Human evolution News

Researchers “very shocked” by recent new genes that form distinctly human brain

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from Gray's Anatomy, the prefrontal cortex

In “New Genes, New Brain” (The Scientist , October 19, 2011), Cristina Luiggi reports,

The evolution of the human brain may have been driven by a group of novel genes that arose fairly recently in primate evolution.

A bevy of genes known to be active during human fetal and infant development first appeared at the same time that the prefrontal cortex—the area of the brain associated with human intelligence and personality—took shape in primates, a new study published yesterday (October 18) in PLoS Biology found. The timing suggests that the new genes may have been intimately tied to the evolution of the human brain.

Previous research focused on older genes conserved across the animal kingdom, looking at new genes is hoped to provide insight. Like:

“We were very shocked that there were that many new genes that were upregulated in this part of the brain,” said Long, who added that he was also taken aback by synchronicity of the origin of the genes and the development of novel brain structures. It seems that around the same time that the neocortex and the prefrontal cortex arose, and then expanded in humans, a large collection of genes also popped up.

That’s something the old genes were never going to tell researchers.

It feels like a rollout of some kind, no?

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77 Replies to “Researchers “very shocked” by recent new genes that form distinctly human brain

  1. 1
    bornagain77 says:

    Lab experiments – several million dollars

    Thoroughly equipped Lab in which to conduct proper experiments- 10’s of millions of dollars

    Scientists being ‘very shocked’ that the findings severely compromise the gradual appearance of humans by neo-Darwinian processes – priceless

  2. 2
    PaV says:

    Maybe Nick Matzke can explain to us how these new genes came about through Darwinian processes in an absolutely short period of time.

    Another day; another bad day for Darwinism!

  3. 3
    bornagain77 says:

    Notes:

    Could Chance Arrange the Code for (Just) One Gene?
    “our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236).”
    http://www.creationsafaris.com/epoi_c10.htm

    Dr. Sanford calculates it would take 12 million years to “fix” a single base pair mutation into a population. He further calculates that to create a gene with 1000 base pairs, it would take 12 million x 1000 or 12 billion years. This is obviously too slow to support the creation of the human genome containing 3 billion base pairs.
    http://www.detectingtruth.com/?p=66

    Waiting Longer for Two Mutations – Michael J. Behe
    Excerpt: Citing malaria literature sources (White 2004) I had noted that the de novo appearance of chloroquine resistance in Plasmodium falciparum was an event of probability of 1 in 10^20. I then wrote that ‘for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years’ (1 quadrillion years)(Behe 2007) (because that is the extrapolated time that it would take to produce 10^20 humans). Durrett and Schmidt (2008, p. 1507) retort that my number ‘is 5 million times larger than the calculation we have just given’ using their model (which nonetheless “using their model” gives a prohibitively long waiting time of 216 million years). Their criticism compares apples to oranges. My figure of 10^20 is an empirical statistic from the literature; it is not, as their calculation is, a theoretical estimate from a population genetics model.
    http://www.discovery.org/a/9461

    “Darwin’s theory is easily the dumbest idea ever taken seriously by science.”
    Granville Sewell – Professor Of Mathematics – University Of Texas – El Paso

    God by the Numbers – Charles Edward White
    Excerpt: “Even if we limit the number of necessary mutations to 1,000 and argue that half of these mutations are beneficial, the odds against getting 1,000 beneficial mutations in the proper order is 2^1000. Expressed in decimal form, this number is about 10^301. 10^301 mutations is a number far beyond the capacity of the universe to generate. Even if every particle in the universe mutated at the fastest possible rate and had done so since the Big Bang, there still would not be enough mutations.”
    http://www.christianitytoday.c.....ml?start=2

    Study Reports a Whopping “23% of Our Genome” Contradicts Standard Human-Ape Evolutionary Phylogeny – Casey Luskin – June 2011
    Excerpt: For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. This encompasses genes and exons to the same extent as intergenic regions. We conclude that about 1/3 of our genes started to evolve as human-specific lineages before the differentiation of human, chimps, and gorillas took place. (of note; 1/3 of our genes is equal to about 7000 genes that we do not share with chimpanzees)
    http://www.evolutionnews.org/2.....47041.html

    Indeed, math is not kind to Darwinism in the least when considering the probability of humans ‘randomly’ evolving:

    In Barrow and Tippler’s book The Anthropic Cosmological Principle, they list ten steps necessary in the course of human evolution, each of which, is so improbable that if left to happen by chance alone, the sun would have ceased to be a main sequence star and would have incinerated the earth. They estimate that the odds of the evolution (by chance) of the human genome is somewhere between 4 to the negative 180th power, to the 110,000th power, and 4 to the negative 360th power, to the 110,000th power. Therefore, if evolution did occur, it literally would have been a miracle and evidence for the existence of God. William Lane Craig

    William Lane Craig – If Human Evolution Did Occur It Was A Miracle – video
    http://www.youtube.com/watch?v=GUxm8dXLRpA

    Along that same line:

    Darwin and the Mathematicians – David Berlinski
    “The formation within geological time of a human body by the laws of physics (or any other laws of similar nature), starting from a random distribution of elementary particles and the field, is as unlikely as the separation by chance of the atmosphere into its components.”
    Kurt Gödel, was a preeminent mathematician who is considered one of the greatest to have ever lived.!
    http://www.evolutionnews.org/2.....cians.html

