution, right?

    Here are some of the comments you’ve made on Uncommon Descent in the past few days ….

    Earth to Larry Moran- Your position cannot account for DNA nor biological reproduction. That is why you need to leave ID alone and focus on your lame position- it needs help, badly.

    And Larry, why do you delete comments from your blog that expose your ignorance and bias? Oops, I know why…

    Which of those four are blind watchmaker mechanisms and how was the determined?

    So you can’t answer the question. Figures…

    Larry Moran is just upset because ID exists due to the total failure of his position to find scientific support. He is just a big baby who can’t get his way.

    LoL! YOU can’t make a scientific case for unguided evolution, Larry. THAT is the point- not one scientist can make a positive case for unguided evolution. It is an untestable position.

    Larry, you are an evo with an agenda and a strong opinion and that is not how a scientist should behave.

    Larry Moran, totally unaware of himself.

    NS includes RM so RM+NS is unnecessarily redundant.

    The sad part is that you don’t have any clue what ID is all about.

    The intelligent design is evidence for an intelligent designer, Larry. If the scientific community could just support their claims then ID would be a non-starter.

    Larry Moran- The whole debate is about whether or not all genetic changes are accidents, errors and mistakes. Yes mutations happen. That doesn’t mean they are accidents, errors and mistakes. It isn’t NS if the mutations are directed. And we see the creative power of directed evolution with genetic and evolutionary algorithms.

    There isn’t any model for evolutionism and no one has won a Nobel Prize for anything to do with unguided evolution. But yes I am sure if someone could actually demonstrate that natural selection and drift could produce something like ATP synthase or the genetic code, they would win a Nobel Prize. If someone could elucidate the evolutionary pathways that led to the emergence of humans they would win a Nobel Prize.

    Perhaps if someone could figure out how to quantify unguided evolution so that it qualifies as science, they would win a Nobel prize.

    Larry Moran- Can you please link to this modern evolutionary theory so we all read what it actually says? How is unguided evolution quantified in the theory? Is it just through population genetics?

    And thank you, Zachriel @ 145, for proving that natural selection is non-random in the most trivial sense. Heck by that standard mutations are non-random.

    “The rate of fixation of neutral mutations is the same as the rate of introduction of neutral mutations,”

    That is the untested claim, anyway.

    Please explain how to test the claim the differences in genomes can account for all of the physiological and morphological differences between humans and chimps.

    Then tell us how to test the claim that drift and natural selection didit.

    Or you can just remain a non-credible supporter of your faith.

    Yes mutations happen and they can accumulate. The BIG questions are – Can accumulations of mutations account for the physiological and morphological change required? How can we test that claim?

    It is very telling that all our opponents can do is equivocate, erect strawman after strawman and misrepresent.

    Zachriel’s continued equivocation is duly noted.

    And the equivocation continues.

    It is very telling that all our opponents can do is equivocate, erect strawman after strawman and misrepresent.

    Pathetic, actually

    A burst of evolution is expected if organisms are designed to evolve. The equivocation comes from using all examples of evolution as support for blind watchmaker evolution.

    That’s because it wasn’t a required change- it wasn’t required for survival.

    How many generations did it take before humans discovered alternating current?

    “And yet we can show that mutations are random with respect to fitness, …”

    OK we are waiting for such a demonstration.

    It is also not a good idea to come here and posts lies, equivocations, misrepresentations and strawmen.

    That study did not show that mutations are random with respect to fitness. It showed that the variation that allowed for fitness in the presence of anti-biotics was already present.

    Only ignorance can make such a determination.

    Natural selection includes mutation.

    It is so awesome having other people see Zachriel for what it is- an insipid troll.

    So something that aids fitness is random with respect to it? Really?

    And last but not least, the most ironic comment of them all ….

    Intelligent Design is not anti-evolution, Larry. ID argues against blind watchmaker evolution having sole dominion and creative powers.

    I read the books you posted, plus many others. The problem is not one offers up a way to objectively test the claim that natural selection and drift produced the diversity of life. Sean Carroll and Neil Shubin are confident that changes in regulatory networks are sufficient to explain the differences in metazoans. Yet no one has taken fish embryos, for example, subjected them to rounds of targeted mutagenesis and had a fish-a-pod arise as a result.

    So the question is why would anyone accept Universal Common Descent without having some prior bias? What makes a human a human, Larry? What makes a chimp a chimp? Evolutionary biologists want us to believe we are the sum of our genome yet no one has ever tested that claim.

    The fact is, larry, both natural selection and drift are impotent with respect to creating complex biological functionality. If you want disease and deformities they are your mechanisms.

    Also the age of the earth depends on how it was formed. Without knowing that the best you can do is find the age of the materials that made it. Is the age of a log cabin the age of the trees or does it start from when the cabin was erected?

    Maybe I’m not seeing the wit and intelligence behind those comments but to me they look an awful lot like attacks on evolution and attacks on evolutionary biologists. I haven’t seen a single comment from you, Virgil Cain, that presents evidence for intelligent design and evidence for an intelligent designer.

    I’ve got nothing against your behavior. This is a social and political battle and all’s fair in love and war.

    But please don’t insult my intelligence by claiming that ID is not anti-evolution.

  67. 67
    Andre says:

    I am now convinced that Prof Larry Moran is an idiot. The issue is not evolution per say Prof Moran the issue is unguided vs. guided. How does one model unguided evolution? Please tell us Prof Moran? How does unguided processes create guided processes to prevent unguided processes from happening in the first place?

    The mind boggles that a supposedly intelligent being can be so utterly dumb.

  68. 68
    Vy says:

    A 4.5x billion year old earth relies on the assumption that the proto-earth was molten and at least 20,000 degrees Kelvin.

    @Virgil @Andre, that and the assumption that the constantly refuted “nebular hypothesis (or hunch, according to the NAS and pals) is somehow a valid representation of reality.

    They assume dust somehow accumulates into planets over X billion Darwin years (with the help of fairy-dust mechanisms) when it is readily observable that the dust does what it’s supposed to do – blow out into interstellar space, fast!

    I mean, seriously, in their own words:

    The discovery of thousands of star systems wildly different from our own has demolished ideas about how planets form. Astronomers are searching for a whole new theory.

    Too bad the “searching for a whole new theory” meant “finding ways to add more superficially normalizing epicycles”.

  69. 69
    bornagain says:

    Given that no one has ever observed unlimited plasticity in an organism, then I don’t think the genetic evidence, (nor the fossil evidence for that matter, Meyer, Luskin, Tattersall), is compelling to the hypothesis of common descent in the least. IMHO, it is a hypothesis in severe want of empirical confirmation.

    The main reason I don’t think the genetic evidence in particular fits the hypothesis of common descent of man, from some hypothetical chimp-like creature, is tied the fact, as iterated in post 27 & 29, that the ‘3-D form’ of an organism cannot be reduced to the sequential information on DNA, (or even completely reduced to any other material particulars in the cell for that matter).

    Moreover, the sequence similarity for a broad range of creatures, not just chimps, is far more similar to humans than is expected on the neo-Darwinian view of things.

    http://www.uncommondescent.com.....ent-584064

    Of related interest to the fact that the 3-D form of an organism is completely beyond the explanatory scope of neo-Darwinism (post 27), Dr. Sternberg, in the following podcast, gives an excellent overview of the fact that the ‘species specific’ differences between creatures is found in how the information is arranged ‘holistically’, and that the ‘species specific’ differences are not found in the gene comparisons between species:

    On Human Origins: Is Our Genome Full of Junk DNA? Pt 2. – Richard Sternberg PhD. Evolutionary Biology
    Excerpt: “Here’s the interesting thing, when you look at the protein coding sequences that you have in your cell what you find is that they are nearly identical to the protein coding sequences of a dog, of a carp, of a fruit fly, of a nematode. They are virtually the same and they are interchangeable. You can knock out a gene that encodes a protein for an inner ear bone in say a mouse. This has been done. And then you can take a protein that is similar to it but from a fruit fly. And fruit flies aren’t vertebrates and they certainly are not mammals., so they don’t have inner ear bones. And you can plug that gene in and guess what happens? The offspring of the mouse will have a perfectly normal inner ear bone. So you can swap out all these files. I mentioning this to you because when you hear about we are 99% similar (to chimps) it is almost all referring to those protein coding regions. When you start looking, and you start comparing different mammals. Dolphins, aardvarks, elephants, manatees, humans, chimpanzees,, it doesn’t really matter. What you find is that the protein coding sequences are very well conserved, and there is also a lot of the DNA that is not protein coding that is also highly conserved. But when you look at the chromosomes and those banding patterns, those bar codes, (mentioned at the beginning of the talk), its akin to going into the grocery store. You see a bunch of black and white lines right? You’ve seen one bar code you’ve seen them all. But those bar codes are not the same.,, Here’s an example, aardvark and human chromosomes. They look very similar at the DNA level when you take small snippets of them. (Yet) When you look at how they are arranged in a linear pattern along the chromosome they turn out to be very distinct (from one another). So when you get to the folder and the super-folder and the higher order level, that’s when you find these striking differences. And here is another example. They are now sequencing the nuclear DNA of the Atlantic bottle-nose dolphin. And when they started initially sequencing the DNA, the first thing they realized is that basically the Dolphin genome is almost wholly identical to the human genome. That is, there are a few chromosome rearrangements here and there, you line the sequences up and they fit very well. Yet no one would argue, based on a statement like that, that bottle-nose dolphins are closely related to us. Our sister species if you will. No one would presume to do that. So you would have to layer in some other presumption. But here is the point. You will see these statements throughout the literature of how common things are.,,, (Parts lists are very similar, but how the parts are used is where you will find tremendous differences)
    http://www.discovery.org/multi.....-dna-pt-2/

    Dr. Bohlin simplifies what Dr. Sternberg said a little bit here:

    “Where (chimps and humans) really differ, and they differ by orders of magnitude, is in the genomic architecture outside the protein coding regions. They are vastly, vastly, different.,, The structural, the organization, the regulatory sequences, the hierarchy for how things are organized and used are vastly different between a chimpanzee and a human being in their genomes.”
    Raymond Bohlin (per Richard Sternberg) – 9:29 minute mark of video
    http://www.metacafe.com/watch/8593991/

    “genomic architecture” is a very apt description of where the species specific differences are, and it is precisely the “genomic architecture”, i.e. the 3-D form, that is beyond explanatory power of reductive materialism.

    These following experiments get this important point of ‘form’ across far more clearly than words could ever do:

    What Do Organisms Mean? Stephen L. Talbott – Winter 2011
    Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: “Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements… take unique meaning from their context.[3]”,,,
    http://www.thenewatlantis.com/.....nisms-mean

    “Last year I had a fair chunk of my nose removed in skin cancer surgery (Mohs). The surgeon took flesh from a nearby area to fill in the large hole he’d made. The pictures of it were scary. But in the healing process the replanted cells somehow ‘knew’ how to take a different shape appropriate for the new location so that the nose now looks remarkably natural. The doctor said he could take only half the credit because the cells somehow know how to change form for a different location (though they presumably still follow the same DNA code) . — I’m getting the feeling that we’ve been nearly as reductionist in the 20-21st century as Darwin and his peers were when they viewed cells as little blobs of jelly.”
    leodp – UD blogger

    Epigenetics and neuroplasticity: The case of the rewired ferrets – April 3, 2014
    Excerpt: Like inventive electricians rewiring a house, scientists at the Massachusetts Institute of Technology have reconfigured newborn ferret brains so that the animals’ eyes are hooked up to brain regions where hearing normally develops.
    The surprising result is that the ferrets develop fully functioning visual pathways in the auditory portions of their brains. In other words, they see the world with brain tissue that was only thought capable of hearing sounds.
    – per UD

    If DNA really rules (morphology), why did THIS happen? – April 2014
    Excerpt: Researchers implanted human embryonic neuronal cells into a mouse embryo. Mouse and human neurons have distinct morphologies (shapes). Because the human neurons feature human DNA, they should be easy to identify.
    Which raises a question: Would the human neurons implanted in developing mouse brain have a mouse or a human morphology?
    Well, the answer is, the human neurons had a mouse morphology. They could be distinguished from the mouse ones only by their human genetic markers.
    If DNA really ruled, we would expect a human morphology.”
    – per UD

    DNA doesn’t even tell teeth what they should look like – April 3, 2014
    Excerpt: A friend writes to mention a mouse experiment where developing tooth buds were moved so that the incisors and the molars were switched. The tooth buds became the tooth appropriate to the switched location, not the original one, in direct contrast to what we would expect from a gene’centric view.
    – per UD

    Moreover, given my brief summation in post 29 & 30 of the necessity of non-local Quantum Information to explain protein folding, I am firmly convinced, from empirical considerations, that the ‘3-D form’ of the organism is forever beyond materialistic explanation:

    Verse:

    139:13-16
    For you created my inmost being;
    you knit me together in my mother’s womb.
    I praise you because I am fearfully and wonderfully made;
    your works are wonderful,
    I know that full well.
    My frame was not hidden from you
    when I was made in the secret place,
    when I was woven together in the depths of the earth.
    Your eyes saw my unformed body;
    all the days ordained for me were written in your book
    before one of them came to be.

  70. 70
    gpuccio says:

    EugeneS:

    Thank you! 🙂

  71. 71
    Virgil Cain says:

    Larry Moran:

    So, you maintain that ID is not mostly about anti-evolution, right?

    Read the essay I linked to and come back when you have something of substance to say about it.

    Do you doubt that natural selection includes random mutation, Larry? Mayr goes over that in “What Evolution Is”.

    And last but not least, the most ironic comment of them all ….

    And yet you failed to cite the irony. You quote me and it is obvious you don’t grasp what you quoted.

    All you have done is prove that you do not understand what ID says nor what is being debated.

  72. 72
    gpuccio says:

    Virgil Cain:

    Common design is a reasonable possible explanation for some features, especially for the functional similarities. However, I think that it cannot explain everything, for example the differences in similar proteins that seem, at least in part, to accumulate because of neutral variation.

    Of course, I have always thought, and affirmed, that much of the differences between sequences which are usually considered neutral could in reality be functional diversifications, and therefore differentiated design could in part explain them. But IMO it is really difficult to think that all the differences in similar sequences are functional. We do know that many variations are really neutral: for example, we see a lot of that variance in human proteins, and they really seem to have no functional effects. Therefore, if we can see (as we do see) some continuity of apparently neutral variation in conserved molecules, which have some correspondence to cronology of species, IMO that is a very strong argument for Common Descent. Frankly, I am not aware of any convincing alternative explanation. I remain open minded, but my intellectual duty is to acc ept the best explanation available.

    Regarding fossils, I don’t know. I have never been really interested in fossils, and it is not my field of knowledge.

  73. 73
    Virgil Cain says:

    Evidence for ID, starting with the letter A:

    ATP synthase- An irreducibly complex system that consists of two subsystems that have two different functions.

    Bacterial Flagella- all of them- more irreducible complexity, not only in the function but also in the assembly. And then there is the command and control the organism has over it.

    Cilia- even more irreducible complexity

    Directed evolution, like we see with evolutionary and genetic algorithms may be able to produce them. But to say they are the result of differing accumulations of genetic accidents, errors and mistakes is an extraordinary claim and as such requires extraordinary evidence.

    But all you can do is attack me, as if that somehow helps. And your attacks have been limp noodles. Surely you can do better than that.

    And if I posted the drool that you do I would find myself a pseudonym to hide behind.

  74. 74
    Virgil Cain says:

    gpuccio- Thanks for the response:

    True, common design only explains the similarities. The differences are explained by the required variations of the theme for the particular environments.

    As for Common Descent- consider this: If the changes in the genomes cannot account for the physiological and morphological differences observed, then what is the mechanism for the changes required? What is modified in the “descent with modification” paradigm to achieve the diversity observed? And how can we test it?

    Why can’t we take fish embryos, subject them to many series of targeted mutagenesis and see if a fish-a-pod eventually develops?

    Have you read “Why is a Fly Not a Horse?” by Giuseppe Sermonti?

  75. 75
    Vy says:

    Given that no one has ever observed unlimited plasticity in an organism, then I don’t think the genetic evidence, (nor the fossil evidence for that matter, Meyer, Luskin, Tattersall), is compelling to the hypothesis of common descent in the least.

    In addition to what BA said in #69 (partly quoted above), I know common descent is nonsense until it’s proven there was anything to “descend” to in the first place – where’s the evidence the mythical first-cell isn’t mythical?
    This requires proving abiogenesis and considering the fact that it’s a rehashed version of a theory that Blaise Pascal and his contemporaries decisively refuted over a century ago, I don’t see any hope in such.

    To the Darwinist, “abiogenesis is NOT evolution!!!!!!! but it’s pretty much a known fact that “you can take a pig out of the sty but you can’t take the sty out of the pig”. Dress it up all you want, give it a new name like, say, “Smrig” but it will never stop being a pig. 😀

    And no, hand-wavings, smokescreens, appeals to the future, double-standard “doesn’t mean Goddidit” while being perfectly A-OK with “probablymaybecouldnessdidit comments, hedging, ad hominems and snide remarks etc. don’t impress me.

    After all, deluding yourself into thinking having a baking device is irrelevant to actually baking doesn’t change the reality of the fact that without that device, you ain’t baking. You might as well call start “mind-cooking”.

  76. 76
    Virgil Cain says:

    Larry Moran- Do you think the genetic code is a real code (like Morse Code is a real code)?

    If you do what would you say to people who claim the genetic code isn’t a real code? Get a real life?

    You ask how can YECs be taken seriously and we ask how can anyone who says the genetic code isn’t really a code be taken seriously?

  77. 77
    Mapou says:

    Andre:

    Please tell us Prof Moran? How does unguided processes create guided processes to prevent unguided processes from happening in the first place?

    Beautiful. This is an excellent question that goes to the heart of the stupidity of Darwinism but don’t ask Moran. He has no clue.

  78. 78
    Virgil Cain says:

    Vy @ 68- Even if the nebula hypothesis is correct, if the proto-earth didn’t reach 20,000 K then the crystals we are testing could easily be from the debris, which would be very old to begin with.

    It’s like trying to find the age of Stonehenge by determining the age of the stones.

  79. 79
    Larry Moran says:

    Virgil Cain asks,

    Larry Moran- Do you think the genetic code is a real code (like Morse Code is a real code)?

    Yes. That’s how I describe it in my textbook.

  80. 80
    ThickPython says:

    @BornAgain:

    “Python, don’t read it. I don’t care. You are certainly not the first atheist on UD to refuse to deal honestly with the evidence that refutes your position.”

    Wow, I asked a genuine question – is there some other method of inheritance that is not DNA – and I get 4 enormous posts back. Granted, some of those links look interesting and I’m certainly open to seeing where they lead. I’m still very skeptical about it though – and I don’t know if this is a parody of your position or not – but are you suggesting that the whole body plan of organisms is somehow determined by the cell membrane? Though I do recall well-qualified people throwing out the words “HOX genes” in reference to body plans … thoughts and feelings please in 250 words or less.

    “I still can’t get over the feeling that there is something very fishy with your results.”

    Sure, will happily engage with on-topic stuff.

    “I have a question, was the chimp genome that you used to compare the human genome to assembled and oriented based on a map/framework built for chimpanzee and not for humans?”

    I actually used two versions of each genome in my paper. The first versions were the older genomes to match those used by Tomkins, meaning my results would be comparable (and those are the versions you quoted in your comment). In the third experiment, where I compared all chromosomes, I used the latest versions at the time – CHIMP2.1.4 (panTro4) and GRCh38. I do recall someone saying that the current chimp assembly is now based on a de novo assembly but I haven’t been able to verify that anywhere yet.

    Whether the assembly I used was based on the human genome as a framework isn’t important in this kind of comparison anyway, because of the way the query sequences were split into small slices. So when it found a match, it didn’t matter where the match was found as long as it found one. In any case, we’ve known since at least 1982 that aren’t any large scale rearrangements between the chimp and human genomes, so in my not so humble opinion this issue is massively overblown.

    “Frankly, I think the whole set up that you used is rigged to give Darwinists the answers they want.”

    Even ignorant people are entitled to their own opinions.

    “Given the fact that the chimpanzee genome is at least 10 percent larger”

    Can you back that up? Whether it is larger or isn’t larger doesn’t bother me much at all, just want to know what you’re basing it on.

    By the way, when you link to scientific papers please link to the paper itself, and not some creationist misinterpretation of it.

  81. 81
    Larry Moran says:

    Mapou says,

    Beautiful. This is an excellent question that goes to the heart of the stupidity of Darwinism but don’t ask Moran. He has no clue.

    So, if I understand you correctly, your view is that evolution and naturalistic science (i.e. “Darwinism”) can’t explain the history of life therefore gods must have done it?

    Is that correct?

  82. 82
    Virgil Cain says:

    Thank you, Larry @ 79. Thank you very much.

    Did you realize the genetic code is evidence for Intelligent Design?

  83. 83
    Larry Moran says:

    Andre says,

    I am now convinced that Prof Larry Moran is an idiot. The issue is not evolution per say Prof Moran the issue is unguided vs. guided. How does one model unguided evolution? Please tell us Prof Moran? How does unguided processes create guided processes to prevent unguided processes from happening in the first place?

    The mind boggles that a supposedly intelligent being can be so utterly dumb.

    We were trying to have a serious discussion about whether most of ID is about attacking evolution or about presenting evidence for an intelligent designer.

    Andre’s contribution is to specify that ID proponents aren’t really attacking evolution, per se, they are only attacking the idea that evolution is due to naturalistic forces.

    Presumably, there’s another version of evolution called “guided evolution” that ID proponents won’t attack.

    Tell me more about this “guided evolution”? Does it involve fossils that are millions of years old, extinct dinosaurs, and genetic differences that look just like naturalistic evolution?

    Where is all the evidence for this version of evolution and why do you call it evolution?

    Oh, you don’t have any evidence, you say? All you can do is attack scientific evolution and show that it’s impossible.

    Hmmmm … isn’t that what I’ve been saying all along?

  84. 84
    Larry Moran says:

    Virgil Cain asks,

    Did you realize the genetic code is evidence for Intelligent Design?

    No. Really?

    OMG! Where’s the nearest church?

    This is getting boring. Is this the best that ID proponents can do?

  85. 85
    Mapou says:

    Moran:

    So, if I understand you correctly, your view is that evolution and naturalistic science (i.e. “Darwinism”) can’t explain the history of life therefore gods must have done it?

    Is that correct?

    Absolutely. There can be no doubt about it. Call them gods, aliens, advanced beings or whatnot. Makes no difference.

    Hint: No stochastic search process can beat the combinatorial explosion. Unless, of course, you’re a Darwinist and you failed at simple math.

  86. 86
    Virgil Cain says:

    Earth to Larry Moran- ID does not require any church. And the genetic code is evidence for ID for the simple reason is that codes only come from intelligence and no one would even know how to test the claim that mother nature can produce one. The genetic code is the same sign for design as the presence of work is the sign for design in archaeology and forensic science. The code is evidence for work.

    What’s the best you can do, Larry? What is the evidence that drift and natural selection can produce ATP synthase? What does such a claim predict?

    If you want boring just post your answers to those questions

  87. 87
    Mapou says:

    Moran:

    Tell me more about this “guided evolution”? Does it involve fossils that are millions of years old, extinct dinosaurs, and genetic differences that look just like naturalistic evolution?

    How do you know it’s naturalistic since you only have exactly 1 sample: living organisms on earth and you weren’t there to see fish turn into reptiles? I don’t see why fossils that are millions of years old and extinct dinosaurs can be used as evidence against design.

    I hypothesize that the designers either had false starts and caused the extinctions themselves or they were just experimenting with different ecosystems starting from way before the Cambrian explosion. In other words, a very long process of terraforming apparently took place over hundreds of millions of years (if you’re immortal, there is no big hurry. Time is all you got). I believe that we humans are the end product of this grand experiment which is still going on as I write.

  88. 88
    beau says:

    Professor Moran I’ve noticed when you get in a position that makes you u uncomfortable you always reach for the “but you haven’t proved the designer” card. You say
    Thus Neo-Darwinism is false.

    It’s just another attack on evolution by an ID proponent who puts his own spin on what evolutionary biologists are saying. There’s not a single word on proving that gods an intelligent designer is behind developmental biology.

    It seems rather lazy to act as if questioning evolution depends on proof of a designer. They could both be false, regardless you’re smart enough to know for other ideas to be taken seriously there has to be doubt cast on the prevailing the theory. Maybe that’s bad wording? If it doesn’t appear to be broke then why try to fix it?

  89. 89
    Smidlee says:

    @ Mapou 85

    In other words you are not a believer in the “principle of continuity” which is not a scientific view but a religious view. No doubt if this principle of continuity is the ultimate “truth” then evolution is without question.
    In my view the evidence doesn’t fit this world view.

  90. 90
    Mapou says:

    Smidlee @89,

    Yes. The Law of continuity is crackpottery, of course. Continuity is about as stupid as it gets. Zeno and Parmenides refuted all that nonsense thousands of years ago. It’s a religion of cretins. Even Einstein, Mr. Continuity, had serious doubts about it at the end of his life. We live in a discrete reality by logical necessity.

  91. 91
    bornagain says:

    Python your disingenuous response is duly noted and filed in the round file cabinet with all the other disingenuous responses I’ve received from atheists through the years.

    Like I said, I don’t care if you read the references or not. I’ve dealt with dishonest atheists for too many years to care anymore. You are on your own, and I’m certainly not going to spoon feed you.

    The references I provided clearly show that DNA is not the only method of inheritance. Which is the specific claim you made. Unless you can show, by experiment, how membranes are encoded by DNA (which they are now shown not to be), as far as empirical science in concerned, your neo-Darwinian position is now considered refuted. It is nothing personal. That is just the way science works.

    The Scientific Method – Richard Feynman – video
    Quote: ‘If it disagrees with experiment, it’s wrong. In that simple statement is the key to science. It doesn’t make any difference how beautiful your guess is, it doesn’t matter how smart you are who made the guess, or what his name is… If it disagrees with experiment, it’s wrong. That’s all there is to it.”
    https://www.youtube.com/watch?v=OL6-x0modwY

    As for you implying that I hold that membrane patterns encode the entire body plan, I never implied such a thing and made it clear that the empirical evidence from protein folding, and proteins in particular, indicates that an additional non-material, beyond space and time, cause must be appealed to in order to explain the ‘non-local’ quantum information now found in proteins, (posts 29 & 30), i.e. appealed to in order to explain even the ‘form’ of proteins themselves.
    Thus, since even the ‘form’ of proteins require such a ‘non-local’ cause to be appealed to, then certainly ‘body plans’ also need to appeal to a non-local, i.e. beyond space and time, cause as well.

    As to you calling me an idiot for mistrusting evidence coming from Darwinists, all I can say is that, given the long history of fraudulent claims from Darwinists (i.e. Piltdown man, Nebraska man, Vestigial organs, Junk DNA, Nick Matzke, etc.. etc..,,, to name a few frauds off the top of my head), you have to be a complete idiot to trust anything Darwinists ever say about anything without checking their claim from multiple independent, trustworthy, and unbiased, sources.

    Other than atheists being completely dishonest with even the simplest of evidence that might hint at design in the least, I’m sure that Darwinists might be a good group of people overall.

    Too bad that ‘being good’, per se, does not get you to heaven, and only accepting the forgiveness of Christ does.

  92. 92
    Mapou says:

    Moran:

    OMG! Where’s the nearest church?

    Moran’s purpose here has nothing to do with science. He is just another Dawkins who’s only interested in bashing Christianity. Like Dawkins, he must have been molested by some priest or some Church pastor as a kid.

    But then again, the purpose of Darwinism has always been to bash Christianity.

  93. 93
    ThickPython says:

    @BornAgain:

    Please read my “disingenous response” again, but this time, remove the ants from your pants before doing so:

    “Granted, some of those links look interesting and I’m certainly open to seeing where they lead.”

    And I mean that. I’d never come across this ‘membrane’ claim before today, and it’s worthy of some investigation. Still, at this point I’m quite skeptical – saying it is “at least as important as DNA” is a pretty hefty burden of proof to assume.

    Also, I asked you about your claim that the chimpanzee genome is 10% larger than the human genome. Please read my recent blog post on this topic before responding:

    https://roohif.wordpress.com/2015/10/19/how-big-is-the-chimpanzee-genome/

  94. 94
    mike1962 says:

    Moran: Tell me more about this “guided evolution”? Does it involve fossils that are millions of years old, extinct dinosaurs, and genetic differences that look just like naturalistic evolution?

    Mapou: How do you know it’s naturalistic.

    Moran and his ilk assume the fossils are the result of a “natural” entirely blind evolution – because that’s their ideology – and then challenge you explain why your guided evolution is “just like” his assumed blind evolution.

    The reality is neither he nor anyone else knows to what extent any of the evolution recorded in the fossils required intelligent intervention and/or front-loading, and what was obtained by “blind” processes.

    Moran and his ilk don’t have the humility to admit that they simply don’t know if their vaunted blind evolution is capable of producing all of the organisms found in the fossils. Hell, we have living organisms, humans and chimps, available for extremely detailed examination, and they cannot give us anything close to a detailed account of what kind of variations/mutations, and in what order, it takes to turn something like a chimp’s brain into a human brain. And yet they expect people to buy their snake oil story telling about the extremely limited evidence from eons past. Uh huh.

    Doubtful you will convert the faithful. The best you can do is challenge them and allow them to express their ideology for all to see and assess.

  95. 95
    ThickPython says:

    @jeffblue10

    Sorry for not responding earlier, I completely missed your post.

    “a single query is not a valid debunking or criticism of Tomkins work. According to his own paper on chromosome 20 using Numcer he received results ranging from 61% to 100% from multiple queries when comparing chimpanzee to human dna,”

    I think you are fundamentally misunderstanding the problem with Tomkins’ methodology, and then what I have done in response. Both of our studies take a large number of queries into account to come to a final result – not just a single query. The problem with Tomkins’ study is that he includes matches that should not be included. That is, he should only be including the “best hit” for that query sequence (and has previously acknowledged explicitly that this is what should be done). If you include every hit as he does in his newest study, then – if your query sequences contains a well known repeat – you will be including all those hits across the chromosome. To demonstrate the absurdity of this, I used the same method to compare a human chromosome to itself and came to a result of 88%.

    “IMO, Williamson needs to perform the same amount of queries comparing human to human using Numcer too see whether or not there is a trend near 100% before debunking Tompkins use of the average between human and ape.”

    No, it is precisely because Tomkins is returning too many alignments that is the problem. His alignments cover the target sequence around twenty to thirty times, due to his inclusion of many millions of “false hits” for well known repeat sequences.

    I think I understand what your concern is though, as it relates to his 2013 paper, and my (unpublished) response (see Dropbox link in the OP). Tomkins did a “comprehensive” comparison – that is he attempted to align the entire query sequence against the target, while I only performed 10,000 queries per chromosome (something around 2%-3% of the total genome). I realise people have a “common sense” objection to this – “he only did 3% of the genome!” – but this is one of those cases where “common sense” is actually wrong. Please read the explanation (and link) in my paper, or consult a statistician 🙂

  96. 96
    mike1962 says:

    Virgil: Did you realize the genetic code is evidence for Intelligent Design?

    Larry Moran: No. Really?

    Yep. SETI is looking for coded information as a sign of intelligence.

    One need look no farther than the genetic code.

    From SETI web site:

    How do you know if you’ve detected an intelligent, extraterrestrial signal?

    The main feature distinguishing signals produced by a transmitter from those produced by natural processes is their spectral width, i.e. how much room on the radio dial do they take up? Any signal less than about 300 Hz wide must be, as far as we know, artificially produced. Such narrow-band signals are what all SETI experiments look for. Other tell-tale characteristics include a signal that is completely polarized or the existence of coded information on the signal.

    http://www.seti.org/faq

    Larry Moran: OMG! Where’s the nearest church?

    Pure presumptive bigotry. What does that have to do with the fact that coded information (one of the things SETI is looking for as a sign of intelligence) exists in each cell in your decrepit old body? (Although if I did meet whoever(s) designed the DNA/ribosome coded information system, I might be a little bit tempted to bow down in obeisance.)

    I suggest you get some humility.

  97. 97
    bornagain says:

    DNA is not nearly as important as you think it is Python. Besides Wells’s work I suggest that you look at Noble’s and Shapiro’s work, (as well as Talbott’s work) etc….

    The Third Way – people
    http://www.thethirdwayofevolution.com/people

    How life changes itself: the Read-Write (RW) genome. – 2013
    Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.
    http://www.ncbi.nlm.nih.gov/pubmed/23876611

    James Shapiro on “dangerous oversimplifications” about the cell – August 6, 2013
    Excerpt: “Depending upon the energy source and other circumstances, these indescribably complex entities can reproduce themselves with great reliability at times as short as 10-20 minutes. Each reproductive cell cycle involves literally hundreds of millions of biochemical and biomechanical events. We must recognize that cells possess a cybernetic capacity beyond our ability to imitate. Therefore, it should not surprise us when we discover extremely dense and interconnected control architectures at all levels. Simplifying assumptions about cell informatics can be more misleading than helpful in understanding the basic principles of biological function.
    Two dangerous oversimplifications have been (i) to consider the genome as a mere physical carrier of hypothetical units called “genes” that determine particular cell or organismal traits, and (ii) to think of the genome as a digitally encoded Read-Only Turing tape that feeds instructions to the rest of the cell about individual characters [4].”
    http://www.uncommondescent.com.....-the-cell/

    Revisiting the Central Dogma in the 21st Century – James A. Shapiro – 2009
    Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112).
    http://shapiro.bsd.uchicago.ed.....0Dogma.pdf

    “The genome is an ‘organ of the cell’, not its dictator”
    – Denis Noble – President of the International Union of Physiological Sciences

    Modern Synthesis Of Neo-Darwinism Is False – Denis Noble – video
    http://www.metacafe.com/w/10395212
    ,, In the preceding video, Dr Nobel states that around 1900 there was the integration of Mendelian (discrete) inheritance with evolutionary theory, and about the same time Weismann established what was called the Weismann barrier, which is the idea that germ cells and their genetic materials are not in anyway influenced by the organism itself or by the environment. And then about 40 years later, circa 1940, a variety of people, Julian Huxley, R.A. Fisher, J.B.S. Haldane, and Sewell Wright, put things together to call it ‘The Modern Synthesis’. So what exactly is the ‘The Modern Synthesis’? It is sometimes called neo-Darwinism, and it was popularized in the book by Richard Dawkins, ‘The Selfish Gene’ in 1976. It’s main assumptions are, first of all, is that it is a gene centered view of natural selection. The process of evolution can therefore be characterized entirely by what is happening to the genome. It would be a process in which there would be accumulation of random mutations, followed by selection. (Now an important point to make here is that if that process is genuinely random, then there is nothing that physiology, or physiologists, can say about that process. That is a very important point.) The second aspect of neo-Darwinism was the impossibility of acquired characteristics (mis-called “Larmarckism”). And there is a very important distinction in Dawkins’ book ‘The Selfish Gene’ between the replicator, that is the genes, and the vehicle that carries the replicator, that is the organism or phenotype. And of course that idea was not only buttressed and supported by the Weissman barrier idea, but later on by the ‘Central Dogma’ of molecular biology. Then Dr. Nobel pauses to emphasize his point and states “All these rules have been broken!”.
    Professor Denis Noble is President of the International Union of Physiological Sciences.

    “Physiology Is Rocking the Foundations of Evolutionary Biology”: Another Peer-Reviewed Paper Takes Aim at Neo-Darwinism – Casey Luskin March 31, 2015
    Excerpt: Noble doesn’t mince words:
    “It is not only the standard 20th century views of molecular genetics that are in question. Evolutionary theory itself is already in a state of flux (Jablonka & Lamb, 2005; Noble, 2006, 2011; Beurton et al. 2008; Pigliucci & Muller, 2010; Gissis & Jablonka, 2011; Shapiro, 2011). In this article, I will show that all the central assumptions of the Modern Synthesis (often also called Neo-Darwinism) have been disproved.”
    Noble then recounts those assumptions: (1) that “genetic change is random,” (2) that “genetic change is gradual,” (3) that “following genetic change, natural selection leads to particular gene variants (alleles) increasing in frequency within the population,” and (4) that “inheritance of acquired characteristics is impossible.” He then cites examples that refute each of those assumptions,,,
    He then proposes a new and radical model of biology called the “Integrative Synthesis,” where genes don’t run the show and all parts of an organism — the genome, the cell, the body plan, everything — is integrated.
    http://www.evolutionnews.org/2.....94821.html

    As to the 10% difference claim, it is not something I’m wedded to. Like I said, my evidence against common ancestry, as far as DNA is concerned, is, first and foremost, based on the established fact that Body Plans are not reducible to DNA in the first place.
    As far as hard ball empirical science is concerned, that fact renders your neo-Darwinian claims moot and void!

    Moreover, as much importance as you seem to be placing on the similarity of DNA in order to try to establish your case for common descent, it seems clear that you are hedging your bets a little bit at the end of your paper. i.e. your claim is ‘hesitant’ in its certainty as to exact degree of similarity and/or dissimilarity.

    As far as hard nose established facts are concerned, I’m less than impressed with your claim to put it mildly. (and even if I fully accepted your claim, so what? The evidence still does not go one inch towards solving your elephant in the living room problem of DNA not being the major player that you, and all other neo-Darwinists, thought it was!)

  98. 98
    ThickPython says:

    @BornAgain:

    “Moreover, as much importance as you seem to be placing on the similarity of DNA in order to try to establish your case for common descent”

    No, please read post #22. Genetic similarity – in and of itself – is not evidence of common descent. For me, the proof of common descent lies in the fact that there are different protein sequences across the spectrum of organisms but these sequences are functionally equivalent (which has been tested empirically). These sequences can then be used to build a phylogenetic tree, and that tree matches other trees built using independent data. As I said, the differences between these sequences do not affect the level of function of the protein, so design and/or creation is a very poor explanation of their existence. On the other hand, common descent is an excellent explanation – these differences (and similarities) are neutral mutations that became fixed in a common ancestor.

    ” … it seems clear that you are hedging your bets a little … “

    No, please read the last paragraph of post #6. In my paper, I’m (rather clumsily) saying that the number is most certainly up around 97%, but there are various methods that can give slightly higher or slightly lower numbers, and the merits of those methods are up for debate. I’m saying the method I used in my paper is one of the more conservative methods.

  99. 99
    vjtorley says:

    I would like to remind readers that when we have a distinguished guest commenting on Uncommon Descent, a certain level of civility is warranted. Larry Moran is a Professor of Biochemistry at the University of Toronto. Calling a professor an “idiot” or a “big baby” is downright rude, and I expect the guilty parties to be manful enough to apologize.

    I’d like to conclude with a quote from a 2004 article by Dr. William Dembski, titled, Dealing with the Backlash against Intelligent Design:

    Fighting, however, is not advised either. The problem with fighting is that it consumes valuable energies and is motivated by anger, which always distorts mental clarity and distracts from the real issues. As John Cassian noted over 1,500 years ago,

    No matter what provokes it, anger blinds the soul’s eyes, preventing it from seeing the Sun of righteousness. Leaves, whether of gold or lead, placed over the eyes, obstruct the sight equally, for the value of the gold does not affect the blindness it produces. Similarly, anger, whether reasonable or unreasonable, obstructs our spiritual vision. Our incensive power can be used in a way that is according to nature only when turned against our own impassioned or self-indulgent thoughts.

    So, let’s put anger aside. Let the other side fume with indignation.

  100. 100
    vjtorley says:

    Professor Moran,

    Thank you very much for your response (#57). Commenting on the article by Jonathan Wells which I recommended to you, you wrote:

    It’s just another attack on evolution by an ID proponent who puts his own spin on what evolutionary biologists are saying. There’s not a single word on proving that gods an intelligent designer is behind developmental biology.

    Two quick points in response:

    1. Dr. Wells was writing a science article. He was trying to stick to the facts. I imagine that’s why he avoided speculation about an intelligent designer, although I would have had no problem with him discussing that.

    2. In any case, it seems to me that the real problem is that there are several distinct codes inside the living cell. Theories of unguided evolution need to explain how these distinct codes in the cell managed to co-ordinate their evolution, over four billion years. Obviously, an explanation which focuses on just one code (the genetic code) is not going to do the job. The only kind of agent known to be capable of co-ordinating multiple disparate processes towards a common goal is an intelligent agent. The only way that a defender of unguided evolution could rebut this claim, it seems to me, is to argue that in reality, these codes are not separate from one another, but that something is co-ordinating the evolution of all these codes in each lineage of living organisms.

  101. 101
    vjtorley says:

    Hi gpuccio,

    Thank you very much for your reflections at #55 above. I pretty much agree with what you wrote, and I greatly appreciate the depth of thought you have given to these issues. Clearly, there is much that we do not know, but design remains the most valid explanation for the origin of the genetic code, and for the vast amount of functional information found in proteomes and genomes. Thank you once again.

  102. 102
    vjtorley says:

    Hi Virgil Cain,

    You ask: “Have you considered a common design to account for the genetic similarities and the appearance of the fossil succession is due to terraforming?”

    I certainly believe that terraforming is an excellent explanation of the fossil succession. I believe that the Earth was deliberately designed to be shaped by successive waves of organisms (including the dinosaurs) until it became hospitable for intelligent life.

    Re common design vs. common descent: I believe in both. They complement each other. However, common design alone cannot explain why we find switched-off genes coding for the production of egg yolks in human DNA. Only the hypothesis that humans are descended from an eggg-laying ancestor can explain that.

  103. 103
    bornagain says:

    Python first off, until you establish that mutations to DNA can effect Body Plan morphogenesis (Meyer’s ‘Darwin’s Doubt’), all you have are imaginary conjectures based on biased sequence comparisons.

    You simply do not have the real time empirical evidence you need to make your case.

    Without you having that real time empirical evidence, you telling me that you think common descent is a better explanation for life is about as meaningful as you saying that you prefer the color blue to orange.

    So what? I don’t care for what you prefer to be true. I only care for what you can empirically demonstrate in real time to be true.

    Which brings me to my second point. That point being, despite the programming of the cell being orders of magnitude more advanced than anything man has ever programmed in his computers, you, nor any other neo-Darwinists, have any real time empirical evidence whatsoever for your claim that unguided material processes can create non-trivial functional information. NONE, ZILCH, NADA!!!

    For instance, The last four decades worth of lab work are surveyed here, and no evidence for neo-Darwinian evolution surfaces. Not even a single gene and protein was created. In fact, breaking stuff in order to gain a short term advantage was the ‘rule’:

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.
    http://behe.uncommondescent.co.....evolution/

    How about the oft cited example from neo-Darwinists of antibiotic resistance?

    List Of Degraded Molecular Abilities Of Antibiotic Resistant Bacteria:
    Excerpt: Resistance to antibiotics and other antimicrobials is often claimed to be a clear demonstration of “evolution in a Petri dish.” ,,, all known examples of antibiotic resistance via mutation are inconsistent with the genetic requirements of evolution. These mutations result in the loss of pre-existing cellular systems/activities, such as porins and other transport systems, regulatory systems, enzyme activity, and protein binding.
    per True Origin

    That doesn’t seem to be helping.
    How about we look really, really, close at very sensitive growth rates and see if we can find any evidence for neo-Darwinian evolution?

    Unexpectedly small effects of mutations in bacteria bring new perspectives – November 2010
    Excerpt: Most mutations in the genes of the Salmonella bacterium have a surprisingly small negative impact on bacterial fitness. And this is the case regardless whether they lead to changes in the bacterial proteins or not.,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed.
    http://www.physorg.com/news/20.....teria.html

    Well, that doesn’t seem to be helping either.
    How about if we just try to fix an unconditionally ‘beneficial’ mutation by sustained selection?

    Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) – October 2010
    Excerpt: “Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, “This research really upends the dominant paradigm about how species evolve,” said ecology and evolutionary biology professor Anthony Long, the primary investigator.
    http://www.arn.org/blogs/index.....ruit_flies

    Well that’s certainly disappointing.
    How about if try to help neo-Darwinian evolution out a little and just saturate genomes with mutations until we can actually see some ‘evolution’ in action?

    Response to John Wise – October 2010
    Excerpt: A technique called “saturation mutagenesis”1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans–because none of the observed developmental mutations benefit the organism.
    http://www.evolutionnews.org/2.....38811.html

    Now this is starting to get a little frustrating.
    Perhaps we just have to give neo-Darwinian evolution a little ‘room to breathe’?
    How about we ‘open the floodgates’ and look at Lenski’s Long Term Evolution Experiment and see what we can find after 50,000 generations, which is equivalent to somewhere around 1,000,000 years of supposed human evolution?

    Richard Lenski’s Long-Term Evolution Experiments with E. coli and the Origin of New Biological Information – September 2011
    Excerpt: The results of future work aside, so far, during the course of the longest, most open-ended, and most extensive laboratory investigation of bacterial evolution, a number of adaptive mutations have been identified that endow the bacterial strain with greater fitness compared to that of the ancestral strain in the particular growth medium. The goal of Lenski’s research was not to analyze adaptive mutations in terms of gain or loss of function, as is the focus here, but rather to address other longstanding evolutionary questions. Nonetheless, all of the mutations identified to date can readily be classified as either modification-of-function or loss-of-FCT.
    (Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” Quarterly Review of Biology, Vol. 85(4) (December, 2010).)
    http://www.evolutionnews.org/2.....51051.html

    Lenski’s Long-Term Evolution Experiment: 25 Years and Counting – Michael Behe – November 21, 2013
    Excerpt: Twenty-five years later the culture — a cumulative total of trillions of cells — has been going for an astounding 58,000 generations and counting. As the article points out, that’s equivalent to a million years in the lineage of a large animal such as humans. Combined with an ability to track down the exact identities of bacterial mutations at the DNA level, that makes Lenski’s project the best, most detailed source of information on evolutionary processes available anywhere,,,
    ,,,for proponents of intelligent design the bottom line is that the great majority of even beneficial mutations have turned out to be due to the breaking, degrading, or minor tweaking of pre-existing genes or regulatory regions (Behe 2010). There have been no mutations or series of mutations identified that appear to be on their way to constructing elegant new molecular machinery of the kind that fills every cell. For example, the genes making the bacterial flagellum are consistently turned off by a beneficial mutation (apparently it saves cells energy used in constructing flagella). The suite of genes used to make the sugar ribose is the uniform target of a destructive mutation, which somehow helps the bacterium grow more quickly in the laboratory. Degrading a host of other genes leads to beneficial effects, too.,,, –
    http://www.evolutionnews.org/2.....79401.html

    Now that just can’t be right.
    We should really start to be seeing some neo-Darwinian fireworks by 50,000 generations!
    Hey, I know what we can do. How about we see what happened when the ‘top five’ ‘beneficial mutations from Lenski’s experiment were combined?
    Surely now the Darwinian magic will start flowing?

    Mutations : when benefits level off – June 2011 – (Lenski’s e-coli after 50,000 generations)
    Excerpt: After having identified the first five beneficial mutations combined successively and spontaneously in the bacterial population, the scientists generated, from the ancestral bacterial strain, 32 mutant strains exhibiting all of the possible combinations of each of these five mutations. They then noted that the benefit linked to the simultaneous presence of five mutations was less than the sum of the individual benefits conferred by each mutation individually.
    http://www2.cnrs.fr/en/1867.htm?theme1=7

    Now something is going terribly wrong here. Isn’t neo-Darwinian evolution an established fact on par with gravity?
    Tell you what, let’s just forget trying to observe evolution in the lab. I mean it really is kind of cramped in the lab, and let’s REALLY open the floodgates and let’s see what neo-Darwinian evolution can do with the ENTIRE WORLD at its disposal.
    Surely now neo-Darwinian evolution will flex its awesomely powerful muscles for all to see and forever make those IDiots, who believe in Intelligent Design, cower in terror!

    A review of The Edge of Evolution: The Search for the Limits of Darwinism
    The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155).
    http://creation.com/review-mic.....-evolution

    “The immediate, most important implication is that complexes with more than two different binding sites-ones that require three or more proteins-are beyond the edge of evolution, past what is biologically reasonable to expect Darwinian evolution to have accomplished in all of life in all of the billion-year history of the world. The reasoning is straightforward. The odds of getting two independent things right are the multiple of the odds of getting each right by itself. So, other things being equal, the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the world in the last 4 billion years, so the odds are against a single event of this variety in the history of life. It is biologically unreasonable.”
    – Michael Behe – The Edge of Evolution – page 146

    Now, there is something terribly wrong here!
    After looking high and low and everywhere in between, we can’t seem to find any substantiating evidence for neo-Darwinism anywhere!
    It is as if the whole neo-Darwinian theory, relentlessly sold to the general public as it was the gospel truth, is nothing but a big fat lie!

    Verse:

    John 1:1-3
    In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made.

  104. 104
    Virgil Cain says:

    vjtorley- Thank you for your response. You say:

    However, common design alone cannot explain why we find switched-off genes coding for the production of egg yolks in human DNA.

    It would depend if they were always off, ie never expressed. Do you have a reference?

    Only the hypothesis that humans are descended from an egg-laying ancestor can explain that.

    By what mechanism are humans descended from egg-layers?

  105. 105
    Mapou says:

    Larry Moran does not deserve any respect. He deserves the same disdain and mockery that he uses on others. If I offended Moran, well, whoop-dee-doo! He will get no apology from me, that’s for sure. I hope others feel likewise.

  106. 106
    ThickPython says:

    @BornAgain:

    ” … based on biased sequence comparisons”

    Please explain your use of the word “biased”.

  107. 107
    bornagain says:

    “we find switched-off genes coding for the production of egg yolks in human DNA. Only the hypothesis that humans are descended from an eggg-laying ancestor can explain that.”

    I can think of other hypothesis, one good one being that you don’t have a real clue what the sequence actually does in humans.

    But then again, don’t let me stop you from falling into the Darwinian trap of thinking you are smarter than God.

    i.e. the old ‘God would have not done it that way therefore Darwinism must be true’ argument.

