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.tabOutput:
1.71549e+09
1.52439e+11
88.8601So 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.s011These 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.
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.faThe problem here is the
maxmatchparameter 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. Thismaxmatchparameter 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. 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).
Dr. Torley, ORFans are not so easily dismissed as you seem to believe:
Moreover, there is a disconnect between protein sequences and gene sequences:
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??
Other than those of Tomkins, which other results were invalidated? Surely Tomkins was not singled out.
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
maxmatchthere 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%.
Latest findings indicate Chimps are only 82.3% Chimpanzee!
Okay, we are a 101% match with Chimps. Now what?
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!).
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
Glenn Williamson:
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.
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
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”.
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:
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?
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.
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.
Hi bornagain,
You write:
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:
ORFan genes are quite real.
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.
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.
“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.
@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?
@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?
@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.
@Mung:
“What other frauds have you exposed?”
Ha! Don’t get me started on Tomkins’ work on the fusion in chromosome 2 …
@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.
Python you ask:
“Are you saying that there is some other method of inheriting traits that is not passed on via DNA?”
Hi bFast,
I was intrigued by your comment:
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.
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:
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 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) ‘.
And protein folding is found to be ‘NP-complete’
Yet it is exactly this type of ‘traveling salesman problem’ that quantum computers excel at:
And proteins, like DNA, are found to have Quantum Information within them so as to be able to perform quantum computation
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?’)
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:
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!
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.
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:
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:
Verse and Music:
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.
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?
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.
@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.
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.
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.
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.
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’
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.
as to:
“Very few of these ORFan “genes” have proven to be actual functioning genes.”
and yet:
It must be hard to stay up with current evidence when you are stuck defending a 19th century dinosaur of a theory! 🙂
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?
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
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,
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.
And Larry, why do you delete comments from your blog that expose your ignorance and bias? Oops, I know why…
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.
Larry Moran:
Which of those four are blind watchmaker mechanisms and how was the determined?
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.
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?
Larry Moran:
Then you should be deleting your posts and comments.
My comment in 36 shows that your “point” is moot.
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.
Moreover, there was this recent telling admission
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.
Larry Moran:
So you can’t answer the question. Figures…
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!
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.
Let is ask Prof Moran then.
Prof Moran can your position account for how DNA came about? Do you have any testable results?
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.
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?
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.
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.
GP,
Welcome back.
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
godsan 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.
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?
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.
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?
Larry Moran:
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.
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?
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.
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.
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.
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 ….
And last but not least, the most ironic comment of them all ….
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.
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.
@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:
Too bad the “searching for a whole new theory” meant “finding ways to add more superficially normalizing epicycles”.
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:
Dr. Bohlin simplifies what Dr. Sternberg said a little bit here:
“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:
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:
EugeneS:
Thank you! 🙂
Larry Moran:
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 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.
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.
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.
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?
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”.
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?
Andre:
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.
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.
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.
@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.
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?
Thank you, Larry @ 79. Thank you very much.
Did you realize the genetic code is evidence for Intelligent Design?
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?
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?
Moran:
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.
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
Moran:
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.
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?
@ 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.
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.
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.
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.
Moran:
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.
@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/
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.
@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 🙂
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.
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.
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….
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!)
@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.
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:
Professor Moran,
Thank you very much for your response (#57). Commenting on the article by Jonathan Wells which I recommended to you, you wrote:
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.
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.
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.
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’:
How about the oft cited example from neo-Darwinists of antibiotic resistance?
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?
Well, that doesn’t seem to be helping either.
How about if we just try to fix an unconditionally ‘beneficial’ mutation by sustained selection?
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?
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?
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?
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!
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:
vjtorley- Thank you for your response. You say:
It would depend if they were always off, ie never expressed. Do you have a reference?
By what mechanism are humans descended from egg-layers?
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.
@BornAgain:
” … based on biased sequence comparisons”
Please explain your use of the word “biased”.
“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! 🙂
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.
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…
“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.
bloodymurderlive:
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
VJT:
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.
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?
@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.
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.
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;
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.
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.
Prof Moran
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?
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.
Prof Moran
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?
Prof Moran
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.
Prof Moran
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.
Prof Moran
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/
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.
Prof Moran
futher in Eugene Koonin’s conclusion and this is for you specifically…..
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?
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.
Moran:
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.
VJ @ 100
– 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!
Virgil Cain @ #74:
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.
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
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.
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.
Larry Moran:
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.
So all things evolution support unguided evolution? Is that your “argument”?
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
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):
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
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?
Dr. Moran @ 117:
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:
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?
bfast said:
VT said:
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.
VT wrote:
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
Andre:
Of course it is guided common descent. I have never thought anything different.
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?
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.
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
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.
Larry Moran:
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”:
Larry:
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!
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”.