    Stephen Meyer – Functional Proteins And Information For Body Plans – video
    http://www.metacafe.com/watch/4050681

    Phillips, Craig & Dean – Open the Eyes of My Heart
    http://www.youtube.com/watch?v=hwToU_wfj8s

  4. 4
    PaV says:

    This is from the above cited article:

    Finally, 54 of the 280 genes found to be unique to humans were also highly expressed in the developing prefrontal cortex, which grew considerably in humans after the human chimpanzee lineages broke off around 5 to 7 million years ago. (The human prefrontal cortex is six times larger than the chimpanzee’s.)

    From: “Induced gene expression in human brain after the split from chimpanzee”

    In summary, our analysis has provided statistical evidence to show that after the split of humans and chimpanzees, the change of expression pattern in the human brain was more dramatic than that in the chimpanzee [5]. Moreover, we have shown that these changes in the human brain involved induction (increased gene expression) much more frequently than repression. This pattern is not observed in chimpanzee brain, nor in the liver of humans or chimpanzees. The enhanced expression of genes in the human brain since the split from chimpanzees could be important in the emergence of human beings, and certainly deserves further investigation. [Jianying Gu and Xun Gu, 2003)

    I suppose all these neutral mutations were just right there when they were needed. And, of course, in 5 to 7 million years, NS could have done, what? Well, per a recently cited article, two authors took exception to Behe’s characterizations in EoE, and said that it would only take 31.6 million years to fixate two amino acid substitutions in a mammalian population.

    But, of course, if you believe in magic, anything is possible.

  5. 5
    PaV says:

    Here’s some more:

    The researchers also determined that the majority of these new genes underwent strong positive selection in humans, further supporting the hypothesis that the genes contributed to the evolution of important functions in the brain.

    “All of this is circumstantial evidence that supports this more broad idea that these new genes have something interesting to say about primate-specific or human-specific brain function,” Vallender said.

    Every Darwinian description needs a translation.

    So, when they say “the majority of these new genes underwent strong positive selection in humans”, what they really mean is that these new genes are “highly conserved”; which means they’re almost identical across populations (if not completely identical)—testimony to their evident importance.

    So, not only do we have 54 new genes expressed in the pre-frontal cortex, but they don’t allow any substitutions (effectively ruling out neutral drift); and all this in 5-7 million years. I tell you, that NS+RV is really something (And let’s not even talk about evo-devo here, because we’re not dealing with Hox genes; we’re dealing with de novo genes. And evo-devo is simply about shifting around gene expression patterns. It says nothing at all about the de novo development of genes)

    Any intellectually honest Darwinist should, based on this evidence alone, abandon the theory.

  6. 6
    PaV says:

    BornAgain77:

    I just saw your additional post. You know, Darwinism is just an absolute affront to reason. The numbers we’re talking about here in de novo generation of genes is simply mind-boggling long. And now we need 54 of them.

    They accuse us of being creationists. Well, I’m Catholic—just like Ken Miller. What they’re really accusing us of is not being impartial, of having an agenda, and of thus not being able to follow where the evidence leads. Well, who’s guilty of that?!!

    When will they give up the ghost?

  7. 7
    PaV says:

    It gets even worse for Darwinism:

    From the PLoS article, author’s summary:

    Our data reveal that evolutionary change in the development of the human brain happened at the protein level by gene origination and also via evolution of regulatory networks, as intimated by the enrichment of primate-specific transcriptional regulators in our dataset.

    All you Darwinists out there: give up the ghost! Please!

  8. 8
    PaV says:

    And worse still:

    We found these genes are scattered across the whole genome, demonstrating that they are generated by many independent events (Figure S5). Moreover, based on chromosomal coordinates, we pooled neighboring genes into clusters if they share the same age and transcriptional bias. Given two distance cutoffs (100,000 bases and 1 million bases), young transcriptional clusters continue to be more often expressed in the fetal brain compared to old transcriptional clusters.

    . . . these genes are scattered across the whole genome, demonstrating that they are generated by many independent events.

    Kind of like what a computer programmer might do in developing an updated version of his software!

  9. 9
    bornagain77 says:

    Let’s not forget this PaV;

    A bevy of genes known to be active during human fetal and infant development first appeared at the same time that the prefrontal cortex

    These are not ‘newly added’ unique ORFan genes, on top of existing genes, since many are expressed early in development prior to the expression of ‘older genes’:

    notes:

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

    Moreover the ‘anomaly’ of unique ORFan genes is found in every new genome sequenced:

    Widespread ORFan Genes Challenge Common Descent – Paul Nelson – video with references
    http://www.vimeo.com/17135166

    Genomes of similar species – Cornelius Hunter PhD.
    Excerpt: Different variants of the Escherichia coli bacteria, for instance, each have hundreds of unique genes. And some of these genes have been found to have important functions, such as helping to construct proteins. [8]
    Massive genetic differences were also found between different fruit fly species. The fruit fly is one of the most intensely researched organisms and in recent years a systematic study of the genomes of a dozen different species was undertaken. Evolutionists were surprised to find novel features in the genomes of each of these different fruit fly species. Thousands of genes showed up missing in many of the species, and some genes showed up in only a single species. [9] As one science writer put it, “an astonishing 12 per cent of recently evolved genes in fruit flies appear to have evolved from scratch.” [10] These so-called novel genes would have had to have evolved over a few million years—a time period previously considered to allow only for minor genetic changes. [11,12] ,,, etc.. etc…
    http://www.darwinspredictions.com/#_4.2_Genomes_of

    etc.. etc.. etc..