    By golly it is about time we had an ID proponent who thought he was smarter than God too! I’m tired of Darwinists being the only ones who think that! 🙂

    Methodological Naturalism: A Rule That No One Needs or Obeys – Paul Nelson – September 22, 2014
    Excerpt: It is a little-remarked but nonetheless deeply significant irony that evolutionary biology is the most theologically entangled science going. Open a book like Jerry Coyne’s Why Evolution is True (2009) or John Avise’s Inside the Human Genome (2010), and the theology leaps off the page. A wise creator, say Coyne, Avise, and many other evolutionary biologists, would not have made this or that structure; therefore, the structure evolved by undirected processes. Coyne and Avise, like many other evolutionary theorists going back to Darwin himself, make numerous “God-wouldn’t-have-done-it-that-way” arguments, thus predicating their arguments for the creative power of natural selection and random mutation on implicit theological assumptions about the character of God and what such an agent (if He existed) would or would not be likely to do.,,,
    ,,,with respect to one of the most famous texts in 20th-century biology, Theodosius Dobzhansky’s essay “Nothing in biology makes sense except in the light of evolution” (1973).
    Although its title is widely cited as an aphorism, the text of Dobzhansky’s essay is rarely read. It is, in fact, a theological treatise. As Dilley (2013, p. 774) observes:
    “Strikingly, all seven of Dobzhansky’s arguments hinge upon claims about God’s nature, actions, purposes, or duties. In fact, without God-talk, the geneticist’s arguments for evolution are logically invalid. In short, theology is essential to Dobzhansky’s arguments.”,,
    http://www.evolutionnews.org/2.....89971.html

    Nothing in biology makes sense except in light of theology? – Dilley S. – 2013
    Abstract
    This essay analyzes Theodosius Dobzhansky’s famous article, “Nothing in Biology Makes Sense Except in the Light of Evolution,” in which he presents some of his best arguments for evolution. I contend that all of Dobzhansky’s arguments hinge upon sectarian claims about God’s nature, actions, purposes, or duties. Moreover, Dobzhansky’s theology manifests several tensions, both in the epistemic justification of his theological claims and in their collective coherence. I note that other prominent biologists–such as Mayr, Dawkins, Eldredge, Ayala, de Beer, Futuyma, and Gould–also use theology-laden arguments. I recommend increased analysis of the justification, complexity, and coherence of this theology.
    http://www.ncbi.nlm.nih.gov/pubmed/23890740

  108. 108
    bornagain says:

    Python, I will as soon as you produce real time empirical evidence to back up your grandiose claims for unguided material processes producing functional information that far exceeds our best efforts.

    First things first as far as empirical science is concerned, OK?

    Moreover, since I’m not into playing stupid games with atheists who refuse to deal honestly with real time empirical evidence that clearly refutes their position, I’m out of here.

    Good night and good bye.

  109. 109
    bloodymurderlive says:

    Moran @ 84
    Well, yeah… a “code” is good evidence for ID. Unless Moran knows of a way these kinds of information systems emerge spontaneously from natural processes…

  110. 110
    ThickPython says:

    “Python, I will as soon as you produce real time empirical evidence to back up your grandiose claims for unguided material processes producing functional information that far exceeds our best efforts.”

    Easy tiger.

    Mutations can and do occur randomly, and can become fixed in a genome. I think Lenski’s experiment is good evidence of both of those things. Notice I’m not saying that all mutations are random, just that randomness is one of the drivers of mutation. As for the functional equivalence of certain proteins, i think Hampsey 1986 is an excellent demonstration of that – http://www.jbc.org/content/261/7/3259.abstract. So you’ve got all these similarities and differences that map out nicely onto a phylogenetic tree derived from other, independent data. Common descent explains it easily.

    How do you explain that from a design perspective? Why is the human sequence 100% identical to the chimpanzee sequence? When you look at all the sequences across the biosphere, you’ll see that there is quite the variation in sequence, but they are functionally equivalent. On what grounds can you invoke a design inference when there is no difference in function?

    And can I just say that I’ve never made the claim that “unguided material processes produc[ed] functional information”. For the sake of argument, I’ll happy accept that this designer created the first living cell with a broad set of functional genes. The problem is that you need to explain the sequences we see in the current day.

    “Good night and good bye.”

    Night night, princess. Sleep tight xx.

  111. 111
    Mapou says:

    bloodymurderlive:

    Moran @ 84
    Well, yeah… a “code” is good evidence for ID. Unless Moran knows of a way these kinds of information systems emerge spontaneously from natural processes…

    Moran is caught between a code and a hard place. Let’s see how good he is at squeezing himself through the eye of a needle. I’ll be watching him squirm with a bag of cheetos in one hand, a beer in the other and a smile on my face.

    LOL

  112. 112
    Mapou says:

    VJT:

    Re common design vs. common descent: I believe in both. They complement each other. However, common design alone cannot explain why we find switched-off genes coding for the production of egg yolks in human DNA. Only the hypothesis that humans are descended from an eggg-laying ancestor can explain that.

    Why is that? Why could not a designer simply switch off an unneeded gene that is part of an existing (pre-designed) organism or genome? But then again, maybe early humans used to lay eggs. Maybe early humans were originally designed as egg-laying hermaphrodites. There is evidence in the book of Genesis and other ancient mythological stories for this.

  113. 113
    nkendall says:

    Dear Dr. Moran and ThickPython

    The opening statements of James Shapiro’s book entitled, Evolution: A View from the 21st Century are:

    “Innovation, not selection, is the critical issue in evolutionary change. Without variation and novelty, selection has nothing to act upon. So this book is dedicated to considering the many ways that living organisms actively change themselves. Uncovering the molecular mechanisms by which living organisms modify their genomes is a major accomplishment of late 20th Century molecular biology. Conventional evolutionary theory made the simplifying assumption that inherited novelty was the result of chance or accident.”

    He goes on to explain that these innovations are not random “mutations”. Rather they are engineered by the cell using “natural Genetic Engineering” techniques which he says were present even in the earliest cells. He does not know how these marvelous natural engineering techniques arose. But it strikes me that the only way one could hold to a darwinian view point given what Dr. Shapiro is presenting as scientific fact, is to suggest that these natural genetic engineering mechanisms, which he seems to suggest account for the entire range of adaptations from macro changes involving new organs and cell types and proteins to the micro changes such as the variety of colors on a butterfly’s wing, are themselves the result of the tandem neo-darwinian mechanisms of random mutation and natural selection. However:

    1) How can it be imagined that even simple adaptations require sophisticated natural genetic engineering mechanisms while the far more complex function of a system for engineering all variety of adaptive changes would have had to have evolved by chance and selection?

    2) How could such a sophisticated set of techniques have arisen so quickly by chance and without any immediate survival need of the present organism?

    3) How could an engineering technique, which according to darwinists must have evolved by chance and selection, have the foreknowledge to engineer extraordinarily complex adaptations far in the future and do so time and time again?

  114. 114
    ThickPython says:

    @nkendall:

    “He does not know how these marvelous natural engineering techniques arose.”

    I don’t know either, and I don’t claim to.

    Like I said above, I’m happy to accept for the sake of argument that life was designed by an intelligence and plonked into a primordial soup, because even if that’s true, common descent is still by far the best explanation for the diversity of species we see today.

  115. 115
    computerist says:

    He goes on to explain that these innovations are not random “mutations”. Rather they are engineered by the cell using “natural Genetic Engineering” techniques which he says were present even in the earliest cells. He does not know how these marvelous natural engineering techniques arose. But it strikes me that the only way one could hold to a darwinian view point given what Dr. Shapiro is presenting as scientific fact, is to suggest that these natural genetic engineering mechanisms, which he seems to suggest account for the entire range of adaptations from macro changes involving new organs and cell types and proteins to the micro changes such as the variety of colors on a butterfly’s wing, are themselves the result of the tandem neo-darwinian mechanisms of random mutation and natural selection. However:

    Indeed, darwinian/evomat explanations have in my view always been lagging relative to the evidence, aka: they’re far too simplistic, and “under-violate” ocaam’s razor. One question that comes to my mind is; is it easier to be an ID proponent or an evomat relative to the evidence and its necessary explanatory requirements? I find that the answer is always the latter case. Design as a result of various design implementations can sometimes be tricky to parse, I feel that darwinian explanations have taken a major shortcut in accounting for the mechanisms in question and in the process they have created the illusion of explanatory power. It’s more Evoillusion than anything else, so to speak.

  116. 116
    Andre says:

    Dr Torley

    Looks like I have to defend my comment on calling Prof Moran an idiot, so in what context do I do so? Well an idiot is defined as;

    Idiot

    a stupid person.
    synonyms: fool, ass, halfwit, dunce, dolt, ignoramus, cretin, moron, imbecile, simpleton; informaldope, ninny, nincompoop, chump, dimwit, dumbo, dummy, dum-dum, loon, dork, sap, jackass, blockhead, jughead, bonehead, knucklehead, fathead, butthead, numbskull, numbnuts, dumb-ass, doofus, clod, dunderhead, ditz, lummox, knuckle-dragger, dipstick, thickhead, meathead, meatball, wooden-head, airhead, pinhead, lamer, lamebrain, peabrain, birdbrain, mouth-breather, scissorbill, jerk, nerd, donkey, nitwit, twit, boob, twerp, hoser, schmuck, bozo, turkey, chowderhead, dingbat, mook;
    vulgar slangasshat

    I’ve highlighted the one I meant in context of this discussion. I will ignore all the other descriptions and make my case for Prof Moran’s ignorance.

    He quoted Virgil can several times and most of those quotes only dispute unguided evolution yet Prof Moran kept on insisting that Virgil Cain is just anti-evolution The only reasonable explanation for this is of course Prof Moran’s ignorance.

    A Ph.D is not a free pass to negate idiocy.

  117. 117
    Larry Moran says:

    Mapou says,

    Moran is caught between a code and a hard place. Let’s see how good he is at squeezing himself through the eye of a needle. I’ll be watching him squirm with a bag of cheetos in one hand, a beer in the other and a smile on my face.

    I’m not sure why you say this. There are several reasonable explanations for the evolution of the modern genetic code without the necessity of an intelligent designer.

    Are you saying that you have carefully examined all of these explanations and you can prove that none of them are possible therefore gods must have done it?

    We have some very clear examples of changes in the genetic code for several different amino acids. Are you rejecting all of the data and evidence for these minor variants? If not, doesn’t that show that at least some parts of a genetic code can evolve by natural means?

    It’s pretty easy to imagine how the codon for selencysteine could have evolved and also the codons for N-formymethionine and pyrrolysine. Tell me why you don’t believe that those explanations are feasible.

    We’re almost certain that we know how the codons for asparagine and glutamine arose because we have examples of intermediates in bacteria.

    These examples establish the principle that parts of a genetic code can arise by unguided evolution. Do you reject them all? Am I supposed to be squirming because you arbitrarily reject all evidence of the evolution of the genetic code after having looked carefully at the data?

    I’m sure you must be familiar with all the evidence and the explanations because otherwise you would have no right to be so cocky. Please tell my why you reject Jeff Wong’s theory of the origin of the genetic code? (He was one of my colleagues in the Department of Biochemistry at the University of Toronto.) It’s one of the most popular explanations so I’m sure you must have thought carefully about it in order to prove that it’s impossible.

  118. 118
    Andre says:

    Prof Moran

    Where is all the evidence for this version of evolution and why do you call it evolution?

    1. The DNA Code
    2. The DNA Integrity Check systems (evolutionary conserved)
    3. The DNA Repair Mechanisms (evolutionary conserved)
    4. The DNA Apoptosis mechanisms (evolutionary conserved)
    5. The DNA Necrotic System. (evolutionary conserved)

    If you can demonstrate that such a system can come about by natural processes Prof Moran then I will gladly abandon my view that it requires Intelligence to build such systems. What we see here is engineering principles like, redundancy, trade-offs, backups etc.

    I said before I’m not attached to an outcome I’m open to it. So please can you in any way demonstrate that its even plausible for natural processes to build these systems?

    And if you can’t why do you still think its possible?

  119. 119
    bFast says:

    ThickPython, “So you’ve got all these similarities and differences that map out nicely onto a phylogenetic tree derived from other, independent data. Common descent explains it easily.”

    Thick, I bumped into this video ( https://youtu.be/arSkMn5UwGM?t=5m23s ) recently. It has kinda shaken me. He starts with Dawkins’ claim that the FOXP2 gene is a great example of this wonderful tree. Well, it isn’t. The chimp is way the heck in the wrong place. Its not a bit wrong, it’s way wrong. The video goes on to look at the FOXP1 and FOXP3. They describe two totally different trees re the primates. So I have been playing evolution in my little mind with these guys. I thought, well, maybe this gene just edited a little slower and that a little faster. Maybe the molecular clocks aren’t ticking in perfect sync, they often don’t. But it doesn’t work. These different trees do not synchronize in the least little way. Well, that’s not totally accurate, but they do not produce a mapping that is in any way close enough to be explained by common descent with gradual modification. Just these three genes say NO!

    Please help me out here. Though I hold to ID, I also have held to universal common descent. Yet the FOXP* genes (and I understand, most other genes. Remember, this was selected because it was Dawkins’ poster child.) seem to defy UCD.

  120. 120
    Andre says:

    Prof Moran

    We have some very clear examples of changes in the genetic code for several different amino acids. Are you rejecting all of the data and evidence for these minor variants? If not, doesn’t that show that at least some parts of a genetic code can evolve by natural means?

    The variants of course say nothing about how such an actual code came about. Can you give us any account how natural processes can actually manufacture such a code from scratch?

  121. 121
    Andre says:

    Prof Moran

    These examples establish the principle that parts of a genetic code can arise by unguided evolution. Do you reject them all? Am I supposed to be squirming because you arbitrarily reject all evidence of the evolution of the genetic code after having looked carefully at the data?

    Are you saying now that NS and RM increase information? Did you not say earlier that NS removes information? So now NS is both a destroyer and a creator?

    But you are still not addressing the issue on how such a code started de novo using material processes, you seem to assume the code already intact and only then evolution can work its magic.

  122. 122
    Andre says:

    Prof Moran

    It’s pretty easy to imagine how the codon for selencysteine could have evolved and also the codons for N-formymethionine and pyrrolysine. Tell me why you don’t believe that those explanations are feasible.

    It’s also easy to imagine That cold fusion can work, and that is the problem our imagination trying to find answers to things instead of the actual facts on how it is.

    You just gave your A game away, all you have is your imagination on it.

  123. 123
    Andre says:

    Prof Moran

    Please tell my why you reject Jeff Wong’s theory of the origin of the genetic code? (He was one of my colleagues in the Department of Biochemistry at the University of Toronto.) It’s one of the most popular explanations so I’m sure you must have thought carefully about it in order to prove that it’s impossible.

    Firstly, something being popular has no bearing on its truthfulness. Secondly Eugene Koonin has already debunked any notion that a genetic code has the ability to create itself and the only work around is a multiverse, Do you consider a multiverse science Prof Moran?

    Here is a link to his paper, Origin and evolution of the genetic code;

    http://www.ncbi.nlm.nih.gov/pm.....MC3293468/

    Thus, many years of experimentation including the latest extensive studies on aptamer selection show that the code is not based on a straightforward stereochemical correspondence between amino acids and their cognate codons (or anticodons). Direct interactions between amino acids and polynucleotides might have been important at some early stages of code’s evolution but hardly could have been the principal factor of the code’s evolution. Almost the same seems to apply to the coevolution theory: the possibility exists that evolution of amino acid metabolism and evolution of the code were, to some extent, linked, but this coevolution cannot fully explain the properties of the code. The verdict on the adaptive theory of code evolution, in particular, the hypothesis that the code was shaped by selection for error minimization, is different: in our view, this is the only concept of the code evolution that can legitimately claim to be positively relevant as (so far) no attempt to explain the observed robustness of the code to translation errors without invoking at least some extent of selection has been convincing.

    So what do we have? NS & RM, drift, neutral theory all have an influence on the code (not a single Creationist or ID person disputes this to my knowledge) but they cannot explain how the code originated. Should we stop trying to find a natural mechanism for the possible creation of the genetic code? No we should keep probing but the least anyone can do and that includes you Prof Moran is sell a story that believes it knows how this happened, you simply do not, regardless of how much your imagination thinks it might be.

  124. 124
    Andre says:

    Prof Moran

    futher in Eugene Koonin’s conclusion and this is for you specifically…..

    Before closing this discussion, it makes sense to ask: do the analyses described here, focused on the properties and evolution of the code per se, have the potential to actually solve the enigma of the code’s origin? It appears that such potential is problematic because, out of necessity, to make the problems they address tractable, all studies of the code evolution are performed in formalized and, more or less, artificial settings (be it modeling under a defined set of code transformation or aptamer selection experiments) the relevance of which to the reality of primordial evolution is dubious at best. The hypothesis on the causal connection between the universality of the code and the collective character of primordial evolution characterized by extensive genetic exchange between ensembles of replicators (118) is attractive and appears conceptually important because it takes the study of code evolution from being a purely formal exercise into a broader and more biologically meaningful context. Nevertheless, this proposal, even if quite plausible, is only one facet of a much more general and difficult problem, perhaps, the most formidable problem of all evolutionary biology. Indeed, it stands to reason that any scenario of the code origin and evolution will remain vacuous if not combined with understanding of the origin of the coding principle itself and the translation system that embodies it. At the heart of this problem is a dreary vicious circle: what would be the selective force behind the evolution of the extremely complex translation system before there were functional proteins? And, of course, there could be no proteins without a sufficiently effective translation system.

    That raise the question of course, if the code built itself (Your view) from scratch how did the translation system come about at the same time?

  125. 125
    Andre says:

    Prof Moran

    I’m going to use a real world code as an example of why your imagination just don’t work. I have Windows 10, I install a clean copy of it, I use the system and over time it accumulates junk, faults, and garbage but never ever does the code with any accumulation of that said junk, and garbage turn into Linux. No matter how long I run the system and even if it finally meets its doom via the dreaded Blue screen of death it remained just that; A Windows Operating System.

    It never built itself and it could never ever evolve into anything other than Windows unless the designers intervened and programmed it to do so.

    The same principles apply to our genetic code. Now it might become Windows 11 with specific updates that is released by the designers, and the current Windows 10 code will have included in the source code a provision for that to happen, thus guided evolution of Windows 10 to Windows 11.

    I suspect our own genetic code works in much the same way. We have provisioning mechanisms for upgrades or possible downgrades.

  126. 126
    Mapou says:

    Moran:

    Mapou says,

    Moran is caught between a code and a hard place. Let’s see how good he is at squeezing himself through the eye of a needle. I’ll be watching him squirm with a bag of cheetos in one hand, a beer in the other and a smile on my face.

    I’m not sure why you say this. There are several reasonable explanations for the evolution of the modern genetic code without the necessity of an intelligent designer.

    Are you saying that you have carefully examined all of these explanations and you can prove that none of them are possible therefore gods must have done it?

    I knew you’d be squirming. I got a bag cheetos in one hand and a beer in the other, just for the occasion. LOL.

    The answer is that all I need to do is to falsify just one aspect of your randomly-created DNA code hypothesis. Just one. And it’s very easy to falsify your pseudoscience. The combinatorial explosion (CE) simply kills it before it was born. This is the fate of all stochastic search mechanisms. You could have a random search mechanism as big as zillions upon zillions of universes and it would not make a difference. And the mechanism would have to be actively looking for something. But, if it were, that would destroy the randomness of it all, would it not? Now imagine how big the search space for a mosquito or a rat genome is.

    But it gets worse, much worse. If a search mechanism has no idea what it’s looking for, the search space becomes infinite. Read it and weep.

    Conclusion: Every so-called plausible explanation you may have for the origin of DNA is just pseudoscience based on wishful thinking and superstition. And it will always be that way, you know why? It’s because (say it real loud now) the combinatorial explosion kills it. Thank you very much.

    The CE is a bitch, I know.

  127. 127
    butifnot says:

    VJ @ 100

    2. In any case, it seems to me that the real problem is that there are several distinct codes inside the living cell.

    – Exponentially more complex – distinct yet interacting/interconnected
    – An absolute roadblock to natural explanation

    – That we know of so far
    – Let alone ‘meta-codes’, codes manipulating other codes!

  128. 128
    gpuccio says:

    Virgil Cain @ #74:

    True, common design only explains the similarities. The differences are explained by the required variations of the theme for the particular environments.

    As for Common Descent- consider this: If the changes in the genomes cannot account for the physiological and morphological differences observed, then what is the mechanism for the changes required? What is modified in the “descent with modification” paradigm to achieve the diversity observed? And how can we test it?

    As I have said in my previous post, I do believe that a significant part of the differences is functional, and is responsible, at least in part, for functional differences and adaptations between different species. In that sense, this part could be explained by common design.

    I don’t believe, however, that all the differences are functional. I think that there is ample evidence for neutral variation. And neutral variation is evidence for common descent.

    As I have said, I remain open minded about common descent, but with the available evidence I strongly accept it. I have no ideological issues about CD: it’s just the facts that bring me to accept it. If you believe differently, I certainly respect your judgement.

    I can only support VJ’s statement:

    “Re common design vs. common descent: I believe in both.”

    I believe in common and differentiated intelligent design through common descent. That is, IMO, the only theory which can explain the functional similarities, the functional differences, and the non functional similarities and differences.

    I have read Sermonti, probably not that specific book, but I know his ideas, and I agree with them. Today, epigenetics is a new source of understanding about many of the problems highlighted by Sermonti, first of all the problem of form in biological beings.

    But our understanding of epigenetics is at present still primordial. And there is no doubt that epigenetics, at all its levels, is a depository of astounding functional complexity, that we are just beginning to decode.

  129. 129
    Andre says:

    Gpuccio.

    I can only accept common descent if it’s a guided process, an unguided process is very unlikely to lead to universal common decent. I share the same sentiments as Dr. Craig Venter. It was a breath of fresh air that somebody of his stature would openly deny the dogma.

    https://www.youtube.com/watch?v=MXrYhINutuI

  130. 130
    Vy says:

    We have some very clear examples of changes in the genetic code for several different amino acids

    So all you have is “changes”, eh? And that relates to how the thing that is being changed came into existence how???

    I have clear examples of changes in the JS, HTML and CSS code of a webpage from the webpage itself, it doesn’t explain where the JS, HTML and CSS code came from.

    You, oh “distinguished” one, are grasping at MEGASIZED straws.

  131. 131
    Vy says:

    We have some very clear examples of changes in the genetic code for several different amino acids.

    So all you have is “changes”, eh? And that relates to how the thing that is being changed came into existence how???

    I have clear examples of changes in the JS, HTML and CSS code of a webpage from the webpage itself, it doesn’t explain where the JS, HTML and CSS code came from.

    You, oh “distinguished” one, are grasping at MEGASIZED straws.

  132. 132
    Virgil Cain says:

    Larry Moran:

    There are several reasonable explanations for the evolution of the modern genetic code without the necessity of an intelligent designer.

    then someone should be testing them to see if they pan out.

    There is a 3.1 million dollar offer to anyone who can demonstrate such a thing. Technology Prize for Origin of Information

    If Wong is right then he should have no problem collecting- if he can actually demonstrate what he says.

    These examples establish the principle that parts of a genetic code can arise by unguided evolution.

    So all things evolution support unguided evolution? Is that your “argument”?

  133. 133
    Virgil Cain says:

    There are several reasonable explanations for the evolution of the modern genetic code without the necessity of an intelligent designer.

    The evolution of the modern genetic code from a primitive genetic code does not explain the origin of the genetic code. You need to be able to account for the origin of the genetic code. Also the alleged evolution of the modern genetic code is not, by itself, evidence for unguided evolution.

    Failure 101, Larry

  134. 134
    bornagain says:

    The hypothesis of common descent has far deeper problems than many Darwinists, and apparently some ID proponents, are willing to believe.

    Dr. Hunter observes these following fundamental falsified predictions coming from the hypothesis of common descent (among many other falsifications of neo-Darwinian predictions):

    Common descent predictions

    The pentadactyl pattern and common descent
    Serological tests reveal evolutionary relationships
    Biology is not lineage specific
    Similar species share similar genes
    MicroRNA

    Evolutionary phylogenies predictions

    Genomic features are not sporadically distributed
    Gene and host phylogenies are congruent
    Gene phylogenies are congruent
    The species should form an evolutionary tree
    https://sites.google.com/site/darwinspredictions/home

    etc.. etc..

    If you take the time to read those falsifications on Dr. Hunter’s site, you can see those certainly are not minor falsifications of the predictions stemming from the hypothesis of common descent, but indeed go to the very heart of the hypothesis and show it to be very highly questionable if not completely false, (i.e. see Imre Lakatos: Science and Pseudoscience).

    For instance, there are ‘remarkably discontinuous’ glycans which are not reducible to the DNA code in the first place

    The Membrane Code: A Carrier of Essential Biological Information That Is Not Specified by DNA and Is Inherited Apart from It – Jonathan Wells – published online May 2013
    Excerpt: ,,In 1985 Ronald Schnaar wrote, “There appears to be a code on the surface of each cell that specifies its function and directs its interactions with other cells, a code in some ways comparable to the genetic code carried on the DNA molecules inside each cell.” The “letters” of the cell surface code to which Schnaar was referring are sugar molecules. A few monosaccharide building blocks can produce the enormous diversity of “words” needed to identify the many different kinds of cells in a complex organism, Schnaar explained, because “each building block can assume several different positions. It is as if an A could serve as four different letters, depending on whether it was standing upright, turned upside down, or laid on either of its sides. In fact, seven simple sugars can be rearranged to form hundreds of thousands of unique words, most of which have no more than five letters. (This alphabet is even more efficient than the genetic code: the four nucleic acids that constitute DNA — guanine, adenine, thymine, and cytosine — can be connected only front to back, like roller coaster cars.) So, not only are sugars in the right place to serve as the alphabet for the cell-surface code, they have the requisite structural flexibility too.” Schnaar concluded, “It may be that as much control over the cell’s fate, and as much of the language of life’s unfolding, reside on the cell’s surface as in its nucleus” [63].,,
    Membrane patterns in ciliates are known to be heritable independently of the information in DNA sequences, and there is evidence that some cytoskeletal and membrane patterns in the cells of multicellular organisms can also be inherited apart from the DNA. Taken together, the data suggest that embryo development is not controlled by DNA alone, and thus that DNA mutations are not sufficient to provide raw materials for evolution.
    http://www.worldscientific.com.....08728_0021

    Glycans: What Makes Them So Special? – The Complexity Of Glycans – short video
    http://www.youtube.com/watch?v=WXez_OyNBQA

    This Non Scientific Claim Regularly Appears in Evolutionary Peer Reviewed Papers – Cornelius Hunter – April 2012
    Excerpt: Indeed these polysaccharides, or glycans, would become rather uncooperative with evolution. As one recent paper explained, glycans show “remarkably discontinuous distribution across evolutionary lineages,” for they “occur in a discontinuous and puzzling distribution across evolutionary lineages.” This dizzying array of glycans can be (i) specific to a particular lineage, (i) similar in very distant lineages, (iii) and conspicuously absent from very restricted taxa only. In other words, the evidence is not what evolution expected.
    Here is how another paper described early glycan findings:
    There is also no clear explanation for the extreme complexity and diversity of glycans that can be found on a given glycoconjugate or cell type. Based on the limited information available about the scope and distribution of this diversity among taxonomic groups, it is difficult to see clear trends or patterns consistent with different evolutionary lineages. It appears that closely related species may not necessarily share close similarities in their glycan diversity, and that more derived species may have simpler as well as more complex structures. Intraspecies diversity can also be quite extensive, often without obvious functional relevance.
    http://darwins-god.blogspot.co.....larly.html

    Did you guys catch that? “occur in a discontinuous and puzzling distribution across evolutionary lineages.”?

    That is certainly not something to be ignored for anyone who is trying to be truthful to the evidence at hand both for and against common descent.

    My question is why do ID proponents so willingly ignore all these major flaws in the hypothesis of common descent, (see Dr. Hunter’s site), but so willingly accept the hypothesis as a fact? Especially without any real time empirical support for the presumption of unlimited plasticity? and Especially since it is based on such biased methodology for extracting ‘cooperative sequences’ as is practiced in the field?

    “These incongruities have forced evolutionists to filter the data carefully in order to obtain evolutionary trees. As one paper explains, “selecting genes with strong phylogenetic signals and demonstrating the absence of significant incongruence are essential for accurately reconstructing ancient divergences.” (Salichos and Rokas) But this raises the question of whether the resulting tree is real: “Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL [tree of life] rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true.” (Doolittle and Bapteste).”
    https://sites.google.com/site/darwinspredictions/the-species-should-form-an-evolutionary-tree

  135. 135
    tjguy says:

    Dr. Moran @ 117:

    There are several reasonable explanations for the evolution of the modern genetic code without the necessity of an intelligent designer.

    Reasonable is a subjective term, not a scientific term. If it could be tested, then that would be quite a powerful argument, but lacking that ability, so many assumptions must be made to interpret what we see.

    Dr. Moran says to Mung:

    So, if I understand you correctly, your view is that evolution and naturalistic science (i.e. “Darwinism”) can’t explain the history of life therefore gods must have done it?
    Is that correct?

    Since Darwinism cannot explain the history of life, is it possible that gods(God) might have done it?

    Is that a possible answer to the problem or does your worldview preclude you from even entertaining that as a possibility?

  136. 136
    tjguy says:

    bfast said:

    I think it reasonable to assume that de novos grew in the “junk” until they were ready to be implemented. But why the heck would a gene that has meaning grow in junk that has no guidance.

    VT said:

    You suggest that de novo genes “are not ‘poofed’ into existence, but that they do grow, mutation by mutation,” and you propose that they may be growing in “DNA used for some purpose other than protein coding.”

    Now that’s an interesting suggestion, which I hadn’t considered. If true, it would explain why these genes need to be built up step by step.

    I find this suggestion to be quite incredible. Like bfast said: “But why the heck would a gene that has meaning grow in junk that has no guidance?”

    How could this be possible? Did it just happen to build the perfect gene necessary for the new function? How could such genes just happen into existence by totally blind random directionless mutations? How many such mutations would be necessary to produce the denovo gene?

    Could it have happened once or twice? Perhaps, but are you suggesting this is a common process that happened over and over again in the history of life? That just does not seem rational to me. Is there a way to test the credibility of such an idea? Are there such genes being built now in our genome? Sure would be nice if this hypothesis could be tested.

  137. 137
    Sebestyen says:

    VT wrote:

    “You suggest that de novo genes “are not ‘poofed’ into existence, but that they do grow, mutation by mutation,” and you propose that they may be growing in “DNA used for some purpose other than protein coding.”

    Now that’s an interesting suggestion, which I hadn’t considered. If true, it would explain why these genes need to be built up step by step.”

    That’s like saying a feasible way to add a new function to a piece of software is by filling a module with random letters and then let a script randomly exchange letters at random positions until the module successfully compiles.

    I hope I don’t have to emphasize how utterly retarded that idea is.

    Sebestyen

  138. 138
    gpuccio says:

    Andre:

    Of course it is guided common descent. I have never thought anything different.

  139. 139
    Box says:

    What it boils down to, professor Moran, is that you are just a bag filled with chemicals. And none of those molecules can be said to have “you” in mind. None of those molecules is interested in “you”.

    It follows then that, in fact, there is no “you”. Is there? Isn’t that “your” key message?
    According to “your” precious naturalism, there is no person ‘in there’, so to speak, who controls the molecules. The molecules obey just one master: the law of nature.

    So, professor Moran, it is not really “you” who is in control and writes posts. In fact non-rational molecules subordinate to non-rational laws of nature are doing the “thinking”.

    Can “you” — read: bag filled with molecules — give us one reason why we should give serious consideration to what non-rational purposeless blind molecules subordinate to purposeless blind non-rational laws of nature have to say?

    Reppert: . . let us suppose that brain state A, which is token identical to the thought that all men are mortal, and brain state B, which is token identical to the thought that Socrates is a man, together cause the belief that Socrates is mortal. It isn’t enough for rational inference that these events be those beliefs, it is also necessary that the causal transaction be in virtue of the content of those thoughts . . . [But] if naturalism is true, then the propositional content is irrelevant to the causal transaction that produces the conclusion, and [so] we do not have a case of rational inference. In rational inference, as [C S] Lewis puts it, one thought causes another thought not by being, but by being seen to be, the ground for it. But causal transactions in the brain occur in virtue of the brain’s being in a particular type of state that is relevant to physical causal transactions.

  140. 140
    Larry Moran says:

    Andre says,

    If you can demonstrate that such a system can come about by natural processes Prof Moran then I will gladly abandon my view that it requires Intelligence to build such systems. What we see here is engineering principles like, redundancy, trade-offs, backups etc.

    I said before I’m not attached to an outcome I’m open to it. So please can you in any way demonstrate that its even plausible for natural processes to build these systems?

    I understand your position. You, personally, can’t see any rational and reasonable naturalistic explanation for the existence of the genetic code therefore you conclude that an intelligent designer exists who could make species and insert into them the necessary genes and proteins for interpreting the genetic code.

    I say that you are basing your conclusion on attacking and rejecting evolutionary explanations rather than on presenting positive evidence that such an intelligent designer actually exists and is capable of doing what you claim.

    For some reason you disagree. Why? Your position isn’t that the mere existence of the genetic code proves intelligent design because surely you agree that there could, in theory, be a naturalistic explanation. Your position has to be based on the idea that such a naturalistic explanation is impossible or highly improbable to you.

    From there you leap to the idea of an intelligent designer who can create species. That’s not a logical leap unless you already believe in the existence of such a designer based on entirely different “evidence.”

    The vast majority of scientists who are knowledgeable about this topic do not see it the way you do. We do not think that a naturalistic explanation can be ruled out based on our knowledge of biochemistry and molecular biology. Therefore, we do not feel compelled to invent a story about a supernatural intelligent designer.

    Why do you think you have a better insight than these experts? It’s possible that you have studied biochemistry and molecular biology and that you know more than we do. It wouldn’t be the first time that experts have been proven wrong by better experts. What what I’ve seen over the past few days I’m confident that you are not very knowledgeable about this topic.

    Another possibility is that you actually don’t know a lot about the genetic code and molecular biology but you do know a lot about how people think. You conclude that the vast majority of experts must be wrong because they have a materialistic bias that prevents them from seeing the explanation you prefer.

    I suspect that this is your main rationalization. That’s fine but you need to be honest enough to admit it when you are advancing your case.

    In conclusion, your “evidence” for the existence of an intelligent designer is based on your pre-existing, non-scientific, belief that such a being exists plus your rejection of any naturalistic explanation. Your rejection is probably not based on expert knowledge and you almost certainly realize that the traditional experts don’t agree with you. Thus, an important part of your logic relies on discrediting the experts, probably by claiming that they have a materialistic bias that prevents them from seeing alternative explanations involving gods.

    But that position, anti-materialism, is itself based on a prior commitment to a belief in supernatural beings.

    I conclude that in spite of what you say you are not providing evidence for the existence of gods based just on the existence of a genetic code.

    We been over this ground many time in discussions about irreducible complexity. That argument has two parts just like the the existence of the genetic code. The first part is whether irreducibly complex things exist. They do. The second part is whether they can be explained by unguided evolution. Some of them can. It’s the second part that’s important.

    You’re asking me to “demonstrate that such a system can come about by natural processes.” On the surface this looks like a perfectly reasonable request from someone who really wants to learn about biochemistry. But that not the case here. You have already made up your mind that the existence of the genetic code is evidence of an intelligent designer and that MUST mean that you have already rejected the possibility of any naturalistic explanation.

    Since your rejection is not based on knowledge of the topic, it must be based on your distrust of scientists. Many of your comments confirm that you won’t ever believe anything a scientist says. I conclude that no answer from a scientist will ever satisfy you.

  141. 141
    bornagain says:

    Larry Moran, we know for a 100% fact that intelligence can produce codes. Whereas no one has ever seen unguided material processes do it.

    Deal with it.

    If you want to get into further argument as to Who the Intelligence is behind that code, perhaps you can talk to Dawkins, Crick, and even Hoyle, who all, at one time or the other, admitted that aliens could be the ‘intelligence’ behind DNA

    Ben Stein vs. Richard Dawkins Interview (3:20 mark)
    https://youtu.be/GlZtEjtlirc?t=200

    PANSPERMIA
    Excerpt: *Francis Crick received the Noble Prize for his discovery of the DNA molecule. In his 1981 book, Life Itself, he fills the first half of the book with reasons why life could not originate on our planet—and then he proceeds to suggest that it came from outer space on rockets!
    http://www.pathlights.com/ce_e.....hist11.htm

    i.e. The inference to Intelligence is based on what we do know about the cause and effect structure of the world, it is not based on what we don’t know.

    “Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source — from a mind or personal agent.”
    (Stephen C. Meyer, “The origin of biological information and the higher taxonomic categories,” Proceedings of the Biological Society of Washington, 117(2):213-239 (2004).)

    “As the pioneering information theorist Henry Quastler once observed, “the creation of information is habitually associated with conscious activity.” And, of course, he was right. Whenever we find information—whether embedded in a radio signal, carved in a stone monument, written in a book or etched on a magnetic disc—and we trace it back to its source, invariably we come to mind, not merely a material process. Thus, the discovery of functionally specified, digitally encoded information along the spine of DNA, provides compelling positive evidence of the activity of a prior designing intelligence. This conclusion is not based upon what we don’t know. It is based upon what we do know from our uniform experience about the cause and effect structure of the world—specifically, what we know about what does, and does not, have the power to produce large amounts of specified information.”
    – Stephen Meyer
    http://www.signatureinthecell......l-falk.php

    Information Enigma – 22 minute video (Meyer – Axe)
    https://www.youtube.com/watch?v=aA-FcnLsF1g

    “A code system is always the result of a mental process (it requires an intelligent origin or inventor). It should be emphasized that matter as such is unable to generate any code. All experiences indicate that a thinking being voluntarily exercising his own free will, cognition, and creativity, is required. ,,,there is no known law of nature and no known sequence of events which can cause information to originate by itself in matter.
    Werner Gitt 1997 In The Beginning Was Information pp. 64-67, 79, 107.”
    (The retired Dr Gitt was a director and professor at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt, Braunschweig), the Head of the Department of Information Technology.)

  142. 142
    Virgil Cain says:

    Larry Moran:

    I understand your position. You, personally, can’t see any rational and reasonable naturalistic explanation for the existence of the genetic code therefore you conclude that an intelligent designer exists who could make species and insert into them the necessary genes and proteins for interpreting the genetic code.

    It has nothing to do with us, personally. It is that such an explanation would be like explaining cars and computers by calling on mother nature and father time. As Dr Behe said in “Darwin’s Black Box”:

    ” Might there be some as-yet-undiscovered natural process that would explain biochemical complexity? No one would be foolish enough to categorically deny the possibility. Nonetheless, we can say that if there is such a process, no one has a clue how it would work. Further, it would go against all human experience, like postulating that a natural process might explain computers.”

    Larry:

    I say that you are basing your conclusion on attacking and rejecting evolutionary explanations rather than on presenting positive evidence that such an intelligent designer actually exists and is capable of doing what you claim.

    The evidence for the designer comes from the evidence for design. How do we know that the peoples of thousands of years ago were capable of building Stonehenge, Larry? The structure itself!

    Your position isn’t that the mere existence of the genetic code proves intelligent design because surely you agree that there could, in theory, be a naturalistic explanation. Your position has to be based on the idea that such a naturalistic explanation is impossible or highly improbable to you.

    Then all you have to do is step up and actually demonstrate such a thing is possible, larry. Do that and not only will you win 3.1 million dollars you will also get a Nobel Prize- more money- and you will have refuted ID.

    BTW, ID does not require the supernatural. With ID “natural” is contrasted with “artificial”.

    We been over this ground many time in discussions about irreducible complexity. That argument has two parts just like the the existence of the genetic code. The first part is whether irreducibly complex things exist. They do. The second part is whether they can be explained by unguided evolution. Some of them can. It’s the second part that’s important.

    By what evidence can unguided evolution produce IC systems?

    My rejection is based on my knowledge of both codes and of cause and effect relationships. Other people have anted up 3.1 million dollars because they know it is safe from being taken.

    Since your rejection is not based on knowledge of the topic, it must be based on your distrust of scientists. Many of your comments confirm that you won’t ever believe anything a scientist says. I conclude that no answer from a scientist will ever satisfy you.

    LoL! Larry just says that so he doesn’t have to try to demonstrate his case.

  143. 143
    gpuccio says:

    bFast at #119:

    I think that one of the problems when neo darwinists try to build trees according to protein genes is that all the differences are considered more or less as the result of neutral evolution, and therefore markers of evolutionary distance. My point is that a significant part of the differences, IOWs of the non conserved AA sites, is probably functional, and is part of the substrate for functional differences between species. Those differences are the result of design, not of random variation through time, and therefore they are not markers of evolutionary distance.

    That is particularly evident in transcription factors, like those you mention. If you look at distant species, you can see an interesting pattern. The DNA binding site is highly con served, but most of the rest of the protein is not. You can see that blasting the human protein against, say, drosophila.

    If you go to vertebrates, the similarity greatly increses, and so to mammals, or primates, where there is almost identity of all the molecule.

    However, the DNA binding site is in general the most conserved part of the molecule, as it happens constantly with transcription factors.

    Now, what does that mean? Is the DNA binding site (a tiny part of the molecule) the only functional part, and all the rest is useless sequence, which varies according to neutral mutations and proportionally to time separations?

    I don’t think so. While the DNA binding site is responsible for a function which remaisn rather constant, the rest of the molecule is probably responsible for functions which vary mych more from one species to another: for example, protein protein interactions which are probably very specific in each species, and define the regulatory pattern of transcription factors in different species.

    However, as I have said, it is really difficult to think that part of the variation is not neutral. I strongly beliebe that both functional variation and neutral variation occur in similar proteinsin different species. The functional variation is the result of design, ad is not related to time distance, but rather to functional purposes. The neutral variation, instead, is grossly related to time distances.

    Unfortumately, we cannot easily distinguish between the two kinds of differences. Usually, variation is considered by default the result of neutral random mutations. Trees are base on that assumption, and therefore I am not surprised that they give sometimes contradictory results.

  144. 144
    Zachriel says:

    gpuccio: Usually, variation is considered by default the result of neutral random mutations. Trees are base on that assumption, and therefore I am not surprised that they give sometimes contradictory results.

    The nested hierarchy is observed, regardless of any theory of explanation.

  145. 145
    Larry Moran says:

    Andre says,

    Firstly, something being popular has no bearing on its truthfulness. Secondly Eugene Koonin has already debunked any notion that a genetic code has the ability to create itself and the only work around is a multiverse, Do you consider a multiverse science Prof Moran?

    What you say is not correct. Eugen Koonin has published two excellent papers on the evolution of the genetic code.

    Wolf, Y.I. and Koonin, E.V. (2007) On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization. Biology Direct. 2007;2:14. [doi:10.1186/1745-6150-2-14]

    Koonin, E.V. and Novozhilov, A.S. (2009) Origin and evolution of the genetic code: the universal enigma. Iubmb Life. 2009;61(2):99-111. [doi:10.1002/iub.146].

    The papers are wonderful examples of how science works. They discuss the pros and cons of several models of genetic code evolution and conclude that right now we don’t have a really good explanation that satisfies all of the data.

    He DOES NOT conclude that a naturalistic explanation for the origin of the genetic code is impossible and he did not convert to Intelligent Design Creationism.

    It’s the second paper that is extensively quote-mined by creationists to give the impression that Eugene Koonin supports intelligent design.

    Here’s the abstract. You can see that Koonin and Novozhilov do NOT claim to have debunked that idea that the genetic code has evolved. They simply point out that it’s a difficult problem. (There’s no mention of a multiverse.)

    The genetic code is nearly universal, and the arrangement of the codons in the standard codon table is highly non-random. The three main concepts on the origin and evolution of the code are the stereochemical theory, according to which codon assignments are dictated by physico-chemical affinity between amino acids and the cognate codons (anticodons); the coevolution theory, which posits that the code structure coevolved with amino acid biosynthesis pathways; and the error minimization theory under which selection to minimize the adverse effect of point mutations and translation errors was the principal factor of the code’s evolution. These theories are not mutually exclusive and are also compatible with the frozen accident hypothesis, i.e., the notion that the standard code might have no special properties but was fixed simply because all extant life forms share a common ancestor, with subsequent changes to the code, mostly, precluded by the deleterious effect of codon reassignment. Mathematical analysis of the structure and possible evolutionary trajectories of the code shows that it is highly robust to translational misreading but there are numerous more robust codes, so the standard code potentially could evolve from a random code via a short sequence of codon series reassignments. Thus, much of the evolution that led to the standard code could be a combination of frozen accident with selection for error minimization although contributions from coevolution of the code with metabolic pathways and weak affinities between amino acids and nucleotide triplets cannot be ruled out. However, such scenarios for the code evolution are based on formal schemes whose relevance to the actual primordial evolution is uncertain. A real understanding of the code origin and evolution is likely to be attainable only in conjunction with a credible scenario for the evolution of the coding principle itself and the translation system.

    (Incidentally, it would be wonderful to see a skeptical self-critical paper like this on the possible models for how an intelligent designer made the genetic code and when it happened.)

    Andre continues,

    Should we stop trying to find a natural mechanism for the possible creation of the genetic code? No we should keep probing but the least anyone can do and that includes you Prof Moran is sell a story that believes it knows how this happened, you simply do not, regardless of how much your imagination thinks it might be.

    I do not know how the genetic code came to be. I’m confident that I know how some of the variant codon assignments evolved and that demonstrates that part of a code can arise by purely naturalistic means.

    I may not know exactly how the core of the genetic code arose but I also don’t presume to conclude that the evolution of the genetic code is impossible by naturalistic means—therefore intelligent design.

    Andre has already made that illogical leap in spite of what he says above because when I asked for evidence of an intelligent designer, he said “the Genetic Code.” You can’t have it both ways, Andre. You can’t say that we simply don’t know whether the genetic code evolved by naturalistic means and also say that it’s proof of intelligent design.

    Now it’s interesting that creationists reject just about everything that evolutionary biologists say except when they say something that appears to support intelligent design. Then, all of a sudden, that scientist becomes an authority worth quoting.

    Eugene Koonin has just been elevated to that high status so let’s see what he has to say about evolution in The Logic of Chance: The Nature and Origin of Biological Evolution.

    The evolution of life is largely a stochastic process based on historical contingency, substantially constrained by various requirements for the maintenance of basic biological organization, and modulated by adaptation. (p. 397)

    And what does this “creationist authority” have to say about intelligent design?

    ID is malicious nonsense. (p. 780)

  146. 146
    vjtorley says:

    Professor Moran writes (to Mapou):

    Please tell my why you reject Jeff Wong’s theory of the origin of the genetic code? (He was one of my colleagues in the Department of Biochemistry at the University of Toronto.) It’s one of the most popular explanations so I’m sure you must have thought carefully about it in order to prove that it’s impossible.

    If Mapou or anybody else is looking for good, solid scientific reasons why the various scientific hypotheses put forward to explain the origin of the genetic code won’t work, then the online article, Origin and evolution of the genetic code (IUBMB Life. 2009 Feb; 61(2): 99–111. doi: 10.1002/iub.146) by evolutionary biologist Dr. Eugene Koonin and Artem S. Novozhilov is an excellent reference.

    Here’s a brief excerpt which discusses the merits of Wong’s coevolution theory:

    Two major criticisms of the coevolution theory have been put forward. First, the coevolution scenario is very sensitive to the choice of amino acid precursor-product pairs, and the choice of these pairs is far from being straightforward. Indeed, in the original formulation of the coevolution theory, Wong did not directly use biochemically established relationships between amino acids but instead employed inferred reactions of primordial metabolism that remain debatable (70, 103). Amirnovin (108) generated a large set of random codes and found that, if the original 8 precursor-product pairs proposed by Wong (70) are considered, the standard code shows a substantially higher codon correlation score (a measure that calculates number of adjacent codons coding for precursor-product amino acids) than most of the random codes (only 0.1% of random codes perform better). However, after the pairs Gln-His and Val-Leu are removed (the validity of the latter pair has been questioned (109)), the proportion of better random codes rises to 3.6%, and if the precursor-product pairs are taken from the well-characterized metabolic pathways of E. coli, the proportion that a random code shows a stronger correlation reaches 34%. Second, the biological validity of the statistical analysis of Wong (70) appears dubious (109). Ronneberg et al., together with consistent definition of amino acid precursor-product pairs, suggested that, according to the wobble rule, the genetic code contains not 61 functional codons coding for amino acids, but 45 codons, where each two codons of the form NNY are considered as one because no known tRNA can distinguish codons with U or C in the third base position. Under this assumption, there was no statistical support for the coevolution scenario of the evolution of the code (109) (but see (110)).

    I hope that helps.

  147. 147
    EugeneS says:

    Folks,

    I personally don’t care if Eugene Koonin excepts or rejects ID. If he does I will mentally tick against his name that he is a sensible person. That’s all. All I really care about is what I accept or reject myself. While Koonin or anybody else for that matter is providing input of various degrees of trustworthiness and common sense, this input should be judged for what it actually is irrespective of the accolades or curses it generates. ‘Do not swim upstream or downstream. Swim where you need’, as Kozma Prutkov put it.

    The multiverse that Koonin attempts to rescue evolutionism with, is not scientific whatever they say. However, the fact itself that he understands what the problem is, is telling me volumes.

    With research, to fit any data into the desired curve sometimes all you need is a thick marker and an expression of confidence on your face.

    Nature cannot explain nature. Period. All attempts to explain nature naturalistically are Sisyphus labor.

    Thankfully, the scientific community have reached a consensus not to take seriously any attempts to disprove the validity of the 2nd law. Well done! For that, the collective intelligence of the scientific elite was enough.

    But it is just as futile to try to explain life and its irreducible core containing data, the program and the processor, all three in one holistic autonomous replicating and metabolizing whole, – as a frozen accident.

    The design of life is obvious and takes children’s level of knowledge and common sense to acknowledge. Children can sometimes teach an adult a very good lesson.

  148. 148
    bornagain says:

    As to a critique of Koonin’s own many world’s model, here is a good video.

    Dr. Paul Giem did a lecture on Dr. Koonin’s paper. In the lecture, it was found that Eugene Koonin’s estimates are grossly overly optimistic. It was almost comical to learn some of the erroneous assumptions made by Dr. Koonin to get his ‘low’ 1 in 10^1018 probability for life originating:

    Eugene Koonin and the Origin of Life 3-7-2015 by Paul Giem – video
    https://www.youtube.com/watch?v=gkB8VcfvcBQ&index=17&list=PLHDSWJBW3DNUUhiC9VwPnhl-ymuObyTWJ

  149. 149
    Andre says:

    Prof Moran

    I understand your position. You, personally, can’t see any rational and reasonable naturalistic explanation for the existence of the genetic code therefore you conclude that an intelligent designer exists who could make species and insert into them the necessary genes and proteins for interpreting the genetic code.