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.
LoL! Larry just says that so he doesn’t have to try to demonstrate his case.
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.
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.
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.)
(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.
And what does this “creationist authority” have to say about intelligent design?
Professor Moran writes (to Mapou):
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:
I hope that helps.
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.
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
Prof Moran
No you don’t understand my position, matter of fact I am certain you don’t understand the ID position at all.
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?
A digital code arising by chance and luck in a happenstance manner is highly improbable don’t you agree?
Where did I say this?
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?
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?
Am I a reading a response here from a Professor at a University or is this the standard school yard bully response?
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?
Really who is really the faithful here? I already told you give me the testable results to your claims and I’ll shut up.
I’m not an anti-materialist what ever that means. If I was I’d picket for the destruction of all matter.
How did we go from design to gods? Only you keep doing that.
What can be explained by unguided evolution? Can you model unguided evolution for us?
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?
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.
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!
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
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
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?
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!
Zachriel:
A nested hierarchy should not exist given descent with modification and transitional forms.
Larry Moran:
No materialist would. They will do whatever it takes until they die so that they can die a materialist.
Mapou writes:
Adam and Eve laid eggs! You heard it here first, folks!
Well Nick Matzke, evolutionists lay eggs every time we ask them to support the claims of unguided evolution. So there you have it. 😛
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.
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.)
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?
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.)
Larry Moran-
We conclude that it was something else. Then, via our knowledge of cause and effect relationships, we infer it was via some intelligent agency.
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.
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.
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.
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.
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:
Sheer dumb luck, Larry? Really?
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.
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.
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.
Prof Moran
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?
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.
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.
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.
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
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………
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.
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
Nick Matzke
Really? some scientists noticed this apparent agreement too and cautioned against it!
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.
@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.
No, Incomplete Lineage Sorting means the *sorting* is incomplete. And you are a silly person. Try google, man.
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?
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?
@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”.
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.
Thickpython
Oh so when it conflicts with your beliefs it’s wrong? Gotcha.
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.
So Nick what you are saying then is scientists with a certain biases cherry pick the data. Got it thanks.
@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.
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?
NickMatzke_UD:
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.
ThickPython:
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?
“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?
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.
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.
@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”.
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.
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.
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.
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.
@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!
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?
so it is admitted the programs are ‘not perfect’ and yet Python claims
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:
A few more notes:
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:
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’.
A few more notes:
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…
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…
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.
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.
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!
Circular reasoning anyone?? How about affirming the consequence???
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.
Much ado about a “bush” of life. Or is that “circle” of life?
Oh well.
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.
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.
Did you read the rest of Zachriel’s post? Convergence can often be tested, including by the way he suggests.
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.
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 .
Sebesteyen at #137,
After I wrote back to bFast:
you commented:
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.
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…
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.
J-Mac @217, here’s more:
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?”
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”.
Theory? What theory?
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
LOL 😀
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/
bFast at 211 no problem
Of related interest:
ENV reported on the subsequent failed attempt by Darwinists to ‘explain away’ Peterson’s very un-Darwinian findings of microRNAs:
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:
Of semi-related note, messenger RNAs are found to have ‘evolved major differences’ between chimps and humans
Verse and Music:
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.
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.
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?
Prestin is a good example of what unguided evolution could never produce.
Vy,
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.
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?
Vy:
Because it could. I bet it freaked itself out. 😉
What? What’s being avoided when we conclude a trait has evolved convergent?
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.
Apparently I am too late to edit my comment in 233 which should actually feature JDD’s odd comment:
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.
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.
NickMatzke:
Umm, phylogenetics doesn’t yield a nested hierarchy. Linnaean Taxonomy is a nested hierarchy. Nice clean distinct sets
the best way to control a complex design is to set it up in a nested hierarchy and then carry it out.
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.
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.
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
Yup after all this “evolution” a vole is still a vole. This study alone should cast a huge shadow over evolutionism and macroevolution
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
NickMatzke:
OK so there isn’t really a scientific theory of evolution. Got it.
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.
No, sorry. It’s the naturalistic and assumed, yet totally unproven, ancestor of all known life.
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.
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 …
NickMatzke_UD:
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?
I went to that “29+ [delusional interpretations of reality to support common descent]” and found this:
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!!!”
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.)
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.
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
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.
EDTA:
http://www.uncommondescent.com.....ent-584872
“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?
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:
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):
Weinberg himself admits that atheists are in a ‘fix’
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”.
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.
@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
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.
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?
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?
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.
Andre, you’re gonna kill the dirt worshipper. 😀
@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.
NickMatzke_UD:
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.
@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.
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?
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.
@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
Thickpython
@196 – Are you trying to label me a creationist that believe in barminology? Try again!
@264 – Wikipedia? Really? The unemployed atheist playground? Really?