  10. 10
    bornagain77 says:

    This is really something!!!,,,

  11. 11
    DrREC says:

    “Such a pattern is consistent with the hourglass model recently observed in zebrafish, where the oldest genes are transcribed in the phylotypic stage (supposedly the stage of ancient evolutionary origin) and younger genes are expressed in the more divergent ontogenic stages [40].”

    Oops.

    I do hope there is a follow-up paper on the ‘de novo’ genes. Data on whether these actually are real genes is pretty light: “Such a trend continues into the hominoid lineages with 198 genes upregulated in PFC (Figure 6). Up to 54 of them were human-specific, i.e. they originated after human lineage diverged from the other hominoids. Although these 198 genes have been subject to less experimental investigations, expression of 33 genes in fetal or infant brain was demonstrated by UniGene EST data (Table 3), four of which have been confirmed to encode proteins, as revealed by Pride peptide data [27].”

    From their tables, searching the chimp genome for a few of the de-novo genes turned up some nearly identical matches, particularly for ARL17.

    I’d bet a few are genuine de novo genes. I’d bet some aren’t.

  12. 12
    DrREC says:

    Careful there, young in that figure means primate-specific, not human specific.

  13. 13
    GilDodgen says:

    The massively profound discontinuity between humans (especially the human mind and brain) and all other life forms should be obvious to anyone with even minimal reasoning power.

    The notion that this discontinuity is the result of randomly produced gene disparity is irrational and superbly unsupported by any concrete evidence, only Alice-in-Wonderland fantastic speculation. Something else is going on — something powerful, creative, and with purpose.

  14. 14
    Eocene says:

    GilDodgen:

    “Something else is going on — something powerful, creative, and with purpose.”
    ====

    You mean other than a Gerald Joyce ‘Master Chef’ chemical cocktail soup experiment ???

  15. 15
    ThoughtSpark says:

    Shocked?? I’m shocked that they’re shocked. Really, you had to go to a lab to find out that humans are different?

  16. 16
    Clive Hayden says:

    That scientific gentleman with the bald, egg-like head and the bare, bird-like neck had no real right to the airs of science that he assumed. He had not discovered anything new in biology; but what biological creature could he have discovered more singular than himself?

    ~G. K. Chesterton, The Man Who Was Thursday

  17. 17

    Well, you could read the paper 🙂

    http://www.plosbiology.org/art.....rticles%29

    It’s really interesting.

    Incidentally, the authors talk about both “young genes” (genes unique to primates) and “human-specific genes”, some of both of which they find upregulated in PFC during human development.

    They also show that the number of new genes separating our nearest relations are roughly similar – 318 between Rhesus monkey and orangutan, 72 expressed in PFC; 372 between orangutan and chimp, 72 expressed in PFC; and 280 between chimp and human, 54 expressed in PFC.

    It’s a really interesting paper, not exactly “another bad day for Darwinism”! It actually tests specific Darwinian hypotheses!

  18. 18

    Oh, golly, PaV, you have read the paper!

    I think you should stop “translating” it and just read what it says!

    I think your babelfish is on the blink.

  19. 19

    Why, PaV?

    Seriously, I am not seeing the point you are making. The paper gives a data-supported account of primate and human brain evolution.

    And you are reading it as some kind of falsification of Darwinism?

    I see you quote parts, but I’m simply not seeing your argument.

    What is it, specifically, that you think refutes Darwinism in that paper?

    I’m seeing a beautiful family tree of new genes along the hominid lineage, with a substantial proportion expressed in PFC.

    What on earth refutes Darwinian evolution of the human PFC in that account? And why do you think the authors aren’t seeing it, and make the quite contrary point?

  20. 20
    bornagain77 says:

    As well, besides these 54 novel human ORFan genes that were found in this study, (which is devastating to neo-Darwinian gradualism despite what the ‘true believers’ may say) I would like to point out this following study, in this following study the authors tried to remove over 1000 unique ORFan genes from the human gene count simply because it was ‘not expected’ by the neo-Darwinian mindset:

    notes:

    This following article, which has a direct bearing on the 98.8% genetic similarity myth, shows that over 1000 ‘ORFan’ genes, that are completely unique to humans and not found in any other species, and that very well may directly code for proteins, were stripped from the 20,500 gene count of humans simply because the evolutionary scientists could not find corresponding genes in primates. In other words evolution, of humans from primates, was assumed to be true in the first place and then the genetic evidence was directly molded to fit in accord with their unproven assumption. It would be hard to find a more biased and unfair example of practicing science!