    No you don’t understand my position, matter of fact I am certain you don’t understand the ID position at all.

    I say that you are basing your conclusion on attacking and rejecting evolutionary explanations rather than on presenting positive evidence that such an intelligent designer actually exists and is capable of doing what you claim.

    Can we be more specific here? Do I reject unguided evolutionary explanations or do I reject guided ones? Is the bona fida Digital code of DNA not positive evidence?

    For some reason you disagree. Why? Your position isn’t that the mere existence of the genetic code proves intelligent design because surely you agree that there could, in theory, be a naturalistic explanation. Your position has to be based on the idea that such a naturalistic explanation is impossible or highly improbable to you.

    A digital code arising by chance and luck in a happenstance manner is highly improbable don’t you agree?

    From there you leap to the idea of an intelligent designer who can create species. That’s not a logical leap unless you already believe in the existence of such a designer based on entirely different “evidence.”

    Where did I say this?

    The vast majority of scientists who are knowledgeable about this topic do not see it the way you do. We do not think that a naturalistic explanation can be ruled out based on our knowledge of biochemistry and molecular biology. Therefore, we do not feel compelled to invent a story about a supernatural intelligent designer.

    The vast majority of scientists in the 16th century believed that the Ptolemaic system was true. Was it? If you actually have testable results for your claim can we have it?

    Why do you think you have a better insight than these experts? It’s possible that you have studied biochemistry and molecular biology and that you know more than we do. It wouldn’t be the first time that experts have been proven wrong by better experts. What what I’ve seen over the past few days I’m confident that you are not very knowledgeable about this topic.

    I don’t think I have better insight only that my a priori view does not cloud my judgement. Then a nice snipe at you just don’t know….. Is that your best charge against me?

    Another possibility is that you actually don’t know a lot about the genetic code and molecular biology but you do know a lot about how people think. You conclude that the vast majority of experts must be wrong because they have a materialistic bias that prevents them from seeing the explanation you prefer.

    Am I a reading a response here from a Professor at a University or is this the standard school yard bully response?

    I suspect that this is your main rationalization. That’s fine but you need to be honest enough to admit it when you are advancing your case.

    I’ve been honest with you give us a testable scenario for your claim and what we have to say will collapse spectacularly. Can you do that?

    In conclusion, your “evidence” for the existence of an intelligent designer is based on your pre-existing, non-scientific, belief that such a being exists plus your rejection of any naturalistic explanation. Your rejection is probably not based on expert knowledge and you almost certainly realize that the traditional experts don’t agree with you. Thus, an important part of your logic relies on discrediting the experts, probably by claiming that they have a materialistic bias that prevents them from seeing alternative explanations involving gods.

    Really who is really the faithful here? I already told you give me the testable results to your claims and I’ll shut up.

    But that position, anti-materialism, is itself based on a prior commitment to a belief in supernatural beings.

    I’m not an anti-materialist what ever that means. If I was I’d picket for the destruction of all matter.

    I conclude that in spite of what you say you are not providing evidence for the existence of gods based just on the existence of a genetic code.

    How did we go from design to gods? Only you keep doing that.

    We been over this ground many time in discussions about irreducible complexity. That argument has two parts just like the the existence of the genetic code. The first part is whether irreducibly complex things exist. They do. The second part is whether they can be explained by unguided evolution. Some of them can. It’s the second part that’s important.

    What can be explained by unguided evolution? Can you model unguided evolution for us?

    You’re asking me to “demonstrate that such a system can come about by natural processes.” On the surface this looks like a perfectly reasonable request from someone who really wants to learn about biochemistry. But that not the case here. You have already made up your mind that the existence of the genetic code is evidence of an intelligent designer and that MUST mean that you have already rejected the possibility of any naturalistic explanation.

    There is no “on the surface” here, give us the testable models so we can verify your claim, that is all I’m asking you or should I just take your word for it?

    Since your rejection is not based on knowledge of the topic, it must be based on your distrust of scientists. Many of your comments confirm that you won’t ever believe anything a scientist says. I conclude that no answer from a scientist will ever satisfy you.

    I don ‘t have knowledge of the topic at hand? Are you just making this up because you’re uncomfortable with my request to backup your claim with testable results? Seems to me my questions make you uncomfortable so you’ve got your defenses up and the best way to shut me up instead of showing the goods is to tell me how I don’t know.

  150. 150
    Andre says:

    I linked this paper by Eugene Koonin in an earlier post, and he makes it clear that the digital code is an enigma……

    Here is a link to his paper, Origin and evolution of the genetic code;

    http://www.ncbi.nlm.nih.gov/pm.....MC3293468/

    What is an enigma Professor Moran? Can you help this guy (me) that in your own words don’t know anything?

    Nowhere does his paper say that the digital code evolved from scratch, if anything he makes it clear that it did not!

  151. 151
    bornagain says:

    I wonder if bullying is the way Moran treats his students who won’t buckle under to his Darwinian belief system?

    Judging from the comments on rate my professor, his class must be one of the least enjoyable classes to attend at the university he teaches at.

    http://www.ratemyprofessors.co.....?tid=39948

  152. 152
    Box says:

    Moran: I understand your position. You, personally, can’t see any rational and reasonable naturalistic explanation for the existence of the genetic code therefore you conclude that an intelligent designer exists who could make species and insert into them the necessary genes and proteins for interpreting the genetic code.

    First, I can’t see any rational and reasonable naturalistic explanation for the existence of consciousness, rationality and the universe.
    Next I cannot see any rational and reasonable naturalistic explanation for matter self-organizing into living organisms.
    Third I can’t see any rational and reasonable naturalistic explanation for the existence of all the fancy stuff in life.

    edit: *rational and reasonable naturalistic explanation* is an oxymoron, because rationality and reason cannot be grounded under naturalism ;see post # 139

  153. 153
    bFast says:

    Zachriel, “The nested hierarchy is observed, regardless of any theory of explanation.”

    In comment 119 I link to a video that discusses the trees represented by FOXP2, P1 and P3. Each tree is substantially different from each other. My understanding of the logic of mutations as they flow through time is that this class of differences should not form. If the UCA of two species has a particular mutation, both children will have it. Once in a gazillion moons a mutation will be mutated upon, but multiple such key mutations would not realistically all disappear. Yet somehow the chimp ends up closer to the squirrel than to the human. Whassup?

  154. 154
    vh says:

    This is off topic here but I’m debating someone in another forum, a biologist, and he claims that this paper demonstrates that mutations add new information….I admit I don’t understand all the jargon and ramifications of the paper but if someone could help me out I’d truly appreciate it.

    http://journals.plos.org/ploso.....ne.0000096

    if you’d like to join in and converse with him the active thread is here: https://plus.google.com/117832126042339109939/posts/BJdNPwwRK8G

    thanks!

  155. 155
    Virgil Cain says:

    Zachriel:

    The nested hierarchy is observed, regardless of any theory of explanation.

    A nested hierarchy should not exist given descent with modification and transitional forms.

  156. 156
    Virgil Cain says:

    Larry Moran:

    He DOES NOT conclude that a naturalistic explanation for the origin of the genetic code is impossible and he did not convert to Intelligent Design Creationism.

    No materialist would. They will do whatever it takes until they die so that they can die a materialist.

  157. 157
    NickMatzke_UD says:

    Mapou writes:

    112
    October 25, 2015 at 9:21 pm
    VJT:
    Re common design vs. common descent: I believe in both. They complement each other. However, common design alone cannot explain why we find switched-off genes coding for the production of egg yolks in human DNA. Only the hypothesis that humans are descended from an eggg-laying ancestor can explain that.
    Why is that? Why could not a designer simply switch off an unneeded gene that is part of an existing (pre-designed) organism or genome? But then again, maybe early humans used to lay eggs. Maybe early humans were originally designed as egg-laying hermaphrodites. There is evidence in the book of Genesis and other ancient mythological stories for this.

    Adam and Eve laid eggs! You heard it here first, folks!

  158. 158
    Virgil Cain says:

    Well Nick Matzke, evolutionists lay eggs every time we ask them to support the claims of unguided evolution. So there you have it. 😛

  159. 159
    beau says:

    I don’t know much about science. I do know a little bit about Jesus teachings. I can’t imagine the way Professor Moran is being treated is a great tool to entice him into considering becoming a believer. I know he can be bit disrespectful on his blog but as believers we shouldn’t reciprocate with the same type of behaviour. You may not be able to prove God to him scientifically but you can demonstrate the love of Christ in how you interact with him.

  160. 160
    bFast says:

    tjguy(136), “Could it have happened once or twice? Perhaps, but are you suggesting this is a common process that happened over and over again in the history of life?”

    What we do know is that de novo genes are EXTREMELY common. This is a phenomenon, not an odd exception.

    tjguy, “That just doesn’t seem rational to me.”

    I think that this is the “naturalistic” voice speaking to you. It is inherently not a naturalistic perspective. It is, however, consistent with my own experience — plenty frequently enough conditions in the real world have aligned to represent themselves to me as “miracles”. It also is what the Bible portrays about many of the miracles: “In those days Caesar Augustus issued a decree that a census should be taken of the entire Roman world.” (Luke 2:1)

    I do present a couple of hypotheses, however. (These are not my own, though I like ’em.)

    One would suggest that the quanta (or maybe the strings) is a giant quantum computer. This suggestion is that this giant quantum computer is “conscious”, and able to self-manipulate. If so, all is made from this giant, conscious computer. We are all god-stuff.

    The other would suggest that the quanta allow for all possibilities, that what becomes fixed as “real” is determined by observation. Observation establishes, and fixes, reality. If so, an observer established the big bang out of “all of the possibilities”. This observer, by choosing which chance to go with, makes all reality happen (except when we become the observer, which is another story.) This observer, of necessity, would be able to decide what to observe (where we as observer only get to find out).

    These are two hypotheses of who the designer is. Both would be compatible with the slow growth of de novo genes in a UCA environment. (That said, in this topic I present the challenge of the FOXP* genes that suggest that UCA is, well, wrong.)

  161. 161
    Larry Moran says:

    Vincent Torley says,

    If Mapou or anybody else is looking for good, solid scientific reasons why the various scientific hypotheses put forward to explain the origin of the genetic code won’t work, then the online article, Origin and evolution of the genetic code (IUBMB Life. 2009 Feb; 61(2): 99–111. doi: 10.1002/iub.146) by evolutionary biologist Dr. Eugene Koonin and Artem S. Novozhilov is an excellent reference.

    Koonin and Novozhilov conclude that in 2009 we didn’t have a completely naturalistic explanation of the origin of the genetic code. They prefer some combination of the main competing explanations.

    Let’s assume that this is still true. Let’s assume that we still don’t know for certain how the genetic code arose early in the history of life.

    What do you conclude from that? Do you conclude that this is evidence for an intelligent designer who was capable of creating the genetic code and all the enzymes required to interpret it and then inserting them into one or more primitive species about 3 billion years ago? If so, could you please explain the logic behind such a leap?

    As you know, there are many interesting controversies in science and many things we don’t know. Do you think that just because we don’t know something it must mean that intelligent designers did it?

    If not, what criteria do you use to distinguish between those areas where lack of knowledge is just temporary and those areas where lack of knowledge is proof that something cannot possibly have evolved?

    Finally, do you agree that when Virgil Cain says, “No materialist would. They will do whatever it takes until they die so that they can die a materialist” then that’s evidence that ID isn’t just about science?

  162. 162
    Larry Moran says:

    bornagain says,

    Whereas no one has ever seen unguided material processes do it.

    Then a few lines later she says,

    The inference to Intelligence is based on what we do know about the cause and effect structure of the world, it is not based on what we don’t know.

    She probably doesn’t even see the irony.

    (Note: When dealing with people who hide their identity I try not to make sexist assumptions about their gender.)

  163. 163
    Virgil Cain says:

    Larry Moran-

    Let’s assume that this is still true. Let’s assume that we still don’t know for certain how the genetic code arose early in the history of life.

    What do you conclude from that?

    We conclude that it was something else. Then, via our knowledge of cause and effect relationships, we infer it was via some intelligent agency.

    Do you conclude that this is evidence for an intelligent designer who was capable of creating the genetic code and all the enzymes required to interpret it and then inserting them into one or more primitive species about 3 billion years ago? If so, could you please explain the logic behind such a leap?

    The same logic that went into determining Stonehenge was designed, ie we observe something that intelligent agencies can do and nature cannot. It is an example of work/ counterflow.

    If geological forces and environmental pressures could shape stones such that mortice and tenon joints were formed a key entailment of work would be taken away from Stonehenge.

    Finally, do you agree that when Virgil Cain says, “No materialist would. They will do whatever it takes until they die so that they can die a materialist” then that’s evidence that ID isn’t just about science?

    No, Larry, it is a sign that materialism isn’t about science as nothing will ever convince you of Intelligent Design short of meeting the designer(s) and getting answers to all of your inane questions.

    Furthermore inferring Intelligent Design in biology would mean we can A) stop wasting money on abiogenesis research and B) focus the resources to figure out the software, the “elan vital”, that makes living things very different from mere matter and energy. It would also go to serve notice that there is a higher purpose in life, that we are here for a reason other than the mundane.

  164. 164
    Larry Moran says:

    Virgil Cain says,

    It has nothing to do with us, personally.

    Don’t be ridiculous. This entire debate is about our personal opinions. They may or may not be informed by facts and data but it’s our opinion nevertheless.

    I’d like to think that my opinion is based on evidence and logic and I’m pretty sure you feel the same way. Nevertheless, both our views are personal and subjective to varying degrees.

    Let’s not pretend that the debate over intelligent design is going to be settled any time soon by entirely objective criteria that are completely independent of personal opinion.

    I’m an atheist and most ID proponents are Christians. That’s personal and it’s what this debate is all about in spite of the fact some of you won’t admit it. It’s not about science. It’s about religion.

  165. 165
    Virgil Cain says:

    Larry Moran- Strange that you can only accuse bornagain of some irony. We have never seen mother nature produce a Stonehenge. So our knowledge base doesn’t include such a thing. That is we know that mother nature isn’t up to the task. Couple that with the knowledge that humans use mortice and tenon joints and can arrange large stones for their purpose and the knowledge base is complete enough to make a scientific inference that Stonehenge was designed.

    That said, if some future discovery uncovers mother nature producing Stonehenges we would have to readdress the claim that Stonehenge was designed. That is how rival archaeologists used to debunk each other’s claims- by showing the alleged tooling could be easily accounted for by the environment.

  166. 166
    Virgil Cain says:

    Larry, I was an evolutionist and left Christianity many decades ago. The way I see it either we are here on purpose, ie Intelligent Design, or this is all some happy accident. And only intelligent design can be explored scientifically- we have modeled intelligent design evolution with genetic and evolutionary algorithms. We see its power and ability.

    Just how do you recommend we model physiochemical processes producing a genetic code? Just how the heck did mother nature get the ability to produce an arbitrary code complete with proof-reading and editing?

    Then when you look at all of the evidence- for example:

    “The same narrow circumstances that allow us to exist also provide us with the best over all conditions for making scientific discoveries.”

    “The one place that has observers is the one place that also has perfect solar eclipses.”

    “There is a final, even more bizarre twist. Because of Moon-induced tides, the Moon is gradually receding from Earth at 3.82 centimeters per year. In ten million years will seem noticeably smaller. At the same time, the Sun’s apparent girth has been swelling by six centimeters per year for ages, as is normal in stellar evolution. These two processes, working together, should end total solar eclipses in about 250 million years, a mere 5 percent of the age of the Earth. This relatively small window of opportunity also happens to coincide with the existence of intelligent life. Put another way, the most habitable place in the Solar System yields the best view of solar eclipses just when observers can best appreciate them.”

    Sheer dumb luck, Larry? Really?

  167. 167
    bFast says:

    Larry Moran, “This entire debate is about our personal opinions. They may or may not be informed by facts and data but it’s our opinion nevertheless.”

    Yes! Yes!

    “I’m an atheist and most ID proponents are Christians. That’s personal and it’s what this debate is all about in spite of the fact some of you won’t admit it. It’s not about science. It’s about religion.”

    This is a highly interesting statement. It implies, and rightly so I believe, that your position is a religious position. Yet our governments, in the attempt to be areligious, are allowing your position to be presented, but not ours.

    “I’d like to think that my opinion is based on evidence and logic and I’m pretty sure you feel the same way.”

    Yes and Yes.

    The evidence and logic, however, pushes us from “our option” to “the truth”. It doesn’t drop us there, but it coaxes us to that position. The key, therefore, to these discussions is that evidence and logic be presented. When a compelling case is made by either side, the size of the other side will become as small as the size of the “flat earth” community (90% I am sure are flat earthers because it is fun, not because it is believable.)

    Larry, in post 153 above, I challenge Zachriel to explain the differential in the trees of the FOXP1, P2 and P3 genes. I challenge you with the same question. I have for a long time held to UCD. This data seriously challenges my position. I cannot find logic to fit the FOXP data into a mutation + descendant model. In fact, I have a very hard time explaining it with any model at all, including the ID model I have internally developed to make sense of the data.

  168. 168
    Box says:

    My posts #139 & #152 are being ignored by Larry Moran. A possible explanation for the cold shoulder treatment is that Larry took offense being called a “bag filled with chemicals”.
    If that is indeed the reason, then it is not a valid one, since “being just a bag filled with chemicals” is exactly what Larry desperately wants to be true and he has in fact dedicated his entire adult life to the service of this message to humanity.

  169. 169
    bFast says:

    Larry Moran, “(Note: When dealing with people who hide their identity I try not to make sexist assumptions about their gender.)”

    Bull! You just did. It is possible to write in a totally gender-neutral way, you know.

    “She probably doesn’t even see the irony.”

    Nor do I, BA presents lots of evidence that is easily explained with ID, but is not explicable via naturalistic evolutionary theory.

    I present my own evidence above, something to do with FOXes. Please show me how the FOXP* genes can form inconsistent trees. This makes no NET (Naturalistic Evolutionary Theory) sense to me whatsoever.

  170. 170
    Andre says:

    Prof Moran

    Don’t be ridiculous. This entire debate is about our personal opinions. They may or may not be informed by facts and data but it’s our opinion nevertheless.

    You are of course entitled to your own opinion your own facts? Not so much.

    Lets try and use logic and reason (since you say you do use them).

    Perhaps we should change the approach here. I’ll ask you a question and you can answer.

    Prof Moran can a digital code like the Windows Operating system ever spontaneously generate itself? Is it possible in this universe? Is it possible in any universe?

  171. 171
    NickMatzke_UD says:

    119
    bFastOctober 25, 2015 at 11:21 pm
    ThickPython, “So you’ve got all these similarities and differences that map out nicely onto a phylogenetic tree derived from other, independent data. Common descent explains it easily.”

    Thick, I bumped into this video ( https://youtu.be/arSkMn5UwGM?t=5m23s ) recently. It has kinda shaken me. He starts with Dawkins’ claim that the FOXP2 gene is a great example of this wonderful tree. Well, it isn’t. The chimp is way the heck in the wrong place. Its not a bit wrong, it’s way wrong. The video goes on to look at the FOXP1 and FOXP3. They describe two totally different trees re the primates. So I have been playing evolution in my little mind with these guys. I thought, well, maybe this gene just edited a little slower and that a little faster. Maybe the molecular clocks aren’t ticking in perfect sync, they often don’t. But it doesn’t work. These different trees do not synchronize in the least little way. Well, that’s not totally accurate, but they do not produce a mapping that is in any way close enough to be explained by common descent with gradual modification. Just these three genes say NO!

    Please help me out here. Though I hold to ID, I also have held to universal common descent. Yet the FOXP* genes (and I understand, most other genes. Remember, this was selected because it was Dawkins’ poster child.) seem to defy UCD.

    Dude. Make a friggin’ effort. The video you link just quotes this video: https://www.youtube.com/watch?v=IfFZ8lCn5uU

    Comment #1 on that video points out:

    “FOXP3 – You’re once again using incomplete data. The Chimp protein (ENSPTRP00000037587) is only 265 amino acids long in Ensembl. Have a look over in UniProt – run an alignment on the Human, Chimp, Gorilla and Orangutan proteins – all of which are 431 amino acids long, and you will get a tree that matches the consensus tree.”

    The other comments are also informative.

    Other things to think about:

    1. Not all sequence entries in all databases are complete. Not all species labels on all databased sequences are correct. Automated alignment algorithms aren’t perfect either, and if an alignment is screwed up, the tree will be screwed up.

    2. Not every web program that produces some kind of tree is doing a formal phylogenetic analysis. Trees of sequence similarity or BLAST scores are just versions of “distance measures”, these are the crudest phylogenetic methods, so crude that in the serious phylogenetics journals you can’t publish with them. BLAST is meant to be a rapid search tool for finding things quickly, not a serious phylogenetic method by itself.

    (I don’t know what exactly the youtuber did – a real scientist would write up a description of their methods, not post some youtube video.)

    3. When there are only a few mutations between sequences, just random chance in the mutation process can accidentally produce slightly different trees.

    4. Incomplete lineage sorting is a well-known phenomenon that can produce slightly different histories (and phylogenies). ILS is an inevitable consequence of population genetics. Which leads to:

    5. Phylogenies have *degrees* of similarity/difference. It’s not all or nothing. Items #1-2 can produce huge differences from the multigene consensus phylogeny, but these are errors. Items #3-4 can produce small differences, and these are seen somewhat regularly.

    Overall, we see statistically huge agreement between different sequence datasets for the same basic phylogenetic tree. This is Dawkins’s point.

    6. Neither the original youtuber, nor the one you link to, has much of any idea what they are talking about.

  172. 172
    Virgil Cain says:

    Common designs have degrees of similarities and differences. Phylogenetic analysis, like homology, is based in the assumption of common descent. Change that assumption and you can build a tree based on a common design, as Linnaean Taxonomy does.

  173. 173
    Mapou says:

    I noticed that Moran and the other Darwinists steered clear of my argument that the combinatorial explosion kills all purely stochastic search mechanisms dead, including Darwinian evolution and abiogenesis. There can be no denying the power of simple math.

    The truth hurts.

  174. 174
    bornagain says:

    bfast, you might find this analysis of Matzke’s less than forthright methods informative:

    A One-Man Clade – David Berlinski – July 18, 2013
    http://www.evolutionnews.org/2.....74601.html

    Hopeless Matzke -David Berlinski & Tyler Hampton August 18, 2013
    http://www.evolutionnews.org/2.....75631.html

  175. 175
    Andre says:

    Nick Matzke

    Seriously point 1 to 6 is your answer?

    1. The data is incomplete….. blah blah blah…. if it is why are you so sure of your position?

    2. Web programs are incomplete….. blah blah blah why are you so sure of your position?

    3. Can you demonstrate your assumption? Testable results please?

    4. The lineages are incomplete….. blah blah blah why are you so sure of your position?

    5. Can you demonstrate this? Testable results please?

    6. And neither do you! If you did you’d shut us up with the results of your testable experiments. Can we have them please?

    I read allot of huffing but there just is no puffing………

  176. 176
    bornagain says:

    Moran, for all your bluff and bluster as to how great of a scientist you and all the other Darwinists are, I find that you, and they, do not even have the first clue as to how science actually works.

    The question that needs to be answered with real time empirical evidence, and not with rhetoric, by you and and all the other Darwinists is really quite simple. “Where did the information come from?”

    Yes, the question is so ridiculously simple that even someone who thinks he is smarter than Almighty God, like you apparently do Dr. Moran, can understand it.

    Information Enigma – (Where did the information come from?) – video
    https://www.youtube.com/watch?v=aA-FcnLsF1g

    It is not as if the empirical threshold is too high to be met either. In fact, if Darwinism were actually true, you should have countless thousands of examples from thousands of experiments that you could point to so as to falsify ID. Yet you can’t point to even one example of unguided material processes creating non-trivial functional information

    In fact, my argument for intelligent design is open to direct experimental rebuttal. Here is a thought experiment that makes the point clear. In Darwin’s Black Box (Behe 1996) I claimed that the bacterial flagellum was irreducibly complex and so required deliberate intelligent design. The flip side of this claim is that the flagellum can’t be produced by natural selection acting on random mutation, or any other unintelligent process. To falsify such a claim, a scientist could go into the laboratory, place a bacterial species lacking a flagellum under some selective pressure (for mobility, say), grow it for ten thousand generations, and see if a flagellum–or any equally complex system–was produced. If that happened, my claims would be neatly disproven.”
    Michael Behe
    – clipped from: Confirmation of intelligent design predictions
    http://reasonandscience.heaven.....redictions

    The Law of Physicodynamic Incompleteness – David L. Abel
    Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”
    If only one exception to this null hypothesis were published, the hypothesis would be falsified. Falsification would require an experiment devoid of behind-the-scenes steering. Any artificial selection hidden in the experimental design would disqualify the experimental falsification. After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided.
    The time has come to extend this null hypothesis into a formal scientific prediction:
    “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.”
    https://www.academia.edu/Documents/in/The_Law_of_Physicodynamic_Incompleteness

  177. 177
    Andre says:

    Nick Matzke

    Overall, we see statistically huge agreement between different sequence datasets for the same basic phylogenetic tree.

    Really? some scientists noticed this apparent agreement too and cautioned against it!

    phylogenomics is becoming synonymous with evolutionary analysis of genome-scale and taxonomically densely sampled data sets. In phylogenetic inference applications, this translates into very large data sets that yield evolutionary and functional inferences with extremely small variances and high statistical confidence (P value). However, reports of highly significant P values are increasing even for contrasting phylogenetic hypotheses depending on the evolutionary model and inference method used, making it difficult to establish true relationships.

    http://mbe.oxfordjournals.org/.....2/457.full

    It’s a very good thing that some scientists still actually do science, unlike Dawkins, Prof Moran, Lawrence Krauss, Jerry Coyne, and Nick Matzke who just advocate their own religion.

    There are many things people can be uncertain about but one thing you can be absolutely sure of is this, when its from Nick Matzke’s mouth you can confidently know it is absolute rubbish.

  178. 178
    ThickPython says:

    @bFast (#119, #153, #160, #167, #169)

    Yeah sorry, I saw this yesterday and meant to respond, but poker was beckoning 🙂

    As Nick Matzke has pointed out, the video you linked to is just a rehash of Hugenex2000’s video, and those comments that Nick refers to are mine (i.e. I am roohif on Youtube). The person behind that Youtube channel is a guy named Eugene and Eugene is very sloppy in his analyses. I interacted with him over the course of about a year but he no longer makes videos.

    I strongly endorse Nick’s comments regarding the data on these websites – he is spot on for all 6 of his points.

  179. 179
    NickMatzke_UD says:

    4. The lineages are incomplete….. blah blah blah why are you so sure of your position?

    No, Incomplete Lineage Sorting means the *sorting* is incomplete. And you are a silly person. Try google, man.

  180. 180
    Andre says:

    Thickpython

    I’ve already refuted Nick’s claim with an actual paper are you sure as a gambler you want to back the wrong horse?

  181. 181
    Andre says:

    If Nick Matzke calls you silly it’s certain you are onto something.

    Nick I’ve posted S. Kumar’s paper did you actually read it? It cautions exactly on your idea about statistically huge agreemens between the different sequence datasets.

    So is he a liar for Jesus or are you a liar for Darwin?

  182. 182
    ThickPython says:

    @Andre

    This is a great opportunity for you to do some of your own research, rather than have everything spoon fed to you.

    1. and 2. The software used to automatically annotate the genomes isn’t perfect. Humans can spot these errors. In fact, one of the ways to spot these sort of errors is when the data are in apparent conflict with common descent! 😀

    3. Dude, you can demonstrate this to yourself.

    4. Google it. I know Biologos have a very easy to understand explanation of it.

    5. If you understand points #1 – #4, this becomes self-evident.

    6. And neither does your mum. Sorry, “mom”.

  183. 183
    NickMatzke_UD says:

    177
    AndreOctober 26, 2015 at 1:03 pm
    Nick Matzke

    Overall, we see statistically huge agreement between different sequence datasets for the same basic phylogenetic tree.

    Really? some scientists noticed this apparent agreement too and cautioned against it!

    phylogenomics is becoming synonymous with evolutionary analysis of genome-scale and taxonomically densely sampled data sets. In phylogenetic inference applications, this translates into very large data sets that yield evolutionary and functional inferences with extremely small variances and high statistical confidence (P value). However, reports of highly significant P values are increasing even for contrasting phylogenetic hypotheses depending on the evolutionary model and inference method used, making it difficult to establish true relationships.

    http://mbe.oxfordjournals.org/…..2/457.full

    It’s a very good thing that some scientists still actually do science, unlike Dawkins, Prof Moran, Lawrence Krauss, Jerry Coyne, and Nick Matzke who just advocate their own religion.

    There are many things people can be uncertain about but one thing you can be absolutely sure of is this, when its from Nick Matzke’s mouth you can confidently know it is absolute rubbish.

    Um…you are misinterpreting your quote. P-values have little to do with inferring phylogenies. In the paper, they are talking about p-values as ways of detecting selection, e.g. by rejecting a null hypothesis of neutral evolution for some particular gene. Such a test requires a phylogeny, but estimating the phylogeny is a different thing.

    Now, there are various issues with inferring phylogenies from massive phylogenomic datasets, which the paper also talks about apart from the p-value discussion, but these boil down to basically (1) lots of sequence, but poor taxon sampling, and (2) heavily saturated sequence and sequence evolution models that start to break down when sequences are saturated.

    Some scientists have had the idea that by throwing more and more saturated sequence at very remote divergences, phylogenetic resolution will improve. This was feasible to try due to the cheapness of genome sequencing, but was never that great of an idea if you understood the issue of sequence saturation. If you want to resolve, say, divergence 300 million years ago, it’s better to use 20 or so well-conserved genic sequences for 500 taxa than to do full genomes of 20 species and throw all of their unconserved junk DNA etc. into the analysis.

    Anyhow, these issues basically apply to ancient divergence that were close in time. No matter how these are resolved in detail, the trees are still basically pretty similar. Learn about the statistics of tree similarity please.

  184. 184
    Andre says:

    Thickpython

    Oh so when it conflicts with your beliefs it’s wrong? Gotcha.

  185. 185
    Barry Arrington says:

    Nick,

    Do you still contend that a design inference would not necessarily be warranted if you encountered 500 coins on a table all heads?

    Just checking.

  186. 186
    Andre says:

    So Nick what you are saying then is scientists with a certain biases cherry pick the data. Got it thanks.

  187. 187
    ThickPython says:

    @Andre:

    “I’ve already refuted Nick’s claim with an actual paper are you sure as a gambler you want to back the wrong horse?”

    “Refuted”? Maybe you should pose your little conundrum to the authors of the paper. What would you like to ask them – is phylogenetics useless? Should we throw out P-values? Is common descent false?

    I already know what they would say, so I’m happy to “gamble” if you want to use that word. I get called a “professional gambler” from time to time and it’s always from people who have no idea about what I actually do.

  188. 188
    Andre says:

    Thickpython

    You said you were playing poker ???? None of those would be my questions.

    But what I would ask is what would the relationships look like if there was no inference to a common ancestor and we build an unrooted tree from the data?

  189. 189
    Mapou says:

    NickMatzke_UD:

    Adam and Eve laid eggs! You heard it here first, folks!

    You’re clueless, Matzke. You have no clue what the words Adam and Eve mean other than what you learned in Sunday school from some fundamentalist preacher. The Adam and Eve story in the garden of Eden is purely metaphorical.

    Adam or rather, “the Adam”, as the original Hebrew has it, means mankind. Yahweh Elohim first created the Adam in their image and made them male and female (not men and women, as most people believe) and told them to go forth and multiply. My interpretation is that the first humans were hermaphrodites and could self reproduce. Then Yahweh decided that this was not a good idea because the Adam were lonely even after spending a long time classifying all the animals that existed at the time. So he changed them and separated them into two groups, men and women. It is not farfetched to suppose that, in the beginning, the Adam were designed to procreate via egg laying. After all, this is not unheard of among mammals. If you are Yahweh and you have great genetic engineering resources at your disposition, this is perfectly plausible.

  190. 190
    Mung says:

    ThickPython:

    I get called a “professional gambler” from time to time and it’s always from people who have no idea about what I actually do.

    Well, we do know what you don’t do.

    Let’s try this again. There was a bug in a piece of software. You pointed out that Tomkins used that software while the bug was present. Who else used that software while the bug was present? No one? You don’t care?

  191. 191
    ThickPython says:

    “Oh so when it conflicts with your beliefs it’s wrong? Gotcha.”

    The data is in accord with common descent – that’s precisely why I believe it. When the data is not in accord with common descent, I investigate. Every investigation to date has been resolved by one of the first four points that Nick put forward. When a theory responds well to challenges and always comes out the winner, then maybe .. just maybe .. that theory is true?

  192. 192
    Andre says:

    Please read my question post 188…

    If we assume no common ancestor and we build an unrooted tree what will we get?

    Let me be clear I’m not opposed to UCD. I just don’t think there is enough convincing evidence for it. Circumstantial evidence yes, enough for a conviction not yet.

  193. 193
    Andre says:

    Thickpython

    Darwin’s tree of life is not a true reflection of the domains of life on this planet, there are multiple life forms and they do not all fit into a rooted tree. Dr. Craig Venter knows allot more about this than you, me or Nick Matzke and he denies common descent and a rooted tree.

  194. 194
    ThickPython says:

    @Andre:

    “You said you were playing poker ????”

    Ha! Yes, yes I did. I wasn’t referring to poker, but even if I was – poker is a game of skill, not luck. It’s not “gambling”.

    “But what I would ask is what would the relationships look like if there was no inference to a common ancestor and we build an unrooted tree from the data?”

    I think I know what you’re trying to get at. If creationism were true, then phylogenetic trees [would | could | should] resemble an “orchard” rather than a single rooted tree, yeah? This is precisely why baraminologists struggle so hard when it comes to the demarcation of Biblical kinds. They want to use genetic data to delineate kinds, but they know that the data implies a continuous line of descent, rather than there being a “cat tree” and a “dog tree”. For example, we all agree (or do we?) that all cats descended from an original “cat kind”, and we use phylogenetic methods to construct that tree. Unfortunately for creationists, the “cat kind” is an arbitrary distinction when looking at the genetic data. The method you use to join “big cats” to “small cats” is the same method you use to join “cats” to “dogs”, and then “cats and dogs” to “carnivorans”. Rinse and repeat.

    If this “orchard” were a true representation of reality, then it would be obvious in phylogenetics. The root of the “cat tree” would bear no resemblance to the root of the “dog tree”.

  195. 195
    bFast says:

    Nick, thanks for the answers (except the derogatory, self-aggrandizing comments, of course.)

    Let me respond to each of your points:

    “The video you link just quotes this video.” Actually it doesn’t “just”. I was perfectly aware that the one quoted the other. I chose to publish the one I did because it added commentary that I thought was useful.

    1 – Not all sequence entries in all databases are complete …
    I am a computer programmer of some skill. I do not have the expertise to separate intron from exon in a DNA sequence. However, I can envision what the results of “incomplete” or “alignment is screwed up” would look like. If I were writing the program, they would not look like “oh, it doesn’t look like an chimp, it looks like a squirrel”. Rather my results would be, “Oh, it doesn’t look like a chimp, it looks like something extremely different altogether.

    2 – “Not every web program that produces some kind of tree is doing a formal phylogenetic analysis. Trees of sequence similarity or BLAST scores are just versions of “distance measures”, these are the crudest phylogenetic methods”

    They are not siting “the crudest phylogenetic methods”, they are specifically siting ensembl.org. Do you have reason to believe that ensembl.org merely uses “distance measures”? It certainly doesn’t appear to, especially when it images the bar graph of the relevant DNA.

    3 – “When there are only a few mutations between sequences, just random chance in the mutation process can accidentally produce slightly different trees.” How so? It would seem to me that once you have any mutations in the LUCA of two species, that mutation should show up in both. If you have no such mutation, then the ensembl program appears to place the two species on the same level, rather than shifting one name to the right by one notch.

    5 – “Phylogenies have *degrees* of similarity/difference. It’s not all or nothing.” It should be very nearly all or nothing. As I play my mental mutation/generation engine, I can see two possible ways to not get “all or nothing”:
    > The extremely unlikely scenario of a mutation happening that “undoes” a previous mutation (particularly unlikely in a low mutation environment.
    > The scenario species that had spats of separation followed by spats of reconnection — maybe.

    “Overall, we see statistically huge agreement between different sequence datasets for the same basic phylogenetic tree. This is Dawkins’s point.”

    I would say that overall we MUST see near perfect agreement between different species or UCD is toast.

    Lastly, please provide me with similar trees for the FOXP1, P2 and P3, trees that include at least 50% of the species that are generated via ensembl. Please allow me to see that “proper data” produces the UCD-like tree.

    As it is, I have held to UCD for a long time. This data alone, if validated, throws my belief in UCD out the window.

  196. 196
    ThickPython says:

    Andre:

    “Dr. Craig Venter knows allot more about this than you, me or Nick Matzke and he denies common descent and a rooted tree.”

    No, Craig Venter does not deny common descent. Yes, he denies a simplistic, singly rooted tree, but then again so do I.

    These things have nuance, Andre. I suggest you spend more time reading, less time spouting.

  197. 197
    bFast says:

    bornagain, I know you to be a treasure trove of interesting articles. Do you have anything on this topic? I seem to recall articles that say that using genetics to reconstruct the tree have proven difficult at best.

  198. 198
    Andre says:

    Thickpython

    Would you care to ask him? He has publicly stated.that he does not accept common descent and neither does he agree with the Darwinian tree of life. He said its an artifact that is not holding up. I agree with him.

  199. 199
    ThickPython says:

    @Mung:

    “Well, we do know what you don’t do.”

    And what would that be … ?

    “Let’s try this again. There was a bug in a piece of software. You pointed out that Tomkins used that software while the bug was present. Who else used that software while the bug was present? No one? You don’t care?”

    Haven’t I already addressed that in post #24?

    Maybe lots of people used the software while the bug was present. Maybe one of them discovered the bug. Maybe they reported it to the developers. Maybe they fixed (tried to fix?) it in the next release. Maybe they even sent an email to “blast-announce” to tell everyone about it?

    Do you have a reason for bringing this up again that wasn’t addressed in my previous post?

    I’ll check back in later .. enjoy!

  200. 200
    NickMatzke_UD says:

    bFast — every one of your points indicates utterly basic misunderstanding. Random ones include: ensemble.org has a great many tools, but you seem to think it’s just one thing. We don’t even know which ones the YouTuber used, with what settings. Various tools have various usages, and typically with web tools the usual purpose is finding data and very basic explorations, not thorough phylogenetic analyses. Yet you assume the programmers would have your goals, instead of the typical data-retrieval and basic explorations goal.

    That’s just for starters. You also clearly don’t get the stochasticity inherent in data when there are just a few mutations in the dataset, for example. But why should I spend more time when you just misunderstand and/or distort everything I say? If you really don’t believe me, don’t ask me to do all your work for you. I quoted the quote pointing out the data problem with one of the sequences used in YouTube video, yet you still seem to think even that is up for debate.

    Given all of this — which comes down to laziness and the williness to confidently expound opinions without studying an issue first — why should I then volunteer to do all of the work for you? You should yourself go on Genbank, download a bunch of FoxP1, FoxP2, and FoxP3 sequences from mammals, align each gene by hand yourself, and count up the differences. Or, you could learn some basic alignment and phylogeny software.

    It’s fine if you don’t want to, but why should anyone who is familiar with all this stuff after years of coursework and practical research experience take your totally uninformed opinion seriously?

  201. 201
    bornagain says:

    so it is admitted the programs are ‘not perfect’ and yet Python claims

    “, one of the ways to spot these sort of errors is when the data are in apparent conflict with common descent!”

    Interesting belief, but what if the ‘not perfect’ programs are set up to give common descent the most favorable outcome in the first place even if the assumption of common descent is wrong? How ‘not perfect’ would that make the programs?

    A few notes in that ‘not perfect’ regards:

    Pattern pluralism and the Tree of Life hypothesis – 2006
    Excerpt: Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true.
    http://www.pnas.org/content/104/7/2043.abstract

    “The computer programs that analyze the sequence similarities, or differences, are programmed in advance to generate a tree-like pattern. In other words, the assumption of a common ancestor is built into the way in which the analysis is performed. So there is no way you would get anything other than the conclusion,,, It’s a question begging assumption.”
    Stephen Meyer – on the Cambrian Explosion – podcast (15:25 minute mark)
    http://intelligentdesign.podom.....3_15-07_00

    Contradictory Trees: Evolution Goes 0 For 1,070 – Whif
    Excerpt: One of evolution’s trade secrets is its prefiltering of data to make it look good, but now evolutionists are resorting to postfiltering of the data as well.,,,
    Prefiltering is often thought of merely as cleaning up the data. But prefiltering is more than that, for built-in to the prefiltering steps is the theory of evolution. Prefiltering massages the data to favor the theory. The data are, as philosophers explain, theory-laden.
    But even prefiltering cannot always help the theory.,,,
    http://darwins-god.blogspot.co.....oes-0.html

    Richard Dawkins: How Could Anyone “Possibly Doubt the Fact of Evolution” – Cornelius Hunter – February 27, 2014
    Excerpt: there is “no known mechanism or function that would account for this level of conservation at the observed evolutionary distances.”,,,
    the many examples of nearly identical molecular sequences of totally unrelated animals are “astonishing.”,,,
    “data are routinely filtered in order to satisfy stringent criteria so as to eliminate the possibility of incongruence.”,,,
    he has not found “a single example that would support the traditional tree.” It is, another evolutionist admitted, “a very serious incongruence.”
    “the more molecular data is analysed, the more difficult it is to interpret straightforwardly the evolutionary histories of those molecules.”
    And yet in public presentations of their theory, evolutionists present a very different story. As Dawkins explained, gene comparisons “fall in a perfect hierarchy, a perfect family tree.” This statement is so false it isn’t even wrong—it is absurd. And then Dawkins chastises anyone who “could possibly doubt the fact of evolution.” Unfortunately this sentiment is typical. Evolutionists have no credibility.
    http://darwins-god.blogspot.co.....nyone.html

    Darwin’s Tree of Life is a Tangled Bramble Bush – May 15, 2013
    Excerpt: ,,, One whole subsection in the paper is titled, “All gene trees differ from species phylogeny.” Another is titled, “Standard practices do not reduce incongruence.” A third, “Standard practices can mislead.” One of their major findings was “extensive conflict in certain internodes.”
    The authors not only advised throwing out some standard practices of tree-building, but (amazingly) proposed evolutionists throw out the “uninformative” conflicting data and only use data that seems to support the Darwinian tree: “the subset of genes with strong phylogenetic signal is more informative than the full set of genes, suggesting that phylogenomic analyses using conditional combination approaches, rather than approaches based on total evidence, may be more powerful.”,,,
    ,,,tossing out “uninformative” data sets and only using data that appear to support their foreordained conclusion. Were you told this in biology class? Did your textbook mention this?
    http://crev.info/2013/05/darwi.....mble-bush/

    “there is a great deal of preferential and selective treatment of the data being analyzed. In many cases, only the most promising data such as gene-rich sequences that exist in both species (homologs) is utilized from a much larger data pool. This pre-selected data is often further subjected to more filtering before being analyzed and discussed. Non-alignable regions and large gaps in DNA sequence alignments are also typically omitted, thus increasing the levels of reported similarity.”
    Jeffrey Tomkins

    A few more notes:

    Do Molecular Clocks Run at All? A Critique of Molecular Systematics – Jeffrey H. Schwartz, Bruno Maresca
    Abstract: Although molecular systematists may use the terminology of cladism, claiming that the reconstruction of phylogenetic relationships is based on shared derived states (synapomorphies), the latter is not the case. Rather, molecular systematics is (largely) based on the assumption, first clearly articulated by Zuckerkandl and Pauling (1962), that degree of overall similarity reflects degree of relatedness. This assumption derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change. Review of the history of molecular systematics and its claims in the context of molecular biology reveals that there is no basis for the “molecular assumption.”.. For historians and philosophers of science the questions that arise are how belief in the infallibility of molecular data for reconstructing evolutionary relationships emerged, and how this belief became so central …
    http://www.pitt.edu/~jhs/artic.....clocks.pdf

    Fudging Evolution to Avoid Falsification – March 12, 2015
    Evolutionary theory follows Finagle’s Rule #4: “Draw your curves, then plot your data.”
    Excerpt: “The fact that the clock is so uncertain is very problematic for us,” David Reich of Harvard said at a recent meeting where no consensus was reached. “It means that the dates we get out of genetics are really quite embarrassingly bad and uncertain.” The solution for some has been to invoke “rate heterogeneity”: mutations rates that speed up or slow down as needed to keep the theory intact. –
    http://crev.info/2015/03/fudging-evolution/

    Evolution Makes No Sense on This Molecular Clock Problem – Cornelius Hunter – June 15, 2015
    Excerpt: The theory-laden measurements are based on evolutionary theory. The theory-neutral measurements do not entail evolutionary thinking. In other words, making measurements based on evolutionary theory leads to problems. The resulting DNA mutation rates are not even close to what we can measure more directly, free from theoretical assumptions.
    As is often the case, these discrepancies between the evidence and the theory leave evolutionists unsure and of differing opinions. As one evolutionist admitted:
    “The fact that the clock is so uncertain is very problematic for us, It means that the dates we get out of genetics are really quite embarrassingly bad and uncertain.”
    http://darwins-god.blogspot.co.....-this.html

    Molecular Data Wreak Havoc on the Tree of Life – Casey Luskin – February 7, 2014
    Excerpt: After citing Pauling and Zuckerkandl’s test, Douglas Theobald claims in his “29+ Evidences for Macroevolution” that “well-determined phylogenetic trees inferred from the independent evidence of morphology and molecular sequences match with an extremely high degree of statistical significance.”26
    In reality, however, the technical literature tells a different story. Studies of molecular homologies often fail to confirm evolutionary trees depicting the history of the animal phyla derived from studies of comparative anatomy. Instead, during the 1990s, early into the revolution in molecular genetics, many studies began to show that phylogenetic trees derived from anatomy and those derived from molecules often contradicted each other.
    Probably the most protracted conflict of this type concerns a widely accepted phylogeny for the bilaterian animals. This classification scheme was originally the work of the influential American zoologist Libbie Hyman.27 Hyman’s view, generally known as the “Coelomata” hypothesis, was based on her analysis of anatomical characteristics, mainly germ (or primary tissue) layers, planes of body symmetry, and especially the presence or absence of a central body cavity called the “coelom,” which gives the hypothesis its name. In the Coelomata hypothesis, the bilaterian animals were classified in three groups, the Acoelomata, the Pseudocoelomata, and the Coelomata, each encompassing several different bilaterian animal phyla.28 (See Fig. 6.1a.)
    Then, in the mid-1990s, a very different arrangement of these animal groups was proposed based on the analysis of a molecule present in each (the 18S ribosomal RNA; see Fig. 6.1b). The team of researchers who proposed this arrangement published a groundbreaking paper in Nature with a title that surprised many morphologists: “Evidence for a Clade of Nematodes, Arthropods and Other Moulting Animals.”29 The paper noted the conventional wisdom, based on Hyman’s hypothesis, that arthropods and annelids were closely related because both phyla had segmented body plans.30 But their study of the 18S ribosomal RNA suggested a different grouping, one that placed arthropods close to nematodes within a group of animals that molt, which they called “Ecdysozoa.” This relationship surprised anatomists, since arthropods and nematodes don’t exactly look like kissing cousins. Arthropods (such as trilobites and insects) have coeloms, whereas nematodes (such as the tiny worm Caenorhabditis elegans) do not, leading many evolutionary biologists to believe nematodes were early branching animals only distantly related to arthropods.31 The Nature paper explained how unexpected this grouping of arthropods and nematodes was: “Considering the greatly differing morphologies, embryological features, and life histories of the molting animals, it was initially surprising that the ribosomal RNA tree should group them together.”32
    [and S. Meyer goes on several pages building his case based on several distinct arguments and many references to scientific papers]
    Stephen Meyer – Darwin’s Doubt – (pp. 122-123)
    ,,,Moreover, when complex parts that are shared by different animals aren’t distributed in a treelike pattern, that wreaks havoc on the assumption of homology that’s used to build phylogenetic trees. In other words, this kind of extreme convergent evolution refutes the standard assumption that shared biological similarity (especially complex biological similarity like a brain and nervous system) implies inheritance from a common ancestor.
    If brains and nervous systems evolved multiple times, this undermines the main assumptions used in constructing phylogenetic trees, calling into question the very basis for inferring common ancestry.,,,
    http://www.evolutionnews.org/2.....81981.html

  202. 202
    bornagain says:

    Logged Out – Scientists Can’t Find Darwin’s “Tree of Life” Anywhere in Nature by Casey Luskin – Winter 2013
    Excerpt: the (fossil) record shows that major groups of animals appeared abruptly, without direct evolutionary precursors.
    Because biogeography and fossils have failed to bolster common descent, many evolutionary scientists have turned to molecules—the nucleotide and amino acid sequences of genes and proteins—to establish a phylogenetic tree of life showing the evolutionary relationships between all living organisms.,,,
    Many papers have noted the prevalence of contradictory molecule-based phylogenetic trees. For instance:
    • A 1998 paper in Genome Research observed that “different proteins generate different phylogenetic tree[s].”6
    • A 2009 paper in Trends in Ecology and Evolution acknowledged that “evolutionary trees from different genes often have conflicting branching patterns.”7
    • A 2013 paper in Trends in Genetics reported that “the more we learn about genomes the less tree-like we find their evolutionary history to be.”8
    Perhaps the most candid discussion of the problem came in a 2009 review article in New Scientist titled “Why Darwin Was Wrong about the Tree of Life.”9 The author quoted researcher Eric Bapteste explaining that “the holy grail was to build a tree of life,” but “today that project lies in tatters, torn to pieces by an onslaught of negative evidence.” According to the article, “many biologists now argue that the tree concept is obsolete and needs to be discarded.”,,,
    Syvanen succinctly summarized the problem: “We’ve just annihilated the tree of life. It’s not a tree any more, it’s a different topology entirely. What would Darwin have made of that?” ,,,
    “battles between molecules and morphology are being fought across the entire tree of life,” leaving readers with a stark assessment: “Evolutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology.”10,,,
    A 2012 paper noted that “phylogenetic conflict is common, and [is] frequently the norm rather than the exception,” since “incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species.”12,,,
    http://www.salvomag.com/new/ar.....ed-out.php

    Here is another article, written by a leading researcher in the world, that states the true pattern found for life, from comparative genetic evidence, is certainly not the tree pattern that Darwin had originally envisioned:

    A New Model for Evolution: A Rhizome – Didier Raoult – May 2010
    Excerpt: Thus we cannot currently identify a single common ancestor for the gene repertoire of any organism.,,, Overall, it is now thought that there are no two genes that have a similar history along the phylogenic tree.,,,Therefore the representation of the evolutionary pathway as a tree leading to a single common ancestor on the basis of the analysis of one or more genes provides an incorrect representation of the stability and hierarchy of evolution. Finally, genome analyses have revealed that a very high proportion of genes are likely to be newly created,,, and that some genes are only found in one organism (named ORFans). These genes do not belong to any phylogenic tree and represent new genetic creations.
    http://darwins-god.blogspot.co.....izome.html

    Of note: Didier Raoult, who authored the preceding paper, has been referred to as ‘Most Productive and Influential Microbiologist in France’. He has unambiguously said that ‘Darwin’s theory is wrong’.