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
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:
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?
http://onlinelibrary.wiley.com.....7/abstract
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.
Bfast
http://www.genomebiology.com/2015/16/1/50
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.
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
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
BFast, pretty pervasive
NickMatzke:
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.
Nick Matzke:
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…
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–
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.
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:
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:
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:
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.
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
Interestingly, Al-Khalili comparison of the orderliness of life to the ordiliness of a Bose-Einstein condensate was just recently confirmed in protein molecules
The implication of finding quantum non-locality in molecular biology on a massive scale is fairly, and pleasantly, obvious:
Verse and Music:
Virgil Cain
In Theobald’s article he says;
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?
@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.
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.
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.
bornagain:
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,
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.
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.
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.
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.
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.
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.
bornagain:
Fuzzy makes you warm. And warm makes you comfortable. However comfortable does not make for good science.
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
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.
A few pertinent notes from the fossil record that run directly contrary to the, IMHO, all to easily accepted hypothesis of CD:
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.,,,
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.
Moreover, there are ‘yawning chasms’ in the ‘morphological space’ between the phyla which suddenly appeared in the Cambrian Explosion,,,
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.
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’:
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:
Of related note from the genetic evidence:
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.
NickMatzke_UD and the infamous cladograms are dealt with here:
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.
Cladograms are just our way of trying to understand evolutionary history. Neither evolution nor Common Descent predicted any of the cladograms science has constructed.
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
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.
NickMatzke_UD: and you are not saying what you mean by “fish”.
Be honest, Nick. Are you a “fish”?
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.
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.
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.
NickMatzke:
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
cladistics:
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
I thought you understood biology, Nick? Do all mammals have some fish as an ancestor or not, Nick?
NickMatzke:
Then it is strange that they all depict a direction. Even darwin’s tree does.
and
and
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?
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.)
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*.
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.
Nick M:
And where in the cladogram are the groups?
Virgil Cain:
From wikipedia:
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?
NickMatzke:
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.
The clade is not constructed based on ancestor-descendent relationships, those are assumed. And ancestor-descendent relationships form a non-nested hierarchy
NickMatzke:
You are full of bluff and bluster, Nick.
The nodes, ie the points of divergence, are alleged ancestral populations, Nick. The sister relationships are made through those nodes.
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.
NickMatzke:
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.
NickMatzke:
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.
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?
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.
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.
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?
Nick the only person confused here are those that think they have fish brains.
I am now convinced that flat earthers are more rational and reasonable than the fish people believers.
– Joel Cracraft & Niles Eldridge. Phylogenetic Analysis and Paleontology. 1979.
OT:
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
What was that remark about living in crazy land Matzke?
Wow, what a genuinely sensible comment. I wonder which version of him was in control.
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.
Zachrial wrote:
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
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.
– Robert M. Schoch. Phylogeny Reconstruction in Paleontology. 1986.
@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.
@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.
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.
@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?
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.
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?
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?
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.
Franklin
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.
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.
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.
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….
TP:
Equidistance of something your position cannot explain in the first place? LoL!
Looks like you’re stuck in fantasy-ville.
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.
@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?
SqueakPython says:
And yet only a few umpteen comments earlier, he said:
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!
@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.
Right.
TP:
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.
Right.
When evodelusionsts accuse you of quote-mining, you know you’ve got something.
@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.
Thickpython
You start with the assumption that CD is true and that is why you can’t see the wood from the trees……
Squeak, those were your words not mine.
They are your own words so stop imagining straw men.
Vy
And when they say “You don’t understand”
Andre, yup.
Apparently, they think that we’re obliged to believe that the random reactions in their brains can differentiate between reality and fantasy.
More:
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!
@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.
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
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!
@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.
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
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.
@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!
Oh yes, when your fallacious reasoning was found out.
However, it did not contradict your earlier statement:
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.
<blockquoteSqueakPythonYou also said:
… and:
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:
Damn Squeak, “too_much_reality”> overload? I mean, look at what that did to the multi-person entity, Zachriel.
Talk about a quote taken out of context:
Damn Squeak, “too_much_reality” overload? I mean, look at what that did to the multi-person entity, Zachriel.
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.
What’s going on here? I would like to know the real percentage of human-chimp DNA similarity.
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.
What’s a baseless tree called?
As stated in post 293, the fossil record certainly, when looked at in its entirety, does not support the hypothesis of common descent,
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:
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:
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:
Meyers puts the one of the primary reasons why mutations to DNA cannot change one creature into another creature like this
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:
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:
Moreover, there are very good mathematical reasons why overlapping coding within DNA will prevent one creature from ever being changed into another creature.
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.
Which is translated ;
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:
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 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:
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:
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:
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
Yet it is exactly in these genetic regulatory networks that ‘orders of magnitude’ differences are found between species:
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’:
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:
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.