    Human Gene Count Tumbles Again – 2008
    Excerpt: Scientists on the hunt for typical genes — that is, the ones that encode proteins — have traditionally set their sights on so-called open reading frames, which are long stretches of 300 or more nucleotides, or “letters” of DNA, bookended by genetic start and stop signals.,,,, The researchers considered genes to be valid if and only if similar sequences could be found in other mammals – namely, mouse and dog. Applying this technique to nearly 22,000 genes in the Ensembl gene catalog, the analysis revealed 1,177 “orphan” DNA sequences. These orphans looked like proteins because of their open reading frames, but were not found in either the mouse or dog genomes. Although this was strong evidence that the sequences were not true protein-coding genes, it was not quite convincing enough to justify their removal from the human gene catalogs. Two other scenarios could, in fact, explain their absence from other mammalian genomes. For instance, the genes could be unique among primates, new inventions that appeared after the divergence of mouse and dog ancestors from primate ancestors. Alternatively, the genes could have been more ancient creations — present in a common mammalian ancestor — that were lost in mouse and dog lineages yet retained in humans. If either of these possibilities were true, then the orphan genes should appear in other primate genomes, in addition to our own. To explore this, the researchers compared the orphan sequences to the DNA of two primate cousins, chimpanzees and macaques. After careful genomic comparisons, the orphan genes were found to be true to their name — they were absent from both primate genomes.
    http://www.sciencedaily.com/re.....161406.htm

    The sheer, and blatant, shoddiness of the science of the preceding study should give everyone who reads it severe pause whenever, in the future, someone tells them that genetic studies have proven evolution to be true.

    If the authors of the preceding study were to have actually tried to see if the over 1000 unique ORFan genes of humans may actually encode for proteins, instead of just written them off because they were not found in other supposedly related species, they would have found that there is ample reason to believe that they may very well encode for biologically important proteins:

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

    Dr. Howard Ochman – Dept. of Biochemistry at the University of Arizona
    Excerpt of Proposal: The aims of this proposal are to investigate this enigmatic class of genes by elucidating the source and functions of “ORFans”, i.e., sequences within a genome that encode proteins having no homology (and often no structural similarity) to proteins in any other genome. Moreover, the uniqueness of ORFan genes prohibits use of any of homology-based methods that have traditionally been employed to establish gene function.,,, Although it has been hypothesized that ORFans might represent non-coding regions rather than actual genes, we have recently established that the vast majority that ORFans present in the E. coli genome are under selective constraints and encode functional proteins.
    http://www.uncommondescent.com.....ent-358868

    In fact it turns out that the authors of the ‘kick the ORFans out in the street’ paper actually did know that there was unbiased evidence strongly indicating the ORFan genes encoded proteins but chose to ignore it in favor of their preconceived evolutionary bias:
    http://www.uncommondescent.com.....ent-358547

    This following study found much more dramatic differences for unique ORFan genes:

    Study Reports a Whopping “23% of Our Genome” Contradicts Standard Human-Ape Evolutionary Phylogeny – Casey Luskin – June 2011
    Excerpt: For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. This encompasses genes and exons to the same extent as intergenic regions. We conclude that about 1/3 of our genes started to evolve as human-specific lineages before the differentiation of human, chimps, and gorillas took place. (of note; 1/3 of our genes is equal to about 7000 genes that we do not share with chimpanzees)
    http://www.evolutionnews.org/2.....47041.html

  21. 21
    PaV says:

    Dear Elizabeth:

    Since you seem to claim to have read the paper, then perhaps you can point out where they explain just exactly ‘where’ and ‘how’ these new genes came about.

    Could you do that for us? 🙂

    They also show that the number of new genes separating our nearest relations are roughly similar – 318 between Rhesus monkey and orangutan, 72 expressed in PFC; 372 between orangutan and chimp, 72 expressed in PFC; and 280 between chimp and human, 54 expressed in PFC.

    How is this in any way relevant to the problems facing Darwinism indicated by these results?

    And just so you can’t just say, “What problems?”, let’s remember this:

    We were very shocked that there were that many new genes that were upregulated in this part of the brain,” said Long, who added that he was also taken aback by synchronicity of the origin of the genes and the development of novel brain structures.

    Why were they “shocked”? Why? Because they knew this was completely contrary to Darwinian expectations. That’s why.

    IOW, they knew this was a huge problem for Darwinism. Let’s not pretend here.

  22. 22
    PaV says:

    Elizabeth:

    I think you are the one indulging in “babelfish”. If I have improperly interpreted the Darwinian code words, then please tell me where. But, if not, then it should be apparent that a huge part of the problem with biology is that Darwinian presumptions have crept into the language that is used.

  23. 23
    PaV says:

    Elizabeth:

    Darwinism refutes Darwinism. It is an incoherent theory.

    Isn’t it obvious why I highlighted the words in the post you’re responding to?

    Not only do de novo genes need to be accounted for, but also the rise of an integrated system—that is, “new” regulatory networks.

    This only confounds the task of Darwinism. It is like trying to haul away the Himilayans with a Tonka truck.

    I’m seeing a beautiful family tree of new genes along the hominid lineage, with a substantial proportion expressed in PFC.

    You see what you want to see. Don’t you see that Darwinism has absolutely no way of explaining how all these new genes arose in an evolutionary ‘blink of an eye’?