    The “Most Productive and Influential Microbiologist in France” Is a Furious Darwin Doubter – March 2012
    Excerpt: Controversial and outspoken, Raoult last year published a popular science book that flat-out declares that Darwin’s theory of evolution is wrong.
    http://www.evolutionnews.org/2.....57081.html

    A few more notes:

    Here Are Those Incongruent Trees From the Yeast Genome – Case Study – Cornelius Hunter – June 2013
    Excerpt: We recently reported on a study of 1,070 genes and how they contradicted each other in a couple dozen yeast species. Specifically, evolutionists computed the evolutionary tree, using all 1,070 genes, showing how the different yeast species are related. This tree that uses all 1,070 genes is called the concatenation tree. They then repeated the computation 1,070 times, for each gene taken individually. Not only did none of the 1,070 trees match the concatenation tree, they also failed to show even a single match between themselves. In other words, out of the 1,071 trees, there were zero matches. Yet one of the fundamental predictions of evolution is that different features should generally agree. It was “a bit shocking” for evolutionists, as one explained: “We are trying to figure out the phylogenetic relationships of 1.8 million species and can’t even sort out 20 yeast.”
    In fact, as the figure above shows, the individual gene trees did not converge toward the concatenation tree. Evolutionary theory does not expect all the trees to be identical, but it does expect them to be consistently similar. They should mostly be identical or close to the concatenation tree, with a few at farther distances from the concatenation tree. Evolutionists have clearly and consistently claimed this consilience as an essential prediction.
    But instead, on a normalized scale from zero to one (where zero means the trees are identical), the gene trees were mostly around 0.4 from the concatenation tree with a huge gap in between. There were no trees anywhere close to the concatenation tree. This figure is a statistically significant, stark falsification of a highly acclaimed evolutionary prediction.
    http://darwins-god.blogspot.co.....-from.html

    You Won’t Believe This New Epicycle: Both Congruence & Incongruence are Powerful Phylogenetic Signals – October – 7, 2013
    Excerpt: Similar evolution trees are derived from completely different genes. Such congruence of independent data was predicted by evolution and evolutionists have consistently proclaimed it as a powerful confirmation of the fact of evolution. It is, as evolutionists like to say, a powerful phylogenetic signal. There’s only one problem: all of this is false. It is yet another example of evolution’s theory-laden science where the findings are dictated not by the data but by the doctrine. There is no powerful phylogenetic signal. That is a myth. For when evolutionists construct their phylogenies, they first filter out the anatomical comparisons that don’t cooperate. But that is not enough so after their first try they filter some more. As one evolutionist admitted, “We are trying to figure out the phylogenetic relationships of 1.8 million species and can’t even sort out 20 [types of] yeast.” And so it is good to see a new paper that admits that data are routinely filtered in order to satisfy stringent criteria so as to eliminate the possibility of incongruence.
    And what is the solution to this dilemma? As usual, a theoretical failure is converted into a success by adding yet more epicycles. Or as Lakatos might have put it, the core idea is protected by the addition of yet more auxiliary hypotheses. In this case, the incredible emerging view is that incongruence is now to be interpreted as a powerful phylogenetic signal that is desirable, as it often illuminates previously poorly understood evolutionary phenomena. Once again a prediction that was hailed as a powerful proof of evolution turns out to be false, and the story is simply flipped on its head, thus preserving the success of the theory. Where congruence was once claimed as a powerful phylogenetic signal, now incongruence takes its place as the powerful phylogenetic signal. You cannot make this stuff up.
    http://darwins-god.blogspot.co.....cycle.html

  203. 203
    Dr JDD says:

    Andre:

    If you want to look yourself at how closely protein sequences are to each other that is quite straightforward and anyone can have a go.

    Go to:

    http://www.uniprot.org

    Type in the search box your gene name of interest (e.g. FOXP2) and it will come up with loads. Then check on the left hand side to restrict to particular organisms or search for one not listed (e.g. pan troglodites) and when you click on the relevant entry, you can scroll down to see a protein sequence.

    If you copy that protein amino acid sequence as is (don’t worry about the fact it is in a form with numbers in it), you can paste it here:

    http://blast.ncbi.nlm.nih.gov/.....eq_protein

    Then click the “Align two or more sequences” and you can paste those sequences for different organisms into different boxes, hit BLAST and it will align them giving you sequence identity.

    IF you have 2 sequences it will put them on top of each other and in between them it will state the same amino acid if they are identical, a gap if they are quite different, a “+” if they are conservative changes (e.g. an R changed to a K is conservative as they are structurally quite similar amino acids with similar proterties) and a “-” if there has been a gap (indel) when aligning.

    But crudely, you will see a % identify and % sequence coverage. So if you do homo sapiens vs pan tr for FOXP2 as you stated above, the amino acid sequence homology is 99% with only 4 amino acid differences I believe. If you do homo sap vs orangutan you get 99% homology with only 4 differences.

    You can also do this with genetic code which is subject to greater change/mutation (amino acid hides mutants through redundancy) just use the “blastn” version rather than blastp.

    It is quite easy to do and worth doing yourself when someone makes a claim that a particular gene/protein is completely different in chimp than human vs other species. This is unfortunately often out-dated info (assuming the uniprot entry is correct) and really is not a wise argument for ID to labour over. For years many pro-ID people have argued that homology does not = common descent and is expected with common design and is not really any more evidence for one than the other so actually when people claim things don’t align when they do does more harm than good! Especially when it is so easy to do a simple alignment when talking about a specific gene…

  204. 204
    J-Mac says:

    Larry Moran wrote:

    “Don’t be ridiculous. This entire debate is about our personal opinions. They may or may not be informed by facts and data but it’s our opinion nevertheless.”

    Yes, professor Moran; They are your personal opinions too, just in case you think that your opinions carry more weight…

    You have been selling those same your own personal opinions to everyone as facts though. Can you explain why?

    Well, we have it on record now…. You have admitted to it.
    Can you see the difference between an opinion vs faith?
    I don’t, especially when someone is spreading his own personal opinions with religious conviction…

  205. 205
    bFast says:

    Further to 195, I think that multiple alleles of the same gene could result in a juggling order in the charts — albeit not by much.

    “Given all of this — which comes down to laziness and the williness to confidently expound opinions without studying an issue first — why should I then volunteer to do all of the work for you?”

    If you want to prove a point, you’ve got to provide the proof.

  206. 206
    Zachriel says:

    bFast: My understanding of the logic of mutations as they flow through time is that this class of differences should not form.

    That is incorrect. If there are similar selective constraints, they may converge. However, that does not apply to silent mutations, which generally support the standard phylogeny. In any case, it’s the overall pattern that is objectively observed independent of any explanation.

    bFast: I would say that overall we MUST see near perfect agreement between different species or UCD is toast.

    No. Perfect agreement is not expected due to a number of factors, including convergence. See Darwin, Origin of Species, 1859.

  207. 207
    Mung says:

    ThickPython @ 24: Are you suggesting that only creationists have been affected by this bug?

    Certainly not. That was the point of my questions. So who else have you unmasked, other than Tomkins? No one?

    Such a good sleuth you are!

  208. 208
    Vy says:

    In fact, one of the ways to spot these sort of errors is when the data are in apparent conflict with common descent!

    Circular reasoning anyone?? How about affirming the consequence???

  209. 209
    Dr JDD says:

    Convergence is the great “heads I win tails you lose” argument of evolution.

    No real difference to assuming a Creator God who spoke and created ex nihilo.

  210. 210
    Vy says:

    Much ado about a “bush” of life. Or is that “circle” of life?

    Oh well.

  211. 211
    bFast says:

    Bornagain, you are a veritable treasure trove!

    Dr. JDD (203) thanks. I may play with this if I have time. Dying to see what I learn.

    NickMatzke_UD, see, you don’t have to be a holier-than-thou (or in your case smarter-than-thou) A$#. Had you given me what Dr. JDD gave me, I would have been impressed and pleased.

  212. 212
    Vy says:

    Convergence is the great “heads I win tails you lose” argument of evolution.

    It’s a nonsensical cop out from the reality of no descent.

    It assumes evolution has some sort of “successful randomizations for habitat type X” cabinet where it frequently goes in to pull out stuff to reapply on unrelated organisms.

  213. 213
    wd400 says:

    Convergence is the great “heads I win tails you lose” argument of evolution.

    No real difference to assuming a Creator God who spoke and created ex nihilo.

    Did you read the rest of Zachriel’s post? Convergence can often be tested, including by the way he suggests.

  214. 214
    bFast says:

    Zachriel (206) “That is incorrect. If there are similar selective constraints, they may converge.”

    Yes, convergence could produce a fixing of the same mutation in two threads. I studied this with the langur monkey. There was some realistic convergence with cows. The convergence was slight, and the motivation to converge (both are ungulates) was very strong. ‘Could be a factor, but not likely a strong one.

  215. 215
    Dr JDD says:

    Yes wd400 I did read his post thanks. Convergence is still a copout at the molecular level whether you can test it (under evolutionary paradigms and assumptions) or not .

  216. 216
    vjtorley says:

    Sebesteyen at #137,

    After I wrote back to bFast:

    “You suggest that de novo genes “are not ‘poofed’ into existence, but that they do grow, mutation by mutation,” and you propose that they may be growing in “DNA used for some purpose other than protein coding.”

    Now that’s an interesting suggestion, which I hadn’t considered. If true, it would explain why these genes need to be built up step by step.”

    you commented:

    That’s like saying a feasible way to add a new function to a piece of software is by filling a module with random letters and then let a script randomly exchange letters at random positions until the module successfully compiles.

    I hope I don’t have to emphasize how utterly retarded that idea is.

    Just to be clear:

    (i) I was referring to the suggestion of bFast’s that de novo genes may appear arise from “DNA used for some purpose other than protein coding.” The notion that such DNA could gradually be refined into a protein-coding gene does not strike me as absurd;

    (ii) I have made it abundantly clear that I believe families of proteins (and the genes that code for them) arose via a guided process. It doesn’t follow from that that each and every gene was designed. Some genes may have required only slight alterations from pre-existing genetic material – and as we’ve seen, in this case, the pre-existing genetic material was 98% similar. I’d be hesitant to say that guidance would have been required for the changes that occurred here.

    tjguy at #136: please see my reply above.

  217. 217
    J-Mac says:

    Since the famous Nick Mitzke joined the crowd, it is a double opportunity for me to get the double confirmation on the issue that has not been answered for such a long time…
    Since Larry and Nick represent a large crowd of believers, I would like them to provide me with one answer only;

    1.What was the ONE piece of scientific evidence that convinced you personally that life must have originated without an interference of a superior and Intelligent Designer. Please do not overwhelm this blog with too much scientific evidence!!!

    2.Larry and Nick M; let’s move beyond OOL. I’m not going to even mention the problems that lead to this issue, after the life originated.

    The living cell even after the miracles formation of unknown mechanisms ( I will let it go for now) cannot reproduce unless there are very complex molecules present. But here is the real kicker; they are all interdependent; or in the real world, they have to be present at the same time or…:

    Enzymes are needed to produce energy ATP, but energy from ATP is required to make the enzymes. Here is the kicker;

    DNA is absolutely essential to make enzymes, but enzymes can’t be absolutely be made without DNA. It gets worst; proteins can be made only by a full functioning cell, but a cell can’t be made without proteins.

    It is your time too shine Larry and Nick…

  218. 218
    Virgil Cain says:

    Convergent evolution via differing accumulations of genetic accidents, ie NS and drift, strains credibility. Convergent evolution was invented just for cases when the phylogenetic tree didn’t match expectations/ failed to support Common Descent.

  219. 219
    Vy says:

    J-Mac @217, here’s more:

    Thus the [genetic] code can not be translated except by using certain products of its translation. This constitutes a baffling circle; a really vicious circle, it seems, for any attempt to form a model or theory of the genesis of the genetic code.

    Good luck finding a “step-by-step” way out of that circle.

    I guess these evodelusionists didn’t notice the fact that Andre was being generous when he asked them “can a digital code like the Windows Operating system ever spontaneously generate itself?”

  220. 220
    Vy says:

    Virgil @218, convergent evolution is perfect example of why the only place you find true (not twisted) evidence for evolution is in the theory itself; it’s the only thing so far that seems to be“evolving”.

  221. 221
    Virgil Cain says:

    Theory? What theory?

  222. 222
    Sebestyen says:

    (i) I was referring to the suggestion of bFast’s that de novo genes may appear arise from “DNA used for some purpose other than protein coding.” The notion that such DNA could gradually be refined into a protein-coding gene does not strike me as absurd;

    It’s one thing to assume that a gene can get altered so it fulfills a more or less different function but changing a completely different part to a protein coding gene makes no sense at all.

    Besides that, I’d wait until the code of the genome is completely or at least very well understood before giving that idea any merit.

    Sebestyen

  223. 223
    Vy says:

    LOL 😀

  224. 224
    NickMatzke_UD says:

    217
    J-Mac

    October 26, 2015 at 4:03 pm

    Since the famous Nick Mitzke joined the crowd, it is a double opportunity for me to get the double confirmation on the issue that has not been answered for such a long time…
    Since Larry and Nick represent a large crowd of believers, I would like them to provide me with one answer only;

    1.What was the ONE piece of scientific evidence that convinced you personally that life must have originated without an interference of a superior and Intelligent Designer. Please do not overwhelm this blog with too much scientific evidence!!!

    Um, what? Only in crazy-land would someone think major scientific theories come down to ONE piece of evidence. You have to start with the dozens of independent lines of evidence for common ancestry. Start here: http://www.talkorigins.org/faqs/comdesc/

  225. 225
    bornagain says:

    bFast at 211 no problem

    Of related interest:

    Phylogeny: Rewriting evolution – Tiny molecules called microRNAs are tearing apart traditional ideas about the animal family tree. – Elie Dolgin – 27 June 2012
    Excerpt: “I’ve looked at thousands of microRNA genes, and I can’t find a single example that would support the traditional tree,” he says. “…they give a totally different tree from what everyone else wants.” (Phylogeny: Rewriting evolution, Nature 486,460–462, 28 June 2012) (molecular palaeobiologist – Kevin Peterson)
    Mark Springer, (a molecular phylogeneticist working in DNA states),,, “There have to be other explanations,” he says.
    Peterson and his team are now going back to mammalian genomes to investigate why DNA and microRNAs give such different evolutionary trajectories. “What we know at this stage is that we do have a very serious incongruence,” says Davide Pisani, a phylogeneticist at the National University of Ireland in Maynooth, who is collaborating on the project. “It looks like either the mammal microRNAs evolved in a totally different way or the traditional topology is wrong.
    http://www.nature.com/news/phy.....on-1.10885

    ENV reported on the subsequent failed attempt by Darwinists to ‘explain away’ Peterson’s very un-Darwinian findings of microRNAs:

    MicroRNAs Still Do Not Support an Evolutionary “Tree of Life” – July 31, 2014
    Excerpt: Nature News,,, ended on a despairing note:
    “For Ken Halanych, an evolutionary biologist at Auburn University in Alabama, today’s paper provides a critical analysis of a method that he has long doubted. Why did microRNAs get so much attention? “Because we are hopeful,” he says. A simple tool to decode how animals have evolved over hundreds of millions of years would certainly be nice — but it is looking unlikely that one exists.”
    At best, this “explains away” the microRNA mismatch. But if a “simple tool to decode how animals have evolved” does not exist, evolutionists are left with a collection of methods that either disagree with one another, or rely on ad hoc fudge factors to bring the data into agreement with expectations. That’s hardly a good situation to be in for arguing the empirical reliability of any scientific theory.
    http://www.evolutionnews.org/2.....88431.html

    Here is a nice video on the whole episode and how Darwinists never allow their theory to be falsified, not even allowing their theory to be falsified by such severely in-congruent data:

    micro-RNAs and Non-Falsifiable Phylogenetic Trees – video
    http://www.youtube.com/watch?v=qv-i4pY6_MU

    Of semi-related note, messenger RNAs are found to have ‘evolved major differences’ between chimps and humans

    Gene Regulation Differences Between Humans, Chimpanzees Very Complex – Oct. 17, 2013
    Excerpt: Although humans and chimpanzees share,, similar genomes, previous studies have shown that the species evolved major differences in mRNA expression levels.,,,
    http://www.sciencedaily.com/re.....144632.htm

    Verse and Music:

    2 Peter 1:16
    For we did not follow cleverly devised stories when we told you about the coming of our Lord Jesus Christ in power, but we were eyewitnesses of his majesty.

    Mandisa – Overcomer – music video
    https://www.youtube.com/watch?v=b8VoUYtx0kw

  226. 226
    Vy says:

    Another question for the “distinguished” ones: Why did the first cell reproduce?

    It was the fittest. It had no idea of death. It had no idea of reproduction.

  227. 227
    Zachriel says:

    bFast: convergence could produce a fixing of the same mutation in two threads.

    A good example is prestin, which is a motor protein found in the hair cells of the inner ear of the mammalian cochlea. Prestin is crucial for high-frequency hearing. There is convergence of prestin in bats and whales, both of which use echolocation. However, synonymous substitutions support the standard phylogeny.

    More generally, a whale and a fish both have hydrodynamic traits, requiring a large number of adaptations. However, when we look at the overall organism, it’s clear that whales are best classified with mammals.

    Dr JDD: Convergence is still a copout at the molecular level whether you can test it (under evolutionary paradigms and assumptions) or not .

    It’s understandable why you might reject convergence if it weren’t testable, but you are saying you reject it even if it is testable.

    Sebestyen: That’s like saying a feasible way to add a new function to a piece of software is by filling a module with random letters and then let a script randomly exchange letters at random positions until the module successfully compiles.

    See Hayashi et al., Experimental Rugged Fitness Landscape in Protein Sequence Space, PLOS ONE 2006. They replace a section of a phage genome crucial for infectivity with a random sequence, then they mutate and select for infectivity. Guess what happens.

  228. 228
    Virgil Cain says:

    NickMatzke- Theobald says that a nested hierarchy is evidence for Common Descent yet Common Descent expects an abundance of transitional forms whose very existence would make forming a nested hierarchy virtually impossible.

    Fundamental unity is evidence for a common design.

    All of Theobald’s evidences require you to assume he knows what pattern would emerge from a very complex process. There isn’t one essay that tells us what genes were changed or added to produce all of the physical changes required.

    What, exactly, gets modified?

  229. 229
    Virgil Cain says:

    A good example is prestin,…

    Prestin is a good example of what unguided evolution could never produce.

  230. 230
    goodusername says:

    Vy,

    Another question for the “distinguished” ones: Why did the first cell reproduce?

    It was the fittest. It had no idea of death. It had no idea of reproduction.

    If you mean the cell that’s the ancestor of all known life, it had to reproduce or it wouldn’t be the ancestor of any life. How or why it reproduced, we don’t know.

    There may have been earlier cells that didn’t reproduce, but it’s safe to say that they aren’t our ancestors.

  231. 231
    Virgil Cain says:

    And NickMatzke- Could you please link to ten theory of evolution so we can see if it is indeed a major scientific theory? I bet you can’t even say who the author was nor when it was published.

    Does it provide a way to quantify anything to do biological evolution?

    Dr. Giuseppe Sermonti wrote in 2004 that there isn’t a scientific theory of evolution. If there is no one seems to be able to find it. Did the NCSE lock it away for safe keeping?

  232. 232
    Virgil Cain says:

    Vy:

    Why did the first cell reproduce?

    Because it could. I bet it freaked itself out. 😉

  233. 233
    wd400 says:

    wd400, it’s not random because only a subset of the genetic sequences are mutabl

    What? What’s being avoided when we conclude a trait has evolved convergent?

  234. 234
    NickMatzke_UD says:

    228
    Virgil Cain
    October 26, 2015 at 6:19 pm

    NickMatzke- Theobald says that a nested hierarchy is evidence for Common Descent yet Common Descent expects an abundance of transitional forms whose very existence would make forming a nested hierarchy virtually impossible.

    That just ain’t so. Do Google Images on transitional fossil phylogeny: https://www.google.com/search?q=transitional+fossil+phylogeny&es_sm=119&biw=1333&bih=655&tbm=isch&tbo=u&source=univ&sa=X&ved=0CBwQsARqFQoTCJn18MGy4cgCFcubHgod9SQFGQ


    Fundamental unity is evidence for a common design.

    And The Designer apparently just happens to like putting the similarities and differences in a tree pattern that just happens to match geographic distribution, DNA, fossils, etc. Yeah, right.

    All of Theobald’s evidences require you to assume he knows what pattern would emerge from a very complex process.

    It’s not so hard. Organisms resemble their parents, but not exactly. Over great amounts of time, populations split and gradually acquire differences through well-known genetic and population genetic processes. This simple process produces a treelike pattern, produces fossils that gradually acquire the characteristics of organisms currently living, etc.

    There isn’t one essay that tells us what genes were changed or added to produce all of the physical changes required.

    What, exactly, gets modified?

    Genes and gene regulation get modified. Easy question.

    Or did you mean to say, “I want a single, simple, essay that explains in detail the evolution of 20,000 or so genes in humans and every other of millions of living and extinct species.”

    If that’s your standard, you need to justify it. Over here in real science, we form hypotheses and test them with the data we can actually get. We don’t require omniscience before concluding that some hypothesis explains the patterns in the data quite well.

  235. 235
    wd400 says:

    Apparently I am too late to edit my comment in 233 which should actually feature JDD’s odd comment:

    Convergence is still a copout at the molecular level whether you can test it (under evolutionary paradigms and assumptions) or not .

  236. 236
    NickMatzke_UD says:

    231
    Virgil Cain
    October 26, 2015 at 6:25 pm
    And NickMatzke- Could you please link to ten theory of evolution so we can see if it is indeed a major scientific theory? I bet you can’t even say who the author was nor when it was published.

    Does it provide a way to quantify anything to do biological evolution?

    Dr. Giuseppe Sermonti wrote in 2004 that there isn’t a scientific theory of evolution. If there is no one seems to be able to find it. Did the NCSE lock it away for safe keeping?

    C’mon, this is childish. Any modern scientific theory is the product of hundreds or thousands of scholars over generations. Replace “evolution” with “plate tectonics” or “atomic theory” or “the germ theory of disease” in your question, then provide the answers.

    Us reasonable people over in noncrazy land recognize that major scientific theories get treated in textbooks. There are textbooks and college courses on evolutionary biology all over the place. Google is your friend.

  237. 237
    bFast says:

    VJTorley(216)

    I was referring to the suggestion of bFast’s that de novo genes may appear arise from “DNA used for some purpose other than protein coding.” The notion that such DNA could gradually be refined into a protein-coding gene does not strike me as absurd;

    I actually would find this to be very amazing! (That said, a lot about DNA is amazing.) It would be equivalent to writing a paragraph in a foreign language, running the results throug a simple character for character exchange and having the results be meaningful.

  238. 238
    Virgil Cain says:

    NickMatzke:

    That just ain’t so. Do Google Images on transitional fossil phylogeny:

    Umm, phylogenetics doesn’t yield a nested hierarchy. Linnaean Taxonomy is a nested hierarchy. Nice clean distinct sets

    And The Designer apparently just happens to like putting the similarities and differences in a tree pattern that just happens to match geographic distribution, DNA, fossils, etc

    the best way to control a complex design is to set it up in a nested hierarchy and then carry it out.

    Organisms resemble their parents, but not exactly. Over great amounts of time, populations split and gradually acquire differences through well-known genetic and population genetic processes.

    Humans will always be humans, Nick. Either that or we will go extinct. There isn’t any known process that can turn a fin into a leg, Nick.

    Genes and gene regulation get modified.

    yes, they do. However there isn’t any evidence that those modifications can account for all of the physiological and morphological changes required for UCD.

    Over here in real science, we form hypotheses and test them with the data we can actually get.

    So how can you test the hypothesis that drift and natural selection can produce a human from some chimp-like ancestor?

    And what about voles? Voles- A lot of micro but no macro

    The study focuses on 60 species within the vole genus Microtus, which has evolved in the last 500,000 to 2 million years. This means voles are evolving 60-100 times faster than the average vertebrate in terms of creating different species. Within the genus (the level of taxonomic classification above species), the number of chromosomes in voles ranges from 17-64. DeWoody said that this is an unusual finding, since species within a single genus often have the same chromosome number.  

    Among the vole’s other bizarre genetic traits:  

    •In one species, the X chromosome, one of the two sex-determining chromosomes (the other being the Y), contains about 20 percent of the entire genome. Sex chromosomes normally contain much less genetic information.
    •In another species, females possess large portions of the Y (male) chromosome.
    •In yet another species, males and females have different chromosome numbers, which is uncommon in animals. 

    A final “counterintuitive oddity” is that despite genetic variation, all voles look alike, said DeWoody’s former graduate student and study co-author Deb Triant. 

    “All voles look very similar, and many species are completely indistinguishable,” DeWoody said.  

    In one particular instance, DeWoody was unable to differentiate between two species even after close examination and analysis of their cranial structure; only genetic tests could reveal the difference.  

    Nevertheless, voles are perfectly adept at recognizing those of their own species.

    Yup after all this “evolution” a vole is still a vole. This study alone should cast a huge shadow over evolutionism and macroevolution

  239. 239
    bornagain says:

    NickMatzke_UD, you keep using the word crazy like you know what it actually means.

    You don’t!

    Let me give you a small clue what crazy REALLY means Matzke.

    Crazy, I mean REALLY batshit, lunatic foaming at the mouth, crazy, (not your normal everyday crazy mind you), is believing that your brain, which is far, far, more complex than the entire internet combined, came about by completely undirected material processes.

    that level of crazy is just not natural. It takes extreme effort to warp your God given brain/mind so badly that it believes such a completely insane BS.

    Yet, in spite of the fact that you are certifiably insane for believing such non-sense as you do about your own brain, you apparently have made it your life’s mission to become even more insane than you already are and to try to drag others down the Alice in Wonderland rabbit hole that you live in.

    As I heard one man say Matzke, “you are either on drugs or you need to start taking some!” 🙂

    Here are few notes on the ‘beyond belief’ brain
    http://www.uncommondescent.com.....ent-573329

  240. 240
    Virgil Cain says:

    NickMatzke:

    Any modern scientific theory is the product of hundreds or thousands of scholars over generations.

    OK so there isn’t really a scientific theory of evolution. Got it.

    Us reasonable people over in noncrazy land recognize that major scientific theories get treated in textbooks. There are textbooks and college courses on evolutionary biology all over the place. Google is your friend.

    So the “theory” is things change and sometimes they don’t. We don’t know the details but we are comforted by the fact that evolution has occurred.

    Without a means of quantification it isn’t a theory, Nick. And no one can quantify unguided evolution’s ability to produce ATP synthase. the premise doesn’t make any predictions.

    What does unguided evolution predict, Nick? Einstein’s predictions were very specific. His is a major scientific theory. I am pretty sure it was in a published paper, too.

  241. 241
    Vy says:

    If you mean the cell that’s the ancestor of all known life

    No, sorry. It’s the naturalistic and assumed, yet totally unproven, ancestor of all known life.

    it had to reproduce or it wouldn’t be the ancestor of any life. How or why it reproduced, we don’t know.

    The more realistic and sensible thing to say would be: it didn’t exist.

    There’s no “it had to reproduce”, that’s just false. Read my post again.

  242. 242
    Vy says:

    Because it could. I bet it freaked itself out.

    Lol!

    “Ahhh! Kwhat whash dhadt? Shid Dhi yust shee mye riflektion inn dhe shoup bowwl?” (I don’t speak bacter too well).

    I guess it couldn’t stand the loneliness, and since it’s got no ribs …

  243. 243
    Mapou says:

    NickMatzke_UD:

    Us reasonable people over in noncrazy land

    So why is it you people have such a hard time understanding a simple truth like the combinatorial explosion kills any stochastic search mechanism (such as RM+NS) dead? Are you people in noncrazy land stupid or something?

  244. 244
    Vy says:

    I went to that “29+ [delusional interpretations of reality to support common descent]” and found this:

    Furthermore, because it is not part of evolutionary theory, abiogenesis also is not considered in this discussion of macroevolution: abiogenesis is an independent hypothesis. In evolutionary theory it is taken as axiomatic that an original self-replicating life form existed in the distant past, regardless of its origin.

    So here’s mine:

    “Fantasy-ville: Mix all the ingredients you need to make a cake but don’t worry about the baking device because that’s not necessary for baking. Assume that, irregardless of where that device comes from, when the time comes it will reveal itself to you. Now wait and watch. Oh, and don’t clean up.

    Reality-ville:

    2 days later …

    What the? Did something die in kitchen??? Gosh, that stinks!!!”

  245. 245
    EDTA says:

    Sorry that I’m late to this fun party, but I have a question for the people assembled here: Are we certain that the DNA sequence matching algorithm(s) used to obtain the 98% similarity result don’t rely on any circular assumptions, such as common ancestry?

    (There has been much discussion in years past that methods for reconstructing phylogenies rely on the assumption of common ancestry–is why I ask.)

  246. 246
    NickMatzke_UD says:

    240
    Virgil Cain

    October 26, 2015 at 6:59 pm
    NickMatzke:

    Any modern scientific theory is the product of hundreds or thousands of scholars over generations.

    OK so there isn’t really a scientific theory of evolution. Got it.

    Dude! Listen to yourself! Do you really think all theories in science have a single author with a single definitive publication? Even Einstein’s wasn’t a single publication. He had a number of papers, as did a number of other scientists, improving, refining, and testing it. Modern relativity theory is based on Einstein and large number of other people.

    You are just being contrarian because you don’t want to admit you made a silly mistake to one of those evil Darwinists.

  247. 247
    NickMatzke_UD says:

    245
    EDTA

    October 26, 2015 at 7:41 pm

    Sorry that I’m late to this fun party, but I have a question for the people assembled here: Are we certain that the DNA sequence matching algorithm(s) used to obtain the 98% similarity result don’t rely on any circular assumptions, such as common ancestry?

    (There has been much discussion in years past that methods for reconstructing phylogenies rely on the assumption of common ancestry–is why I ask.)

    Pairwise BLAST and similar algorithms do not. Here’s a classic pairwise alignment algorithm, it’s not that complicated.

    https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm

    Dot-plots are a simple way of visualizing pairwise matches in sequences:

    https://en.wikipedia.org/wiki/Dot_plot_(bioinformatics)

    http://www.nature.com/nature/j.....0-f2.2.jpg

  248. 248
    NickMatzke_UD says:

    Umm, phylogenetics doesn’t yield a nested hierarchy. Linnaean Taxonomy is a nested hierarchy. Nice clean distinct sets

    Uh…nested hierarchy means “groups within groups”. A phylogeny has these. Why am I even talking to you guys? Up means down with you guys, if that’s what you have to assert to avoid conceding some point about evolution.

  249. 249
  250. 250
    bornagain says:

    “Modern relativity theory is based on Einstein and large number of other people.”

    Really?

    and other than the extremely finely tuned 1 in 10^120 cosmological constant, what addition to general relativity has there ever been Matzke?

    And how did that addition to GR possibly confirm your atheistic delusions?

    Hugh Ross PhD. – Scientific Evidence For Cosmological Constant (1 in 10^120 Expansion Of The Universe)
    http://www.metacafe.com/watch/4347218/

    (Commenting on the 1 in 10^120 fine tuning of the expansion of the universe), “Hugh Ross states an analogy that does not even come close to describing the precarious nature of this cosmic balance [between too fast and too slow] would be a billion pencils all simultaneously positioned upright on their sharpened points on a smooth glass surface with no vertical supports.”
    Eric Metaxas – Miracles – page 49

    Here are the verses from the Bible which Dr. Ross listed, which were written well over 2000 years before the discovery of the finely tuned expansion of the universe, that speak of God ‘Stretching out the Heavens’; Job 9:8; Isaiah 40:22; Isaiah 44:24; Isaiah 48:13; Zechariah 12:1; Psalm 104:2; Isaiah 42:5; Isaiah 45:12; Isaiah 51:13; Jeremiah 51:15; Jeremiah 10:12. The following verse is my favorite out of the group of verses:

    Job 9:8
    He alone stretches out the heavens and treads on the waves of the sea.

    The Truman Show – Truman walking on water – screenshot picture
    http://gaowsh.files.wordpress......0-pm-2.jpg

    Here is the paper from the atheistic astrophysicists, that Dr. Ross referenced in the preceding video, that speaks of the ‘disturbing implications’ of the finely tuned expanding universe (1 in 10^120 cosmological constant):

    Disturbing Implications of a Cosmological Constant – Dyson, Kleban, Susskind (each are self proclaimed atheists) – 2002
    Excerpt: “Arranging the universe as we think it is arranged would have required a miracle.,,,”
    “The question then is whether the origin of the universe can be a naturally occurring fluctuation, or must it be due to an external agent which starts the system out in a specific low entropy state?”
    page 19: “A unknown agent [external to time and space] intervened [in cosmic history] for reasons of its own.,,,”
    Page 21 “The only reasonable conclusion is that we don’t live in a universe with a true cosmological constant”.
    http://arxiv.org/pdf/hep-th/0208013.pdf

    Weinberg himself admits that atheists are in a ‘fix’

    Quote:
    “I don’t think one should underestimate the fix we are in. That in the end we will not be able to explain the world. That we will have some set of laws of nature (that) we will not be able to derive them on the grounds simply of mathematical consistency. Because we can already think of mathematically consistent laws that don’t describe the world as we know it. And we will always be left with a question ‘why are the laws nature what they are rather than some other laws?’. And I don’t see any way out of that.
    The fact that the constants of nature are suitable for life, which is clearly true, we observe,,,”
    (Weinberg then comments on the multiverse conjecture of atheists)
    “No one has constructed a theory in which that is true. I mean,, the (multiverse) theory would be speculative, but we don’t even have a theory in which that speculation is mathematically realized. But it is a possibility.”
    Steven Weinberg – as stated to Richard Dawkins at the 8:15 minute mark of the following video

    Leonard Susskind – Richard Dawkins and Steven Weinberg – 1 in 10^120 – Cosmological Constant points to intelligent design – video
    https://youtu.be/z4E_bT4ecgk?t=495

  251. 251
    bFast says:

    EDTA (245) “Are we certain that the DNA sequence matching algorithm(s) used to obtain the 98% similarity result don’t rely on any circular assumptions, such as common ancestry?”

    Actually, in the software world we have used similar technologies for years. We use it for “version control” systems: We record all changes made to a document (usually computer program) so that we can figure out why the new version is somehow worse than the old, etc. We also use it for software patches: A difference engine is run between old and new version of the machine language version of software. Rather than sending the end user a new version of the program, we just send the necessary changes.

    There is fundamentally no difference between these technologies, therefore I don’t see any need for an “assumption of UCD”.

  252. 252
    aarceng says:

    Now, granted that I only looked at the very first one (“ZNF843?), it was quite easy to find the corresponding DNA on the chimpanzee chromosome, with approximately 98.5% identity.

    What does this really mean? A “gene” compared randomly to another section of DNA should have an average of 25% similarity because there are only 4 bases. You can then “correct for indels” to improve the match. But if you scan an entire genome looking for a best match you can have billions of trials and expect to get some with high similarity by chance. This does not mean that they are both derived from a gene in a common ancestor.

  253. 253
    ThickPython says:

    @aarceng:

    “you can have billions of trials and expect to get some with high similarity by chance”

    http://blast.ncbi.nlm.nih.gov/.....FAQ#expect

  254. 254
    Andre says:

    Nick

    Why did you link TalkOrigins as some sort of valid site to make your point? The site even has a page on how to debate creationists hardly scientific if you ask me.

  255. 255
    Andre says:

    EDTA

    That is my question exactly if we don’t infer common descent and we build an unrooted tree what will it look like? I noticed Nick and Thickpython has completely ignored this. I wonder why that is?

  256. 256
    Andre says:

    Nick Matzke is a reasonable person?

    Let’s test that claim.

    This is a guy that believe that dirt not only made itself but magically became alive.

    Is that reasonable?

    Nick if there is no reason for anything why are you trying to use reason to deny reason exist?

    Is that reasonable?

    Nick thinks that through small incremental random copy errors, deletions over a long period of time the mind of a monkey can grow convictions.

    Is that reasonable?

  257. 257
    Andre says:

    Ever since Darwin drew his tree every person of a dubious mind has tried to fit data into his supposed and assumed tree. As Dr. Craig Venter said it’s an artifact and the data does not hold up, sadly those with dubious minds are still trying to force the data to fit the artifact.

  258. 258
    Mapou says:

    Andre, you’re gonna kill the dirt worshipper. 😀

  259. 259
    ThickPython says:

    @Andre:

    “That is my question exactly if we don’t infer common descent and we build an unrooted tree what will it look like? I noticed Nick and Thickpython has completely ignored this. I wonder why that is?”

    See post #194.

  260. 260
    Mapou says:

    NickMatzke_UD:

    Umm, phylogenetics doesn’t yield a nested hierarchy. Linnaean Taxonomy is a nested hierarchy. Nice clean distinct sets

    Uh…nested hierarchy means “groups within groups”. A phylogeny has these. Why am I even talking to you guys? Up means down with you guys, if that’s what you have to assert to avoid conceding some point about evolution.

    A truly nested hierarchy via common descent does not allow horizontal gene transfers. HGTs are all over the place, thus falsifying common descent and Darwin’s strictly nested hierarchy. Wake up Nicky.

    PS. A hierarchy that allows multiple inheritance (HGTs) is precisely what one would expect from intelligent design over time. Ask any software designer.

  261. 261
    ThickPython says:

    @EDTA:

    “Sorry that I’m late to this fun party, but I have a question for the people assembled here: Are we certain that the DNA sequence matching algorithm(s) used to obtain the 98% similarity result don’t rely on any circular assumptions, such as common ancestry?”

    It lines up two sequences as best as it can, and then counts the differences. It’s not rocket surgery.

    There are no assumptions about common ancestry built into the software, although if you feel less than secure in your womanhood, you can call the differences putative mutations and putative indels.

  262. 262
    bFast says:

    Mapou, “HGTs are all over the place.”
    Ok, gurus, help me out here. To what extent is this statement true? I understand that HGT is pervasive within bacteria and archaea. How pervasive is it in eukaryotes? In mammals?

  263. 263
    Mapou says:

    bFast,

    Anytime the place of an organism in the tree is ambiguous, meaning that the organism seems to belong to multiple branches simultaneously, you can bet the reason is HGT. I am willing to bet that a systematic search for HGTs in higher organisms will unearth many big surprises. But then again we would need a few honest scientists in biology, not a bunch of dirt worshippers.

  264. 264
    ThickPython says:

    @bFast:

    “How pervasive is it in eukaryotes? In mammals?”

    Here, let me Google that for you.

    https://en.wikipedia.org/wiki/Horizontal_gene_transfer#Eukaryotes

  265. 265
    Andre says:

    Thickpython

    @196 – Are you trying to label me a creationist that believe in barminology? Try again!

    @264 – Wikipedia? Really? The unemployed atheist playground? Really?

  266. 266
    Dr JDD says:

    Starting point on LGT/HGT

    http://www.sciencedirect.com/s.....7414001854

    Lateral gene transfers and the origins of the eukaryote proteome: a view from microbial parasitesRobert P HirtCecilia AlsmarkT Martin Embley

  267. 267
    vjtorley says:

    Dr. Ann Gauger raises some interesting questions in her 2013 article, Orphan Genes — A Guide for the Perplexed. Here’s an excerpt from her conclusion:

    Thus, the existence and prevalence of orphan genes raises a number of significant questions.

    1. Do orphan genes encode functional proteins? In many cases there is evidence to suggest that they do. Some are highly conserved, even essential for viability to the organism from which they come. Some are involved in important species-specific or group-specific functions.

    2. Will similar sequences be found in other genomes, as we obtain more data? This could be the case if orphans are simply the result of our having sampled too little of worldwide genomic diversity. Orphan genes could be examples of once common genes now lost in most other species, or they could be far voyagers, come from other life forms and integrated into new contexts (this is especially possible among bacteria). This is unlikely to be the case for all orphan genes, however, because we keep discovering more as we sequence more genomes.

    3. Will orphan proteins show structural similarity, if not sequence similarity, to known proteins? This would suggest that orphan genes started out with sequence similarity, but have lost it because of rapid adaptive evolution or, alternatively, long-term neutral evolution. The current answer would seem to suggest that at least some orphan genes have no known structural similarity. It is too soon to say whether that will always be the case.

    4. Given the fact that such surprising species- or clade-specific proteins exist, it raises interesting questions about where orphans come from. Some might have come from gene duplication followed by rapid adaptive evolution (see #3 above). If that is the case we should see traces left behind in the orphan protein’s three-dimensional structure. Some propose recruitment from non-coding DNA by a combination of mechanisms, including insertion of transposable elements. This is possible, but it would require that the insertion or other mechanism(s) be lucky events in order to produce a stable, functional protein, that is, one that is of use to the organism. Exactly how lucky is one of the issues we are debating.

    5. Then there is the elephant in the room that evolutionary biologists don’t want to acknowledge. Perhaps we see so many species- and clade-specific orphan genes because they are uniquely designed for species- and clade-specific functions. Certainly, this runs contrary to the expectation of common descent.

    We have seen that orphan genes in humans bear striking similarity to DNA sequences in chimpanzees and other apes. In the light of that information, which of Ann Gauger’s five alternatives do readers favor?

  268. 268
  269. 269
    Andre says:

    Dr. Torley

    I think it is safe to say we can rule out luck having anything to do with it. If it was luck it means multiple jackpots over and over and over and over and over. That simply does not fit the data.

  270. 270
  271. 271
    Mapou says:

    Take 4 and raise it to the average size (number of base pairs) of an orphan gene (or any gene) and you have the size of the search space that RM+NS would have to go through in order to evolve that gene. The math does not lie. The whole thing is laughable because it’s based on pure superstition and wishful thinking.

  272. 272
    Andre says:

    Bfast

    Here is Prof Moran agreeing with me! We have no difference here in opinion, as the facts speak for them-self, where the difference does split our opinion is that Prof Moran presupposes Common Descent and I do not.

    HGT is not good for common descent, It makes common descent a non-starter.

    http://sandwalk.blogspot.co.za.....-life.html

  273. 273
    Andre says:

    For those that have not seen Dr Craig Venter’s discussion, with a panel of mostly militant atheists that swear by common descent he showed some balls here. The truth is unstoppable.

    https://www.youtube.com/watch?v=MXrYhINutuI

  274. 274
  275. 275
    Virgil Cain says:

    NickMatzke:

    Do you really think all theories in science have a single author with a single definitive publication?

    No, Nick. I do know scientific theories should be published so that people can read what they actually say. To say that a scientific theory is ion the aether, as you are doing, is a sure sign of desperation.

    What does unguided evolution predict, Nick? Why did you avoid all the questions that pertain to this alleged theory, Nick?

    Pathetic.

    There isn’t any way to quantify unguided evolution and science requires quantification. Without quantification you cannot have a scientific theory. Not that I would expect NickMatzke to understand that simple point.

  276. 276
    Virgil Cain says:

    Nick Matzke:

    Uh…nested hierarchy means “groups within groups”. A phylogeny has these.

    Linnaean Taxonomy has that. In what way does phylogeny have that? Please be specific or admit that you are a bluffing fool.

    If population A gives rise to populations B and C, do populations B and C constitute groups within population A? No, Nick, B and C are not within A.

    Why am I even talking to a known evoTARD like you, anyway…

  277. 277
    Virgil Cain says:

    First I will note that Theobald, who Nick cites, says that Linnaean Taxonomy is the nested hierarchy. It is right there in his article. That said:

    Nested Hierarchy and Common Descent

    Potential falsification:
    It would be very problematic if many species were found that combined characteristics of different nested groupings.

    Yet that is exactly what we would observe if all the alleged transitional forms were still alive- combined characteristics of different nested groups. Mammals are a nested group and reptiles are a nested group. Mammal-like reptiles and reptile-like mammals are on the outside, looking in.

  278. 278
    bornagain says:

    Dr. Torley. I like Dr. Gauger’s “Elephant in the living room” picture in her article summing up the state of evidence for ORFan genes:

    http://31.media.tumblr.com/114.....qz4rgp.jpg

    They say that a picture can say a thousand words, but I think that particular picture says a ‘billion-trillion words’ when is comes to these debates on origins.

    Stephen Talbott does an excellent job of highlighting that ‘billion-trillion’ elephant in the living room question that is never really honestly addressed in any of these debates on origins:

    HOW BIOLOGISTS LOST SIGHT OF THE MEANING OF LIFE — AND ARE NOW STARING IT IN THE FACE – Stephen L. Talbott – May 2012
    Excerpt: “If you think air traffic controllers have a tough job guiding planes into major airports or across a crowded continental airspace, consider the challenge facing a human cell trying to position its proteins”. A given cell, he notes, may make more than 10,000 different proteins, and typically contains more than a billion protein molecules at any one time. “Somehow a cell must get all its proteins to their correct destinations — and equally important, keep these molecules out of the wrong places”. And further: “It’s almost as if every mRNA [an intermediate between a gene and a corresponding protein] coming out of the nucleus knows where it’s going” (Travis 2011),,,
    Further, the billion protein molecules in a cell are virtually all capable of interacting with each other to one degree or another; they are subject to getting misfolded or “all balled up with one another”; they are critically modified through the attachment or detachment of molecular subunits, often in rapid order and with immediate implications for changing function; they can wind up inside large-capacity “transport vehicles” headed in any number of directions; they can be sidetracked by diverse processes of degradation and recycling… and so on without end. Yet the coherence of the whole is maintained.
    The question is indeed, then, “How does the organism meaningfully dispose of all its molecules, getting them to the right places and into the right interactions?”
    The same sort of question can be asked of cells, for example in the growing embryo, where literal streams of cells are flowing to their appointed places, differentiating themselves into different types as they go, and adjusting themselves to all sorts of unpredictable perturbations — even to the degree of responding appropriately when a lab technician excises a clump of them from one location in a young embryo and puts them in another, where they may proceed to adapt themselves in an entirely different and proper way to the new environment. It is hard to quibble with the immediate impression that form (which is more idea-like than thing-like) is primary, and the material particulars subsidiary.
    Two systems biologists, one from the Max Delbrück Center for Molecular Medicine in Germany and one from Harvard Medical School, frame one part of the problem this way:
    “The human body is formed by trillions of individual cells. These cells work together with remarkable precision, first forming an adult organism out of a single fertilized egg, and then keeping the organism alive and functional for decades. To achieve this precision, one would assume that each individual cell reacts in a reliable, reproducible way to a given input, faithfully executing the required task. However, a growing number of studies investigating cellular processes on the level of single cells revealed large heterogeneity even among genetically identical cells of the same cell type. (Loewer and Lahav 2011)”,,,
    And then we hear that all this meaningful activity is, somehow, meaningless or a product of meaninglessness. This, I believe, is the real issue troubling the majority of the American populace when they are asked about their belief in evolution. They see one thing and then are told, more or less directly, that they are really seeing its denial. Yet no one has ever explained to them how you get meaning from meaninglessness — a difficult enough task once you realize that we cannot articulate any knowledge of the world at all except in the language of meaning.,,,
    http://www.netfuture.org/2012/May1012_184.html#2

    In these debates on origins, Darwinists, and apparently people who believe in Theistic evolution, (i.e. Biologos, Dr. Torley, gpuccio), think that they have made their case for common descent primarily based on how similar they think the genes and proteins are.
    In other words, Darwinists and Theistic evolutionists try to ‘explain away’ as much dissimilarity in genes and proteins as they possibly can. Apparently with the erroneous assumption that if there is very little dissimilarity between genes and proteins then that finally explains how the human body attained its unique ‘form’.

    That approach to answering the question is, to put it kindly, ‘not even wrong’.

    i.e. That approach, as Talbott highlighted, is not even close to being the right approach in regards to trying explain how not only the human ‘form’ exists, but also how each individual human body of a billion-trillion protein molecules was created.

    The problem is further clearly illustrated here by Talbott:

    What Do Organisms Mean? Stephen L. Talbott – Winter 2011
    Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: “Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements… take unique meaning from their context.[3]”,,,
    http://www.thenewatlantis.com/.....nisms-mean

    In other words, the right approach in trying to figure out how the human form was created is not to ‘explain away’ dissimilarity in proteins and genes but is to try to figure out what in blue blazes is controlling the billion trillion protein molecules of a human body, telling them exactly where to go and what to do, for precisely a lifetime and not a moment longer.

    The Unbearable Wholeness of Beings – Stephen L. Talbott – 2010
    Excerpt: Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary.
    ,,, the question, rather, is why things don’t fall completely apart — as they do, in fact, at the moment of death. What power holds off that moment — precisely for a lifetime, and not a moment longer?
    Despite the countless processes going on in the cell, and despite the fact that each process might be expected to “go its own way” according to the myriad factors impinging on it from all directions, the actual result is quite different. Rather than becoming progressively disordered in their mutual relations (as indeed happens after death, when the whole dissolves into separate fragments), the processes hold together in a larger unity.
    http://www.thenewatlantis.com/.....-of-beings

    picture – What power holds off that moment — precisely for a lifetime, and not a moment longer?
    http://cdn-4.spiritscienceandm.....ardd-2.jpg

    Any other argument as to how human ‘form’ was created, such as the ‘genetic similarity argument’ currently being used by Darwinists and Theistic evolutionists, is to miss the elephant in the living room problem of explaining exactly how a billion-trillion protein molecules can possibly cohere as a single unified whole for precisely a lifetime and not a moment longer.