@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.
@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?
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.
Peer, EugeneS,
I second EugeneS’ request.
I’m sure the name “ThickPython” is just randomly chosen 🙂
@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
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.
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
BA77, if someone wants to do a guest post, I am willing to host. KF
Cornelius Hunter:
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?
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
And yet the average human has about 175 mutations.
Who are you calling average?
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.
Kf, Bornagain,
Great offer kf!
Yes, it is indeed.
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.
Yes, Mapou, two sentences could be 98% similar and yet mean opposite things. A 1% change to an operating system could wreak havoc.
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.
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……
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.
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.
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.
@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.
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.
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.
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?
JoeCoder, you ask Dr. Hunter
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”
Thus, JoeCoder’s question to Dr. Hunter,,,,
,,, Thus, JoeCoder’s question to Dr. Hunter is actually better phrased as such,,,
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:
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:
@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.
What’s not amazing is ThickPython’s selective criticism.
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!
@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.
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)
@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.
An evolutionist actually used “mathematically impossible” in a sentence?? 🙂
@bornagain:
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???
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 😀
@BornAgain:
Yes, and I used it correctly. What you’ve just written is “mathematically very very unlikely”.
I do realize that you took his comment out of context. Full Stop.
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?
Andre: I love it when you comment on things you know nothing about.
We’re willing to learn. Let’s take the first citation.
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.
To clarify as to how the 500 bit universal limit is found for ‘structured, functional information’:
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
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:
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):
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.
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
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)
@Peer, #357:
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:
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 …
Yup, everyone he’s claimed to seek “clarification” from has left him hanging.
@Cornelius:
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.
@BornAgain:
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.
Yes.
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.
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.
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.
Are you suggesting that Nature would be interested in a paper titled “Creationist gets it wrong”?
Really?
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
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;
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:
You live in a fantasy land if you think the molecular data fits a tree pattern
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).
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.
@BornAgain:
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.
@Cornelius:
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.
Well, I was looking for something to disagree with. But I agree with your specific criticism.
Sorry, I misunderstood your argument.
@BornAgain:
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.
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.
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?
@BornAgain:
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.
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.
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.
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
ThickPython:
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?
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.
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!
@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.
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!
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.
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.
@Cornelius:
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.
@JoeCoder:
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.
@Cornelius, #434:
Are you suggesting that these proteins perform some known function? If so, what are their respective functions?
@Mung, #432:
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.
Numerator.
You’re welcome.
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?
@Mung, #430:
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.
There is a link to my paper in the OP. It’s been there since the start.
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.
Aww man, STOP IT! That hurts my feelings.
@BornAgain, #429:
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.
Thickpython
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
@Cornelius, #442:
“voila”.
And what will you say if 500bp upstream and downstream of these genes also shows 98%-ish identity?
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 …
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.
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:
//follow-up #448//
More S.L.Talbott:
— on histones and gene expression:
— DNA in knots:
Box
Talbott’s paper is poetry…..
I hope Prof Moran has read it……
ThickPython:
I think he was calculating the probability with a zero in the numerator, not that they “evolved out of nothing.”
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).
Dr. Hunter, big fan of your books.
Anything new in the works that you can share?
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
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.
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.
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.
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.
ThickPython:
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.
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.”
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?
…
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’?
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? 🙂
// – – – –
Good to hear that you enjoyed it!
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
@Mung:
Jeff Tomkins did. Check out the pretty graph in his 2013 paper.
Fixed.
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?
@Mung:
You sir, are an imbecile. The reason he got those results was due to the bug in the software. Please try to keep up.
@Big Snake…
What program did you run? NCBI Blast or WU Blast?
If you used NCBI Blast…that would explain a lot.
Peer, kf has offered to host a guest post by you on this subject.
@Peer, #468:
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.
@BornAgain:
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.
@ big snake ,
that was not my question.
my question was: what did you run…WU or NCBI….?
I would like to see both results.
@Peer, #472:
And I answered it: “Jeff Tomkins used NCBI BLAST, so clearly I have to use it …”.
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.
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:
Would this be your position?
Dr. Torley, this article that Dr. Nelson posted today may interest you
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.
@Cornelius, #476:
Are you sure about that?
Also, I notice you haven’t yet responded to post #458, which is the topic of the OP.
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.
Nick
We don’t assume it and since you make the claim that unguided processes can do this please show us.
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.
Folks: I repeat, I am willing to host guest post(s). I may be contacted through the web page linked from my handle. KF
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
S.L. Talbot says,
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 …
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 ….
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.
Larry Moran:
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.
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/
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.
How was it determined that gene duplication is a blind watchmaker process?
Nick M:
Hey, I never thought of it like that before!
You’re right. I can no longer believe the glacial theory.
Thanks!
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