    But, of course, you don’t see—-because you refuse to see. Or to answer. Or to explain. Just vague generalities.

  24. 24
    PaV says:

    Even if the point is conceded, does that give us an extra five million years? Does that solve this problem at all.

  25. 25
    DrREC says:

    55-65 million. Details…..

    “Does that solve this problem at all.”

    What problem?

  26. 26
    PaV says:

    DrREC:

    The fact that cytochrome C is essential to cell division and replication, and that it is found, relatively unchanged, in all animal forms, even from the very earliest living descendants, convinced Sir Fred Hoyle, the renowned astrophysicist, that the Darwinist solution to evolution was impossible.

    Cytochrome C is a fairly short protein as proteins go. So, really, just ONE de novo gene is beyond Darwinian explanations. So, now what are you going to do if TWO of the genes prove to be de novo.?

  27. 27
    PaV says:

    Gil:

    You wrote:

    The notion that this discontinuity is the result of randomly produced gene disparity is irrational and superbly unsupported by any concrete evidence, only Alice-in-Wonderland fantastic speculation. Something else is going on — something powerful, creative, and with purpose.

    You can’t load Windows Vista operating system on a machine with very little data storage capacity. You have to upgrade to a larger system. The hardware is not the same as the software; but they need to be compatible. We’re only dealing, metaphorically, with hardware issues right now.

  28. 28
    PaV says:

    What’s your point?

  29. 29
    PaV says:

    What is, IMO, extremely enlightening about all of this is: We are perhaps looking at what a “true”, macroevolutionary speciation event looks like; i.e., the introduction of a host of new genes, in locations all throughout the genome, with the added addition of new regulatory regimes, leading to a complete break with the prior lineage.

    IOW, we may not have been around for the Cambrian Explosion, but it is not entirely off the mark to retroject this finding to exactly what happened back then. This, then, could be posited as the “mechanism” for macroevolution; and, for the time being, as studies further confirm or disconfirm, it could be called a “design intervention.”

  30. 30
    DrREC says:

    “The fact that cytochrome C is essential to cell division and replication, and that it is found, relatively unchanged, in all animal forms”

    But it isn’t essential for all life-certainly not archaea, bacteria, and some fungi. The further you go from animals, the more divergent the sequence

    “So, really, just ONE de novo gene is beyond Darwinian explanations.”

    Why? There are several examples of de novo genes with tractable origins. A recombination of two genes, retrotransposition of an exon into a pseudogene, mutations at a transcribed, but non-translatable region, yielding a new ORF.

  31. 31
    PaV says:

    They’re talking about “clusters”. Obviously, de novo genes would be “clustered” with the “young” genes. Hence, the independence stems from these de novo genes being spread out amongst the clusters, and not just in one or two.

  32. 32
    DrREC says:

    Why would de novo (human only) and young (primate) genes be clustered, if they formed in independent events?

    They are found throughout the genome.

  33. 33
    bornagain77 says:

    DrREC states:

    There are several examples of de novo genes with tractable origins. A recombination of two genes, retrotransposition of an exon into a pseudogene, mutations at a transcribed, but non-translatable region, yielding a new ORF.

    Unfortunately for DrREC hopeless nihilistic atheism (which he apparently places so much hope in), he has ZERO evidence of completely random neo-Darwinian mechanisms generating a single novel gene or protein in life, and indeed the changes we do witness in the genome, some of which DrREC listed, point to higher levels of ‘epigenetic’ programming information in the ‘information hierarchy’ of the cell which is directly orchestrating the ‘base level of information’ of DNA sequences to be in prescribed patterns dictated by that epigenetic information. i.e. This ‘information hierarchy’, though DrREC will never admit it (and indeed he will keep repeating something that is falsified over and over), is devastating to the genetic reductionism model of neo-Darwinism!!!

    notes:

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

    ‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does insure that proteins, cell types, tissues, organs, will all be arranged in the body. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’ – Stephen Meyer – (excerpt taken from Meyer/Sternberg vs. Shermer/Prothero debate – 2009)

    Stephen Meyer – Functional Proteins And Information For Body Plans – video
    http://www.metacafe.com/watch/4050681

    A few comments on ‘non-local’ epigenetic information:
    https://docs.google.com/document/pub?id=1iNy78O6ZpU8wpFIgkILi85TvhC9mSqzUSE_jzbksoHY

    Falsification Of Neo-Darwinism by Quantum Entanglement/Information
    https://docs.google.com/document/d/1p8AQgqFqiRQwyaF8t1_CKTPQ9duN8FHU9-pV4oBDOVs/edit?hl=en_US

    Does Quantum Biology Support A Quantum Soul? – Stuart Hameroff – video (notes in description)
    http://vimeo.com/29895068

  34. 34
    PaV says:

    Expression data covering numerous subregions of the developing brain further demonstrate that these young genes are mainly upregulated in the neocortex. They originated in the evolutionary period during which the neocortex was expanding, suggesting the functional association of new genes with this newly evolving brain structure.