    Indeed the whole idea that a billion-trillion protein molecules could possibly cohere as a single unified whole, for precisely a life time and not a moment longer, is very antithetical to the entire philosophy of reductive materialism (which is the philosophy that undergirds neo-Darwinian thought).

    Of supplemental note, as briefly highlighted in posts 29, 30, and 31, of this thread, quantum nonlocality has now been found in molecular biology on a massive scale.
    And in addition to post 29, 30, and 31, is the following quote

    Jim Al-Khalili, at the 2:30 minute mark of the following video states,
    “Biologists, on the other hand have got off lightly in my view. They are very happy with their balls and sticks models of molecules. The balls are the atoms. The sticks are the bonds between the atoms. And when they can’t build them physically in the lab nowadays they have very powerful computers that will simulate a huge molecule.,, It doesn’t really require much in the way of quantum mechanics in the way to explain it.”
    At the 6:52 minute mark of the video, Jim Al-Khalili goes on to state:
    “To paraphrase, (Erwin Schrodinger in his book “What Is Life”), he says at the molecular level living organisms have a certain order. A structure to them that’s very different from the random thermodynamic jostling of atoms and molecules in inanimate matter of the same complexity. In fact, living matter seems to behave in its order and its structure just like inanimate cooled down to near absolute zero. Where quantum effects play a very important role. There is something special about the structure, about the order, inside a living cell. So Schrodinger speculated that maybe quantum mechanics plays a role in life”.
    Jim Al-Khalili – Quantum biology – video
    https://www.youtube.com/watch?v=zOzCkeTPR3Q

    Interestingly, Al-Khalili comparison of the orderliness of life to the ordiliness of a Bose-Einstein condensate was just recently confirmed in protein molecules

    Quantum coherent-like state observed in a biological protein for the first time – October 13, 2015
    Excerpt: If you take certain atoms and make them almost as cold as they possibly can be, the atoms will fuse into a collective low-energy quantum state called a Bose-Einstein condensate. In 1968 physicist Herbert Fröhlich predicted that a similar process at a much higher temperature could concentrate all of the vibrational energy in a biological protein into its lowest-frequency vibrational mode. Now scientists in Sweden and Germany have the first experimental evidence of such so-called Fröhlich condensation (in proteins).,,,
    The real-world support for Fröhlich’s theory (for proteins) took so long to obtain because of the technical challenges of the experiment, Katona said.
    http://phys.org/news/2015-10-q.....otein.html

    The implication of finding quantum non-locality in molecular biology on a massive scale is fairly, and pleasantly, obvious:

    Does Quantum Biology Support A Quantum Soul? – Stuart Hameroff – video
    https://www.youtube.com/watch?v=iIyEjh6ef_8

    Verse and Music:

    Acts 17:28
    For in him we live and move and have our being.’ As some of your own poets have said, ‘We are his offspring.’

    Todd Agnew – This Fragile Breath
    http://www.youtube.com/watch?v=hoGPG4JOcXs

  279. 279
    Andre says:

    Virgil Cain

    In Theobald’s article he says;

    Hierarchical classifications for inanimate objects don’t work for the very reason that unlike organisms, rocks and minerals do not evolve by descent with modification from common ancestors.

    Common descent is presupposed that is why they have to mangle the data to fit the model.

    I think this is where the problem starts, its assumed. with this kind of dogmatic view how else can we do rational open scientific inquiries?

  280. 280
    ThickPython says:

    @Andre:

    “Are you trying to label me a creationist that believe in barminology? Try again!”

    I’ve already had to guess what your question actually means, because if you’re using the term “unrooted tree” correctly, your question is fairly trivial.

    So how about you try again to make your question clearer.

  281. 281
    Virgil Cain says:

    The US Army is a nested hierarchy and I am pretty sure it did not arise via descent with modification from common ancestors.

    And Linnaean Taxonomy doesn’t have anything to do with descent with modification from common ancestors and it is a nested hierarchy.

    When I was a network admin I used a nested hierarchy to set up directory access. That was how I was taught to do it. It seems that is standard operating procedure.

  282. 282
    Andre says:

    Thickpython

    I am saying that the data does not show common descent it is forced to fit the assumption of common descent. If we remove the assumption what do we get? I think Dr. Venter answers it aptly.

  283. 283
    gpuccio says:

    bornagain:

    In these debates on origins, Darwinists, and apparently people who believe in Theistic evolution, (i.e. Biologos, Dr. Torley, gpuccio), think that they have made their case for common descent primarily based on how similar they think the genes and proteins are.
    In other words, Darwinists and Theistic evolutionists try to ‘explain away’ as much dissimilarity in genes and proteins as they possibly can. Apparently with the erroneous assumption that if there is very little dissimilarity between genes and proteins then that finally explains how the human body attained its unique ‘form’.

    I don’t want to take again the discussion about CD with you, we have alredy debated much about that.

    However, please consider the following two points, just for the sake of truth:

    1) I am not a believer in Theistic evolution. I have never been, I never will be. There are probably not many things that I dislike as much as Theistic evolution.

    2) Your summary of what I would think about CD, while certainly in perfect good faith, is completely wrong. I don’t think those things. You can refer to my posts to find out what I do think, if you like,

  284. 284
    NickMatzke_UD says:

    281
    Virgil Cain

    October 27, 2015 at 6:20 am
    The US Army is a nested hierarchy and I am pretty sure it did not arise via descent with modification from common ancestors.

    And Linnaean Taxonomy doesn’t have anything to do with descent with modification from common ancestors and it is a nested hierarchy.

    When I was a network admin I used a nested hierarchy to set up directory access. That was how I was taught to do it. It seems that is standard operating procedure.

    This would only be a good analogy for the biological data if each soldier’s billions of DNA base pairs of genome sequence fit the military nested hierarchy so well that you could infer that hierarchy just by looking at the DNA.

    This is what we see in biology that we don’t see in human-constructed hierarchies. The latter typically only describe a few characters and cannot be retrieved with multiple independent datasets unrelated to function, geography, etc.

  285. 285
    bornagain says:

    gpuccio, I did read your posts and was very disappointed with the ‘fuzziness’ with which you accept CD.

    The posts, IMHO, are very uncharacteristic of your usual posts when you argue solely for ID in very a crisp, clear, and precise manner.

    I’m sorry that you don’t like being grouped with BioLogos and will gladly change my opinion of you (and of Dr. Torley) if you guys are more clear in distancing yourself from the BioLogos crowd in the superficial type of argumentation you guys are using to try to establish CD as valid.

    Until then, the differences I see between you and them, (and even between you and neo-Darwinists), are very murky when it comes to the argumentation of CD in particular. i.e. It is hard for me to see a clear distinction between your argumentation and theirs so as to distinctly separate you guys on the issue of CD.

  286. 286
    Virgil Cain says:

    Earth to NickMatzke- There is a huge difference between a nested hierarchy and a mere hierarchy.

    With a nested hierarchy levels consist of and contain the lower levels. The Animal Kingdom consists of and contains Phyla, which consist of and contain Classes and so on.

    We shouldn’t see that level of containment with Common Descent. Transitional forms, by their very nature, do not fit into nice neat sets, Nick.

    Even Darwin recognized that fact.

  287. 287
    Zachriel says:

    Andre: HGT is not good for common descent, It makes common descent a non-starter.

    The nested hierarchy doesn’t have to be perfect for it to be objectively identifiable. There is a strong signal of the nested hierarchy for eukaryotes, but it is not perfect, and there are a number of anomalies, many with known causes (e.g. convergence, endogenous retroviruses, hybridization, endosymbiosis, incomplete lineage sorting). The signal is fuzzier at the trunk of the tree, and the early branches do not seem to form a single trunk, even though the branches appear to share a common ancestral population.

  288. 288
    Virgil Cain says:

    The nested hierarchy doesn’t have to be perfect for it to be objectively identifiable.

    Common Descent does not produce a nested hierarchy. Even YOU admitted that a family tree is not a nested hierarchy and yet it is an example of Common Descent.

    Zachriel is lying as all of this has been pointed out to him already and he still persists with this nonsense.

  289. 289
    Virgil Cain says:

    Parent populations do NOT consist of nor do they contain any of their daughter populations. Nested hierarchies are all about the consisting and containment entailments.

  290. 290
    Virgil Cain says:

    bornagain:

    gpuccio, I did read your posts and was very disappointed with the ‘fuzziness’ with which you accept CD.

    Fuzzy makes you warm. And warm makes you comfortable. However comfortable does not make for good science.

  291. 291
    NickMatzke_UD says:

    Virgil Cain, you are really not even getting the basics of what a cladogram is. It is literally a groups-within-groups statement. A cladogram and a perfectly-nested Venn Diagram contain identical information.

    And, yes, you can put transitional fossils in cladograms and Venn diagrams. Transitional fossils are put in cladograms all the time — every phylogenetic analysis of fossils, in fact.

    See the figures here:

    http://superoceras.blogspot.co.....-life.html

  292. 292
    Virgil Cain says:

    NickMatzke- I know what a cladogram is. Venn diagrams allow for overlapping and nested hierarchies cannot have overlapping.

    A cladogram is set up by using shared characteristics and then determine ancestor-descendent relationships based on that. However with evolution defining traits can be lost, meaning a descendent may not have a defining characteristic of its ancestors. That means it could be easily placed in the wrong group.

    Also the nodes of cladograms are alleged populations. Those populations do not consist of nor contain any of their alleged daughter populations.

    Cladograms are semi-nested hierarchies at best- see Knox, “The use of hierarchies as organizational models in systematics”, Biological Journal of the Linnean Society (1998), 63: 1–49.

  293. 293
    bornagain says:

    A few pertinent notes from the fossil record that run directly contrary to the, IMHO, all to easily accepted hypothesis of CD:

    What Types of Evolution Does the Cambrian Explosion Challenge? – Stephen Meyer – video – (challenges Universal Common Descent and the Mechanism of Random Variation/Natural Selection)
    https://www.youtube.com/watch?v=AaF7t5wRFtA&list=UUUMhP2x7_7psVO-H4MJFpAQ

    Cambrian Explosion Ruins Darwin’s Tree of Life (2 minutes in 24 hour day) – Jonathan Wells – video (2:55 minute mark)
    https://www.youtube.com/watch?v=vA2LDiWeWb4

    As Dr. Wells pointed out in the preceding video, Darwin predicted that minor differences (diversity) between species would gradually appear first and then the differences would grow larger (disparity) between species as time went on. i.e. universal common descent as depicted in Darwin’s tree of life. What Darwin predicted should be familiar to everyone and is easily represented in the following graph.,,,

    The Theory – Diversity precedes Disparity – graph
    http://www.veritas-ucsb.org/JOURNEY/IMAGES/F.gif

    disparity
    [dih-spar-i-tee] noun, plural disparities.
    1. lack of similarity or equality; inequality; difference:

    But that ‘tree pattern’ that Darwin predicted is not what is found in the fossil record. The fossil record reveals that disparity (the greatest differences) precedes diversity (the smaller differences), which is the exact opposite pattern for what Darwin’s theory predicted.

    The Actual Fossil Evidence- Disparity precedes Diversity – graph
    http://www.veritas-ucsb.org/JOURNEY/IMAGES/G.gif

    Jerry Coyne’s Chapter on the Fossil Record Fails to Show “Why Evolution is True” – Jonathan M. – December 4, 2012
    Excerpt: Taxonomists classify organisms into categories: species are the very lowest taxonomic category. Species are classified into different genera. Genera are classified into different families. Families are classified into different orders. Orders are classified into different classes. And classes are classified into different phyla. Phyla are among the very highest taxonomic categories (only kingdom and domain are higher), and correspond to the high level of morphological disparity that exists between different animal body plans. Phyla include such groupings as chordates, arthropods, mollusks, and echinoderms.
    Darwin’s theory would predict a cone of diversity whereby the major body-plan differences (morphological disparity) would only appear in the fossil record following numerous lower-level speciation events. What is interesting about the fossil record is that it shows the appearance of the higher taxonomic categories first (virtually all of the major skeletonized phyla appear in the Cambrian, with no obvious fossil transitional precursors, within a relatively small span of geological time). As Roger Lewin (1988) explains in Science,
    “Several possible patterns exist for the establishment of higher taxa, the two most obvious of which are the bottom-up and the top-down approaches. In the first, evolutionary novelties emerge, bit by bit. The Cambrian explosion appears to conform to the second pattern, the top-down effect.”
    Erwin et al. (1987), in their study of marine invertebrates, similarly conclude that,
    “The fossil record suggests that the major pulse of diversification of phyla occurs before that of classes, classes before that of orders, orders before that of families. The higher taxa do not seem to have diverged through an accumulation of lower taxa.”
    Indeed, the existence of numerous small and soft-bodied animals in the Precambrian strata undermines one of the most popular responses that these missing transitions can be accounted for by them being too small and too-soft bodied to be preserved.
    http://www.evolutionnews.org/2.....67021.html

    Investigating Evolution: The Cambrian Explosion Part 1 – (4:45 minute mark – upside-down fossil record) video
    http://www.youtube.com/watch?v=4DkbmuRhXRY
    Part 2 – video
    http://www.youtube.com/watch?v=iZFM48XIXnk

    Challenging Fossil of a Little Fish
    Excerpt: “In Chen’s view, his evidence supports a history of life that runs opposite to the standard evolutionary tree diagrams, a progression he calls top-down evolution.”
    Jun-Yuan Chen is professor at the Nanjing Institute of Paleontology and Geology
    http://www.fredheeren.com/boston.htm

    Timeline graphic on Cambrian Explosion – ‘Darwin’s Doubt’ (Disparity preceding Diversity) – infographic
    http://www.evolutionnews.org/2.....74341.html

  294. 294
    bornagain says:

    Evolutionists Are Losing Ground Badly: Both Pattern and Process Contradict the Aging Theory – Cornelius Hunter – July 2012
    Excerpt: Contradictory patterns in biology include the abrupt appearance of so many forms and the diversity explosions followed by a winnowing of diversity in the fossil record. It looks more like the inverse of an evolutionary tree with bursts of new species which then die off over time.
    http://darwins-god.blogspot.co.....badly.html

    “Darwin had a lot of trouble with the fossil record because if you look at the record of phyla in the rocks as fossils why when they first appear we already see them all. The phyla are fully formed. It’s as if the phyla were created first and they were modified into classes and we see that the number of classes peak later than the number of phyla and the number of orders peak later than that. So it’s kind of a top down succession, you start with this basic body plans, the phyla, and you diversify them into classes, the major sub-divisions of the phyla, and these into orders and so on. So the fossil record is kind of backwards from what you would expect from in that sense from what you would expect from Darwin’s ideas.”
    James W. Valentine – as quoted from “On the Origin of Phyla: Interviews with James W. Valentine” – (as stated at 1:16:36 mark of video)
    https://www.youtube.com/watch?v=xtdFJXfvlm8&feature=player_detailpage#t=4595

    Erwin and Valentine’s The Cambrian Explosion Affirms Major Points in Darwin’s Doubt: The Cambrian Enigma Is “Unresolved” – June 26, 2013
    Excerpt: “In other words, the morphological distances — gaps — between body plans of crown phyla were present when body fossils first appeared during the explosion and have been with us ever since. The morphological disparity is so great between most phyla that the homologous reference points or landmarks required for quantitative studies of morphology are absent.”
    Erwin and Valentine (p. 340)
    http://www.evolutionnews.org/2.....73671.html

    Moreover, there are ‘yawning chasms’ in the ‘morphological space’ between the phyla which suddenly appeared in the Cambrian Explosion,,,

    “Over the past 150 years or so, paleontologists have found many representatives of the phyla that were well-known in Darwin’s time (by analogy, the equivalent of the three primary colors) and a few completely new forms altogether (by analogy, some other distinct colors such as green and orange, perhaps). And, of course, within these phyla, there is a great deal of variety. Nevertheless, the analogy holds at least insofar as the differences in form between any member of one phylum and any member of another phylum are vast, and paleontologists have utterly failed to find forms that would fill these yawning chasms in what biotechnologists call “morphological space.” In other words, they have failed to find the paleolontogical equivalent of the numerous finely graded intermediate colors (Oedleton blue, dusty rose, gun barrel gray, magenta, etc.) that interior designers covet. Instead, extensive sampling of the fossil record has confirmed a strikingly discontinuous pattern in which representatives of the major phyla stand in stark isolation from members of other phyla, without intermediate forms filling the intervening morphological space.”
    Stephen Meyer – Darwin’s Doubt (p. 70)

    Moreover, this top down pattern in the fossil record, which is the complete opposite pattern as Darwin predicted for the fossil record, is not only found in the Cambrian Explosion, but this ‘top down’, disparity preceding diversity, pattern is found in the fossil record subsequent to the Cambrian explosion as well.

    Scientific study turns understanding about evolution on its head – July 30, 2013
    Excerpt: evolutionary biologists,,, looked at nearly one hundred fossil groups to test the notion that it takes groups of animals many millions of years to reach their maximum diversity of form.
    Contrary to popular belief, not all animal groups continued to evolve fundamentally new morphologies through time. The majority actually achieved their greatest diversity of form (disparity) relatively early in their histories.
    ,,,Dr Matthew Wills said: “This pattern, known as ‘early high disparity’, turns the traditional V-shaped cone model of evolution on its head. What is equally surprising in our findings is that groups of animals are likely to show early-high disparity regardless of when they originated over the last half a billion years. This isn’t a phenomenon particularly associated with the first radiation of animals (in the Cambrian Explosion), or periods in the immediate wake of mass extinctions.”,,,
    Author Martin Hughes, continued: “Our work implies that there must be constraints on the range of forms within animal groups, and that these limits are often hit relatively early on.
    Co-author Dr Sylvain Gerber, added: “A key question now is what prevents groups from generating fundamentally new forms later on in their evolution.,,,
    http://phys.org/news/2013-07-s.....ution.html

    In Allaying Darwin’s Doubt, Two Cambrian Experts Still Come Up Short – October 16, 2015
    Excerpt: “A recent analysis of disparity in 98 metazoan clades through the Phanerozoic found a preponderance of clades with maximal disparity early in their history. Thus, whether or not taxonomic diversification slows down most studies of disparity reveal a pattern in which the early evolution of a clade defines the morphological boundaries of a group which are then filled in by subsequent diversification. This pattern is inconsistent with that expected of a classic adaptive radiation in which diversity and disparity should be coupled, at least during the early phase of the radiation.”
    – Doug Erwin
    What this admits is that disparity is a worse problem than evolutionists had realized: it’s ubiquitous (throughout the history of life on earth), not just in the Cambrian (Explosion).
    http://www.evolutionnews.org/2.....00111.html

    “In virtually all cases a new taxon appears for the first time in the fossil record with most definitive features already present, and practically no known stem-group forms.”
    TS Kemp – Fossils and Evolution,– Curator of Zoological Collections, Oxford University, Oxford Uni Press, p246, 1999

    “What is missing are the many intermediate forms hypothesized by Darwin, and the continual divergence of major lineages into the morphospace between distinct adaptive types.”
    Robert L Carroll (born 1938) – vertebrate paleontologist who specializes in Paleozoic and Mesozoic amphibians

    Moreover, as with the rest of the fossil record that clearly shows sudden appearance of new ‘forms’ throughout the history of life on earth, there is also an unmistakable gap in the fossil record leading up to the human ‘form’:

    No Known Hominin Is Common Ancestor of Neanderthals and Modern Humans, Study Suggests – Oct. 21, 2013
    Excerpt: The article, “No known hominin species matches the expected dental morphology of the last common ancestor of Neanderthals and modern humans,” relies on fossils of approximately 1,200 molars and premolars from 13 species or types of hominins — humans and human relatives and ancestors. Fossils from the well-known Atapuerca sites have a crucial role in this research, accounting for more than 15 percent of the complete studied fossil collection.,,,
    They conclude with high statistical confidence that none of the hominins usually proposed as a common ancestor, such as Homo heidelbergensis, H. erectus and H. antecessor, is a satisfactory match.
    “None of the species that have been previously suggested as the last common ancestor of Neanderthals and modern humans has a dental morphology that is fully compatible with the expected morphology of this ancestor,” Gómez-Robles said.
    http://www.sciencedaily.com/re.....153202.htm

    Skull “Rewrites” Story of Human Evolution — Again – Casey Luskin – October 22, 2013
    Excerpt: “There is a big gap in the fossil record,” Zollikofer told NBC News. “I would put a question mark there. Of course it would be nice to say this was the last common ancestor of Neanderthals and us, but we simply don’t know.” –
    http://www.evolutionnews.org/2.....78221.html

    “A number of hominid crania are known from sites in eastern and southern Africa in the 400- to 200-thousand-year range, but none of them looks like a close antecedent of the anatomically distinctive Homo sapiens…Even allowing for the poor record we have of our close extinct kin, Homo sapiens appears as distinctive and unprecedented…there is certainly no evidence to support the notion that we gradually became who we inherently are over an extended period, in either the physical or the intellectual sense.”
    Dr. Ian Tattersall: – paleoanthropologist – emeritus curator of the American Museum of Natural History – (Masters of the Planet, 2012)

    Also of related interest, over the last 30,000 years, where the fossil record for humans is the most complete and reliable, we find this very un-Darwinian fact:

    Are brains shrinking to make us smarter? – February 2011
    Excerpt: Human brains have shrunk over the past 30,000 years,
    http://www.physorg.com/news/20.....arter.html

    If Modern Humans Are So Smart, Why Are Our Brains Shrinking? – January 20, 2011
    Excerpt: John Hawks is in the middle of explaining his research on human evolution when he drops a bombshell. Running down a list of changes that have occurred in our skeleton and skull since the Stone Age, the University of Wisconsin anthropologist nonchalantly adds, “And it’s also clear the brain has been shrinking.”
    “Shrinking?” I ask. “I thought it was getting larger.” The whole ascent-of-man thing.,,,
    He rattles off some dismaying numbers: Over the past 20,000 years, the average volume of the human male brain has decreased from 1,500 cubic centimeters to 1,350 cc, losing a chunk the size of a tennis ball. The female brain has shrunk by about the same proportion. “I’d call that major downsizing in an evolutionary eyeblink,” he says. “This happened in China, Europe, Africa—everywhere we look.”
    http://discovermagazine.com/20.....-shrinking

  295. 295
    bornagain says:

    Scientists Discover Proof That Humanity Is Getting Dumber, Smaller And Weaker By Michael Snyder, on April 29th, 2014
    Excerpt: An earlier study by Cambridge University found that mankind is shrinking in size significantly.
    Experts say humans are past their peak and that modern-day people are 10 percent smaller and shorter than their hunter-gatherer ancestors.
    And if that’s not depressing enough, our brains are also smaller.
    The findings reverse perceived wisdom that humans have grown taller and larger, a belief which has grown from data on more recent physical development.
    The decline, said scientists, has happened over the past 10,000 years.
    http://thetruthwins.com/archiv.....and-weaker

    Of related note from the genetic evidence:

    Human Genetic Variation Recent, Varies Among Populations – (Nov. 28, 2012)
    Excerpt: Nearly three-quarters of mutations in genes that code for proteins — the workhorses of the cell — occurred within the past 5,000 to 10,000 years,,,
    “One of the most interesting points is that Europeans have more new deleterious (potentially disease-causing) mutations than Africans,”,,,
    “Having so many of these new variants can be partially explained by the population explosion in the European population. However, variation that occur in genes that are involved in Mendelian traits and in those that affect genes essential to the proper functioning of the cell tend to be much older.” (A Mendelian trait is controlled by a single gene. Mutations in that gene can have devastating effects.) The amount variation or mutation identified in protein-coding genes (the exome) in this study is very different from what would have been seen 5,000 years ago,,,
    The report shows that “recent” events have a potent effect on the human genome. Eighty-six percent of the genetic variation or mutations that are expected to be harmful arose in European-Americans in the last five thousand years, said the researchers.
    The researchers used established bioinformatics techniques to calculate the age of more than a million changes in single base pairs (the A-T, C-G of the genetic code) that are part of the exome or protein-coding portion of the genomes (human genetic blueprint) of 6,515 people of both European-American and African-American decent.,,,
    http://www.sciencedaily.com/re.....132259.htm

    “We found an enormous amount of diversity within and between the African populations, and we found much less diversity in non-African populations,” Tishkoff told attendees today (Jan. 22) at the annual meeting of the American Association for the Advancement of Science in Anaheim. “Only a small subset of the diversity in Africa is found in Europe and the Middle East, and an even narrower set is found in American Indians.”
    Tishkoff; Andrew Clark, Penn State; Kenneth Kidd, Yale University; Giovanni Destro-Bisol, University “La Sapienza,” Rome, and Himla Soodyall and Trefor Jenkins, WITS University, South Africa, looked at three locations on DNA samples from 13 to 18 populations in Africa and 30 to 45 populations in the remainder of the world.-

    “…but Natural Selection reduces genetic information and we know this from all the Genetic Population studies that we have…”
    Maciej Marian Giertych – Population Geneticist – member of the European Parliament – EXPELLED
    https://www.youtube.com/watch?v=6z5-15wk1Zk

  296. 296
    NickMatzke_UD says:

    That article is literally all about hierarchies and how cladograms are hierarchies. The debates it is engaging in are very fine points about inclusion of ancestors, what a “species” means through time, etc. — and he basically lost those debates, as Hennig’s view, which was already taking over in 1998, is now dominant. But it doesn’t matter anyway — any way you or Knox 1998 slice it, cladograms represent groups within groups, this is all that is typically meant by nested hierarchy.

  297. 297
    bornagain says:

    NickMatzke_UD and the infamous cladograms are dealt with here:

    A One-Man Clade – David Berlinski – July 18, 2013
    Excerpt: The relationship between cladistics and Darwin’s theory of evolution is thus one of independent origin but convergent confusion. “Phylogenetic systematics,” the entomologist Michael Schmitt remarks, “relies on the theory of evolution.” To the extent that the theory of evolution relies on phylogenetic systematics, the disciplines resemble two biologists dropped from a great height and clutching at one another in mid-air.

    Tight fit, major fail.7

    No wonder that Schmidt is eager to affirm that “phylogenetics does not claim to prove or explain evolution whatsoever.”8 If this is so, a skeptic might be excused for asking what it does prove or might explain?
    http://www.evolutionnews.org/2.....74601.html

  298. 298
    Virgil Cain says:

    In order for a cladogram to be a nested hierarchy the entire cladogram would have to be one. However that is not the case. Also cladograms are constructed on the basis of a nested hierarchy. Each clade is allegedly an ancestor and all of its descendents, but that is based on the number and quality of shared characteristics. Each node of a cladogram represents a population that has specific defining traits. Evolution is OK with defining traits being lost. Mammals allegedly have some fish as an ancestor yet mammals lack gills and fins. Those defining characteristics were lost. That means mammals cannot be placed as a descendent to fish, that is they are not in the same clade. Fish do not occupy any nodes in the clade that includes mammals.

    Also cladograms depict progress and we all know that evolution is not about progress.

    Evolution is much too complex to form nice neat nested hierarchies, Nick. Linnaean Taxonomy was originally based on a Common Design. Evos stole the his Creationist taxonomy and explained the pattern by appeals to timely extinctions, not to mere descent with modification (Darwin 1859).

    If you had to classify every organism that allegedly existed the cladogram would be so messy it wouldn’t make any sense. Every node, in reality, could resemble an asterisk.

  299. 299
    Virgil Cain says:

    Cladograms are just our way of trying to understand evolutionary history. Neither evolution nor Common Descent predicted any of the cladograms science has constructed.

  300. 300
    NickMatzke_UD says:

    Each clade is allegedly an ancestor and all of its descendents, but that is based on the number and quality of shared characteristics. Each node of a cladogram represents a population that has specific defining traits. Evolution is OK with defining traits being lost. Mammals allegedly have some fish as an ancestor yet mammals lack gills and fins. Those defining characteristics were lost. That means mammals cannot be placed as a descendent to fish, that is they are not in the same clade.

    Almost everything here is wrong. You are confusing definition and diagnosis, you are confusing individual characters with the overall pattern in all available characters, and you are not saying what you mean by “fish”.

    See: https://en.wikipedia.org/wiki/Phylogenetic_nomenclature

  301. 301
    NickMatzke_UD says:

    And this is just nuts:

    Also cladograms depict progress and we all know that evolution is not about progress.

    Ladders depict progress. Cladograms have no necessary axis of direction, so they do not.

  302. 302
    Zachriel says:

    NickMatzke_UD: and you are not saying what you mean by “fish”.

    Be honest, Nick. Are you a “fish”?

  303. 303
    Andre says:

    Nick

    Please stop citing wikipedia. You know as well as I do its the hangout of unemployed atheists living in their mom’s basements. It is not a reliable source to substantiate your claim if it was Havard and other universities would not caution against it.

    I bet you if I delve I’ ll find you there as a contributor and as stated last night whatever comes from you is certain rubbish.

  304. 304
    Virgil Cain says:

    Regardless of what is eventually learned about the evolution of Clarkia/Heterogaura, the complex nature of evolutionary processes yields patterns that are more complex than can be represented by the simple hierarchical models of either monophyletic systematization or Linnaean classification.- Knox pg 34

  305. 305
    Box says:

    Foundational to the Darwinian narrative is the assumption that an organism as a unified whole is compatible with some bottom-up naturalistic explanation. That assumption is not even wrong.

    Bornagain: (…) the right approach in trying to figure out how the human form was created is not to ‘explain away’ dissimilarity in proteins and genes but is to try to figure out what in blue blazes is controlling the billion trillion protein molecules of a human body, telling them exactly where to go and what to do, for precisely a lifetime and not a moment longer.

    A billion trillion protein molecules cannot conceivably be orchestrated bottom-up. For one thing it’s incoherent to posit multiple trillions of DNA-molecules as a ‘collective of master-controllers’. Such a collective cannot explain the unity and orchestration of the dynamic equilibrium state that defines an organism. The true cause of unity must enclose overview and the power to direct all the parts, and none of the molecules that constitute an organismal body is a candidate for this role.

    The unity of an organism inexorably points to top-down causation from the level of the whole or beyond.

    // see Bornagain’s posts #278 & #96.

  306. 306
    Virgil Cain says:

    NickMatzke:

    Almost everything here is wrong.

    And yet I can pull the exact thing from textbooks. Clades are based on shared characteristics with ancestor-descendent relationships based on that.

    intro to cladistics

    The basic idea behind cladistics is that members of a group share a common evolutionary history, and are “closely related,” more so to members of the same group than to other organisms. These groups are recognized by sharing unique features which were not present in distant ancestors. These shared derived characteristics are called synapomorphies.

    cladistics:

    Cladistics can be distinguished from other taxonomic systems, such as phenetics, by its focus on shared derived characters (synapomorphies).

    And also what is cladistics?

    The clade is not constructed based on ancestor-descendent relationships, those are assumed. And ancestor-descendent relationships form a non-nested hierarchy

    and you are not saying what you mean by “fish”.

    I thought you understood biology, Nick? Do all mammals have some fish as an ancestor or not, Nick?

  307. 307
    Virgil Cain says:

    NickMatzke:

    Cladograms have no necessary axis of direction, so they do not.

    Then it is strange that they all depict a direction. Even darwin’s tree does.

  308. 308
    Virgil Cain says:

    Extinction has only defined the groups: it has by no means made them; for if every form which has ever lived on this earth were suddenly to reappear, though it would be quite impossible to give definitions by which each group could be distinguished, still a natural classification, or at least a natural arrangement, would be possible.- Charles Darwin chapter 14

    and

    There is another stringent condition which must be satisfied if a hierarchic pattern is to result as the end product of an evolutionary process: no ancestral forms can be permitted to survive. This can be seen by examining the tree diagram on page 135. If any of the ancestors X, Y, or Z, or if any of the hypothetical transitional connecting species stationed on the main branches of the tree, had survived and had therefore to be included in the classification scheme, the distinctness of the divisions would be blurred by intermediate or partially inclusive classes and what remained of the hierarchic pattern would be highly disordered.- Denton, “Evolution: A Theory in Crisis” page 136 (X, Y and Z are hypothetical parental node populations)

    and

    The goals of scientists like Linnaeus and Cuvier- to organize the chaos of life’s diversity- are much easier to achieve if each species has a Platonic essence that distinguishes it from all others, in the same way that the absence of legs and eyelids is essential to snakes and distinguishes it from other reptiles. In this Platonic worldview, the task of naturalists is to find the essence of each species. Actually, that understates the case: In an essentialist world, the essence really is the species. Contrast this with an ever-changing evolving world, where species incessantly spew forth new species that can blend with each other. The snake Eupodophis from the late Cretaceous period, which had rudimentary legs, and the glass lizard, which is alive today and lacks legs, are just two of many witnesses to the blurry boundaries of species. Evolution’s messy world is anathema to the clear, pristine order essentialism craves. It is thus no accident that Plato and his essentialism became the “great antihero of evolutionism,” as the twentieth century zoologist Ernst Mayr called it.- Andreas Wagner, “Arrival of the Fittest”, pages 9-10

  309. 309
    Andre says:

    Nick Matzke gets schooled by the text books he approved. Now that is irony right there.

    Nick I’ll say it again you have no credit here, and whatever you have to say will always be rubbish. When you have actually learned some biology, and humbled yourself come back and we can chat for hours.

    Looking forward.to your.book on macro evolution. Have you made it past the introduction yet?

  310. 310
    NickMatzke_UD says:

    The clade is not constructed based on ancestor-descendent relationships, those are assumed. And ancestor-descendent relationships form a non-nested hierarchy

    You’ve argued in a circle. Cladograms represent sister-group relationships between tips, not direct ancestors. Therefore, on your own argument, cladograms represent nested hierarchies.

    (Direct fossil ancestors is an interesting topic that I actually work on, but you need a sophisticated Bayesian method, not just a cladistic method, to detect them. And in any case, even a direct fossil ancestor still falls perfectly neatly into a phylogenetic representation, they are just sister groups with very short or zero-length branches.)

  311. 311
    NickMatzke_UD says:

    You’re not reading your own quotes:

    though it would be quite impossible to give definitions by which each group could be distinguished, still a natural classification, or at least a natural arrangement, would be possible.- Charles Darwin chapter 14

    He says *would*.

  312. 312
    Andre says:

    Virgil Cain

    You should have not used those text books Nick will be writing to the authors soon and force them to retract it. He will lobby all his pals in their mom’s basements to harras and bully until the stuff is removed. He has done it before because that is how he operates.

  313. 313
    Mung says:

    Nick M:

    Virgil Cain, you are really not even getting the basics of what a cladogram is. It is literally a groups-within-groups statement.

    And where in the cladogram are the groups?

    Virgil Cain:

    A cladogram is set up by using shared characteristics and then determine ancestor-descendent relationships based on that.

    From wikipedia:

    A cladogram is not, however, an evolutionary tree because it does not show how ancestors are related to descendants or how much they have changed; many evolutionary trees can be inferred from a single cladogram.

  314. 314
    NickMatzke_UD says:

    307
    Virgil Cain

    October 27, 2015 at 10:06 am
    NickMatzke:

    Cladograms have no necessary axis of direction, so they do not.

    Then it is strange that they all depict a direction. Even darwin’s tree does.

    Nope. Google “unrooted phylogeny”.

    But: time is a legitimate axis on which to depict phylogenies. Or do you disagree with time along with everything else?

  315. 315
    Virgil Cain says:

    NickMatzke:

    You’re not reading your own quotes:

    though it would be quite impossible to give definitions by which each group could be distinguished, still a natural classification, or at least a natural arrangement, would be possible.- Charles Darwin chapter 14

    He says *would*.

    Buy a vowel, Nick. That natural arrangement would not be a nice neat cladogram. Evolution does not predict any actual pattern other than ancestors give rise to descendants.

  316. 316
    Virgil Cain says:

    The clade is not constructed based on ancestor-descendent relationships, those are assumed. And ancestor-descendent relationships form a non-nested hierarchy

    NickMatzke:

    You’ve argued in a circle.

    You are full of bluff and bluster, Nick.

    Cladograms represent sister-group relationships between tips, not direct ancestors.

    The nodes, ie the points of divergence, are alleged ancestral populations, Nick. The sister relationships are made through those nodes.

  317. 317
    NickMatzke_UD says:

    303
    Andre

    October 27, 2015 at 9:57 am
    Nick

    Please stop citing wikipedia. You know as well as I do its the hangout of unemployed atheists living in their mom’s basements. It is not a reliable source to substantiate your claim if it was Havard and other universities would not caution against it.

    I bet you if I delve I’ ll find you there as a contributor and as stated last night whatever comes from you is certain rubbish.

    Actually, that page is pretty good, and accords with what is taught in mainstream university courses. Unfortunately, you guys don’t even get these basics, so you really don’t even understand what you are talking about. I’m trying to help, but you’re so incredibly biased, or conspiratorial, or just mad for some reason, that nothing is getting through.

    Re: fishes — yes, we are fishes, cladistically speaking. Mammals are a subgroup of tetrapods which are a subgroup of lobe-finned fishes. This has been known for 100+ years based on morphology, and was stunningly confirmed by DNA:

    https://en.wikipedia.org/wiki/Sarcopterygii

    See also Neil Shubin, “Your Inner Fish”. Although tetrapods lost some aquatic characters, they retain a great many characters from that aquatic ancestry.

    Since you guys are clearly confusing definitions based on “key characteristics”, and definitions based on relationship, I will spell out the mainstream understanding:

    In phylogenetic taxonomy, clades are *defined* as the common ancestor of two or more tip species, and all of that common ancestor’s descendants.

    Clades are *diagnosed* (discovered and recognized) by a phylogenetic analysis of all available data — morphological characters, DNA, etc.

    Clades might be given a *name* based on one or more particularly obvious characters, but this is not the *definition*. E.g. tetrapods are called “tetra-pods” because that common ancestor had 4 feet, but not all descendants of that common ancestor retain 4 legs. Thus snakes, whales, etc. remain in the clade Tetrapoda.

    Linnaean and folk/popular taxonomies are an inconsistent mixture of the above, leading to all of the confusion you guys are having. Usually, those groups are based on a few big obvious characters. Often, these turn out to be clades (Class Mammals, Class Birds), but often they do not (Class Reptilia actually has to include Birds, phylogenetically speaking, which means at least one of these can’t be a class, which is why Linnaean taxonomy is being abandoned as unworkable.

  318. 318
    Virgil Cain says:

    NickMatzke:

    Nope. Google “unrooted phylogeny”.

    I should be googling “unrooted cladogram” as a cladogram is a specific subset of phylogenetic trees, right, Nick? And cladograms have a root, ie a LUCA.

  319. 319
    Virgil Cain says:

    NickMatzke:

    Re: fishes — yes, we are fishes, cladistically speaking. Mammals are a subgroup of tetrapods which are a subgroup of lobe-finned fishes. This has been known for 100+ years based on morphology, and was stunningly confirmed by DNA:

    There isn’t any DNA evidence that says the transformations required are even possible, Nick. Your DNA “evidence” assumes we have fish as an ancestor.

    See also Neil Shubin, “Your Inner Fish”

    rea it and he doesn’t have any idea if the changes required are even possible. Why hasn’t he subjected fish embryos to a series of targeted mutagenesis to see if a fish-a-pod eventually develops?

    In phylogenetic taxonomy, clades are *defined* as the common ancestor of two or more tip species, and all of that common ancestor’s descendants.

    We know. As i said those relationships are assumed based on the shred characteristics.

    The point about Linnaean taxonomy is that when it comes to biology it is the only nested hierarchy.

  320. 320
    Virgil Cain says:

    Andre @ 312- My bad. The NCSE did a hack job on Dr Denton after his “Evolution: A Theory in Crisis” was published. No one seemed to notice, though.

  321. 321
    Andre says:

    We are fish?

    Light bulb….

    Nick are you a fish brain? How can we trust the convictions in a fish’es mind? Are there any convictions in such a mind?

  322. 322
    Andre says:

    Nick the only person confused here are those that think they have fish brains.

  323. 323
    Andre says:

    I am now convinced that flat earthers are more rational and reasonable than the fish people believers.

  324. 324
    Mung says:

    A cladogram is literally a hierarchical branching diagram that says something about the shared similarities of the taxa included in that diagram. It does not represent a phylogeny of these taxa – that is the purpose of a tree. A number of trees might be consistent with a given cladogram since the latter says nothing about the nature of the relationships among taxa, only their shared similarities.

    – Joel Cracraft & Niles Eldridge. Phylogenetic Analysis and Paleontology. 1979.

  325. 325
    bornagain says:

    OT:

    Physicists prove ‘quantum spookiness’ and start chasing Schrodinger’s cat – October 26, 2015
    http://phys.org/news/2015-10-p.....r-cat.html

    Miracles Man: Metaxas Vs. Closed Minds And A Closed Universe -Oct 27, 2015
    Excerpt: Last Christmas, Christian apologist, Eric Metaxas published an article in the opinion section of the Wall Street Journal about a ‘miracle’, or perhaps I should say ‘the miracle’ — the origin of the universe. That article, Science Increasingly Makes the Case for God went on to become, if not quite a miracle, at least a sort of wonder. It was shared via email and social media more than any other opinion article in the history of the Wall Street Journal. That’s really saying something, since the Journal is known to have one of the most popular op/ed pages in the world. Former editor Robert Bartley quipped that his was the only opinion page in journalism that actually sold papers.
    Metaxas certainly tapped into something. As of this writing this morning, that article has over 470,000 Facebook shares and well over 9,000 comments. The wonder is not the article itself, but the phenomenon that in an age of angry pop atheism and sloppy ‘God-is-dead’ scientific journalism, intelligent, well-educated people, the kind of people who read the Wall Street Journal, still have minds which are open to the idea that the universe is not closed; that there is something (or Someone) beyond it who can intervene into it, Who started it whirling into existence in the first place.
    I sat down across a Skype line with Metaxas recently to discuss the paperback release of his book, Miracles: What They Are, Why They Happen, and How They Can Change Your Life.,,,
    http://www.forbes.com/sites/je.....-universe/

    As to the ‘closed minds’ of atheists that Metaxas talked about, the following is an interesting finding. It seems shutting down the part of the brain associated with logic and reasoning causes a marked increase in atheism

    Atheists embarrassed: study proves atheism uses less brain function – Oct 26, 2015 by Dr. Joel McDurmon
    Excerpt: This has to be embarrassing . . . if you’re an atheist. A new study performed at the University of York used targeted magnetism to shut down part of the brain. The result: belief in God disappeared among more than 30 percent of participants.
    That in itself may not seem so embarrassing, but consider that the specific part of the brain they frazzled was the posterior medial frontal cortex—the part associated with detecting and solving problems, i.e., reasoning and logic.
    In other words, when you shut down the part of the brain most associated with logic and reasoning, greater levels of atheism result.
    You’ve heard the phrase, “I don’t have enough faith to be an atheist”? Apparently we can now also say, “I have too many brains to be an atheist.”
    For a group that makes so much noise vaunting its superior prowess with logic and reasoning, this study has got to be quite a deflator. For a group that claims to be rooted primarily in logic and reason, and to exist for little reason other than that they have used logic and reason to free themselves from belief in God and, as they allege, superstition and fairy tales, this study is the equivalent of a public depanting­—i.e., the would-be emperor’s got no clothes.
    http://americanvision.org/1263.....-function/

    What was that remark about living in crazy land Matzke?

  326. 326
    Vy says:

    NickMatzke_UD: and you are not saying what you mean by “fish”.

    Zachriel: Be honest, Nick. Are you a “fish”?

    Wow, what a genuinely sensible comment. I wonder which version of him was in control.

  327. 327
    Peer says:

    When the chimp genome consortium published the Chimp-Human whole genome sequence comparison, something was immediately obvious for those who actually read Methode sections: only 2.4 Mb had a match in the 2.85 Mb human probe. Although 8 percent had been omitted from the studies, the consortium did not find this of sufficient importance to discuss this observation.

    Around the same time, Roy Britten showed that the Protein-Coding Part of the chimp and human genomes differ by 5 percent counting indels.

    Further, we know since ages that, by simply weighing, the genome of chimps exceed that of humans by approx 10 percent.

    I recommend Williamson to brush up a bit into the bioscience literature instead of provoking confusion.

  328. 328
    Sebestyen says:

    Zachrial wrote:

    See Hayashi et al., Experimental Rugged Fitness Landscape in Protein Sequence Space, PLOS ONE 2006. They replace a section of a phage genome crucial for infectivity with a random sequence, then they mutate and select for infectivity. Guess what happens.

    I know what happened, the mutation/selection cycles increased the infectivity.

    However, there’s a two things to note:

    a) The phage was still infectious to begin with, the D1 and D3 sections of g3p were still intact. Even with D1 and D2 removed, the infectivity is still there 1.

    b) The infectivity never reached the level of the original D2 sequence and the paper states that other mechanisms than random substitutions must’ve played a role.

    It’s an interesting read but overall I’m less than impressed by the results in regards to the neutral evolution claim.

    [1] L Riechmann, P Holliger
    The C-Terminal Domain of TolA Is the Coreceptor for Filamentous Phage Infection of E. coli
    Cell, 90 (1997), pp. 351–360

  329. 329
    Zachriel says:

    Sebestyen: However, there’s a two things to note:

    a) The phage was still infectious to begin with, the D1 and D3 sections of g3p were still intact. Even with D1 and D2 removed, the infectivity is still there 1.

    Or it wouldn’t have replicated at all.

    Sebestyen: b) The infectivity never reached the level of the original D2 sequence and the paper states that other mechanisms than random substitutions must’ve played a role.

    It also requires recombination to avoid local fitness peaks, which is clear from studies of evolutionary algorithms. In any case, it answers your stated concern: “That’s like saying a feasible way to add a new function to a piece of software is by filling a module with random letters and then let a script randomly exchange letters at random positions until the module successfully compiles.” That’s what they did.

  330. 330
    Mung says:

    …logically and epistemologically cladograms should precede phylogenetic trees, and phylogenetic trees should precede scenarios.

    – Robert M. Schoch. Phylogeny Reconstruction in Paleontology. 1986.

  331. 331
    ThickPython says:

    @Andre, #282:

    “I am saying that the data does not show common descent it is forced to fit the assumption of common descent. If we remove the assumption what do we get?”

    You’re coming at this from the wrong direction – you’re suggesting that data is forced to fit the assumption of common descent, when that’s not what’s happening at all. There are no inbuilt assumptions of common descent in tree building – you can build a tree with whatever kind of data you like (data completely unrelated to biology) but most of them will be garbage. The reason why phylogenetic trees are not garbage, and the reason they strongly indicate common descent is because they consistently match other trees that are built using independent data. Plus we have a very simple, observable theory that would produce such trees: descent with modification.

    “I think Dr. Venter answers it aptly.”

    I think you are missing a lot of nuance from that conversation. I guarantee you that Craig Venter accepts a “tree of life” all the way back to at least metazoans, if not all the way back to eukaryotes. The nuance that Venter is trying to get across in that conversation is that HGT is prevalent in these single celled organisms, so constructing a tree is near impossible, and that’s why he uses the term “bush of life”. That “bush of life” is kind of off to the side and kind of underneath the “tree of life”. He is also conveying that there are several exceptions found to the standard codon table, but again, I guarantee you he will not claim that these belong to a “second genesis”.

    If you’re willing to put something on the line, I’ll ask him these questions myself.

  332. 332
    ThickPython says:

    @Virgil Cain, #320:

    “The NCSE did a hack job on Dr Denton after his “Evolution: A Theory in Crisis” was published. No one seemed to notice, though.”

    Wow. Please don’t tell me you’re going to pull out that equidistance crap? It amazes me that two allegedly smart people – Jonathan Sarfati and Nathaniel Jeanson have actually repeated it.

  333. 333
    Andre says:

    Thickpython

    Who drew the first tree?

    I think us asking Dr Venter for clarity is a very good thing. If I wrong had misunderstood him then I’ll accept that.

  334. 334
    ThickPython says:

    @Peer, #327:

    ” … only 2.4 Mb had a match in the 2.85 Mb human probe.”

    Of course I’ve read that, and done plenty of work on it.

    “Around the same time, Roy Britten showed that the Protein-Coding Part of the chimp and human genomes differ by 5 percent counting indels.”

    And yes, I’ve read that and done my own comparisons.

    “Further, we know since ages that, by simply weighing, the genome of chimps exceed that of humans by approx 10 percent.”

    Have we really? And by “simply weighing” them? I posted on this only last week:

    https://roohif.wordpress.com/2015/10/19/how-big-is-the-chimpanzee-genome/

    “I recommend Williamson to brush up a bit into the bioscience literature instead of provoking confusion.”

    You’ve made three claims above, one of which I happened to address very recently. Now, you can choose one of the remaining two, but before I post some actual results, I’d like to know what you’re risking. Basically I’m getting pretty sick of people just repeating these claims that they hear or read without doing their own research to see if they actually check out.

    So, in the first example, I assume you’re saying that only 2.4Gb of sequence actually aligns. What will you do when I demonstrate that virtually all of it aligns? Will you admit that you are wrong, or will you slink of to another forum and repeat the same crap to another bunch of people?

  335. 335
    Andre says:

    If there is a 98% alignment out of 3 000 000 000 pairs you still have a 60 000 000 Base pair mismatch it really is not almost all aligned no matter how much you want it to be. If there was only 10 Base pairs and 8 lined up with only 2 differences then you would sort of have a case. But yes please come give us an entire Human and chimp genome sequence.

  336. 336
    franklin says:

    Andre in your example you accept that a 20% difference(2:10) is non-asignificant mismatch and deemed worthy of making a case. However, you reject the 60 million out of 3 billion base pair non-alignment as being significantly mismatched and not making a case.

    You do realize that 60 000 000 out of 3 000 000 000 represents a 2% difference in alignment. So you don’t accept an alignment that has an order of magnitude better alignment than what you describe as being acceptable.

    how does that work, exactly?

  337. 337
    franklin says:

    Andre to better represent the conundrum you posed for yourslf if we considerd your 10 base pair alignment with 2 mismatched bases the 60 mil out of 3 bill would be analogous to 9.8 matches out of 10 for the human:chimp sequence alignment.

    how is that not making a case?