    Examination of the gene structure and homology further revealed that these genes were generated by DNA-mediated duplication, RNA-mediated duplication (retroposition), and de novo origination (which created a protein without a parental locus) (Figure 3). In other words, young genes created by all major gene origination mechanisms tend to be upregulated in fetal brain. Such generality suggests that a systematic force instead of a mutational bias associated with a specific origination mechanism contributed to the excess of young genes in the fetal brain.

    DrREC: the details. How do you interpret them?

  35. 35

    There is no “complete break with the prior lineage”, PaV!

    What makes you think that the new genes all arrived at once? The tree they give makes it fairly clear how new genes accumulate between branches.

    Really, you seem to be reading into this something that simply is not there. It’s a very interesting paper, but it’s hard for me to imagine how anyone could read it and not find confirmatory evidence of common descent and the effects of natural selection! It even gives the genetic phylogeny!

    There is no “mechanism” posited here, and you are not in fact positing one. For some reason you seem to have interpreted the finding as evidence for a single “macroevolutionary speciation event”. What, in the paper, leads you to think such an event occurred, and what “mechanism” for such an event do you see evidence for?

    We do not know why the chimp and human lineages originally diverged. It could simply originally have been some kind of physical separation of populations into non-interbreeding groups. At which point, the gradual accumulation of new genes would follow different paths in the two lineages, just as it seems to have done between orangs and champs, and between rhesus monkeys and orangs, and between marmosets and rhesus monkeys.

    However it does look as the there has been steady selection for genes that are beneficially expressed in PFC during development, and for regulatory genes that lead to such expression, not surprisingly, as it looks as though the associated PFC effects lead to greater intelligence, which is likely to have a reproductive advantage.

    So we see a steady accumulation along the homind lineage, from marmosets onwards, of genes that are expressed in the PFC, with various populations (rhesus, orang, chimp) getting of the bus a bit early.

    There is no evidence for sudden explosions of genes at each branch point at all. At least not given in that paper.

  36. 36
    DrREC says:

    bornagain77,

    “Unfortunately for DrREC hopeless nihilistic atheism (which he apparently places so much hope in)”

    I’ve never discussed my faith here.

    “he has ZERO evidence of completely random neo-Darwinian mechanisms generating a single novel gene or protein in life”

    I listed examples, and the mechanisms that created them. Those mechanistically appear random with respect to need, and also cause deleterious effects/disease. I think what you really mean is that I can’t demonstrate they were unguided. Of course I can’t. That isn’t falsifiable, it isn’t science, it is theism attached to evolution–fine as a personal belief. Not science, not support for ID.

    “indeed the changes we do witness in the genome, some of which DrREC listed, point to higher levels of ‘epigenetic’ programming information in the ‘information hierarchy’ of the cell which is directly orchestrating the ‘base level of information’ of DNA sequences to be in prescribed patterns dictated by that epigenetic information. i.e. ‘

    You could have created this paragraph using a mad-lib for all the meaning it has.

    Epigenetic literally means on top of the genome. Epigenetic marks serve to regulate the transcription of genes. They aren’t a creator of new genes. They aren’t even thought to be permanent enough to contribute to evolution in the long run. So you’re really stretching to attribute genome changes to them,

  37. 37
    bornagain77 says:

    DrREC, you atheistic/materialistic faith literally bleeds through in every post you write!!! and If you have the sheer audacity to claim theism as your belief, it will certainly be in name only and completely devoid of any real substance, as for even your very posts witness against you!!!,,, Tell you what DrREC, there is a null hypothesis that you atheistic/materialistic neo-Darwinists need to falsify to even be considered scientifically legitimate in the first place. If You guys falsify this null hypothesis and I will at least concede that you guys have a plausible foundation within science in which to make your, thus far, completely unsubstantiated pseudo-scientific conjectures, for the ability of purely ‘random’ material processes to generate transcendent information!!!

    Three subsets of sequence complexity and their relevance to biopolymeric information – Abel, Trevors
    Excerpt: Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC (Functional Sequence Complexity). FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,,
    Testable hypotheses about FSC
    What testable empirical hypotheses can we make about FSC that might allow us to identify when FSC exists? In any of the following null hypotheses [137], demonstrating a single exception would allow falsification. We invite assistance in the falsification of any of the following null hypotheses:

    Null hypothesis #1
    Stochastic ensembles of physical units cannot program algorithmic/cybernetic function.

    Null hypothesis #2
    Dynamically-ordered sequences of individual physical units (physicality patterned by natural law causation) cannot program algorithmic/cybernetic function.

    Null hypothesis #3
    Statistically weighted means (e.g., increased availability of certain units in the polymerization environment) giving rise to patterned (compressible) sequences of units cannot program algorithmic/cybernetic function.

    Null hypothesis #4
    Computationally successful configurable switches cannot be set by chance, necessity, or any combination of the two, even over large periods of time.

    We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable. We offer the prediction that none of these four hypotheses will be falsified.
    http://www.tbiomed.com/content/2/1/29

    The following describes how quantum entanglement is related to functional information:

    Quantum Entanglement and Information
    Excerpt: A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems.
    http://plato.stanford.edu/entries/qt-entangle/

    further notes:

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

    Meyer and Nelson on a Failed Explanation for the Origin of the Genetic Code
    Jonathan M. – August 2011
    Excerpt: ‘codes and digital information are categories of effects uniformly associated with intelligent causes. Indeed, to the extent that Yarus and others have succeeded in establishing affinities between codons and amino acids, they did so only as a direct consequence of their own intelligent manipulation and intervention.’
    http://www.evolutionnews.org/2.....50121.html

    The Law of Physicodynamic Insufficiency – Dr David L. Abel – November 2010
    Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.”
    http://www-qa.scitopics.com/Th.....iency.html

    The Capabilities of Chaos and Complexity – David L. Abel – 2009
    Excerpt: “A monstrous ravine runs through presumed objective reality. It is the great divide between physicality and formalism. On the one side of this Grand Canyon lies everything that can be explained by the chance and necessity of physicodynamics. On the other side lies those phenomena than can only be explained by formal choice contingency and decision theory—the ability to choose with intent what aspects of ontological being will be preferred, pursued, selected, rearranged, integrated, organized, preserved, and used. Physical dynamics includes spontaneous non linear phenomena, but not our formal applied-science called “non linear dynamics”(i.e. language,information).
    http://www.mdpi.com/1422-0067/10/1/247/pdf

    Stephen C. Meyer – Signature In The Cell:
    “DNA functions like a software program,” “We know from experience that software comes from programmers. Information–whether inscribed in hieroglyphics, written in a book or encoded in a radio signal–always arises from an intelligent source. So the discovery of digital code in DNA provides evidence that the information in DNA also had an intelligent source.”
    http://www.evolutionnews.org/2.....ligen.html

    Three subsets of sequence complexity and their relevance to biopolymeric information – David L Abel and Jack T Trevors:
    Excerpt: Genetic algorithms instruct sophisticated biological organization. Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC). FSC alone provides algorithmic instruction…No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization…It is only in researching the pre-RNA world that the problem of single-stranded metabolically functional sequencing of ribonucleotides (or their analogs) becomes acute.
    http://www.biomedcentral.com/c.....2-2-29.pdf

    Biological Information: The Puzzle of Life that Darwinism Hasn’t Solved – Stephen C. Meyer
    Thus, as my book Signature in the Cell shows, Joyce’s experiments not only demonstrate that self-replication itself depends upon information-rich molecules, but they also confirm that intelligent design is the only known means by which information arises.
    http://www.evolutionnews.org//.....e_puz.html

    The Origin of Life: An RNA World? – Jonathan M. – August 22, 2011 (Refutation of Nick Matzke)
    Excerpt Summary & Conclusion
    We have explored just a small handful of the confounding difficulties confronting the chemical origin of life. This is not a god-of-the-gaps argument, as Matzke claims, but rather a positive argument, based on our uniform and repeated experience of cause-and-effect. It is not based on what we don’t know, but on what we do know: that intelligence is a necessary and sufficient condition for the production of novel complex and functionally specified information. The design inference is based on sound and conventional scientific methodology. It utilizes the historical or abductive method and infers to the best explanation from multiple competing hypotheses.
    http://www.evolutionnews.org/2.....49871.html

    There remains one and only one type of cause that has shown itself able to create functional information like we find in cells, books and software programs — intelligent design. We know this from our uniform experience and from the design filter — a mathematically rigorous method of detecting design. Both yield the same answer. (William Dembski and Jonathan Witt, Intelligent Design Uncensored: An Easy-to-Understand Guide to the Controversy, p. 90 (InterVarsity Press, 2010).

    “Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information.
    “Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information.
    “Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information in the cell.”

    Stephen C. Meyer – The Scientific Basis For the Intelligent Design Inference – video
    http://www.metacafe.com/watch/4104651

    The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.
    http://www.mdpi.com/1422-0067/10/1/247/pdf
    Can We Falsify Any Of The Following Null Hypothesis (For Information Generation)
    1) Mathematical Logic
    2) Algorithmic Optimization
    3) Cybernetic Programming
    4) Computational Halting
    5) Integrated Circuits
    6) Organization (e.g. homeostatic optimization far from equilibrium)
    7) Material Symbol Systems (e.g. genetics)
    8) Any Goal Oriented bona fide system
    9) Language
    10) Formal function of any kind
    11) Utilitarian work
    http://mdpi.com/1422-0067/10/1/247/ag

  38. 38
    bornagain77 says:

    DrREC, you atheistic/materialistic faith literally bleeds through in every post you write!!! and If you have the sheer audacity to claim Theism as your belief, it will certainly be in name only and completely devoid of any real substance, as for even your very posts witness against you in this matter!!!,,, Tell you what DrREC, there is a null hypothesis that you atheistic/materialistic neo-Darwinists need to falsify to even be considered scientifically legitimate in the first place. If You guys falsify this null hypothesis, I will at least concede that you guys have a plausible foundation within science in which to make your, thus far, completely unsubstantiated pseudo-scientific conjectures with, for the ability of purely ‘random’ material processes to generate transcendent information!!!

    Three subsets of sequence complexity and their relevance to biopolymeric information – Abel, Trevors
    Excerpt: Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC (Functional Sequence Complexity). FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,,
    Testable hypotheses about FSC
    What testable empirical hypotheses can we make about FSC that might allow us to identify when FSC exists? In any of the following null hypotheses [137], demonstrating a single exception would allow falsification. We invite assistance in the falsification of any of the following null hypotheses:

    Null hypothesis #1
    Stochastic ensembles of physical units cannot program algorithmic/cybernetic function.