  338. 338
    Andre says:

    Right

    It is true that a 8 out of 10 is a 20% difference, but its a total difference of 2 units.

    If we look at at 2 994 000 000 out of 3 000 000 000 its only a 2% difference but a whopping 60 000 000 unit difference. This is no trivial difference, or almost the same not by a long shot!

    This is not about the difference in percentage but the difference in units….. 60 000 000 of them.

    Now lets chat about the idea that these 60 000 000 base pair difference could become fixed in only 6 000 000 years. That means a whopping 10 million base pair changes fixed in the population for every 1 000 000 years.

    Do we have data that can verify or falsify such a claim? In fact we do, Lenski’s experiment holds about 1 000 000 years of evolution time in the petri dishes, lets see how many changes have become fixed in that time slot? 100? 200? 1000? 5000? 100 000? Not anywhere near 10 000 000 not even close.

    And as I have argued before for these 60 000 000 base pair diffreces to be come fixed in only 6 000 000 years NS & RM, drift, and any other form of evolution has to deal with the following…….

    1.) Multiple DNA Integrity check systems (Evolutionary conserved)
    2.) Multiple DNA Repair Mechanisms (Evolutionary conserved)
    3.) Multiple Apoptosis systems (Evolutionary conserved)
    4.) Necrotic system (Evolutionary conserved)

    You are welcome to believe that these 60 000 000 base pair differences can by some magic process become fixed considering the odds and systems in place to prevent it from happening. Me I just don’t have that much faith.

  339. 339
    Andre says:

    Franklin

    Andre to better represent the conundrum you posed for yourslf if we considerd your 10 base pair alignment with 2 mismatched bases the 60 mil out of 3 bill would be analogous to 9.8 matches out of 10 for the human:chimp sequence alignment.

    how is that not making a case?

    But its not, its a literal 60 000 000 base pair difference the percentage difference is meaningless in regards to the total amount of actual units.

  340. 340
    Andre says:

    Franklin

    you can’t compare 8/10 with 2 994 000 000/3 000 000 000 units in that way but it is the number of actual differences that need to be counted and in this case its 2 vs 60 000 000.

  341. 341
    Andre says:

    To verify what I have to say about mutation rates from Lenski’s lab

    http://www.nature.com/nature/j.....08480.html

    http://www.sciencedirect.com/s.....2209020594

    These numbers are not nearly enough to get to where you want to be. Not even close!

    So if you are honest with yourself, you would know that Lenski’s experiment falsifies Darwinian evolution’s grand claim.

  342. 342
    Andre says:

    Just want to make a correction

    In post 338 & 340

    The figure is actually

    2 940 000 000 and not 2 994 000 000, apologies for the typos….

  343. 343
    Virgil Cain says:

    TP:

    Please don’t tell me you’re going to pull out that equidistance crap?

    Equidistance of something your position cannot explain in the first place? LoL!

  344. 344
    Vy says:

    The reason why phylogenetic trees are not garbage, and the reason they strongly indicate common descent is because they consistently match other trees that are built using independent data

    Looks like you’re stuck in fantasy-ville.

    “For a long time the holy grail was to build a tree of life”, says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. “We have no evidence at all that the tree of life is a reality“, says Bapteste. (Graham Lawton – “Why Darwin Was Wrong About the Tree of Life”, New Scientist. January 21, 2009)

    The problems began in the early 1990s when it became possible to sequence actual bacterial and archaeal genes rather than just RNA. Everybody expected these DNA sequences to confirm the RNA tree, and sometimes they did but, crucially, sometimes they did not. RNA, for example, might suggest that species A was more closely related to species B than species C, but a tree made from DNA would suggest the reverse.

    Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species. (Liliana M. Dávalos, Andrea L. Cirranello, Jonathan H. Geisler, and Nancy B. Simmons, “Understanding Phylogenetic Incongruence: Lessons from Phyllostomid Bats” – Biological Reviews of the Cambridge Philosophical Society, Vol. 87: 991-1024 (2012))

    Phylogenetic conflict is common, and frequently the norm rather than the exception.

    The phylogenetic relationships among most metazoan phyla remain uncertain. (Rokas et al., “Animal Evolution and the Molecular Signature of Radiations Compressed in Time,” Science, Vol. 310: 1933-1938 (December 23, 2005))

    Again, the problem lies in the fact that trees based upon one gene or protein often conflict with trees based upon other genes. Their study employed the many-gene technique, and yet still found that [a] 50-gene data matrix does not resolve relationships among most metazoan phyla.

    The key assumption made when constructing a phylogenetic tree from a set of sequences is that they are all derived from a single ancestral sequence, i.e., they are homologous. (Marketa Zvelebil and Jeremy O. Baum, Understanding Bioinformatics, page 239 (Garland Science, 2008))

    Cladistics can run into difficulties in its application because not all character states are necessarily homologous. Certain resemblances are convergent — that is, the result of independent evolution. We cannot always detect these convergences immediately, and their presence may contradict other similarities, ‘true homologies’ yet to be recognized. Thus, we are obliged to assume at first that, for each character, similar states are homologous, despite knowing that there may be convergence among them. (Guillaume Lecointre & Hervé Le Guyader, The Tree of Life: A Phylogenetic Classification, page 16 (Harvard University Press, 2006))

    So far, all evidence points to the fact that phylogentic trees are in fact garbage and do not point to common descent, much less match independent data.

  345. 345
    ThickPython says:

    @Virgil Cain:

    “Equidistance of something your position cannot explain in the first place? LoL!”

    Just so we’re clear, you’re saying that articles like this:

    https://www.icr.org/article/5867/

    .. are evidence against common descent. Is that your position?

  346. 346
    Vy says:

    SqueakPython says:

    You’re coming at this from the wrong direction – you’re suggesting that data is forced to fit the assumption of common descent, when that’s not what’s happening at all. There are no inbuilt assumptions of common descent in tree building – you can build a tree with whatever kind of data you like (data completely unrelated to biology) but most of them will be garbage

    And yet only a few umpteen comments earlier, he said:

    The software used to automatically annotate the genomes isn’t perfect. Humans can spot these errors. In fact, one of the ways to spot these sort of errors is when the data are in apparent conflict with common descent!

    Anyone who hasn’t got their brain clogged up with fogma (ref: CEH Dictionary) can see the blatant contradiction.

    Squeak, find that fish, it smells!

  347. 347
    ThickPython says:

    @Vy, #344:

    Similar to what I said a few posts back, I’m getting tired of people spouting off crap, and not actually doing the work. You’ve quote-mined like a pro. The first two quotes from the New Scientist article are clearly referring to HGT in bacteria and archaea, and you’d know that if you read and comprehended the article. Please see my post at #331. Regarding incongruence in general, please see Nick’s post at #171 (and my endorsement of it at #178). There are clearly other factors that can cause trees to be incongruent, and the “Lessons from Phyllostomid Bats” paper tries to systematically remove these factors.

    As for your “key assumption” quote, that’s blatantly out of context and I think you should retract. The heading for that section is “Only orthologous genes should be used to construct species phylogenetic trees” – meaning that merely homologous sequences (as opposed to strictly orthologous sequences) can cause incongruence in phylogenetics. Consider an example where, in the common ancestor to species A and B (and C and D and E etc.), a particular gene has undergone duplication. When constructing a phylogenetic tree, care must be taken to ensure that we are not comparing the original gene in species A to the copy of the gene in species B.

  348. 348
    Vy says:

    You’ve quote-mined like a pro

    Right.

  349. 349
    Virgil Cain says:

    TP:

    Just so we’re clear, you’re saying that articles like this:

    https://www.icr.org/article/5867/

    .. are evidence against common descent.

    No. My position is there isn’t any evidence for Universal Common Descent. That is because no one knows what makes an organism what it is.

    Until someone can come up with a way to scientifically test the claim there isn’t any need to refute it.

  350. 350
    Vy says:

    You’ve quote-mined like a pro

    Right.

    When evodelusionsts accuse you of quote-mining, you know you’ve got something.

  351. 351
    ThickPython says:

    @Vy, #346:

    If you’re suggesting that my position is that when I see data that are in apparent conflict with common descent then it is necessarily and automatically an error in the data (or software, whatever), then I don’t see how we can possibly have a respectful and honest conversation.

    See my post at #191, and maybe re-state your argument without the obvious straw man.

  352. 352
    Andre says:

    Thickpython

    You start with the assumption that CD is true and that is why you can’t see the wood from the trees……

  353. 353
    Vy says:

    If you’re suggesting that my position is that when I see data that are in apparent conflict with common descent then it is necessarily and automatically an error in the data (or software, whatever), then I don’t see how we can possibly have a respectful and honest conversation.

    Squeak, those were your words not mine.

    See my post at #191, and maybe re-state your argument without the obvious straw man.

    They are your own words so stop imagining straw men.

  354. 354
    Andre says:

    Vy

    When evodelusionsts accuse you of quote-mining, you know you’ve got something.

    And when they say “You don’t understand”

  355. 355
    Vy says:

    Andre, yup.

    Apparently, they think that we’re obliged to believe that the random reactions in their brains can differentiate between reality and fantasy.

  356. 356
    Vy says:

    More:

    Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves. – Carl Woese, A pioneer of evolutionary molecular systematics

    Hmm, there must be a “deeper” mystical meaning to that. Maybe he’s using evodelusionary English that only the indoctrinated can understand, who knows.

    SqueakPython’s rants remind me of how theistic Darwinists interpret Genesis to make evolution fit it, amazing mental gymnastics!

  357. 357
    Peer says:

    @ThickPython, #334:

    Big Snake says: “You’ve made three claims above, one of which I happened to address very recently. Now, you can choose one of the remaining two, but before I post some actual results, I’d like to know what you’re risking.”

    Peer: I am not risking anything, here, since a don’t care too much about sequence comparisons. I’ve done so many, I know what the assumptions and pitfalls are. And I know that they are usually contrary to evolutionary expectations.

    From the frontloading paradigm (which is the best biological framework to explain what we observe), I expect evolution to preceed by frontloaded activity, which has been identified unequivocally as transposable and transposed elements (TEs). Since TEs are particularly good at driving genetic and epigenetic changes, and thus variation, they should be renamed variation-inducing genetic elements (VIGEs), as I have proposed in the science literature.

    Further, VIGEs knowns as ERVs are the most parsimonious explanation for the existence of RNA viruses, and their non-random (site specific) integration explains part of the homologies between ape and man.

    From the front-loading theory I also expect novel protein-coding genes in man as the result of acquisition of regulatory and control elements, so they can be expressed. This can also be mediated by TEs, which already have the appropriate regulatory sequences. In fact, TEs are jumping genetic regulators for gene expression (promotors and enhancers, sometimes silencers)They only have to be put into the right context. Indeed, 10-30% of all genes start from TEs. Such observations confirm and emphasize that the sequences were frontloaded (because random sequences never have potential functional coding properties).

    Big snake: “Basically I’m getting pretty sick of people just repeating these claims that they hear or read without doing their own research to see if they actually check out.”

    Peer: Basically I’m getting pretty sick of people just repeating the old canards of Darwinism for non-scientific but personal and worldview reasons without ever checking out the heaps of literature opposing the canard.

    Big Snake: “So, in the first example, I assume you’re saying that only 2.4Gb of sequence actually aligns. What will you do when I demonstrate that virtually all of it aligns?”

    Peer: I have always found it peculiar that in the chimp-human comparison 8% of the sequence was omitted from the studies. My own studies show highly divergent sequences even in man, most due to indels.

    Further, I am pretty sure you are able to align virtually all of the sequences. I can do that, too. Leaving out all indels and all pointmutations would make a monkey out of man. I recommend you to submit your papers to a science journal, instead of leaving it to the blogosphere. That is how science proceeds.

    Big Snake: “Will you admit that you are wrong, or will you slink of to another forum and repeat the same crap to another bunch of people?”

    Peer: Wrong in what, snake? If someone is wrong, it is the Chimp Genome Consortium, they omitted 8% of the sequence and did not provide a reason. You may have found the reason, so let them know!

    Slinking of to another forum is not my style. It is usually the other way around: I get banned or kicked out because my knowleghde on biology is superior to that of blog-holders. Ask Larry Moran. He kicked me from his blog, last week.

    The last time we listened to a snake, we were pretty much deceived, big snake. As a scientist, I advice you to better read a bit into the literature on frontloading. Darwin is dead. Try to keep up with the new biology.

  358. 358
    Andre says:

    Papers detailing that the tree of life aka common descent is hogwash

    http://onlinelibrary.wiley.com.....126.x/full

    http://rstb.royalsocietypublis...../1527/2209

    http://www.nature.com/nrg/jour.....g1603.html

    Phew just a few samples showing what Thickpython calls true can simply not be tested….. Love the last paper

    The very nature of the evolutionary history of organisms and the limitations of current phylogenetic reconstruction methods mean that part of the tree of life might prove difficult, if not impossible, to resolve with confidence.

    Fear not Nick Matzke, Thickpython, Prof Moran and the Zachriel have it all figured out. They just know it… How so? Because they believe it! Their faith is unshaken!

  359. 359
    ThickPython says:

    @Vy, #352:

    “Squeak, those were your words not mine.”

    And so are these words: “When the data is not in accord with common descent, I investigate.”

    If this is the kind of crap you’re going to pull, then it just confirms for me that there’s no way we can have an honest conversation.

  360. 360
    Andre says:

    Thickpython

    And we have made several suggestions like maybe not presuppose common descent? Even in your response in @358 you show your bias.

    Blinkers off for a change…… The truth will really set you free

  361. 361
    EugeneS says:

    Peer #356,

    Thanks for your comment.

    Could you write an OP on this. I am sure it will serve a good purpose. I hate to see UD sinking into arguments about people, who said or did not say what, sort of thing. It is better to concentrate on the subject matter.

  362. 362
    ThickPython says:

    @Peer:

    You said previously:

    Further, we know since ages that, by simply weighing, the genome of chimps exceed that of humans by approx 10 percent.

    Right. Approximately 10% (plus or minus 37%!).

    You also said:

    … only 2.4 Mb had a match in the 2.85 Mb human probe

    … and:

    I am pretty sure you are able to align virtually all of the sequences.

    Which is it? Can it all be aligned, or is there a large proportion (450Mbp?) that can’t be aligned?

    “I recommend you to submit your papers to a science journal, instead of leaving it to the blogosphere. That is how science proceeds.”

    I agree, which is why I submitted a paper to Answers Research Journal in September last year. Next time you speak to Andrew Snelling, please ask him why he rejected that paper, because he refuses to give me any reasons. Weird, given that my paper was explicitly stated as the catalyst for Jeff Tomkins’ reanalysis. I’ve heard stories about creationists being shunned from secular journals, but when the shoe is on the other foot .. sheesh!

    Anyway my little cherubs, it’s past my bedtime. Sleep tight!

  363. 363
    Vy says:

    And so are these words: “When the data is not in accord with common descent, I investigate.”

    Oh yes, when your fallacious reasoning was found out.

    However, it did not contradict your earlier statement:

    The software used to automatically annotate the genomes isn’t perfect. Humans can spot these errors. In fact, one of the ways to spot these sort of errors is when the data are in apparent conflict with common descent!

    i.e. it’s an error if it doesn’t match the illusory presupposition of common descent.

    You have clearly shown that the software assumes common descent is true and if the results don’t match that illusion, you, in your own words “investigate”.

    Squeak, you’re squeaking your worth into oblivion. Shush up before it’s too late.

  364. 364
    Vy says:

    <blockquoteSqueakPythonYou also said:

    Peer:. … only 2.4 Mb had a match in the 2.85 Mb human probe

    … and:

    Peer:. I am pretty sure you are able to align virtually all of the sequences.

    Which is it? Can it all be aligned, or is there a large proportion (450Mbp?) that can’t be aligned?

    Talk about a quote taken out of context:

    Further, I am pretty sure you are able to align virtually all of the sequences. I can do that, too. Leaving out all indels and all pointmutations would make a monkey out of man

    Damn Squeak, “too_much_reality”> overload? I mean, look at what that did to the multi-person entity, Zachriel.

  365. 365
    Vy says:

    SqueakPython: You also said:

    Peer: … only 2.4 Mb had a match in the 2.85 Mb human probe

    … and:

    Peer:. I am pretty sure you are able to align virtually all of the sequences.

    SqueakPython: Which is it? Can it all be aligned, or is there a large proportion (450Mbp?) that can’t be aligned?

    Talk about a quote taken out of context:

    Peer: Further, I am pretty sure you are able to align virtually all of the sequences. I can do that, too. Leaving out all indels and all pointmutations would make a monkey out of man

    Damn Squeak, “too_much_reality” overload? I mean, look at what that did to the multi-person entity, Zachriel.

  366. 366
    Zachriel says:

    Andre: And as I have argued before for these 60 000 000 base pair diffreces to be come fixed in only 6 000 000 years NS & RM, drift, and any other form of evolution has to deal with the following…….

    1.) Multiple DNA Integrity check systems (Evolutionary conserved)
    2.) Multiple DNA Repair Mechanisms (Evolutionary conserved)
    3.) Multiple Apoptosis systems (Evolutionary conserved)
    4.) Necrotic system (Evolutionary conserved)

    And yet the average human has about 175 mutations.

    Andre: Now lets chat about the idea that these 60 000 000 base pair difference could become fixed in only 6 000 000 years.

    The rate of fixation of neutral mutations is the same as the rate of introduction of neutral mutations. Humans each have about 175 mutations, most of them neutral. After six million years, that is about 50 million mutations, well within the required magnitude.

  367. 367
    Box says:

    Peer: I have always found it peculiar that in the chimp-human comparison 8% of the sequence was omitted from the studies. My own studies show highly divergent sequences even in man, most due to indels.
    (…)
    If someone is wrong, it is the Chimp Genome Consortium, they omitted 8% of the sequence and did not provide a reason.

    What’s going on here? I would like to know the real percentage of human-chimp DNA similarity.

  368. 368
    Zachriel says:

    Andre: Papers detailing that the tree of life aka common descent is hogwash

    Your first citation directly contradicts your position, though suggests that prokaryotes are derived not ancestral. Your second citation concerns only prokaryote evolution, which is already known to be obscured by horizontal mechanisms. That still leaves the rest of the tree largely intact. Your third citation states that part of the tree may be difficult to unravel.

    In any case, the tree is objectively determinable. Eukaryotes show a strong signal of a tree, while it is less clear for prokaryotes, and at the base of the tree.

  369. 369
    Vy says:

    What’s a baseless tree called?

  370. 370
    bornagain says:

    As stated in post 293, the fossil record certainly, when looked at in its entirety, does not support the hypothesis of common descent,

    (Disparity consistently precedes diversity in the fossil record)
    disparity
    [dih-spar-i-tee] noun, plural disparities.
    1. lack of similarity or equality; inequality; difference:
    http://www.uncommondescent.com.....ent-585067

    And as stated in post 278, trying to ‘explain away’ as much dissimilarity as possible between the genomes of chimps and humans is ‘not even wrong’ in trying to establish if it is even realistically plausible that humans could have morphed into their present ‘form’ from some hypothetical chimp-like ancestor:

    Darwinists and Theistic evolutionists try to ‘explain away’ as much dissimilarity in genes and proteins as they possibly can. Apparently with the erroneous assumption that if there is very little dissimilarity between genes and proteins then that finally explains how the human body attained its unique ‘form’.
    That approach to answering the question is, to put it kindly, ‘not even wrong’.
    http://www.uncommondescent.com.....ent-585035

    In fact, as also briefly touched upon in post 278, the ‘argument from form’ also gives us very good evidence that we each must have a soul so as to explain how a billion-trillion protein molecules can possibly cohere as a single unified whole for ‘precisely a lifetime, and not a moment longer’ (Talbott).
    But to further highlight why this approach of appealing to mutations to DNA is ‘not even wrong’ in regards to explaining how the unique human ‘form’ came about, no one has EVER even changed one creature into another creature by mutations to DNA as is presupposed in neo-Darwinian thought:

    Response to John Wise – October 2010
    Excerpt: A technique called “saturation mutagenesis”1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans–because none of the observed developmental mutations benefit the organism.
    http://www.evolutionnews.org/2.....38811.html

    ‘No matter what we do to a fruit fly embryo there are only three possible outcomes, a normal fruit fly, a defective fruit fly, or a dead fruit fly. What we never see is primary speciation much less macro-evolution’ –
    Jonathan Wells
    Darwin’s Theory – Fruit Flies and Morphology – video
    http://www.youtube.com/watch?v=hZJTIwRY0bs

    “While it may be an adequate scenario for the refinement of some already-existing characters — the beaks of finches, color intensity of moths — the “microevolutionary” process envisioned by Darwin and his successors does not account in any plausible way for “macroevolutionary” patterns such as the differences between oysters and grasshoppers, fish and birds. ”
    ~ Stuart Newman, “Where do complex organisms come from.”

    Nor, despite the fact that Darwinists claim their theory is on par with gravity, has anyone ever even seen one creature change into another creature:

    Scant search for the Maker
    Excerpt: But where is the experimental evidence? None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of 20 to 30 minutes, and populations achieved after 18 hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another, in spite of the fact that populations have been exposed to potent chemical and physical mutagens and that, uniquely, bacteria possess extrachromosomal, transmissible plasmids. Since there is no evidence for species changes between the simplest forms of unicellular life, it is not surprising that there is no evidence for evolution from prokaryotic to eukaryotic cells, let alone throughout the whole array of higher multicellular organisms.
    – Alan H. Linton – emeritus professor of bacteriology, University of Bristol.
    http://www.timeshighereducatio.....ode=159282

    A review of The Edge of Evolution: The Search for the Limits of Darwinism
    The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155).
    http://creation.com/review-mic.....-evolution

    Natural Selection and Evolution’s Smoking Gun, – American Scientist – 1997
    Excerpt: “A matter of unfinished business for biologists is the identification of evolution’s smoking gun,”…
    “Perhaps the most obvious challenge is to demonstrate evolution empirically. There are, arguably, some 2 to 10 million species on earth. The fossil record shows that most species survive somewhere between 3 and 5 million years. In that case, we ought to be seeing small but significant numbers of originations (new species) .. every decade.”
    (“the smoking gun of evolution is speciation, not local adaptation and differentiation of populations.”)
    Keith Stewart Thomson, Professor of Biology and Dean of the Graduate School, Yale University (Nov. -Dec. American Scientist, 1997 pg. 516)
    http://www.jstor.org/stable/27.....b_contents

    “The closest science has come to observing and recording actual speciation in animals is the work of Theodosius Dobzhansky in Drosophilia paulistorium fruit flies. But even here, only reproductive isolation, not a new species, appeared.”
    from page 32 “Acquiring Genomes” Lynn Margulis.

    Selection and Speciation: Why Darwinism Is False – Jonathan Wells – 2009
    Excerpt: there are observed instances of secondary speciation — which is not what Darwinism needs — but no observed instances of primary speciation, not even in bacteria. British bacteriologist Alan H. Linton looked for confirmed reports of primary speciation and concluded in 2001: “None exists in the literature claiming that one species has been shown to evolve into another.”
    http://www.evolutionnews.org/2.....why_d.html

    Meyers puts the one of the primary reasons why mutations to DNA cannot change one creature into another creature like this

    ‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does not insure that proteins, cell types, tissues, organs, will all be arranged in the body. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’
    Stephen Meyer – (excerpt taken from Meyer/Sternberg vs. Shermer/Prothero debate – 2009) (52:57 minute mark)
    https://youtu.be/7yqqlZ29gcU?t=3177

  371. 371
    bornagain says:

    Jonathan Wells recently wrote some papers highlighting many of those higher levels of information, that are above the DNA coding, that Dr. Meyer alluded to in his debate with Shermer and Prothero:

    Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA – Jonathan Wells – 2014
    http://bio-complexity.org/ojs/.....O-C.2014.2

    podcast – Dr. Jonathan Wells explains the concept of codes in living things, and how they affect the debate over neo-Darwinism and intelligent design. (at least 5 different codes in life besides the genetic code) – Oct. 2015
    http://www.discovery.org/multi.....more-31141

    Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information – Jonathan Wells – published online May 2013
    Conclusion:,, Recent discoveries of multiple overlapping functions in non-protein-coding DNA show that the biological information in the genome far exceeds that in the protein-coding regions alone. Yet biological information is not limited to the genome. Even at the level of gene expression – transcription and translation — the cell must access information that is not encoded in DNA. Many different RNAs can be generated from a single piece of DNA by alternative splicing, and although some splicing codes occur in intronic DNA there is no empirical justification for assuming that all of the information for tissue- and developmental-stage-specific alternative splicing resides in DNA.,, even after RNA has specified the amino acid sequence of a protein, additional information is needed: Protein function depends on three-dimensional shape, and the same sequence of amino acids can be folded differently to produce proteins with different three-dimensional shapes [144–147]. Conversely, proteins with different amino acid sequences can be folded to produce similar shapes and functions [148,149]. Many scientists have pointed out that the relationship between the genome and the organism – the genotype-phenotype mapping – cannot be reduced to a genetic program encoded in DNA sequences. Atlan and Koppel wrote in 1990 that advances in artificial intelligence showed that cellular operations are not controlled by a linear sequence of instructions in DNA but by a “distributed multilayer network” [150]. According to Denton and his co-workers, protein folding appears to involve formal causes that transcend material mechanisms [151], and according to Sternberg this is even more evident at higher levels of the genotype-phenotype mapping [152]. So non-protein-coding regions of DNA that some previously regarded as “junk” turn out to encode biological information that greatly increases the known information-carrying capacity of DNA. At the same time, DNA as a whole turns out to encode only part of the biological information needed for life.
    http://www.worldscientific.com.....08728_0009

    Besides there being overlapping coding that are, hierarchically, above the coding of DNA, we find that there also is overlapping coding within DNA as well:

    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – published online May 2013
    Excerpt: In the last decade, we have discovered still another aspect of the multi- dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43].
    http://www.worldscientific.com.....08728_0006

    “There is abundant evidence that most DNA sequences are poly-functional, and therefore are poly-constrained. This fact has been extensively demonstrated by Trifonov (1989). For example, most human coding sequences encode for two different RNAs, read in opposite directions i.e. Both DNA strands are transcribed ( Yelin et al., 2003). Some sequences encode for different proteins depending on where translation is initiated and where the reading frame begins (i.e. read-through proteins). Some sequences encode for different proteins based upon alternate mRNA splicing. Some sequences serve simultaneously for protein-encoding and also serve as internal transcriptional promoters. Some sequences encode for both a protein coding, and a protein-binding region. Alu elements and origins-of-replication can be found within functional promoters and within exons. Basically all DNA sequences are constrained by isochore requirements (regional GC content), “word” content (species-specific profiles of di-, tri-, and tetra-nucleotide frequencies), and nucleosome binding sites (i.e. All DNA must condense). Selective condensation is clearly implicated in gene regulation, and selective nucleosome binding is controlled by specific DNA sequence patterns – which must permeate the entire genome. Lastly, probably all sequences do what they do, even as they also affect general spacing and DNA-folding/architecture – which is clearly sequence dependent. To explain the incredible amount of information which must somehow be packed into the genome (given that extreme complexity of life), we really have to assume that there are even higher levels of organization and information encrypted within the genome. For example, there is another whole level of organization at the epigenetic level (Gibbs 2003). There also appears to be extensive sequence dependent three-dimensional organization within chromosomes and the whole nucleus (Manuelides, 1990; Gardiner, 1995; Flam, 1994). Trifonov (1989), has shown that probably all DNA sequences in the genome encrypt multiple “codes” (up to 12 codes).
    Dr. John Sanford; Genetic Entropy 2005

    Moreover, there are very good mathematical reasons why overlapping coding within DNA will prevent one creature from ever being changed into another creature.

    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – May 2013
    Conclusions: Our analysis confirms mathematically what would seem intuitively obvious – multiple overlapping codes within the genome must radically change our expectations regarding the rate of beneficial mutations. As the number of overlapping codes increases, the rate of potential beneficial mutation decreases exponentially, quickly approaching zero. Therefore the new evidence for ubiquitous overlapping codes in higher genomes strongly indicates that beneficial mutations should be extremely rare. This evidence combined with increasing evidence that biological systems are highly optimized, and evidence that only relatively high-impact beneficial mutations can be effectively amplified by natural selection, lead us to conclude that mutations which are both selectable and unambiguously beneficial must be vanishingly rare. This conclusion raises serious questions. How might such vanishingly rare beneficial mutations ever be sufficient for genome building? How might genetic degeneration ever be averted, given the continuous accumulation of low impact deleterious mutations?
    http://www.worldscientific.com.....08728_0006

    A very simple way to understand the monumental brick wall any evolutionary scenario faces with the multiple overlapping coding found in DNA is with the following puzzle found on page 141 of the book ‘Genetic Entropy’ by Dr. Sanford.

    S A T O R
    A R E P O
    T E N E T
    O P E R A
    R O T A S

    Which is translated ;

    THE SOWER NAMED AREPO HOLDS THE WORKING OF THE WHEELS.

    This ancient puzzle, which dates back to at least 79 AD, reads the same four different ways, Thus, If we change (mutate) any letter we may get a new meaning for a single reading read any one way, as in Dawkins weasel program, but we will consistently destroy the other 3 readings of the message with the new mutation (save for the center).
    This is what is meant when it is said that a poly-functional genome is poly-constrained to any random mutations.
    This poly-constrained principle is why we never see the unlimited plasticity in organisms that was, and is, imagined by Darwin and his followers, and is also why random mutations, that have effects that great enough that we are able to measure them, are almost always deleterious in the effects that are measured:

    “Whatever we may try to do within a given species, we soon reach limits which we cannot break through. A wall exists on every side of each species. That wall is the DNA coding, which permits wide variety within it (within the gene pool, or the genotype of a species)-but no exit through that wall. Darwin’s gradualism is bounded by internal constraints, beyond which selection is useless.”
    R. Milner, Encyclopedia of Evolution (1990)

    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – May 2013
    Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11].
    1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696.
    2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19.
    3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358.
    4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144.
    5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47.
    6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501.
    7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117.
    8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526.
    9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685.
    10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079.
    11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501.
    http://www.worldscientific.com.....08728_0006

    Moreover, at the morphological and behavioral level we find that Chimps and Humans are far more different than is commonly believed.
    In fact, King and Wilson, who were the first ones to suggest that we are 98% similar to chimps at the genetic level, said that since the morphological and behavioral disparity between chimps and humans is so great then the morphological and behavioral disparity between humans and apes must be due to variations in their genomic regulatory systems since such similarity in the protein coding regions obviously could not explain that great morphological and behavioral disparity between chimps and humans.

    In “Science,” 1975, M-C King and A.C. Wilson were the first to publish a paper estimating the degree of similarity between the human and the chimpanzee genome. This documented the degree of genetic similarity between the two! The study, using a limited data set, found that we were far more similar than was thought possible at the time. Hence, we must be one with apes mustn’t we? But…in the second section of their paper King and Wilson honestly describe the deficiencies of such reasoning:
    “The molecular similarity between chimpanzees and humans is extraordinary because they differ far more than sibling species in anatomy and way of life. Although humans and chimpanzees are rather similar in the structure of the thorax and arms, they differ substantially not only in brain size but also in the anatomy of the pelvis, foot, and jaws, as well as in relative lengths of limbs and digits (38).
    Humans and chimpanzees also differ significantly in many other anatomical respects, to the extent that nearly every bone in the body of a chimpanzee is readily distinguishable in shape or size from its human counterpart (38).
    Associated with these anatomical differences there are, of course, major differences in posture (see cover picture), mode of locomotion, methods of procuring food, and means of communication. Because of these major differences in anatomy and way of life, biologists place the two species not just in separate genera but in separate families (39). So it appears that molecular and organismal methods of evaluating the chimpanzee human difference yield quite different conclusions (40).”

    King and Wilson went on to suggest that the morphological and behavioral between humans and apes,, must be due to variations in their genomic regulatory systems.
    David Berlinski – The Devil’s Delusion – Page 162&163
    Evolution at Two Levels in Humans and Chimpanzees Mary-Claire King; A. C. Wilson – 1975
    http://academic.reed.edu/biolo.....5(classic).pdf

    In fact, so great are the anatomical differences between humans and chimps that a Darwinist, since pigs are anatomically closer to humans than chimps are, actually proposed that a chimp and pig mated with each other and that is what ultimately gave rise to humans. (I guess even hybidization knows no limits in the minds of some Darwinists).
    Moreover, Physorg published a subsequent article showing that the pig-chimp hybrid theory for human origins is much harder to shoot down than some other Darwinists, who opposed McCarthy’s radical theory, had first supposed it would be:

    Human hybrids: a closer look at the theory and evidence – July 25, 2013
    Excerpt: There was considerable fallout, both positive and negative, from our first story covering the radical pig-chimp hybrid theory put forth by Dr. Eugene McCarthy,,,By and large, those coming out against the theory had surprisingly little science to offer in their sometimes personal attacks against McCarthy.
    ,,,Under the alternative hypothesis (humans are not pig-chimp hybrids), the assumption is that humans and chimpanzees are equally distant from pigs. You would therefore expect chimp traits not seen in humans to be present in pigs at about the same rate as are human traits not found in chimps. However, when he searched the literature for traits that distinguish humans and chimps, and compiled a lengthy list of such traits, he found that it was always humans who were similar to pigs with respect to these traits. This finding is inconsistent with the possibility that humans are not pig-chimp hybrids, that is, it rejects that hypothesis.,,,
    http://phys.org/news/2013-07-h.....dence.html

    Of course there is not one single scrap of empirical evidence that suggests that such radically different creatures, such as pigs and chimps, could ever successfully produce viable offspring.
    But alas, when your theory is built on story telling in the first place, (and not on any real empirical evidence), then of course you are not going to be able to shoot down another ‘just so story’ just because you don’t like how the narrative contradicts your preferred narrative of man ascending from monkeys:

    “We have all seen the canonical parade of apes, each one becoming more human. We know that, as a depiction of evolution, this line-up is tosh (i.e. nonsense). Yet we cling to it. Ideas of what human evolution ought to have been like still colour our debates.”
    Henry Gee, editor of Nature (478, 6 October 2011, page 34, doi:10.1038/478034a),

    In further note to King and Wilson’s observation that ‘nearly every bone in the body of a chimpanzee is readily distinguishable in shape or size from its human counterpart’, this observation by King and Wilson, by itself, places another severe constraint on the Darwinian evolution that, once again, calls the entire theory into question.
    Simply put, since nearly every bone is readily distinguishable between chimps and humans, then multiple simultaneous coordinated changes are required instead of just individual changes, as is envisioned in Darwinism, so as to prevent catastrophic results:

    K´necting The Dots: Modeling Functional Integration In Biological Systems – June 11, 2010
    Excerpt: “If an engineer modifies the length of the piston rods in an internal combustion engine, but does not modify the crankshaft accordingly, the engine won’t start. Similarly, processes of development are so tightly integrated temporally and spatially that one change early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream” (1)
    http://www.uncommondescent.com.....l-systems/

  372. 372
    bornagain says:

    “This is the issue I have with neo-Darwinists: They teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn’t create….
    (Quoted in “Discover Interview: Lynn Margulis Says She’s Not Controversial, She’s Right,” Discover Magazine, p. 68 (April, 2011).)

    “The real number of variations is lesser than expected,,. There are no blue-eyed Drosophila, no viviparous birds or turtles, no hexapod mammals, etc. Such observations provoke non-Darwinian evolutionary concepts. Darwin tried rather unsuccessfully to solve the problem of the contradictions between his model of random variability and the existence of constraints. He tried to hide this complication citing abundant facts on other phenomena. The authors of the modern versions of Darwinism followed this strategy, allowing the question to persist. …However, he was forced to admit some cases where creating anything humans may wish for was impossible. For example, when the English farmers decided to get cows with thick hams, they soon abandoned this attempt since they perished too frequently during delivery. Evidently such cases provoked an idea on the limitations to variability… [If you have the time, read all of the following paper, which concludes] The problem of the constraints on variation was not solved neither within the framework of the proper Darwin’s theory, nor within the framework of modern Darwinism.” (IGOR POPOV, THE PROBLEM OF CONSTRAINTS ON VARIATION, FROM DARWIN TO THE PRESENT, 2009,
    http://www.ludusvitalis.org/te....._popov.pdf

    Perhaps that is why so many engineers support intelligent design since they can readily see the impossibility of the ‘engineering problem’ for Darwinian processes. Namely, Design must be implemented top down, with all the pieces coordinated with one another, so as to avoid catastrophic results for the system as a whole.
    Moreover, in further note to King and Wilson’s contention that the morphological and behavioral disparity between humans and apes must be due to variations in their genomic regulatory systems, (since the genetic similarity obviously cannot explain that great morphological and behavioral disparity between chimps and humans), we find that it is indeed in the genetic regulatory regions that we find ‘orders of magnitude’ and ‘species specific’ differences between not only chimps and humans, but also in other species as well:
    Just a reminder, genetic similarity is far more widespread, across very different species, than Darwinists expected the genetic similarity to be

    Shark and human proteins “stunningly similar”; shark closer to human than to zebrafish – December 9, 2013
    Excerpt: “We were very surprised to find, that for many categories of proteins, sharks share more similarities with humans than zebrafish,” Stanhope said. “Although sharks and bony fishes are not closely related, they are nonetheless both fish … while mammals have very different anatomies and physiologies.
    http://www.uncommondescent.com.....zebrafish/

    Kangaroo genes close to humans
    Excerpt: Australia’s kangaroos are genetically similar to humans,,, “There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order,” ,,,”We thought they’d be completely scrambled, but they’re not. There is great chunks of the human genome which is sitting right there in the kangaroo genome,”
    http://www.reuters.com/article.....P020081118

    First Decoded Marsupial Genome Reveals “Junk DNA” Surprise – 2007
    Excerpt: In particular, the study highlights the genetic differences between marsupials such as opossums and kangaroos and placental mammals like humans, mice, and dogs. ,,,
    The researchers were surprised to find that placental and marsupial mammals have largely the same set of genes for making proteins. Instead, much of the difference lies in the controls that turn genes on and off.
    http://news.nationalgeographic.....m-dna.html

    Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012
    Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,,
    A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species.
    On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,,
    http://www.the-scientist.com/?.....plicing%2F

    Where could we have learned but from Phys.org – Sept. 28, 2014
    Excerpt: “We have basically the same 20,000 (30,000?) protein-coding genes as a frog, yet our genome is much more complicated, with more layers of gene regulation.”
    http://www.uncommondescent.com.....-phys-org/

    Yet it is exactly in these genetic regulatory networks that ‘orders of magnitude’ differences are found between species:

    Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012
    Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,,
    A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species.
    On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,,
    http://www.the-scientist.com/?.....plicing%2F

    Gene Regulation Differences Between Humans, Chimpanzees Very Complex – Oct. 17, 2013
    Excerpt: Although humans and chimpanzees share,, similar genomes, previous studies have shown that the species evolved major differences in mRNA (messenger RNA) expression levels.,,,
    http://www.sciencedaily.com/re.....144632.htm

    “Where (chimps and humans) really differ, and they differ by orders of magnitude, is in the genomic architecture outside the protein coding regions. They are vastly, vastly, different.,, The structural, the organization, the regulatory sequences, the hierarchy for how things are organized and used are vastly different between a chimpanzee and a human being in their genomes.”
    Raymond Bohlin (per Richard Sternberg) – 9:29 minute mark of video
    http://www.metacafe.com/watch/8593991/

  373. 373
    bornagain says:

    On Human Origins: Is Our Genome Full of Junk DNA? Pt 2. – Richard Sternberg PhD. Evolutionary Biology
    Excerpt: “Here’s the interesting thing, when you look at the protein coding sequences that you have in your cell what you find is that they are nearly identical to the protein coding sequences of a dog, of a carp, of a fruit fly, of a nematode. They are virtually the same and they are interchangeable. You can knock out a gene that encodes a protein for an inner ear bone in say a mouse. This has been done. And then you can take a protein that is similar to it but from a fruit fly. And fruit flies aren’t vertebrates and they certainly are not mammals., so they don’t have inner ear bones. And you can plug that gene in and guess what happens? The offspring of the mouse will have a perfectly normal inner ear bone. So you can swap out all these files. I mentioning this to you because when you hear about we are 99% similar (to chimps) it is almost all referring to those protein coding regions. When you start looking, and you start comparing different mammals. Dolphins, aardvarks, elephants, manatees, humans, chimpanzees,, it doesn’t really matter. What you find is that the protein coding sequences are very well conserved, and there is also a lot of the DNA that is not protein coding that is also highly conserved. But when you look at the chromosomes and those banding patterns, those bar codes, (mentioned at the beginning of the talk), its akin to going into the grocery store. You see a bunch of black and white lines right? You’ve seen one bar code you’ve seen them all. But those bar codes are not the same.,, Here’s an example, aardvark and human chromosomes. They look very similar at the DNA level when you take small snippets of them. (Yet) When you look at how they are arranged in a linear pattern along the chromosome they turn out to be very distinct (from one another). So when you get to the folder and the super-folder and the higher order level, that’s when you find these striking differences. And here is another example. They are now sequencing the nuclear DNA of the Atlantic bottle-nose dolphin. And when they started initially sequencing the DNA, the first thing they realized is that basically the Dolphin genome is almost wholly identical to the human genome. That is, there are a few chromosome rearrangements here and there, you line the sequences up and they fit very well. Yet no one would argue, based on a statement like that, that bottle-nose dolphins are closely related to us. Our sister species if you will. No one would presume to do that. So you would have to layer in some other presumption. But here is the point. You will see these statements throughout the literature of how common things are.,,, (Parts lists are very similar, but how the parts are used is where you will find tremendous differences)
    http://www.discovery.org/multi.....-dna-pt-2/

    Moreover, unlike protein coding regions where there is some ‘non-catastrophic’ tolerance to random mutations, randomly mutating gene regulatory networks is found to be ‘always catastrophically bad’:

    A Listener’s Guide to the Meyer-Marshall Debate: Focus on the Origin of Information Question -Casey Luskin – December 4, 2013
    Excerpt: “There is always an observable consequence if a dGRN (developmental gene regulatory network) subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the subcircuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work. And indeed the embryos of each species develop in only one way.” –
    Eric Davidson – developmental biologist
    http://www.evolutionnews.org/2.....79811.html

    Thus, where Darwinists most need plasticity in the genome to be viable as a theory, (i.e. developmental Gene Regulatory Networks), is the place where mutations are found to be ‘always catastrophically bad’. Yet, it is exactly in this area of the genome (i.e. regulatory networks) where substantial, ‘orders of magnitude’, differences are found between even supposedly closely related species.
    Needless to say, this is the exact opposite finding for what Darwinism would have predicted for what should have been found in the genome.
    If Darwinism were a normal science, instead of being basically the unfalsifiable ‘blind faith’ religion of atheists, this finding, by itself, should have been more than enough to falsify neo-Darwinian claims.

    Of supplemental note to Richard Sternberg’s ‘bar codes are not the same’ between species quote. It turns out that the bar code pattern that Dr. Sternberg alluded to is irreducibly complex in its organizational relation to the individual genes:

    Refereed scientific article on DNA argues for irreducible complexity – October 2, 2013
    Excerpt: This paper published online this summer is a true mind-blower showing the irreducible organizational complexity (author’s description) of DNA analog and digital information, that genes are not arbitrarily positioned on the chromosome etc.,,
    ,,,First, the digital information of individual genes (semantics) is dependent on the the intergenic regions (as we know) which is like analog information (syntax). Both types of information are co-dependent and self-referential but you can’t get syntax from semantics. As the authors state, “thus the holistic approach assumes self-referentiality (completeness of the contained information and full consistency of the different codes) as an irreducible organizational complexity of the genetic regulation system of any cell”. In short, the linear DNA sequence contains both types of information. Second, the paper links local DNA structure, to domains, to the overall chromosome configuration as a dynamic system keying off the metabolic signals of the cell. This implies that the position and organization of genes on the chromosome is not arbitrary,,,
    http://www.christianscientific.....omplexity/

    This has been a fairly long post, (even for me 🙂 ), but hopefully for the open minded person who is honestly trying to see if either ID or Darwinism is true, this post has made it abundantly clear that neo-Darwinian explanations are grossly deficient on several different levels as to explaining the amazing integrated complexity we see in life, and that ID explanations are, by far, the most satisfactory explanations for that amazing integrated complexity that we see.

  374. 374
    Peer says:

    @Box, @366:

    “What’s going on here?”

    The big snake is out there to put confusion in your minds. And snakes can be rather succesful there.

    Did you ID guys never read Genesis? It’s about the snake. And how he deceives.

    Better start reading.

  375. 375
    Peer says:

    @Box, @366:

    “I would like to know the real percentage of human-chimp DNA similarity.”

    You never will know. We never will. Nobody will ever know.

    Because it depends on the sequences of the chimp and human analysed, the mood of the programmer, the algorithms used, the settings, the comparison done, and the source codes.

    One thing we know: Darwinians will show you point mutations only (1-2%), creationians will show you point mutations, indels, and unique sequences.

    This is not a fight of flesh and blood, but of the mind. The snake is after your mind, not after your body. Isn’t that clear?

  376. 376
    Andre says:

    Zachriel

    I love it when you comment on things you know nothing about. Nobody here makes you look like a fool that you do all by yourself.

  377. 377
    Box says:

    Peer, EugeneS,

    EugeneS:
    Peer #356,

    Thanks for your comment.

    Could you write an OP on this. I am sure it will serve a good purpose.

    I second EugeneS’ request.

    Peer: The big snake is out there to put confusion in your minds. And snakes can be rather succesful there. Did you ID guys never read Genesis? It’s about the snake. And how he deceives.

    I’m sure the name “ThickPython” is just randomly chosen 🙂

  378. 378
    Peer says:

    @Big Snake, @361

    The big snake says: “I agree, which is why I submitted a paper to Answers Research Journal in September last year.”

    Peer: I don’t recall the human-chimp analysis of the Chimp Genome Consortium was publised in ARJ. If I am not mistaken it was publsihed in Nature. Write the Nature editors a letter, claiming that you know why the consortium was unable to align 100% of the sequences.

    Btw. Good to hear that ARJ is a science journal. Maybe you could also proclaim that over at Larry Moran’s blog. He will surely like that. Thanks.

    I think we can now simply stop discussing here, because there is nothing to discuss. Except of course that Darwinian theory is as dead as a dodo. Every well informed scientist (and others) knows that.

    peer

  379. 379
    Cornelius Hunter says:

    Always interesting to see how evolutionists respond to the evidence. The OP is critical of a post I wrote which reports on the evidence–it repeatedly refers to “claims” that I made about human de novo proteins. But those weren’t my claims–the post was reporting on recent findings. Amazing.

    Apparently the OP also takes issue with my comment, that the de novo proteins are extremely unlikely under evolution, because there are homologous chimp and orangutan sequences at the nucleotide level. Again, sorry but regulatory sequences and machinery are not free. Stuff doesn’t just happen by blind chance. I know that’s inconvenient.

    Furthermore, the homologous chimp and orangutan sequences make the evolution explanation that much more unlikely by removing selection from the supposed coding sequence evolution process–what evolutionists have counted on in trying to explain protein evolution.

  380. 380
    bornagain says:

    Since Dr. Torley basically gave a hard core neo-Darwinist unfettered leeway to present his views on a headlined post on UD, without, IMHO, sufficient feedback from Dr. Tomkins himself, then I certainly think it would be more than fair if Dr. Torley would at least give Peer an opportunity to counter Python’s claims and show why the claims for extreme similarity at the genome level may not be nearly as rock solid as Python, and even Dr. Torley himself, may prefer to believe.

    Thus I third (or forth) the motion for Peer to have an opportunity to post a rebuttal of Python’s claims. (minus calling Python a snake of course. Oh wait a minute Pythons really are snakes! 🙂 )

    Picture
    http://fr.wallpaperswiki.org/w.....Python.jpg

  381. 381
    kairosfocus says:

    BA77, if someone wants to do a guest post, I am willing to host. KF

  382. 382
    Mung says:

    Cornelius Hunter:

    Furthermore, the homologous chimp and orangutan sequences make the evolution explanation that much more unlikely by removing selection from the supposed coding sequence evolution process–what evolutionists have counted on in trying to explain protein evolution.

    Evolutionists count on anything and everything, including the proverbial kitchen sink. Walter ReMine calls evolutionary theory a smorgasbord.

    And when they have nothing, they then turn on the critic and ask what is the alternative hypothesis?

  383. 383
    bornagain says:

    Great offer kf! 🙂 Did you hear that Peer? I know that I would really appreciate a solid rebuttal to Darwinists in this area since it is the one piece of evidence that Darwinists forever try to cling to tenaciously as if it was the be all end all of the debate. I hope that you will take up the ‘mission’ Peer! 🙂

    “Your mission. Should you choose to accept it.”
    https://www.youtube.com/watch?v=F5HMWUBmhS8

    mission impossible theme song
    https://www.youtube.com/watch?v=XAYhNHhxN0A

  384. 384
    Mung says:

    And yet the average human has about 175 mutations.

    Who are you calling average?

  385. 385
    Andre says:

    I have really enjoyed this thread. I would love to see Peer do a guest post.

    Personally I’m tired of assumptions and beliefs trumping facts.

    Bring out the facts.

  386. 386
    EugeneS says:

    Kf, Bornagain,

    Great offer kf!

    Yes, it is indeed.

  387. 387
    Mapou says:

    I have one question for the class about comparing genetic sequences. When comparing two binary numbers, we know that the bits on the left are more significant than the bits on the right. The significance grows exponentially as one moves to the left.

    My point is that one can do a bit comparison of two large numbers and find very little difference (e.g., 1 bit off) but the actual difference could be much greater. I suspect that something similar is happening in the genes. Some base pairs are likely to be more significant than others depending on their placement in the sequence. Thus it is very likely that the 98% similarity claim, which is based on base-pair comparisons, is way off.

  388. 388
    Virgil Cain says:

    Yes, Mapou, two sentences could be 98% similar and yet mean opposite things. A 1% change to an operating system could wreak havoc.

  389. 389
    EugeneS says:

    Virgil Cane #388,

    Yes, e.g. in a boot loader 🙂 all or nothing kind of error.

    The question is, how to measure meaning. How should two logically identical but actually dissimilar functional sequences be measured?

    E.g. in the DNA repair machinery there are logically equivalent mechanisms (achieving the same goal) that involve substantially different protein-protein interactions.

  390. 390
    Andre says:

    EugeneS

    And some people in their heart of hearts believe such a system came about by trial or error I’d laugh at them if it was not so sad……

  391. 391
    EugeneS says:

    Andre,

    Indeed! They cannot tackle this challenge with a non-telic toolkit. However, in their eyes their reputation is at stake. I suspect a majority of them understand the issue but they will never acknowledge it. Never.

    The biological circuitry puts to shame contemporary IT. And all that is essentially by change, selection notwithstanding! Selection is mentioned to make it appear logical. In truth, selection is not and never was a source of information. It is just a passive information reduction filter. So the only causal factor they have is chance.

    Pathetic.

  392. 392
    Andre says:

    I am an engineer and what I design does not come close to the tech we see in biology. The engineering in living system are more than exquisite.

  393. 393
    mike1962 says:

    mapou: Thus it is very likely that the 98% similarity claim, which is based on base-pair comparisons, is way off.

    Right. Consider…

    10000000000000000000000000000000 (binary)
    1000000000000000000000000000000

    A %3 difference, right? Yes, if we’re counting raw digits. But not if the two values represent the start values for a countdown timer. In that case the values are 50% different… just because of a single digit.

  394. 394
    JoeCoder says:

    @Dr. Cornelius Hunter at 379

    If we see a sequence that is protein coding in humans but non-coding in apes, given the difficulties of protein evolution wouldn’t the simplest explanation be that it became disabled in the various ape species?

    Even if they are disabled by identical mutations that seems far more likely–and I think shared identical mutations are more likely than what most people realize. Take a look at Figure 2A from Greene and Jinks-Robinson, 1997. They disabled a gene in yeast via frameshift which put it under selection to be re-enabled via small indels to restore the original reading frame. Some spots received the same 1bp deletion mutation 35 times, with no mutations immediately to the left or right. The clusters of indels usually happened at mononucleotide repeats, but not always.

    I admit I have not taken a close look at those shared sequences between humans and apes, where the human sequence is protein coding.

  395. 395
    Mung says:

    I think we should definitely give ThickPython an opportunity to post an OP on how Tomkins wasn’t the only scientist he exposed for using a software program with a faulty algorithm.

  396. 396
    Mapou says:

    Since the genome is organized hierarchically, it would be very instructive to determine whether most of the differences are located at the higher or the lower levels of the hierarchy. I suspect it is the former because most of the low level sequences already exist in the chimp. Since the higher levels of a hierarchy are much more significant in terms of control power than the lower levels, we can conclude that the 98% claim is about as bogus as can be.

    On a different tangent, how believable is the claim that the chimp genome is 10% larger than the human genome? I find this fascinating because I have a hypothesis that calls for the chimp genome to be more complex than the human genome. The reason is that humans rely almost entirely on their powerful ability to learn almost everything they know and thus do not need nearly as many pre-wired behavioral mechanisms at birth as chimps do.

  397. 397
    Mapou says:

    OT: I remember reading, many years ago, about a Sumerian myth that claimed that the Gods fashioned the first man from an ape. IIRC, the biological tour de force was accomplished by a Goddess. Does anybody know about this?

  398. 398
    bornagain says:

    JoeCoder, you ask Dr. Hunter

    If we see a sequence that is protein coding in humans but non-coding in apes, given the difficulties of protein evolution wouldn’t the simplest explanation be that it became disabled in the various ape species?

    Now to make the question a bit more clear for the rest of us, let’s clarify exactly what JoeCoder means by “difficulties of protein evolution”

    Yockey and a Calculator Versus Evolutionists – Cornelius Hunter PhD – September 25, 2015
    Excerpt: In a 1977 paper published in the Journal of Theoretical Biology, Hubert Yockey used information theory to evaluate the likelihood of the evolution of a relatively simple protein.,,,
    Yockey found that the probability of evolution finding the cytochrome c protein sequence is about one in 10^64. That is a one followed by 64 zeros—an astronomically large number. He concluded in the peer-reviewed paper that the belief that proteins appeared spontaneously “is based on faith.”
    Indeed, Yockey’s early findings are in line with, though a bit more conservative than, later findings. A 1990 study of a small, simple protein found that 10^63 attempts would be required for evolution to find the protein.
    A 2004 study found that 10^64 to 10^77 attempts are required, and a 2006 study concluded that 10^70 attempts would be required.
    These requirements dwarf the resources evolution has at its disposal. Even evolutionists have had to admit that evolution could only have a maximum of 10^43 such experiments. It is important to understand how tiny this number is compared to 10^70. 10^43 is not more than half of 10^70. It is not even close to half. 10^43 is an astronomically tiny sliver of 10^70.
    Furthermore, the estimate of 10^43 is, itself, entirely unrealistic. For instance, it assumes the entire history of the Earth is available, rather than the limited time window that evolution actually would have had.,,,
    http://darwins-god.blogspot.co.....ersus.html

    Is Evolution True? Laying Out the Logic – December 4, 2014
    Excerpt:
    To summarize, the key points of that evolutionary argument are:

    1. Evolution is true. That is, enzymes have evolved new functions by a process of random mutation and natural selection.
    2. Modern enzymes can’t evolve genuinely new functions by random mutation and natural selection but can only tinker with existing functions.
    3. Therefore, ancient enzymes must have been different, capable of carrying out a broad range of enzyme activities.
    4. Those enzymes underwent duplication and diverged from one another, becoming specialized.
    5. How do we know this happened? Because we now see a broad array of specialized enzymes. Evolution is the explanation.

    This begs the question of whether evolution is true. It is a circular argument unsubstantiated by the evidence and unfalsifiable. No one can know what ancient enzymes actually looked like, and whether they really had such broad catalytic specificities.

    In contrast, our argument is as follows:

    1. Is evolution true? Test case: do enzymes evolve by a process of natural selection and random mutation?
    2. Modern enzymes are the only thing we can test.
    3. No one knows if ancient enzymes were different. They are lost in the deep past, so claims with regard to their promiscuity or ability to evolve are hypothetical and unfalsifiable.
    4. Modern enzymes can’t evolve new functions, based on our own experiments.
    5. We haven’t tested the universe of modern enzymes, so our result is qualified, but the nine most similar enzymes did not change function.
    6. Our estimate for the likely waiting time for an enzyme to evolve a new function is at least 10^15 years.
    7. Therefore evolution of enzymes is likely to be impossible.
    8. Given the sophistication of enzymes and the way they work together, intelligent design is the best explanation for the origin and current diversity of modern enzymes.
    http://www.biologicinstitute.o.....-the-logic

    “Enzyme Families — Shared Evolutionary History or Shared Design?” – Ann Gauger – December 4, 2014
    Excerpt: If enzymes can’t be recruited to genuinely new functions by unguided means, no matter how similar they are, the evolutionary story is false.,,,
    Taken together, since we found no enzyme that was within one mutation of cooption, the total number of mutations needed is at least four: one for duplication, one for over-production, and two or more single base changes. The waiting time required to achieve four mutations is 10^15 years. That’s longer than the age of the universe. The real waiting time is likely to be much greater, since the two most likely candidate enzymes failed to be coopted by double mutations.
    We have now addressed two objections raised by our critics: that we didn’t test the right mutation(s), and that we didn’t use the right starting point. We tested all possible single base changes in nine different enzymes, Those nine enzymes are the most structurally similar of BioF’s entire family We also tested 70 percent of double mutations in the two closest enzymes of those nine.
    Finally, some have said we should have used the ancestral enzyme as our starting point, because they believe modern enzymes are somehow different from ancient ones. Why do they think that? It’s because modern enzymes can’t be coopted to anything except trivial changes in function. In other words, they don’t evolve!
    That is precisely the point we are making.
    http://www.evolutionnews.org/2.....91701.html

    Thus, JoeCoder’s question to Dr. Hunter,,,,

    If we see a sequence that is protein coding in humans but non-coding in apes, given the difficulties of protein evolution wouldn’t the simplest explanation be that it became disabled in the various ape species?

    ,,, Thus, JoeCoder’s question to Dr. Hunter is actually better phrased as such,,,

    Since no one has a clue how unguided material processes could create a protein to begin with or how unguided material processes can possibly transform one protein into another type of protein, then is not the best explanation for how humans were created the fact the unguided material processes have not ever created anything and in fact consistently break things that are created?

    With the proper background that I provided, the logic behind that question is, to put it kindly, lacking completeness. Dr. Hunter further comments on a similar argument from a Darwinist here:

    Larry Moran: Vitamin C Pseudogene is Powerful Evidence – Cornelius Hunter – May 2011
    Excerpt: “Evolution and common descent have failed to explain how the original vitamin C gene could have arisen. In fact they fail to explain how any protein could have arisen. They have also failed to explain how all of biology could have arisen. This is not a good start.”
    http://www.uncommondescent.com.....-evidence/

  399. 399
    bornagain says:

    Of supplemental note to pseudogenes: It has long been argued by Darwinists that pseudogenes are irrefutable proof of common descent.
    That argument is now known to be false:

    Another pseudogene shows function – January 9, 2014
    Excerpt: Various non-coding regions of the genome, once presumed to be ‘junk’ DNA, have recently been found to be transcriptionally active. In particular, pseudogenes are now known to have important biological roles. Here we report that transcripts of the two tumour suppressor candidate-2 pseudogenes,,, The pseudogene TUSC2P promotes TUSC2 function by binding multiple microRNAs,,,
    http://www.uncommondescent.com.....-function/

    Pseudogenes and the Origin of Humanity: A Response to the Venema Critique of the RTB Human Origins Model, Part 5 – Fazale Rana
    Excerpt: In his critique, Venema does acknowledge that research shows some pseudogenes are functional, but he dismisses this point by claiming that such pseudogenes are rare. This assertion, however, is not supported by the latest work. In fact, two of the articles on our website discuss papers (published in peer-reviewed journals) that emphasize how widespread pseudogene function actually is.
    Researchers have discovered that the genesis of certain classes of junk DNA is not rare and random, but occurs frequently and in a repeatable manner. (Go here and here to read recent articles.) Scientists have also learned that the order of genes along a chromosome plays a functional role as well.
    http://www.reasons.org/pseudog.....del-part-5

    Another Notable Explosion: Has Darwin’s “Abominable Mystery,” the Origin of Flowering Plants, Been Solved? – Casey Luskin – January 2, 2014
    Excerpt: The paper concludes that “pseudogenes have emerged as a previously unappreciated class of sophisticated modulators of gene expression.” Likewise, a 2012 paper in RNA Biology states that “pseudogenes were long considered as junk genomic DNA” but “pseudogene regulation is widespread in eukaryotes.”
    http://www.evolutionnews.org/2.....80681.html

    Pseudogenes and the Origin of Humanity: A Response to the Venema Critique of the RTB Human Origins Model, Part 7 – Vitamin C refutation
    Excerpt: Yet, as biologist Peter Borger points out, fifty percent of the mutations in the primate and guinea pig exon X sequence are identical. In addition, the guinea pig exon X region shows a mutation at position 97, the location in the primate genomes where a deletion took place. These shared features could not have resulted because guinea pigs and primates shared a common ancestor. Instead, they must reflect nonrandom, reproducible changes.
    http://www.reasons.org/pseudog.....del-part-7

  400. 400
    ThickPython says:

    @Cornelius, #379:

    Cornelius: “6 million years simply would not be enough time to evolve these genes. In fact, 6 billion years would not be enough time.”

    Have you bothered to look at the alignments given in the Supplementary Information? Do you understand that these de novo proteins have been switched on by (usually) a single point mutation? Why couldn’t this be done in 6 million years?

    “But those weren’t my claims – the post was reporting on recent findings. Amazing.”

    What’s amazing is that you’re still defending yourself after you’ve clearly misrepresented the paper.

  401. 401
    Mung says:

    What’s not amazing is ThickPython’s selective criticism.

  402. 402
    bornagain says:

    So Python, you actually believe that a sequence that just might, for no particular reason whatsoever, code for a new protein was sitting there all by its lonesome in the junk DNA nether-land that Darwinists believe in, and then suddenly a mutation, a random mutation of course, for no particular reason whatsoever, kissed the junk DNA sequence on the cheek and said ‘wake up my little princess and make me some essential proteins?”, (preferably bacon, eggs, and coffee, proteins 🙂 )

    If you believe that, I’ve got some ocean front property in Arizona to sell you!

    Proteins by Accident? Replying to a Critic of The Information Enigma
    Douglas Axe October 27, 2015
    http://www.evolutionnews.org/2.....00411.html

  403. 403
    ThickPython says:

    @Vy, #365:

    Vy: “Talk about a quote taken out of context:”

    Peer: “Further, I am pretty sure you are able to align virtually all of the sequences. I can do that, too. Leaving out all indels and all pointmutations would make a monkey out of man”

    You do realise that indels and mutations can only be identified once you have an alignment … ? Insertions and deletions relative to another sequence. Mutations (or polymorphisms) relative to another sequence.

    Peer is trying to say that there are large portions in the genome that do not align with chimpanzee. I challenge him to quantify this. My figure of 96.9% includes both indels and mutations and covers the entire genome of both species.

    Also @Vy:

    “Oh yes, when your fallacious reasoning was found out.”

    You’re wasting your breath.

  404. 404
    bornagain says:

    Python I believe Peer suggested, among other flaws in your method, that the entire data base you used for your comparison is flawed.

    Hopefully he takes up the offer of a guest post by kf to more clearly lay his argument out.

    I wouldn’t mind Tomkins having a chance to defend himself against your arguments either on UD with his own guest post. (but I highly doubt that will happen since Tomkins rarely gets into squabbles on blogs)

  405. 405
    ThickPython says:

    @Mung:

    “I think we should definitely give ThickPython an opportunity to post an OP on how Tomkins wasn’t the only scientist he exposed for using a software program with a faulty algorithm.”

    and:

    “What’s not amazing is ThickPython’s selective criticism.”

    Are you going to make a point eventually? Learn to communicate directly, and not with snide, backhanded sarcsasm. I pity anyone that has to be in a relationship with you.

    If I had to guess, you think I picked out Jeff Tomkins for special criticism because he’s a creationist. Is that correct? And I’ve ignored any secular research that used this software, correct?

    Tomkins is the only one I’ve “exposed” because he is the only one incompetent enough to publish results that are – on their face – mathematically impossible. See post #26, which was addressed to you in the first place.

  406. 406
    bornagain says:

    An evolutionist actually used “mathematically impossible” in a sentence?? 🙂

    Darwin and the Mathematicians – David Berlinski
    “The formation within geological time of a human body by the laws of physics (or any other laws of similar nature), starting from a random distribution of elementary particles and the field, is as unlikely as the separation by chance of the atmosphere into its components.”
    Kurt Gödel, was a preeminent mathematician who is considered one of the greatest to have ever lived. Of Note: Godel was a Theist!
    http://www.evolutionnews.org/2.....cians.html

    Dr. David Berlinski: Head Scratching Mathematicians – video
    http://www.youtube.com/watch?v=hEDYr_fgcP8

    Proteins Did Not Evolve Even According to the Evolutionist’s Own Calculations but so What, Evolution is a Fact – Cornelius Hunter – July 2011
    Excerpt: For instance, in one case evolutionists concluded that the number of evolutionary experiments required to evolve their protein (actually it was to evolve only part of a protein and only part of its function) is 10^70 (a one with 70 zeros following it). Yet elsewhere evolutionists computed that the maximum number of evolutionary experiments possible is only 10^43. Even here, giving the evolutionists every advantage, evolution falls short by 27 orders of magnitude.
    http://darwins-god.blogspot.co.....d-not.html

    HISTORY OF EVOLUTIONARY THEORY – WISTAR DESTROYS EVOLUTION
    Excerpt: A number of mathematicians, familiar with the biological problems, spoke at that 1966 Wistar Institute,, For example, Murray Eden showed that it would be impossible for even a single ordered pair of genes to be produced by DNA mutations in the bacteria, E. coli,—with 5 billion years in which to produce it! His estimate was based on 5 trillion tons of the bacteria covering the planet to a depth of nearly an inch during that 5 billion years. He then explained that the genes of E. coli contain over a trillion (10^12) bits of data. That is the number 10 followed by 12 zeros. *Eden then showed the mathematical impossibility of protein forming by chance.
    http://www.pathlights.com/ce_e.....hist12.htm

    Bernard d’Abrera on Butterfly Mimicry and the Faith of the Evolutionist – October 5, 2011
    Excerpt: For it to happen in a single species once through chance, is mathematically highly improbable. But when it occurs so often, in so many species, and we are expected to apply mathematical probability yet again, then either mathematics is a useless tool, or we are being criminally blind.,,, Evolutionism (with its two eldest daughters, phylogenetics and cladistics) is the only systematic synthesis in the history of the universe that proposes an Effect without a Final Cause. It is a great fraud, and cannot be taken seriously because it outrageously attempts to defend the philosophically indefensible.
    http://www.evolutionnews.org/2.....51571.html

    More from Ann Gauger on why humans didn’t happen the way Darwin said – July 2012
    Excerpt: Each of these new features probably required multiple mutations. Getting a feature that requires six neutral mutations is the limit of what bacteria can produce. For primates (e.g., monkeys, apes and humans) the limit is much more severe. Because of much smaller effective population sizes (an estimated ten thousand for humans instead of a billion for bacteria) and longer generation times (fifteen to twenty years per generation for humans vs. a thousand generations per year for bacteria), it would take a very long time for even a single beneficial mutation to appear and become fixed in a human population.
    You don’t have to take my word for it. In 2007, Durrett and Schmidt estimated in the journal Genetics that for a single mutation to occur in a nucleotide-binding site and be fixed in a primate lineage would require a waiting time of six million years. The same authors later estimated it would take 216 million years for the binding site to acquire two mutations, if the first mutation was neutral in its effect.
    Facing Facts
    But six million years is the entire time allotted for the transition from our last common ancestor with chimps to us according to the standard evolutionary timescale. Two hundred and sixteen million years takes us back to the Triassic, when the very first mammals appeared. One or two mutations simply aren’t sufficient to produce the necessary changes,, in the time available. At most, a new binding site might affect the regulation of one or two genes.
    http://www.uncommondescent.com.....rwin-said/

  407. 407
    ThickPython says:

    @bornagain:

    Python I believe Peer suggested, among other flaws in your method, that the entire data base you used for your comparison is flawed.

    Hopefully he takes up the offer of a guest post by kf to more clearly lay his argument out.

    I wouldn’t mind Tomkins having a chance to defend himself against you either on UD with a guest post.

    I WOULD LOVE IF JEFF TOMKINS CAME TO DEFEND HIMSELF! He is ignoring my emails …

    I would also love anyone to point out flaws in my method. Bring it! I’m a bit puzzled by you saying that “the entire database” is flawed. Sure, there are still gaps in it and it’s not 100% complete – but it’s the best we’ve got, so what database are you expecting me to use???

  408. 408
    Vy says:

    You’re wasting your breath.

    Squuueeeeeak! I’m not the one who believes that probablymaybecouldness formed me. Under your worldview, you are a waste, in fact, in the eyes of the earths_gonna_die people, you and your buddies are an epidemic, teeny weeny squeaking pieces of rubbish.

    And last time I checked, noone here was “talking” so your comment is doubly useless.

    What do I mean? That comment coming from someone like you is a compliment. Thanks 😀

  409. 409
    ThickPython says:

    @BornAgain:

    An evolutionist actually used “mathematically impossible” in a sentence?? 🙂

    Yes, and I used it correctly. What you’ve just written is “mathematically very very unlikely”.

  410. 410
    Vy says:

    You do realise that blah blah blah

    I do realize that you took his comment out of context. Full Stop.

  411. 411
    Cornelius Hunter says:

    TP (400): Actually I did not misrepresent the paper. I did add my own comment about the problem.

    “Do you understand that these de novo proteins have been switched on by (usually) a single point mutation?”

    No, I didn’t know that. Can you elaborate? What makes you think a single mutation supplies all the regulation?

  412. 412
    Zachriel says:

    Andre: I love it when you comment on things you know nothing about.

    We’re willing to learn. Let’s take the first citation.

    Our conclusion is that the assumed anteriority of prokaryotes has no firm basis, does not even appear likely and it is not at all obvious that LGT ever took the proportions required to support the hypothesis of a continuum or even a net.

  413. 413
    bornagain says:

    Python, contrary to what you may think, I’ve been through this argument a few times before. Moreover, you certainly did NOT use the term ‘mathematically impossible’ in a scientifically correct way.

    Programming of Life – Probability – Defining Possible, Probable, Feasible etc.. – video
    http://www.youtube.com/watch?v=kckv0wVBYpA

    The Universal Plausibility Metric (UPM) & Principle (UPP) – Abel – Dec. 2009
    Excerpt: Mere possibility is not an adequate basis for asserting scientific plausibility. A precisely defined universal bound is needed beyond which the assertion of plausibility, particularly in life-origin models, can be considered operationally falsified. But can something so seemingly relative and subjective as plausibility ever be quantified? Amazingly, the answer is, “Yes.”,,,

    c?u = Universe = 10^13 reactions/sec X 10^17 secs X 10^78 atoms = 10^108
    c?g = Galaxy = 10^13 X 10^17 X 10^66 atoms = 10^96
    c?s = Solar System = 10^13 X 10^17 X 10^55 atoms = 10^85
    c?e = Earth = 10^13 X 10^17 X 10^40 atoms = 10^70
    http://www.tbiomed.com/content/6/1/27

    Book Review – Meyer, Stephen C. Signature in the Cell. New York: HarperCollins, 2009.
    Excerpt: As early as the 1960s, those who approached the problem of the origin of life from the standpoint of information theory and combinatorics observed that something was terribly amiss. Even if you grant the most generous assumptions: that every elementary particle in the observable universe is a chemical laboratory randomly splicing amino acids into proteins every Planck time for the entire history of the universe, there is a vanishingly small probability that even a single functionally folded protein of 150 amino acids would have been created. Now of course, elementary particles aren’t chemical laboratories, nor does peptide synthesis take place where most of the baryonic mass of the universe resides: in stars or interstellar and intergalactic clouds. If you look at the chemistry, it gets even worse—almost indescribably so: the precursor molecules of many of these macromolecular structures cannot form under the same prebiotic conditions—they must be catalysed by enzymes created only by preexisting living cells, and the reactions required to assemble them into the molecules of biology will only go when mediated by other enzymes, assembled in the cell by precisely specified information in the genome.
    So, it comes down to this: Where did that information come from? The simplest known free living organism (although you may quibble about this, given that it’s a parasite) has a genome of 582,970 base pairs, or about one megabit (assuming two bits of information for each nucleotide, of which there are four possibilities). Now, if you go back to the universe of elementary particle Planck time chemical labs and work the numbers, you find that in the finite time our universe has existed, you could have produced about 500 bits of structured, functional information by random search. Yet here we have a minimal information string which is (if you understand combinatorics) so indescribably improbable to have originated by chance that adjectives fail.
    http://www.fourmilab.ch/docume.....k_726.html

    To clarify as to how the 500 bit universal limit is found for ‘structured, functional information’:

    Dembski’s original value for the universal probability bound is 1 in 10^150,

    10^80, the number of elementary particles in the observable universe.
    10^45, the maximum rate per second at which transitions in physical states can occur.
    10^25, a billion times longer than the typical estimated age of the universe in seconds.

    Thus, 10^150 = 10^80 × 10^45 × 10^25. Hence, this value corresponds to an upper limit on the number of physical events that could possibly have occurred since the big bang.

    How many bits would that be:

    Pu = 10-150, so, -log2 Pu = 498.29 bits

    Call it 500 bits

    (The 500 bits is further specified as a specific type of information. It is specified as Complex Specified Information by Dembski or as Functional Information by Abel to separate it from merely Ordered Sequence Complexity or Random Sequence Complexity; See Three subsets of sequence complexity)

    Three subsets of sequence complexity and their relevance to biopolymeric information – Abel, Trevors
    http://www.tbiomed.com/content/2/1/29

    This short sentence, “The quick brown fox jumped over the lazy dog” is calculated by Winston Ewert, in this following video at the 10 minute mark, to contain 1000 bits of algorithmic specified complexity, and thus to exceed the Universal Probability Bound (UPB) of 500 bits set by Dr. Dembski

    Proposed Information Metric: Conditional Kolmogorov Complexity – Winston Ewert – video
    http://www.youtube.com/watch?v=fm3mm3ofAYU

    Here are the slides of preceding video with the calculation of the information content of the preceding sentence on page 14
    http://www.blythinstitute.org/.....t_info.pdf

    Moreover, for you to claim that ‘you have not proven Darwinism absolutely mathematically impossible therefore Darwinism must be true’ is an absolutely horrible scientific argument for you, and other Darwinists, to constantly make:

    Darwinism Not Proved Absolutely Impossible Therefore It Must Be True – Plantinga – video
    http://www.metacafe.com/watch/10285716/

    Of related interest: Darwinists blatantly ignore empirical realities in order to try to make their mathematical fantasies in population genetics fit with reality in any conceivable way (i.e. rough matches of pop. gen. math to empirics, no matter how stretched the math is, count as stunning confirmation of evolution for a Darwinist):

    Lynn Margulis Criticizes Neo-Darwinism in Discover Magazine (Updated) – Casey Luskin April 12, 2011
    Excerpt: Population geneticist Richard Lewontin gave a talk here at UMass Amherst about six years ago, and he mathemetized all of it–changes in the population, random mutation, sexual selection, cost and benefit. At the end of his talk he said, “You know, we’ve tried to test these ideas in the field and the lab, and there are really no measurements that match the quantities I’ve told you about.” This just appalled me. So I said, “Richard Lewontin, you are a great lecturer to have the courage to say it’s gotten you nowhere. But then why do you continue to do this work?” And he looked around and said, “It’s the only thing I know how to do, and if I don’t do it I won’t get grant money.” –
    Lynn Margulis – biologist
    per ENV

    Thou Shalt Not Put Evolutionary Theory to a Test – Douglas Axe – July 18, 2012
    Excerpt: “For example, McBride criticizes me for not mentioning genetic drift in my discussion of human origins, apparently without realizing that the result of Durrett and Schmidt rules drift out. Each and every specific genetic change needed to produce humans from apes would have to have conferred a significant selective advantage in order for humans to have appeared in the available time (i.e. the mutations cannot be ‘neutral’). Any aspect of the transition that requires two or more mutations to act in combination in order to increase fitness would take way too long (greater than 100 million years).
    My challenge to McBride, and everyone else who believes the evolutionary story of human origins, is not to provide the list of mutations that did the trick, but rather a list of mutations that can do it. Otherwise they’re in the position of insisting that something is a scientific fact without having the faintest idea how it even could be.” Doug Axe PhD.
    http://www.evolutionnews.org/2.....62351.html

    Michael Behe – Observed 1 in 10^20 Edge of Evolution – video – Lecture delivered in April 2015 at Colorado School of Mines
    25:56 minute quote – “This is not an argument anymore that Darwinism cannot make complex functional systems; it is an observation that it does not.”
    27:50 minute mark: no known, or unknown, evolutionary process helped.
    https://www.youtube.com/watch?v=9svV8wNUqvA

  414. 414
    Box says:

    ThickPython: “Do you understand that these de novo proteins have been switched on by (usually) a single point mutation?”

    Cornelius Hunter: No, I didn’t know that. Can you elaborate? What makes you think a single mutation supplies all the regulation?

    ThickPython here seems to labor under the belief that gene regulation consists of a promoter only. If so, I find this typical for naturalists, who, as I have argued before (see #305), simply assume the unity of an organism.
    Why would the dynamic equilibrium of an organism — which is unexplainable from a naturalistic perspective — not be disturbed by an unregulated de novo protein? This constitutes yet another chicken-egg problem. Regulation has to be already in place otherwise a novel protein causes dis-balance and is detrimental.

  415. 415
    bornagain says:

    As to your data base being flawed Python, I cannot comment on your current data base at this time, but I do know for a fact that a lot of Darwinian bias is hidden in how the overall genetic data is gathered and assembled

    Pattern pluralism and the Tree of Life hypothesis – 2006
    Excerpt: Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true.
    http://www.pnas.org/content/104/7/2043.abstract

    “The computer programs that analyze the sequence similarities, or differences, are programmed in advance to generate a tree-like pattern. In other words, the assumption of a common ancestor is built into the way in which the analysis is performed. So there is no way you would get anything other than the conclusion,,, It’s a question begging assumption.”
    Stephen Meyer – on the Cambrian Explosion – podcast (15:25 minute mark)
    http://intelligentdesign.podom.....3_15-07_00

    Contradictory Trees: Evolution Goes 0 For 1,070 – Whif
    Excerpt: One of evolution’s trade secrets is its prefiltering of data to make it look good, but now evolutionists are resorting to postfiltering of the data as well.,,,
    Prefiltering is often thought of merely as cleaning up the data. But prefiltering is more than that, for built-in to the prefiltering steps is the theory of evolution. Prefiltering massages the data to favor the theory. The data are, as philosophers explain, theory-laden.
    But even prefiltering cannot always help the theory.,,,
    http://darwins-god.blogspot.co.....oes-0.html

    Richard Dawkins: How Could Anyone “Possibly Doubt the Fact of Evolution” – Cornelius Hunter – February 27, 2014
    Excerpt: there is “no known mechanism or function that would account for this level of conservation at the observed evolutionary distances.”,,,
    the many examples of nearly identical molecular sequences of totally unrelated animals are “astonishing.”,,,
    “data are routinely filtered in order to satisfy stringent criteria so as to eliminate the possibility of incongruence.”,,,
    he has not found “a single example that would support the traditional tree.” It is, another evolutionist admitted, “a very serious incongruence.”
    “the more molecular data is analysed, the more difficult it is to interpret straightforwardly the evolutionary histories of those molecules.”
    And yet in public presentations of their theory, evolutionists present a very different story. As Dawkins explained, gene comparisons “fall in a perfect hierarchy, a perfect family tree.” This statement is so false it isn’t even wrong—it is absurd. And then Dawkins chastises anyone who “could possibly doubt the fact of evolution.” Unfortunately this sentiment is typical. Evolutionists have no credibility.
    http://darwins-god.blogspot.co.....nyone.html

    Darwin’s Tree of Life is a Tangled Bramble Bush – May 15, 2013
    Excerpt: ,,, One whole subsection in the paper is titled, “All gene trees differ from species phylogeny.” Another is titled, “Standard practices do not reduce incongruence.” A third, “Standard practices can mislead.” One of their major findings was “extensive conflict in certain internodes.”
    The authors not only advised throwing out some standard practices of tree-building, but (amazingly) proposed evolutionists throw out the “uninformative” conflicting data and only use data that seems to support the Darwinian tree: “the subset of genes with strong phylogenetic signal is more informative than the full set of genes, suggesting that phylogenomic analyses using conditional combination approaches, rather than approaches based on total evidence, may be more powerful.”,,,
    ,,,tossing out “uninformative” data sets and only using data that appear to support their foreordained conclusion. Were you told this in biology class? Did your textbook mention this?
    http://crev.info/2013/05/darwi.....mble-bush/

    “there is a great deal of preferential and selective treatment of the data being analyzed. In many cases, only the most promising data such as gene-rich sequences that exist in both species (homologs) is utilized from a much larger data pool. This pre-selected data is often further subjected to more filtering before being analyzed and discussed. Non-alignable regions and large gaps in DNA sequence alignments are also typically omitted, thus increasing the levels of reported similarity.”
    Jeffrey Tomkins

    Is the same flawed method true for the data base you are currently using Python? I don’t know. That is why I hope Peer can come clear this up a bit more with a post on the subject.

    Of note: Tomkins probably ignores you because you do come off as a Darwinian troll in your interactions with people who disagree with you rather than as a serious scholar.

    Like I said, publish your results in Nature and you will turn far more heads than Dr. Torley’s head (who was biased towards favoring your result anyway)

  416. 416
    ThickPython says:

    @Peer, #357:

    “Wrong in what, snake? If someone is wrong, it is the Chimp Genome Consortium, they omitted 8% of the sequence and did not provide a reason. You may have found the reason, so let them know!”

    Glad you asked, Peer. Yes, I may have found the reason – I sought clarification from them last year but didn’t get a response. The first thing is that this sentence that everyone is making such a fuss about merely introduces the section on nucleotide divergence. This sentence is not a “result” as such, it is saying that the results below it are based on 2.4Gb of sequence. Why only 2.4Gb of sequence? For much of their analysis (especially the chromosome by chromosome analysis), they needed to be sure that they are comparing orthologous sequence, rather than just homologous sequence (see #347). At the time, only 2.4Gb of sequence could be accurately anchored to the human genome:

    At this point scaffolds spanning a total of 2.85 Gb were anchored to the human genome sequence (excluding those in the _random bins). All scaffolds that were completely overlapped by another scaffold based on the human position were then removed. Also removed were the smaller of two neighboring contigs when there was an overlap of 60% (based on human) between neighboring scaffolds. The total anchored sequence after these steps dropped to 2.74 Gb (2.41 Gb of actual contig length), or 88% of the total chimpanzee sequence.

  417. 417
    Cornelius Hunter says:

    Box (414):

    “ThickPython here seems to labor under the belief that gene regulation consists of a promoter only.”

    And then he says I’m the one misrepresenting the science. Amazing. My next question was going to be where the sequence came from in the first place, but on second thought …

  418. 418
    Vy says:

    Tomkins probably ignores you because you do come off as a Darwinian troll in your interactions with people who disagree with you rather than as a serious scholar.

    Yup, everyone he’s claimed to seek “clarification” from has left him hanging.

  419. 419
    ThickPython says:

    @Cornelius:

    No, I didn’t know that. Can you elaborate?

    Sure. Here are two examples from the supplementary material that are representative of the majority:

    ENSG00000206113 – a point mutation changed “ATA” into “ATG” which is a start codon.
    ENSG00000232330 – a point mutation changed “TGA” (which is a stop codon) into “CGA”.

    There are also a handful of examples where indels have caused a frame shift and allowed the translation to continue through what otherwise would have been a premature stop codon.

    What makes you think a single mutation supplies all the regulation?

    I don’t recall saying that it did, at least not in the 6 million years that you are implying here. Whatever regulation is (or isn’t!) there was 98%-ish there already anyway.

  420. 420
    ThickPython says:

    @BornAgain:

    Pattern pluralism and the Tree of Life hypothesis – 2006

    Yes, and one of the only two keywords against that paper is “lateral gene transfer”. See post #331 and try to appreciate some of the nuance in the explanation.

    The computer programs that analyze the sequence similarities, or differences, are programmed in advance to generate a tree-like pattern.

    Yes.

    In other words, the assumption of a common ancestor is built in …

    No. Just building any old tree from any old data does not make common descent true. What makes common descent true (for me at least – I’m sure fossils do it for others) is the fact that trees overlap consistently, and, particularly in the case of functionally equivalent sequences, the only plausible explanation for this is common descent. The mechanisms surrounding why they should overlap (mutation and fixation – descent with modification) are supported empirically.

    Non-alignable regions and large gaps in DNA sequence alignments are also typically omitted, thus increasing the levels of reported similarity.

    Hilarious. You’ve just taken a quote from a paper that has effectively been withdrawn. The result of that paper might have supported the quote, but since the result is wrong, that support disappears. If you’d like to discuss any of the half dozen or so external papers that Tomkins cites to support that position, I’d be happy to engage. Choose one, rather than Gish-galloping as you are prone to do.

    Is the same flawed method true for the data base you are currently using Python?

    No, I don’t pre-filter the data (apart from excluding non-DNA letters – but that’s kinda obvious). I am not filtering for homology, I am not just looking at protein-coding regions, etc.

    Like I said, publish your results in Nature and you will turn far more heads than Dr. Torley’s head (who was biased towards favoring your result anyway)

    Are you suggesting that Nature would be interested in a paper titled “Creationist gets it wrong”?

    Really?

  421. 421
    bornagain says:

    as to:

    “lateral gene transfer”.

    Actually lateral gene transfer is another excellent example of how Darwinists refuse to let their theory be falsified by the data that contradicts their beloved theory

    Common Ancestry: Wikipedia vs. the Data – Casey Luskin – October 5, 2012
    Excerpt: In fact, the largest category of genes here is eukaryotic (cells with a nucleus) genes that have no homolog among prokaryotes (cells without a nucleus) — they don’t even have any possible candidate ancestors to explain where these genes came from, much less a consistent pattern of similarity pointing to one particular ancestor. All this is the opposite of “a direct correlation with common descent.”,,,
    ,,, if two phylogenetic trees aren’t congruent, the problem isn’t that common descent is wrong, but rather the conflict is simply evidence of HGT.,,, Syvanen, (in “Evolutionary Implications of Horizontal Gene Transfer,” Annual Review of Genetics, Vol. 46:339-356 (2012), invokes widespread HGT (Horizontal Gene Transfer), but he’s uncommonly honest about the data and its implications, offering the radical suggestion that “life might indeed have multiple origins.”,,,
    let’s now look within eukaryotes.,,,
    The biochemical organization of the innate immune systems of plants and animals is strikingly similar — but this is a direct non-correlation with common descent. Thus, evolutionary scientists are forced to call them “unexpectedly similar,” postulating that the similarities were “independently derived.” This data is not explained by Darwinian evolution and common descent. It is explained by common design.
    Somehow, something tells me not to expect any corrections over at Wikipedia.
    http://www.evolutionnews.org/2.....65001.html

    The following article goes through a bit of the history of how neo-Darwinists have come to use horizontal gene transfer to explain (away) contradictory patterns in the genetic evidence;

    Evolutionists Celebrated This Prediction But When it Later Failed They Didn’t Care – Cornelius Hunter – April 2012
    Excerpt: Sometimes their use of this lateral or horizontal gene transfer mechanism is a real stretch. And in any case, their story calls for evolution to have created this incredible mechanism which then was so important for adaptation and the supposed subsequent evolution. In other words, evolution created evolution.,,, In some cases evolutionists have no idea, beyond pure speculation, about how it could have happened. As they admit in one paper: “An alternative and more plausible possibility is that the STC gene has been laterally transferred among phylogenetically diverged eukaryotes through an unknown mechanism.”
    http://darwins-god.blogspot.co.....-this.html

    Horizontal Gene Transfer 5-16-2015 by Paul Giem – video
    https://www.youtube.com/watch?v=W6X5sJ62NbE

    Here is a recent article (2015) by Jeffrey Tomkins which shows that the mechanism of Horizontal Gene Transfer does not even begin to explain the dissimilarity in genomes being found:

    Another Horizontal Gene Transfer Fairy Tale by Jeffrey P. Tomkins, Ph.D. – April 6, 2015
    Excerpt: First, the researchers found unique genes in a variety of fruit flies, worms, primates, and humans that had no clear evolutionary ancestry. In other words, each of these genes is specific to a certain type of creature. Scientists have previously termed these “orphan genes”—a unique type of gene that provides a clear anti-evolutionary enigma I have discussed in previous reports.3,4 Some claim these novel orphan sequences evolved suddenly out of non-coding DNA while others, such as the authors of this new report, claim they were derived from HGT.
    The major problem with claiming that these alleged HGT genes are imported or “foreign” (i.e., transferred into the genome from some other creature), is that many of them encode important enzymatic proteins and are key parts of the interconnected gene networks and complex biochemical pathways that are essential to the very life of the organism. The researchers stated, “The majority of these genes are concerned with metabolism.” Clearly, the genes are not foreign at all, but designed to function as key parts of essential biologically complex systems.
    Second, the approach to supposedly identifying many of the foreign genes in animals as microbial in origin was not even based on actual complete gene sequence, but depended upon isolated regions of similarity in the proteins they encode. In mammals, genes are quite complex, and on average only about 10% of the entire gene sequence actually codes for protein, the rest contains a large diversity of regulatory sequences that determine how the gene is to function and its various types of products. In contrast, microbial genes are typically much less complex and lack these intricate and intervening regulatory regions found in animal genes. If the researchers had actually compared the genomic DNA, very little similarity would have been discovered—in other words, they didn’t do their homework correctly. In fact, they admitted their claim that the gene was foreign—or where it originated from—was purely hypothetical, when they stated that “absolute certainty in the assignment of most HGT is unachievable.”
    Third, no mechanism of HGT for any of the hundreds of alleged “foreign genes” they found was either discovered or even suggested. This is due to the fact that the only cases where such gene transfer occurs in nature typically involves a clear host-parasite relationship. Not only that, but the cells of the germline (those that produce sperm and egg) must be specifically targeted or the introgressed genes (those that were incorporated from one species into the genome of another) will not be inherited.
    Unfortunately, evolutionary biologists constantly resort to fictional stories cloaked in technical terminology to escape the straightforward conclusion that the genomes of different creatures were purposefully crafted. Because of their unwavering commitment to evolution, all ideas about these cleverly designed and network-integrated gene sequences being engineered by a Creator are not considered—at least not openly.
    http://www.icr.org/article/ano.....sfer-fairy

    An Enzyme’s Phylogeny Reveals a Striking Case of Convergent Evolution – Jonathan M. – February 11, 2013
    Excerpt: The authors attempt to account for the incongruity by positing that “the STC gene has been laterally transferred among phylogenetically diverged eukaryotes through an unknown mechanism.” They thus attribute the shared genes to horizontal gene transfer (with no offered mechanism), a proposition that has become a catch-all to explain away severe conflicts between evolutionary phylogenies.,,,
    “phylogenetic conflict is common, and frequently the norm rather than the exception”
    (Dávalos et al., 2012).
    Is it possible that the real reason for such striking and widespread phylogenetic discordance is that evolutionary biologists are looking at biology through the wrong lens? Could the reason that there is so much difficulty in correlating organisms to a tree be that no such tree exists?
    http://www.evolutionnews.org/2.....68911.html

    You live in a fantasy land if you think the molecular data fits a tree pattern

    Logged Out – Scientists Can’t Find Darwin’s “Tree of Life” Anywhere in Nature by Casey Luskin – Winter 2013
    Excerpt: the (fossil) record shows that major groups of animals appeared abruptly, without direct evolutionary precursors.
    Because biogeography and fossils have failed to bolster common descent, many evolutionary scientists have turned to molecules—the nucleotide and amino acid sequences of genes and proteins—to establish a phylogenetic tree of life showing the evolutionary relationships between all living organisms.,,,
    Many papers have noted the prevalence of contradictory molecule-based phylogenetic trees. For instance:
    • A 1998 paper in Genome Research observed that “different proteins generate different phylogenetic tree[s].”6
    • A 2009 paper in Trends in Ecology and Evolution acknowledged that “evolutionary trees from different genes often have conflicting branching patterns.”7
    • A 2013 paper in Trends in Genetics reported that “the more we learn about genomes the less tree-like we find their evolutionary history to be.”8
    Perhaps the most candid discussion of the problem came in a 2009 review article in New Scientist titled “Why Darwin Was Wrong about the Tree of Life.”9 The author quoted researcher Eric Bapteste explaining that “the holy grail was to build a tree of life,” but “today that project lies in tatters, torn to pieces by an onslaught of negative evidence.” According to the article, “many biologists now argue that the tree concept is obsolete and needs to be discarded.”,,,
    Syvanen succinctly summarized the problem: “We’ve just annihilated the tree of life. It’s not a tree any more, it’s a different topology entirely. What would Darwin have made of that?” ,,,
    “battles between molecules and morphology are being fought across the entire tree of life,” leaving readers with a stark assessment: “Evolutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology.”10,,,
    A 2012 paper noted that “phylogenetic conflict is common, and [is] frequently the norm rather than the exception,” since “incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species.”12,,,
    http://www.salvomag.com/new/ar.....ed-out.php

    Problem 7: Convergent Evolution Challenges Darwinism and Destroys the Logic Behind Common Ancestry – Casey Luskin February 9, 2015
    Excerpt: Whenever evolutionary biologists are forced to appeal to convergent evolution, it reflects a breakdown in the main assumption, and an inability to fit the data to a treelike pattern. Examples of this abound in the literature,,,,
    Biochemist and Darwin-skeptic Fazale Rana reviewed the technical literature and documented over 100 reported cases of convergent genetic evolution.126 Each case shows an example where biological similarity — even at the genetic level — is not the result of inheritance from a common ancestor. So what does this do to the main assumption of tree-building that biological similarity implies inheritance from a common ancestor? With so many exceptions to the rule, one has to wonder if the rule itself holds merit.,,,
    http://www.evolutionnews.org/2.....91161.html

    Molecular Data Wreak Havoc on the Tree of Life – Casey Luskin – February 7, 2014
    Excerpt: After citing Pauling and Zuckerkandl’s test, Douglas Theobald claims in his “29+ Evidences for Macroevolution” that “well-determined phylogenetic trees inferred from the independent evidence of morphology and molecular sequences match with an extremely high degree of statistical significance.”26
    In reality, however, the technical literature tells a different story. Studies of molecular homologies often fail to confirm evolutionary trees depicting the history of the animal phyla derived from studies of comparative anatomy. Instead, during the 1990s, early into the revolution in molecular genetics, many studies began to show that phylogenetic trees derived from anatomy and those derived from molecules often contradicted each other.
    Probably the most protracted conflict of this type concerns a widely accepted phylogeny for the bilaterian animals. This classification scheme was originally the work of the influential American zoologist Libbie Hyman.27 Hyman’s view, generally known as the “Coelomata” hypothesis, was based on her analysis of anatomical characteristics, mainly germ (or primary tissue) layers, planes of body symmetry, and especially the presence or absence of a central body cavity called the “coelom,” which gives the hypothesis its name. In the Coelomata hypothesis, the bilaterian animals were classified in three groups, the Acoelomata, the Pseudocoelomata, and the Coelomata, each encompassing several different bilaterian animal phyla.28 (See Fig. 6.1a.)
    Then, in the mid-1990s, a very different arrangement of these animal groups was proposed based on the analysis of a molecule present in each (the 18S ribosomal RNA; see Fig. 6.1b). The team of researchers who proposed this arrangement published a groundbreaking paper in Nature with a title that surprised many morphologists: “Evidence for a Clade of Nematodes, Arthropods and Other Moulting Animals.”29 The paper noted the conventional wisdom, based on Hyman’s hypothesis, that arthropods and annelids were closely related because both phyla had segmented body plans.30 But their study of the 18S ribosomal RNA suggested a different grouping, one that placed arthropods close to nematodes within a group of animals that molt, which they called “Ecdysozoa.” This relationship surprised anatomists, since arthropods and nematodes don’t exactly look like kissing cousins. Arthropods (such as trilobites and insects) have coeloms, whereas nematodes (such as the tiny worm Caenorhabditis elegans) do not, leading many evolutionary biologists to believe nematodes were early branching animals only distantly related to arthropods.31 The Nature paper explained how unexpected this grouping of arthropods and nematodes was: “Considering the greatly differing morphologies, embryological features, and life histories of the molting animals, it was initially surprising that the ribosomal RNA tree should group them together.”32
    [and S. Meyer goes on several pages building his case based on several distinct arguments and many references to scientific papers]
    Stephen Meyer – Darwin’s Doubt – (pp. 122-123)
    ,,,Moreover, when complex parts that are shared by different animals aren’t distributed in a treelike pattern, that wreaks havoc on the assumption of homology that’s used to build phylogenetic trees. In other words, this kind of extreme convergent evolution refutes the standard assumption that shared biological similarity (especially complex biological similarity like a brain and nervous system) implies inheritance from a common ancestor.
    If brains and nervous systems evolved multiple times, this undermines the main assumptions used in constructing phylogenetic trees, calling into question the very basis for inferring common ancestry.,,,
    http://www.evolutionnews.org/2.....81981.html

    Moreover, the Tomkin’s quote is still relevant because it is an observation of the method used to assemble the genetic data and was not a result from the flawed computer program that had analyzed the data.

    Moreover, I’ve noticed that you have refused to address any of the meatier matters that make your genetic similarity argument completely null and void, i.e. post 370 onward:
    http://www.uncommondescent.com.....ent-585272

    When you refuse to honestly address the strongest criticisms of your ‘similarity’ theory, it does not reflect well on your integrity in science (or your integrity as a person for that matter, if there even were such a thing as a ‘person’ in reductive materialism).

  422. 422
    Cornelius Hunter says:

    TP (419):

    ======
    Sure. Here are two examples from the supplementary material that are representative of the majority:

    ENSG00000206113 – a point mutation changed “ATA” into “ATG” which is a start codon.
    ENSG00000232330 – a point mutation changed “TGA” (which is a stop codon) into “CGA”.

    There are also a handful of examples where indels have caused a frame shift and allowed the translation to continue through what otherwise would have been a premature stop codon. …

    I don’t recall saying that it did, at least not in the 6 million years that you are implying here. Whatever regulation is (or isn’t!) there was 98%-ish there already anyway.
    ======

    “Whatever regulation is”. So you are clueless, have no idea what you are talking about, and blaming me for misrepresenting the science. Should I laugh or cry? This OP is, frankly, a bizarre mixture of groundless accusations and scientific ignorance. This is yet another good example of the hypocrisy of evolution.

  423. 423
    ThickPython says:

    @BornAgain:

    Moreover, you certainly did NOT use the term ‘mathematically impossible’ in a scientifically correct way.

    If I may quote my own paper:

    Put more simply, a 200 base slice that has – on average – 124 identical nucleotides cannot be split into two 100 base slices that each have – on average – only 28 identical nucleotides.

    That’s mathematically impossible. This has nothing to do with probability.

  424. 424
    ThickPython says:

    @Cornelius:

    “Whatever regulation is”. So you are clueless, have no idea what you are talking about ..

    Wow. You had the choice between:

    A) “Regulation? What’s that? Never heard of it before! But whatever it is …”

    and:

    B) “There may or may not be gene regulation mechanisms in place for these genes, but …”

    And you chose “A”. Really?

    I’m struggling to remember why I previously thought of you with some regard.

  425. 425
    bornagain says:

    Well, I was looking for something to disagree with. But I agree with your specific criticism.

    Sorry, I misunderstood your argument.

  426. 426
    ThickPython says:

    @BornAgain:

    When you refuse to honestly address the strongest criticisms of your ‘similarity’ theory, it does not reflect well on your integrity in science (or your integrity as a person for that matter, if there even were such a thing as a ‘person’ in reductive materialism).

    The posting of a ridiculous number of links and/or excerpts does not constitute an argument. I tend to skip a lot of your posts because you can’t seem to put your argument succinctly, and you rely almost entirely on the words of others. And if it wasn’t Cornelius’ name under your post #421 I doubt I would have bothered looking at this one either.

    Moreover, the Tomkin’s quote is still relevant because it is an observation of the method used to assemble the genetic data and was not a result from the flawed computer program that had analyzed the data.

    His only valid criticism of the genome assembly is that the original version of it was mapped onto the human genome. Since we both used a “sequence slice” method, then the effect this assembly method had on my results was effectively zero.

    And besides, I have been told recently that the latest chimpanzee assembly is a completely de novo assembly anyway. If anyone can verify this, please point me to a link.

    His claims about other researchers filtering data in order to underhandedly boost their results are false. I repeat my offer to you to choose one of those supporting papers and we can discuss it.

  427. 427
    Cornelius Hunter says:

    TP (424):

    You accused me of misrepresenting the science (quote: “What’s amazing is that you’re still defending yourself after you’ve clearly misrepresented the paper.”) The basis of your reasoning was the claim that a single point mutation can turn a non coding sequence into a de novo protein. You then confirmed that, while making accusations of misrepresenting science, you have no idea what you are actually talking about with the response that “Whatever regulation is (or isn’t!) there was 98%-ish there already anyway.”

    Tell us this, why do you think that “98%-ish” of the protein’s regulation was there already?

  428. 428
    ThickPython says:

    @BornAgain:

    So ‘mathematically impossible’ has nothing whatsoever to do with probability?

    In the context of my paper, that’s correct. The probability of getting these results – where 200bp slices have 62% identity and 100 bp slices have 24% identity – is exactly zero. It’s not one chance in 2 ^ 500. It’s zero. It’s mathematically impossible.

  429. 429
    bornagain says:

    You do realize that Dr. Hunter has a PhD in biophysics, whereas you really do not have a clue what you are talking about in molecular biology compared to him? Or did that escape your notice.

  430. 430
    Mung says:

    ThickPython, if you’re going to venture out into the public arena, you might consider growing a thicker skin.

    Have my posts confused you? The implication that you cherry-picked your data not plain enough? I’m sorry. Let me say it straight out. You cherry-picked your data.

    Your method? I’ve been asking you to post it and I’m still waiting. How was it that you came to target Tomkins, of all the people who used BLAST during the period in which it contained the bug?

    Counter-apologetics. Is that a new science? What’s it’s method?

    I just loved the article on Josephus. There were a lot of people named Jesus in the first century. Therefore the reference to Jesus, “who was called Christ” is a Christian interpolation. Simply brilliant.

  431. 431
    bornagain says:

    Python, like I said before, don’t read them. I don’t care. You are not the first dogmatic atheist to ignore the crushing evidence against your position and you certainly won’t be the last. I post the links for people who care about the truth, not for dogmatic atheists like yourself who refuse to ever honestly follow the evidence where it leads and even blatantly lie about evidence in order to protect their atheism.

    In fact, you are a prime example of what is wrong with atheistic thinking.

    i.e. “Shutting down part of the brain that’s responsible for problem solving” causes atheism.

    Shutting down part of brain changes views on God, immigrants: study – October 14, 2015
    Excerpt: Temporarily shutting down part of the brain that’s responsible for problem solving can suppress your religious views and prejudices toward immigrants, a new study has found.
    Researchers out of the University of York, in England, and the University of California, Los Angeles, used magnetic energy to safely and temporarily shut down specific regions of the brain of some study participants.
    When the posterior medial frontal cortex — a part of the brain located near the surface and roughly a few inches up from the forehead — was shut down, participants reported a decrease in their religious convictions and were more positive toward new immigrants critical of their country.
    http://www.ctvnews.ca/health/s.....-1.2609612

  432. 432
    Mung says:

    ThickPython:

    The probability of getting these results – where 200bp slices have 62% identity and 100 bp slices have 24% identity – is exactly zero.

    Exactly zero. Nice. Must be those Counter-apologetics probabilities that you’re using. Do they use zero in the numerator or zero in the denominator?

  433. 433
    Andre says:

    I must admit listening to Thickpython he is making a pretty strong case for ID … dormant proteins being switched on and off just like that. So these proteins have never really evolved they have always been there and are managed by a regulatory switching system. So there is no such thing as a random mutation.

    Thanks for that Thickpython.

  434. 434
    Cornelius Hunter says:

    Andre (433):

    Exactly. What evolutionists do not consider is the problem of where those coding sequences came from. They have always appealed to natural selection for (somehow) causing active proteins to climb the (rugged and flat) fitness landscape. But with findings such as this we must believe the extant coding sequences are already in place before there is a protein and expression!

  435. 435
    JoeCoder says:

    @Cornelius Hunter and ThickPython

    If it’s only a single indel that activates the whole gene in apes, isn’t it far more likely that the sequence was once protein coding in all three species but a frameshift mutation deactivated it in apes? See my post @394.

  436. 436
    bornagain says:

    Let me help you out TP since you seem to be getting pummeled here.

    OK, all you IDiots who insist on putting the evidential horse before the theoretical cart, you IDiots just don’t understand how evolution theory, or empirical science, works!

    How Darwinian science works – picture
    http://www.discerningtheworld......eHorse.jpg

    There you go TP, that will teach those IDiots from messing with someone as smart as ‘you’ are!

    How dare they question something that ‘you’ have declared to be a fact even though you don’t have any evidence for your claim.

    The nerve of them IDiots!

    After all TP, “YOU” are an elite Darwinist who believes ‘you’ don’t even really exist!

    Who are these IDiots who dare question ‘you’ when there is no ‘you’ to question in the first place? 🙂

    Friggin IDiots!

    Don’t they know illusions can’t be questioned?

    Hope ‘you’ feel better TP now that I put those IDiots in their place.

    “Hawking’s entire argument is built upon theism. He is, as Cornelius Van Til put it, like the child who must climb up onto his father’s lap into order to slap his face.
    Take that part about the “human mind” for example. Under atheism there is no such thing as a mind. There is no such thing as understanding and no such thing as truth. All Hawking is left with is a box, called a skull, which contains a bunch of molecules. Hawking needs God In order to deny Him.”
    – Cornelius Hunter

    Photo – an atheist contemplating his mind
    http://3.bp.blogspot.com/-H-kj.....0/rob4.jpg

    “that “You”, your joys and your sorrows, your memories and your ambitions, your sense of personal identity and free will, are in fact no more than the behaviour of a vast assembly of nerve cells and their associated molecules. As Lewis Carroll’s Alice might have phrased: “You’re nothing but a pack of neurons.” This hypothesis is so alien to the ideas of most people today that it can truly be called astonishing.”
    Francis Crick – “The Astonishing Hypothesis” 1994

    “What you’re doing is simply instantiating a self: the program run by your neurons which you feel is “you.””
    Jerry Coyne
    https://whyevolutionistrue.wordpress.com/2015/04/04/eagleton-on-baggini-on-free-will/

    The Confidence of Jerry Coyne – January 6, 2014
    Excerpt: But then halfway through this peroration, we have as an aside the confession that yes, okay, it’s quite possible given materialist premises that “our sense of self is a neuronal illusion.” At which point the entire edifice suddenly looks terribly wobbly — because who, exactly, is doing all of this forging and shaping and purpose-creating if Jerry Coyne, as I understand him (and I assume he understands himself) quite possibly does not actually exist at all? The theme of his argument is the crucial importance of human agency under eliminative materialism, but if under materialist premises the actual agent is quite possibly a fiction, then who exactly is this I who “reads” and “learns” and “teaches,” and why in the universe’s name should my illusory self believe Coyne’s bold proclamation that his illusory self’s purposes are somehow “real” and worthy of devotion and pursuit? (Let alone that they’re morally significant: But more on that below.) Prometheus cannot be at once unbound and unreal; the human will cannot be simultaneously triumphant and imaginary.
    http://douthat.blogs.nytimes.c.....oyne/?_r=0

  437. 437
    Cornelius Hunter says:

    Joe (435):

    No, I don’t think so. My understanding is that these simply are non coding sequences. If, as you suggest, you had a deactivating mutation, of some sort, to an existing protein then you would still have signs of the usual flanking sequences there.

  438. 438
    ThickPython says:

    @Cornelius:

    Tell us this, why do you think that “98%-ish” of the protein’s regulation was there already?

    I never made the positive claim that there is a regulation mechanism in place for these genes, I’m merely responding to your implicit suggestion that not only must the protein evolve de novo, but a regulation mechanism must evolve de novo as well. What I’m saying is that even if these genes required a regulation mechanism (for which the burden lies with you to show that they do), then the underlying framework for that regulation – be it transcription factor, or some other mechanism – is likely to have 98% of its DNA already in the genome.

  439. 439
    ThickPython says:

    @JoeCoder:

    If it’s only a single indel that activates the whole gene in apes, isn’t it far more likely that the sequence was once protein coding in all three species but a frameshift mutation deactivated it in apes? See my post @394.

    The chosen outgroup in that paper is the orangutan, for which there is only a tiny fraction of our genome that might give an incorrect signal due to ILS. So it’s fairly safe to say that these mutations and indels occurred in the human lineage to switch these genes on, rather than identical mutations and indels in other great ape lineages to switch them off.

    I think your phrase “given the difficulties of protein evolution” implies that you believe these de novo proteins actually perform some function, and I don’t think that has been established.

  440. 440
    ThickPython says:

    @Cornelius, #434:

    They have always appealed to natural selection for (somehow) causing active proteins to climb the (rugged and flat) fitness landscape.

    Are you suggesting that these proteins perform some known function? If so, what are their respective functions?

  441. 441
    ThickPython says:

    @Mung, #432:

    Exactly zero. Nice.

    Yes. Zero. If you believe otherwise, then please provide any set of results that can satisfy those conditions (i.e. 200bp average of 62%, 100bp average of 28%). I’ll put up a million dollars.

    Must be those Counter-apologetics probabilities that you’re using. Do they use zero in the numerator or zero in the denominator?

    Numerator.

    You’re welcome.

  442. 442
    Cornelius Hunter says:

    TP (438):

    Clankkkk. In order to get a protein you need a protein-coding gene which has a variety of upstream and downstream segments around an ORF, not to mention the cellular logic to regulate transcription, etc. That doesn’t happen with a single point mutation as you absurdly claimed. Nor is it “98%-ish” already there in non coding sequences, as you also absurdly claimed. Your “the species must have arisen spontaneously” mandate has led you to absurdity and making all kinds of false accusations.

    “then the underlying framework for that regulation – be it transcription factor, or some other mechanism – is likely to have 98% of its DNA already in the genome.”

    A transcription factor? Amazing. All an evolutionist needs is a transcription factor and wala, you have regulation.

    OK, tell us this, how did those Ape/Orangutan/Human homologous non coding sequences evolve in the first place. Random drift or what?

  443. 443
    ThickPython says:

    @Mung, #430:

    Have my posts confused you? The implication that you cherry-picked your data not plain enough? I’m sorry. Let me say it straight out. You cherry-picked your data.

    Yes, your posts confuse me. And so does this one. On what grounds are you saying I’ve cherry picked data? Have you actually read my paper? I use the same data and the same method as Tomkins in order to replicate his results. Then I demonstrate that BLAST behaves differently if you submit multiple queries at once, rather than one at a time (i.e. “the bug”). It’s pretty straight forward.

    Your method? I’ve been asking you to post it and I’m still waiting.

    There is a link to my paper in the OP. It’s been there since the start.

    How was it that you came to target Tomkins, of all the people who used BLAST during the period in which it contained the bug?

    I first contacted him in March 2014 about an article of his regarding orphan genes. During that conversation he pointed out some of the DNA comparison work he had done. His result was clearly in conflict with the “casual” BLASTing I’d done up to that point (and obviously in conflict with the secular studies) so I thought it was worth trying to figure out why they were so different.

    I just loved the article on Josephus. There were a lot of people named Jesus in the first century. Therefore the reference to Jesus, “who was called Christ” is a Christian interpolation. Simply brilliant.

    Aww man, STOP IT! That hurts my feelings.

  444. 444
    ThickPython says:

    @BornAgain, #429:

    You do realize that Dr. Hunter has a PhD in biophysics, whereas you really do not have a clue what you are talking about in molecular biology compared to him? Or did that escape your notice.

    And Jeff Tomkins has a PhD in Genetics (allegedly!) – does that make him right? Would be an odd move to retract an already perfect paper.

  445. 445
    Andre says:

    Thickpython

    So it’s fairly safe to say that these mutations and indels occurred in the human lineage to switch these genes on, rather than identical mutations and indels in other great ape lineages to switch them off.

    Well what do you know Thickpython is absolutely making the case for ID, now if this is the case as you point out then I have no problem with Common Descent deriving from a single blueprint or source code with a switching system to determine the operating system as it is needed, if you ask me this is seriously hot programming!

    A single source code that can be Linux, Windows, IOS and Android. And to switch it on and off it gets its queues from environmental pressures. Now that is some seriously advanced programming

  446. 446
    ThickPython says:

    @Cornelius, #442:

    A transcription factor? Amazing. All an evolutionist needs is a transcription factor and wala, you have regulation.

    “voila”.

    And what will you say if 500bp upstream and downstream of these genes also shows 98%-ish identity?

    OK, tell us this, how did those Ape/Orangutan/Human homologous non coding sequences evolve in the first place. Random drift or what?

    No idea, and I don’t know why I would be expected to know that. Do you know how they evolved? In any case, it’s not the point. The point is that you intimated in your article that these de novo genes basically evolved out of nothing – “6 billion years would not be enough time” – and that’s clearly not what the paper is about. If you’ve admitted to that error, I must have missed it …

  447. 447
    Cornelius Hunter says:

    TP (446):

    “If you’ve admitted to that error, I must have missed it …”

    Actually you have made a series of false accusations about a two-year old post which describes a research study of human de novo genes. There was no “error” in the post. The error, as you have repeatedly proven, is in your ignorance of genetics. And you prove it once again:

    “The point is that you intimated in your article that these de novo genes basically evolved out of nothing”

    The post said no such thing, except in your imagination. In spite of that, and in spite of it being pointed out to you, you continue with the false accusations. I would have hoped for a retraction, but you won’t even stop the falsehoods, though you are backpedaling by saying the post merely “intimated” what you imagined. So now I’m guilty of “intimating.”

    ” ‘6 billion years would not be enough time’ ”

    It wouldn’t be, not by evolution.

    “No idea, and I don’t know why I would be expected to know that. Do you know how they evolved? In any case, it’s not the point.”

    That is convenient. You have “no idea” because, in fact, this is a problem for evolution. Suddenly you need a noncoding sequence to evolve into a functional ORF with no natural selection to help. It is absurd and, yes, 6 billion years would not be enough time, or trillion, etc. And so the evolutionist looks the other way and says it doesn’t matter.

    “Do you know how they evolved?”

    I know that they could not have evolved, unless you call on the multiverse to bail you out.

  448. 448
    Box says:

    ThickPython,

    Like many people, you seem to have a very abstract (and overly simplistic) view of DNA and gene-expression. How to picture these things? Talbott’s writings helped me a lot:

    Talbott:

    If you arranged the DNA in a human cell linearly, it would extend for nearly two meters. How do you pack all that DNA into a cell nucleus just five or ten millionths of a meter in diameter? According to the usual comparison it’s as if you had to pack 24 miles (40 km) of extremely thin thread into a tennis ball. Moreover, this thread is divided into 46 pieces (individual chromosomes) averaging, in our tennis-ball analogy, over half a mile long. Can it be at all possible not only to pack the chromosomes into the nucleus, but also to keep them from becoming hopelessly entangled?

    Obviously it must be possible, however difficult to conceive — and in fact an endlessly varied packing and unpacking is going on all the time. The first thing to realize is that chromosomes do not consist of DNA only. Their actual substance, an intricately woven structure of DNA, RNA, and protein, is referred to as chromatin. Histone proteins, several of which can bind together in the form of an extremely complex histone core particle, are the single most prominent constituent of this chromatin. Every cell contains numerous such core particles — there are some 30 million in a typical human cell — and the DNA double helix, after wrapping a couple of times around one of them, typically extends for a short stretch and then wraps around another one. The core particle with its DNA is referred to as a nucleosome, and between 75 and 90 percent of our DNA is wrapped up in nucleosomes.

    But that’s just the first level of packing; it accounts for relatively little of the overall condensation of the chromosomes. If you twist a long, double-stranded rope, you will find the rope beginning to coil upon itself, and if you continue to twist, the coils will coil upon themselves, and so on without particular limit, depending on the fineness and length of the rope. Something like this supercoiling happens with the chromosome, mediated in part by the histone core particles. As a result the core particles, and the DNA along with them, become tightly packed almost beyond comprehension, in a dense, three-dimensional geometry that researchers have yet to visualize in any detail. This highly condensed state, characterizing great stretches of every chromosome, contrasts with other, relatively uncondensed stretches known as open chromatin.

    With that background, we can gain our first glimpse of the concerted dynamism in which genes participate. At any one time — and with the details depending on the tissue type and stage of the organism’s development, among other things — some parts of every chromosome are heavily condensed while others are open. Every overall configuration represents a unique balance between constrained and liberated expression of our total complement of 21,000 genes This is because the transcription of genes generally requires an open state; genes in condensed chromatin are largely silenced.

    The supercoiling has another direct, more localized role in gene expression. Think again of twisting a rope: depending on the direction of your twist, the two strands of the helix will either become more tightly wound around each other or will be loosened and unwound. (This is independent of the supercoiling, which occurs in either case.) And if, taking a double-stranded rope in hand, you insert a pencil between the strands and force it in one direction along the rope, you will find the strands winding ever more tightly ahead of the pencil’s motion and unwinding behind.

    Recall, then, that the enzyme (RNA polymerase) responsible for transcribing DNA into RNA must separate the two strands as it moves along a gene sequence. This is much easier if the supercoiling of the chromatin has already loosened the strands — and harder if the strands are tightened. So in this way the variations in supercoiling along the length of a chromosome either encourage or discourage the transcription of particular genes. Moreover, by virtue of its own activity in moving along the DNA and separating the two strands, RNA polymerase (like the pencil) tends to unwind the strands in the chromosomal region behind it, rendering that region, too, more susceptible to gene expression. There are proteins that detect such changes in torsion propagating along chromatin, and they read the changes as “suggestions” about helping to activate nearby genes (Lavelle 2009; Kouzine et al. 2008).

    Picture the situation concretely. Every bodily activity or condition presents its own requirements for gene expression. Whether you are running or sleeping, starving or feasting, getting aroused or calming down, suffering a flesh wound or recovering from pneumonia — in all cases the body and its different cells have specific, almost incomprehensibly complex and changing requirements for differential expression of thousands of genes. And one thing necessary for achieving this expression in all its fine detail is the properly choreographed performance of the chromosomes.

    This performance cannot be captured with an abstract code. Interacting with its surroundings, the chromosome belongs as much to a living activity as any other element in its cellular environment. Maybe instead of summoning the image of a rope, I should have invoked a snake, coiling, curling, and sliding over a landscape that is itself in continual movement.
    (…)
    Nucleosomes will sometimes move — or be moved (the distinction between actor and acted upon is forever obscured in the living cell) — rhythmically back and forth along the DNA, shifting between alternative positions in order to enable multiple transcription passes over a gene. In stem cells a process some have called “histone modification pulsing” results in the continual application and removal of both gene-repressive and gene-activating modifications of nucleosomes. In this way a delicate balance is maintained around genes involved in development and cell differentiation. The genes are kept, so to speak, in a finely poised state of “suspended readiness”, so that when the decision to specialize is finally taken, the repressive modifications can be quickly lifted, leading to rapid gene expression (Gan et al. 2007).

  449. 449
    Box says:

    //follow-up #448//

    More S.L.Talbott:

    — on histones and gene expression:

    The canonical nucleosome core particle is a complex of histone proteins, each of which has a flexible, filamentary “tail”. This tail can be modified through the addition of several different chemical groups — acetyl, methyl, phosphate, ubiquitin, and so on — at any of various locations along its length. A great variety of enzymes can apply and remove these chemical groups, and the groups themselves play a role in attracting a stunning array of gene regulatory proteins that restructure chromatin or otherwise help choreograph the drama of gene expression.

    After a few histone tail modifications were found to be rather distinctly associated with active or repressed genes, the forlorn hope arose that we would discover a precise, combinatorial “histone code”. It would provide a fixed and reliable key enabling us to predict the consequences of any arrangement of modifications (Strahl and Allis 2000).

    But this was to ignore the nearly infinite variety of all those contextual factors that blend their voices in concert with the histone modifications. In the plastic organism, what goes on at the local level is always shaped and guided by a larger, coherent context — a context that surely has meaning, but (as in all natural languages) never an absolutely fixed grammar. And, in fact, while overwhelming evidence for a meaningful, gene-regulatory conversation involving histone modifications has emerged, there is little to suggest a rigid code. Shelley Berger of Philadelphia’s Wistar Institute, noting that a single tail modification “recruits numerous proteins whose regulatory functions are not only activating but also repressing” and that “many of these marks have several, seemingly conflicting roles”, summarized the situation this way:

    Although [histone] modifications were initially thought to be a simple code, a more likely model is of a sophisticated, nuanced chromatin ‘language’ in which different combinations of basic building blocks yield dynamic functional outcomes. (Berger 2007)

    And (leaving aside the jarring reference to building blocks) how could it be otherwise? Each histone tail modification re-shapes the physical and electrical structure of the local chromatin, shifting the pattern of interactions among nucleosome, DNA, and associated protein factors. To picture this situation concretely — as opposed to remaining within the straightjacket of code — is immediately to realize that it cannot be captured in purely digital terms. A sculptor does not try to assess the results of a stroke of the hammer as a choice among the possibilities of a digital logic. Berger envisions histone modifications as participating in “an intricate ‘dance’ of associations”.

    There is much much more. The histones making up a nucleosome core particle can themselves be exchanged for noncanonical, or variant histones, which also have recognizable — but not strictly encoded — relations to gene expression. Histones can even be removed from a core particle altogether, leaving it “incomplete”. And certain energy-expending proteins can slide core particles along the DNA, changing their position. We saw above that a shift of position by as little as two or three base pairs can mark the difference between gene activation or repression, as can changes in the rotational orientation of the DNA on the face of the histone core particle. And finally (to artificially limit our consideration): the tails — no doubt depending at least in part on the various modifications and protein associations mentioned earlier — can thread themselves through the encircling double helix, perhaps either loosening it from the core particle or holding it more firmly in place. But some of those same tails are also thought to establish nucleosome-to-nucleosome contacts, helping to compact a stretch of chromatin and repress gene expression.

    — DNA in knots:

    With so much concerted movement going on — not to mention the coiling and packing and unpacking of chromosomes mentioned earlier — how does the cell keep all those “miles of string in the tennis ball” from getting hopelessly tangled? In this case we at least know some of the players addressing the problem. For example, there are enzymes called “topoisomerases”, whose task is to help manage the spatial organization of chromosomes. Demonstrating a spatial insight and dexterity that might amaze those of us who have struggled to sort out tangled masses of thread, these enzymes manage to make just the right local cuts to the strands in order to relieve strain, allow necessary movement of individual genes or regions of the chromosome and prevent a hopeless mass of knots.

    Some topoisomerases cut just one strand of the double helix, allow it to wind or unwind around the other strand, and then reconnect the severed ends. This alters the supercoiling of the DNA. Other topoisomerases cut both strands, pass a loop of the chromosome through the gap thus created, and then seal the gap again. (Imagine trying this with miles of string crammed into a tennis ball!) I don’t think anyone would claim to have the faintest idea how this is actually managed in a meaningful, overall, contextual sense, although great and fruitful efforts are being made to analyze isolated local forces and “mechanisms”.

  450. 450
    Andre says:

    Box

    Talbott’s paper is poetry…..

    Most of this noncoding DNA was at first dismissed as “junk” — meaningless evolutionary detritus accumulated over the ages. At best it was viewed as a kind of bag of spare parts, borne by cells from one generation to another for possible employment in future genomic innovations. But that’s an awful amount of junk for a cell to have to lug around, duplicate at every cell division, and otherwise manage on a continuing basis.

    I hope Prof Moran has read it……

  451. 451
    Mung says:

    ThickPython:

    The point is that you intimated in your article that these de novo genes basically evolved out of nothing – “6 billion years would not be enough time” – and that’s clearly not what the paper is about.

    I think he was calculating the probability with a zero in the numerator, not that they “evolved out of nothing.”

  452. 452
    Cornelius Hunter says:

    Mung (451):

    Well evolving a protein-coding gene from a non coding sequence is yet another one of those probabilities which is difficult to estimate precisely because it is so extremely unlikely. And note that when evolutionists appeal to things like mobile genetic elements to do the heavy lifting then we are no longer talking about evolution (in spite of what they would like to claim).

  453. 453
    Mung says:

    Dr. Hunter, big fan of your books.

    Anything new in the works that you can share?

  454. 454
    Cornelius Hunter says:

    Thanks Mung. Not a lot to report, though I do have a new website surveying evolution’s predictions and their failures:

    https://sites.google.com/site/darwinspredictions/home

  455. 455
    vjtorley says:

    Dr. Hunter:

    Re your assertion (based on a 2011 paper by Wu et al.) that humans have “60 protein-coding genes in humans that are not in the chimp,” how do you explain the fact that these genes have non-coding counterparts in chimpanzees which are 98% similar? I think that’s a legitimate question.

    Also, why would it take more than 6 billion years to get from 98% to 100%?

    Finally, what do you make of this paper in “Nature”?
    http://www.nature.com/nature/j.....11184.html

    Cheers.

  456. 456
    Cornelius Hunter says:

    VJ:

    “how do you explain the fact that these genes have non-coding counterparts in chimpanzees which are 98% similar? I think that’s a legitimate question.”

    The fact that there are homologous ORFs of these genes in the chimp and ape is an enormous problem for evolution. As for an explanation of this fact, that question is beyond current science. We don’t even have basic data to answer such a question. Of course we can speculate. For instance, genetic regulation spans a wide range of time scales (think strategic to tactical) and associated mechanisms. Perhaps this is an example of regulation on the strategic end of the scale, where an ORF is recruited to be integrated with a gene, when needed. Under that idea non coding DNA has raw materials in the form of ORFs, or exons, parts of exons, etc., that can be recruited if/when needed. Obviously that is highly speculative.

    “Also, why would it take more than 6 billion years to get from 98% to 100%?”

    I never said it would and, unfortunately, this question reveals an ignorance of basic genetics and why the OP is groundless. What I explained was that 6 billion years is insufficient to evolve a protein coding gene from non coding DNA. It doesn’t matter if you have an ORF to begin with.

  457. 457
    Cornelius Hunter says:

    VJ:

    “Finally, what do you make of this paper in “Nature”?
    http://www.nature.com/nature/j…..11184.html”

    Actually this is along the lines of my speculation above. As usual the paper is cast into an evolutionary perspective. For example, the abstract makes this absurd conclusion: “Our work illustrates that evolution exploits seemingly dispensable sequences to generate adaptive functional innovation.” There is no special evidence for evolution or common descent here. They write: “Here we formalize an evolutionary model,” in spite of the fact that what they describe is far from evolutionary theory. They describe a whole bunch of molecular machinery operating on a whole bunch of DNA, with regulation, to construct protein genes in response to environmental challenges. That is not evolution.

  458. 458
    ThickPython says:

    Vincent: “Also, why would it take more than 6 billion years to get from 98% to 100%?”

    Cornelius: I never said it would. […] 6 billion years is insufficient to evolve a protein coding gene from non coding DNA.

    The chimpanzee non-coding DNA is the “98%”. The “98%” is the chimpanzee non-coding DNA. The human protein coding gene is the “100%”. The “100%” is the human protein coding gene.

    Please continue.

  459. 459
    Mung says:

    ThickPython:

    The probability of getting these results – where 200bp slices have 62% identity and 100 bp slices have 24% identity – is exactly zero.

    Who on earth are you alleging got those results?

    p.s. If your goal is “Counter-apologetics” then UD might not be the right place for you.

  460. 460
    bornagain says:

    semi related is the podcast from ENV yesterday:

    podcast – Molecular Data Wreak Havoc on the Tree of Life
    http://www.discovery.org/multi.....e-of-life/
    On this episode of ID the Future, hear about a recent article in the science magazine Nautilus (Evolution, You’re Drunk: DNA studies topple the ladder of complexity) that shows animal phylogenetic trees conflicting sharply with genetic data. As Casey Luskin points out, “When Darwinian theory tells us that crucial and complex features like brains or nervous systems evolved independently — or almost as weirdly, evolved and were repeatedly lost throughout life’s history — maybe, it’s time for the “ghost of teleology” to make an appearance in the form of common design.”

  461. 461
    Box says:

    ThickPython:

    The chimpanzee non-coding DNA is the “98%”. The “98%” is the chimpanzee non-coding DNA. The human protein coding gene is the “100%”. The “100%” is the human protein coding gene.

    Please continue.

    No, you continue.

    Some questions:

    What is the 98% non-coding DNA doing there? How did it get there? If it is subjected to random mutations what are the odds that it will ever get to “100%”?
    If it will get to 100% will there be matching regulation in place? If so, where does it come from? What are the odds?

  462. 462
    bornagain says:

    OT: OK, dumb question, but how did random mutations to DNA build such elaborate overlapping random mutation repair mechanisms to prevent random mutations from happening to DNA in the first place?
    Does such a clear contradiction even make sense any where else in science save for the fantasy land that is Darwinian ‘science’?

    New class of DNA repair enzyme discovered – October 29, 2015
    Excerpt: This year’s Nobel Prize in chemistry was given to three scientists who each focused on one piece of the DNA repair puzzle. Now a new study, reported online Oct. 28 in the journal Nature, reports the discovery of a new class of DNA repair enzyme.
    When the structure of DNA was first discovered, scientists imagined it to be extremely chemically stable, which allowed it to act as a blueprint for passing the basic traits of parents along to their offspring. Although this view has remained prevalent among the public, biologists have since learned that the double helix is in fact a highly reactive molecule that is constantly being damaged and that cells must make unceasing repair efforts to protect the genetic information that it contains.,,,
    “More than 10,000 DNA damage events occur each day in every cell in the human body that must be repaired for DNA to function properly,” said first author Elwood Mullins, a postdoctoral research associate in the Eichman lab.
    The newly discovered DNA repair enzyme is a DNA glycosylase, a family of enzymes discovered by Tomas Lindahl, who received this year’s Nobel prize for recognizing that these enzymes removed damaged DNA bases through a process called base-excision repair. It was the first of about 10 different DNA repair pathways that biologists have identified to date.,,,
    “Our discovery shows that we still have a lot to learn about DNA repair, and that there may be alternative repair pathways yet to be discovered. It certainly shows us that a much broader range of DNA damage can be removed in ways that we didn’t think were possible,” said Eichman
    http://phys.org/news/2015-10-class-dna-enzyme.html

  463. 463
    Box says:

    Bornagain, talking about DNA-repair … did you happen to read about “topoisomerases”; see Talbott quote in bottom section post #499 ?
    Utterly phenomenal isn’t it? 🙂

    // – – – –

    Andre: Talbott’s paper is poetry…..

    Good to hear that you enjoyed it!

  464. 464
    bornagain says:

    Box, yes, (@ 448 & 449), I was going to say something along the lines of ‘poetry’ too, but Andre nailed it before me.

    http://www.uncommondescent.com.....ent-585481

  465. 465
    ThickPython says:

    @Mung:

    Who on earth are you alleging got those results?

    Jeff Tomkins did. Check out the pretty graph in his 2013 paper.

    p.s. If your goal is “Counter-apologetics” then UD might not be the right place for you.

    Fixed.

  466. 466
    Mung says:

    Mung: Who on earth are you alleging got those results?

    ThickPython: Jeff Tomkins did. Check out the pretty graph in his 2013 paper.

    And yet you asserted that the probability of obtaining those results was “exactly zero.” You were obviously wrong.

    Now all I have to do is replicate Tomkin’s results and I win a million bucks. Right?

  467. 467
    ThickPython says:

    @Mung:

    And yet you asserted that the probability of obtaining those results was “exactly zero.” You were obviously wrong.

    Now all I have to do is replicate Tomkin’s results and I win a million bucks. Right?

    You sir, are an imbecile. The reason he got those results was due to the bug in the software. Please try to keep up.

  468. 468
    Peer says:

    @Big Snake…

    What program did you run? NCBI Blast or WU Blast?

    If you used NCBI Blast…that would explain a lot.

  469. 469
    bornagain says:

    Peer, kf has offered to host a guest post by you on this subject.

  470. 470
    ThickPython says:

    @Peer, #468:

    What program did you run? NCBI Blast or WU Blast?

    If you used NCBI Blast…that would explain a lot.

    Yes, it explains EVERYTHING. Jeff Tomkins used NCBI BLAST, so clearly I have to use it to demonstrate the bug in it that gave him his 70% result. Please let me know your thoughts on the choice of software, and I’ll pass them on to Dr Jeffrey P. Tomkins.

  471. 471
    ThickPython says:

    @BornAgain:

    Peer, kf has offered to host a guest post by you on this subject.

    Yes, in line with BornAgain’s post in #380, I would love to see a guest post with “sufficient feedback from Dr Tomkins himself”, and would also love to see Peer’s rebuttal as well. Clearly I’ve sought feedback from Tomkins but the silence is deafening.

    What I’d like to see an explanation of:

    1. Why Tomkins chose the “ungapped” parameter, and then how he includes those results in his calculation. Specifically he needs to address the example where an indel is right in the middle of two sequences, and why he includes this as a 50% result.

    2. What result he obtains when he corrects for #1.

    3. Why he continued to use “ungapped” in his most recent paper, when my paper directly pointed out this flaw to him 12 months ago.

    4. Why Tomkins included ALL matches for a given query in his nucmer analysis rather than just taking the best match.

    5. What result he obtains when he corrects for #4.

    6. Why his previous work took only the best match into his calculation, and why he has confirmed in personal correspondence that this is the correct practice.

    7. What feedback he gave to the editor (Andrew Snelling) that caused him to reject my paper for publication.

    I don’t think I’m the only one that would like answers to these questions.

  472. 472
    Peer says:

    @ big snake ,

    that was not my question.

    my question was: what did you run…WU or NCBI….?

    I would like to see both results.

  473. 473
    ThickPython says:

    @Peer, #472:

    my question was: what did you run…WU or NCBI….?

    And I answered it: “Jeff Tomkins used NCBI BLAST, so clearly I have to use it …”.

    I would like to see both results.

    I’m sure you would, but that’s no small amount of work just to satisfy your curiosity. I’ve already put two analyses out there for scrutiny (BLAST and nucmer) and I’m not aware of any criticisms of them in this thread that have held up (please give post #’s, if you think otherwise!).

    If you can get Tomkins to address the seven points above, I will gladly do a WU-BLAST comparison.

  474. 474
    vjtorley says:

    Dr. Hunter,

    When I asked, “How do you explain the fact that these genes have non-coding counterparts in chimpanzees which are 98% similar?”, you replied, “The fact that there are homologous ORFs of these genes in the chimp and ape is an enormous problem for evolution.”

    I have to say I’m a little surprised by this leap of logic. If humans had genes for which there was nothing homologous in the DNA of chimpanzees or other apes, or for that matter other organisms, that would indeed be an “enormous problem for evolution.” But when we find homologs which are 98% similar, obviously the problem is considerably reduced.

    You write that ORFs need to be regulated and recruited, but in that case, Thick Python’s argument that “the underlying framework for that regulation – be it transcription factor, or some other mechanism – is likely to have 98% of its DNA already in the genome” would still apply.

    I am not arguing that orphan genes weren’t designed. I honestly don’t know whether they were or not. But I’d like to ask you a question. Which do you think is the greater leap, in evolutionary terms: (i) the leap from a random string of bases to a non-coding DNA string which is 98% similar to a so-called “de novo” gene, or (ii) the leap from this 98%-similar homolog to a gene which codes for a protein? If the latter, why?

    If you believe that the gene was designed, then why not the 98%-similar homolog? And if you believe that the non-coding DNA wasn’t designed, then doesn’t it seem a bit odd to say that design was required to tweak the last 2%?

    So far, the most sensible suggestion I’ve seen coming from Intelligent Design advocates is one by gpuccio at comment #55 above:

    In the case on new protein coding genes which are protein coding only in humans, but which have large homologies with non coding sequences in primates, that is exactly my idea of one modality about how new protein coding genes may come into existence: by the gradual engineering of non coding sequences into a coding sequence. Some examples have been described, and transposons could have an important role in the process. Which can only be interpreted, obviously, as an intelligent design process.

    Would this be your position?

  475. 475
    bornagain says:

    Dr. Torley, this article that Dr. Nelson posted today may interest you

    “Evolution, in the sense of common descent, is not a theory of similarity. Linnaeus, Cuvier, and Agassiz knew all about similarity, yet they denied common descent. Evolution is a theory of transformation.”,,,
    Paul Nelson – What Evolution Is, and What It’s Not – October 30, 2015
    http://www.evolutionnews.org/2.....00501.html

    Common Descent? – Some Insurmountable Problems for gradualism/transformation
    https://docs.google.com/document/d/1BBU4GVEPIxDDSre6YLqU5zbaXVdSk4RRMD8F7GU3DPM/edit

  476. 476
    Cornelius Hunter says:

    VJ:

    ===========
    When I asked, “How do you explain the fact that these genes have non-coding counterparts in chimpanzees which are 98% similar?”, you replied, “The fact that there are homologous ORFs of these genes in the chimp and ape is an enormous problem for evolution.”

    I have to say I’m a little surprised by this leap of logic. If humans had genes for which there was nothing homologous in the DNA of chimpanzees or other apes, or for that matter other organisms, that would indeed be an “enormous problem for evolution.” But when we find homologs which are 98% similar, obviously the problem is considerably reduced.
    ===========

    One can point to scientific problems, but they never matter to evolutionists. The difficulty here is that evolution assumes the “just-add-water” view of nature. This view lacks any serious reckoning with science.

    The fact that there are homologous ORFs of these human genes in the chimp and ape cannot be scientifically explained by evolution (I’m discounting the multiverse and other just-so stories, which I realize are inevitable). You asked me to explain their existence and I at least had reasonable speculation. I could just as easily ask an evolutionist to explain their existence, and there would be nothing but just-so stories. How do you explain the origin of a non coding DNA that, in the context of a protein coding gene, codes for a functional protein? Evolutionists are unable to explain protein evolution, period. Of course their attempts always rely on natural selection somehow to guide a primitive protein-coding gene under expression. These explanations don’t work but now, in the case of these non coding sequences, you don’t even have selection to hide behind. It is absurd to think drift produced such sequences by chance. Yet you find the evolutionary view compelling.

    ===========
    You write that ORFs need to be regulated and recruited, but in that case, Thick Python’s argument that “the underlying framework for that regulation – be it transcription factor, or some other mechanism – is likely to have 98% of its DNA already in the genome” would still apply.
    ===========

    Arg. The “just-add-water” view again. Where to begin? First, transcription factors simply do not magically regulate ORFs. They are one player of many that regulate protein-coding genes, and you have to have at least some of those other players. Sorry but “just-add-water” doesn’t work. Second, addressing your “some other mechanism” catch-all, yes, if we add the right flanking sequences, create a protein-coding gene, create the regulation logic, then yes, it works. This is *astronomically* unlikely under evolution, and even evolutionists resort to their Aristotelianism as we saw in that paper you asked me about above.

    ===========
    I’d like to ask you a question. Which do you think is the greater leap, in evolutionary terms: (i) the leap from a random string of bases to a non-coding DNA string which is 98% similar to a so-called “de novo” gene, or (ii) the leap from this 98%-similar homolog to a gene which codes for a protein? If the latter, why?
    ===========

    Again your questions reveal the evolutionary view. The chimp and ape non-coding DNA is not 98% similar to the human protein-coding gene, and there was no “98%-similar homolog” to a protein-coding gene. You are envisioning a “just-add-water” kind of world that doesn’t exist.

    ===========
    If you believe that the gene was designed, then why not the 98%-similar homolog? And if you believe that the non-coding DNA wasn’t designed, then doesn’t it seem a bit odd to say that design was required to tweak the last 2%?
    ===========

    This is a non sequitur. Since I don’t recognize this I’ll pass.

    ===========
    So far, the most sensible suggestion I’ve seen coming from Intelligent Design advocates is one by gpuccio at comment #55 above: … Would this be your position?
    ===========

    This is strange since you asked me for an explanation above and I provided one. It was speculative but was, in fact, along the lines of the paper which you asked about. I guess that didn’t take.

  477. 477
    ThickPython says:

    @Cornelius, #476:

    The chimp and ape non-coding DNA is not 98% similar to the human protein-coding gene

    Are you sure about that?

    Also, I notice you haven’t yet responded to post #458, which is the topic of the OP.

  478. 478
    NickMatzke_UD says:

    Cornelius Hunter writes,

    The chimp and ape non-coding DNA is not 98% similar to the human protein-coding gene

    It sounds like it is, or something close to that. What makes these interpretations so implausible:

    1. The ORF is just a junk ORF, and actually isn’t doing much of anything?

    2. The ORF has some weak function — say, interfering with some other pathway, or competing with the expression of something else. This function might not require a tight protein fold, a highly specific binding site, or tight regulation.

    3. Differential tissue expression of either #1 or #2 is just a by-product of some other regulational and/or structural feature nearby — if this portion of the chromosome is unwound in order to express something else, that could up-regulate the accidental expression of a #1 or #2. This would then be interpreted by creationists and other sorts of naive functionalists as evidence of function.

    Or do you really think that because “classic” gene and proteins tend to be highly specific and effectively impossible to originate by all-at-once chance assembly , all ORFs of any short must be, even those that are short and originated recently? That seems to be your assumption — you should defend it rather than just implicitly assume it.

  479. 479
    Andre says:

    Nick

    We don’t assume it and since you make the claim that unguided processes can do this please show us.

  480. 480
    Cornelius Hunter says:

    Nick:

    I never said such interpretations are implausible. In fact my original point was *if* these proteins are like most proteins, then blah, blah, blah.

    As for the Vidal paper,

    http://www.nature.com/nature/j.....11184.html

    it argues that de novo protein evolution is more common than thought because, for one thing, they find expression of some non genic sequences, and such expression is under some sort of differential regulation under stress. Hence selection kicks in and you have protein evolution. Of course we know protein fitness landscapes are flat and rugged, not smooth and sloped, so this idea is problematic right off the bat. But let’s say it turns out to be true. Then what you have are elaborate cellular processes involving all kinds of molecular machinery (including a whole bunch of proteins) to regulate, transcribe, and translate the sequence, as a necessary prerequisite, before you ever get any progress going in protein evolution.

    So now in addition to the enormous landscape problem, you are also circular, requiring an army of proteins in order to achieve protein evolution. This is not evolution, at least not by any normal understanding of the theory.

    The evolutionary explanation for this is that such de novo gene “evolution” is only one of several methods evolution has constructed for evolving proteins. There are others, including the original method that constructed the first proteins.

    This saves the theory from circularity, but otherwise is a problem because you have evolution constructing evolution in non trivial ways. This isn’t merely, “oh, the organism got bigger so there there are more places where it can mutate.” This is evolution constructing entirely new, novel, incredibly intricate, complex means of performing the same task–protein evolution. (Meanwhile we still have the landscape problem that we set aside earlier).

    So the theory takes on enormous levels of complexity in order to fit the evidence. That’s not the way science is supposed to work, and it is not the sign of a true theory.

  481. 481
    kairosfocus says:

    Folks: I repeat, I am willing to host guest post(s). I may be contacted through the web page linked from my handle. KF

  482. 482
    kairosfocus says:

    Dr Hunter, could you discuss protein fitness landscapes a bit (flat + rough vs smooth + rising), with onward links to more details and perhaps a paper or two? Appreciated. I already know that functionally specific, complex organisation and/or associated information (FSCO/I for short) will naturally require tight constraints on parts and how they are arranged and coupled, leading to isolated islands of function (IOF) in flat seas of non-function. Also that if an IOF is rugged and has plateaux, the intervening deep valleys will tend to lock up variation in a local peak or zone, just on the logic. KF

  483. 483
    Larry Moran says:

    S.L. Talbot says,

    Most of this noncoding DNA was at first dismissed as “junk” — meaningless evolutionary detritus accumulated over the ages. At best it was viewed as a kind of bag of spare parts, borne by cells from one generation to another for possible employment in future genomic innovations. But that’s an awful amount of junk for a cell to have to lug around, duplicate at every cell division, and otherwise manage on a continuing basis.

    Andre says @450 that this paper is poetry and he hopes I’ve read it.

    I read the essay. Let’s look a the “poetry” that’s quoted and take the opportunity to address a problem I’ve been discussing recently on ID blogs.

    I maintain that most ID proponents, especially IDiots, don’t understand enough about modern evolution to have an informed opinion. They usually defend against this charge by insisting that they know all they need to know. That “knowledge” is usually restricted to some version of natural selection that may or may not be accurate.

    Let’s do a test. Knowledgeable evolutionary biologists have a perfectly good explanation for why some species would carry around a genome full of junk even though it might be costly to duplicate and maintain all this extra DNA. The explanation is perfectly consistent with everything we know about evolution.

    I claim that the average ID proponent cannot describe the standard explanations for junk DNA, and the evidence supporting junk DNA, in spite of the fact that they are more than willing to declare that “Darwinists” are wrong about junk DNA.

    Here’s good opportunity for Andre to prove that I’m wrong.

    Write a short, one paragraph, summary of what knowledgeable evolutionary biologists say about the idea that cells can “lug around” lots of junk DNA.

    I’d really appreciate it if Andre or some of the rest of you could honestly try to prove that I am wrong.

    Not holding my breath …

  484. 484
    Box says:

    Larry Moran: Here’s good opportunity for Andre to prove that I’m wrong.

    Write a short, one paragraph, summary of what knowledgeable evolutionary biologists say about the idea that cells can “lug around” lots of junk DNA.

    What Larry Moran is asking here reminds me of the (fruitless) forum discussions I had with Islamists years ago. They have a persistent tendency to test your knowledge of the Quran and a few other horrendous books. As if those details matter ….

  485. 485
    Mung says:

    I would take Prof. Moran up on his offer, if only because I think for any sort of fruitful discussion there needs to be some level of respect for each other. It may be irksome to think we would need to show ourselves worthy, but what do we have to lose?

    For references I’d probably turn to T. Ryan Gregory’s The Evolution of the Genome and The Origins of Genome Architecture by Michael Lynch, which, for example, has a section on page 34 titled “The Metabolic Cost of DNA.”

    But I’m tied up right now dealing with code denialism. To me, code denial is worse than just plain ignorance.

  486. 486
    Virgil Cain says:

    Larry Moran:

    Knowledgeable evolutionary biologists have a perfectly good explanation for why some species would carry around a genome full of junk even though it might be costly to duplicate and maintain all this extra DNA. The explanation is perfectly consistent with everything we know about evolution.

    1- Under the framework of drift and NS junk DNA can be explained away

    2- Unfortunately drift and selection cannot explain the species Larry refers to so point 1 is moot.

  487. 487
    NickMatzke_UD says:

    Knowledgeable evolutionary biologists have a perfectly good explanation for why some species would carry around a genome full of junk even though it might be costly to duplicate and maintain all this extra DNA.

    It’s debatable whether it’s costly, at least for large multicellular organisms. E.g.:

    “The energy invested in DNA synthesis is trivial compared with the metabolic energy required for the movement of muscles; thus there was little selective pressure to eliminate nonfunctional DNA in vertebrates.” Lodish et al., Molecular Biology of Cell, http://www.ncbi.nlm.nih.gov/books/NBK21571/

  488. 488
    NickMatzke_UD says:

    Nick:

    I never said such interpretations are implausible. In fact my original point was *if* these proteins are like most proteins, then blah, blah, blah.

    Well then, that’s game over for most ID/creationist arguments about ORFs/ORFans, because those arguments typically blindly assume the ORFs have all of the properties of standard proteins/genes.

    As for the Vidal paper,

    http://www.nature.com/nature/j…..11184.html

    it argues that de novo protein evolution is more common than thought because, for one thing, they find expression of some non genic sequences, and such expression is under some sort of differential regulation under stress. Hence selection kicks in and you have protein evolution. Of course we know protein fitness landscapes are flat and rugged, not smooth and sloped, so this idea is problematic right off the bat. But let’s say it turns out to be true. Then what you have are elaborate cellular processes involving all kinds of molecular machinery (including a whole bunch of proteins) to regulate, transcribe, and translate the sequence, as a necessary prerequisite, before you ever get any progress going in protein evolution.

    So now in addition to the enormous landscape problem, you are also circular, requiring an army of proteins in order to achieve protein evolution. This is not evolution, at least not by any normal understanding of the theory.

    The evolutionary explanation for this is that such de novo gene “evolution” is only one of several methods evolution has constructed for evolving proteins. There are others, including the original method that constructed the first proteins.

    This saves the theory from circularity, but otherwise is a problem because you have evolution constructing evolution in non trivial ways. This isn’t merely, “oh, the organism got bigger so there there are more places where it can mutate.” This is evolution constructing entirely new, novel, incredibly intricate, complex means of performing the same task–protein evolution. (Meanwhile we still have the landscape problem that we set aside earlier).

    So the theory takes on enormous levels of complexity in order to fit the evidence. That’s not the way science is supposed to work, and it is not the sign of a true theory.

    A shorter version of what you are saying is, “I am going to ignore and disregard all of the evidence that gene duplication and similarly well-documented mutation and selection mechanisms can and have produced new genes, until someone explains to me every last detail of the origin of life itself.” That makes about as much sense as saying you’re going to disbelieve the glacial theory for the origin of geological moraines until someone explains the origin of matter to you.

  489. 489
    Virgil Cain says:

    How was it determined that gene duplication is a blind watchmaker process?

  490. 490
    Mung says:

    Nick M:

    That makes about as much sense as saying you’re going to disbelieve the glacial theory for the origin of geological moraines until someone explains the origin of matter to you.

    Hey, I never thought of it like that before!

    You’re right. I can no longer believe the glacial theory.

    Thanks!

  491. 491
    Box says:

    The larger point I would like to make is that naturalism is irrelevant. Even when it is true — which it isn’t — we have to pretend that it isn’t.

    Naturalism has two main problems:
    1) It doesn’t lead to a comprehensive world view. A universe from nothing. Rationality from non-rational particles. Organization from chaos. Life from non