    Null hypothesis #2
    Dynamically-ordered sequences of individual physical units (physicality patterned by natural law causation) cannot program algorithmic/cybernetic function.

    Null hypothesis #3
    Statistically weighted means (e.g., increased availability of certain units in the polymerization environment) giving rise to patterned (compressible) sequences of units cannot program algorithmic/cybernetic function.

    Null hypothesis #4
    Computationally successful configurable switches cannot be set by chance, necessity, or any combination of the two, even over large periods of time.

    We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable. We offer the prediction that none of these four hypotheses will be falsified.
    http://www.tbiomed.com/content/2/1/29

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

    Meyer and Nelson on a Failed Explanation for the Origin of the Genetic Code
    Jonathan M. – August 2011
    Excerpt: ‘codes and digital information are categories of effects uniformly associated with intelligent causes. Indeed, to the extent that Yarus and others have succeeded in establishing affinities between codons and amino acids, they did so only as a direct consequence of their own intelligent manipulation and intervention.’

    The Law of Physicodynamic Insufficiency – Dr David L. Abel – November 2010
    Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.”

    The Capabilities of Chaos and Complexity – David L. Abel – 2009
    Excerpt: “A monstrous ravine runs through presumed objective reality. It is the great divide between physicality and formalism. On the one side of this Grand Canyon lies everything that can be explained by the chance and necessity of physicodynamics. On the other side lies those phenomena than can only be explained by formal choice contingency and decision theory—the ability to choose with intent what aspects of ontological being will be preferred, pursued, selected, rearranged, integrated, organized, preserved, and used. Physical dynamics includes spontaneous non linear phenomena, but not our formal applied-science called “non linear dynamics”(i.e. language,information).
    http://www.mdpi.com/1422-0067/10/1/247/pdf

    Stephen C. Meyer – Signature In The Cell:
    “DNA functions like a software program,” “We know from experience that software comes from programmers. Information–whether inscribed in hieroglyphics, written in a book or encoded in a radio signal–always arises from an intelligent source. So the discovery of digital code in DNA provides evidence that the information in DNA also had an intelligent source.”

    Three subsets of sequence complexity and their relevance to biopolymeric information – David L Abel and Jack T Trevors:
    Excerpt: Genetic algorithms instruct sophisticated biological organization. Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC). FSC alone provides algorithmic instruction…No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization…It is only in researching the pre-RNA world that the problem of single-stranded metabolically functional sequencing of ribonucleotides (or their analogs) becomes acute.

    Biological Information: The Puzzle of Life that Darwinism Hasn’t Solved – Stephen C. Meyer
    Thus, as my book Signature in the Cell shows, Joyce’s experiments not only demonstrate that self-replication itself depends upon information-rich molecules, but they also confirm that intelligent design is the only known means by which information arises.

    The Origin of Life: An RNA World? – Jonathan M. – August 22, 2011 (Refutation of Nick Matzke)
    Excerpt Summary & Conclusion
    We have explored just a small handful of the confounding difficulties confronting the chemical origin of life. This is not a god-of-the-gaps argument, as Matzke claims, but rather a positive argument, based on our uniform and repeated experience of cause-and-effect. It is not based on what we don’t know, but on what we do know: that intelligence is a necessary and sufficient condition for the production of novel complex and functionally specified information. The design inference is based on sound and conventional scientific methodology. It utilizes the historical or abductive method and infers to the best explanation from multiple competing hypotheses.

    There remains one and only one type of cause that has shown itself able to create functional information like we find in cells, books and software programs — intelligent design. We know this from our uniform experience and from the design filter — a mathematically rigorous method of detecting design. Both yield the same answer. (William Dembski and Jonathan Witt, Intelligent Design Uncensored: An Easy-to-Understand Guide to the Controversy, p. 90 (InterVarsity Press, 2010).

    “Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information.
    “Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information.
    “Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information in the cell.”

    Stephen C. Meyer – The Scientific Basis For the Intelligent Design Inference – video
    http://www.metacafe.com/watch/4104651

    The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.
    http://www.mdpi.com/1422-0067/10/1/247/pdf
    Can We Falsify Any Of The Following Null Hypothesis (For Information Generation)
    1) Mathematical Logic
    2) Algorithmic Optimization
    3) Cybernetic Programming
    4) Computational Halting
    5) Integrated Circuits
    6) Organization (e.g. homeostatic optimization far from equilibrium)
    7) Material Symbol Systems (e.g. genetics)
    8 ) Any Goal Oriented bona fide system
    9) Language
    10) Formal function of any kind
    11) Utilitarian work

    http://mdpi.com/1422-0067/10/1/247/ag

  39. 39
    bornagain77 says:

    Of interest to this ‘regulatory network’ quote at post 6 by PaV:

    Our data reveal that evolutionary change in the development of the human brain happened at the protein level by gene origination and also via evolution of regulatory networks,

    When they claim evolution of regulatory networks, they are in fact claiming the origination of a novel regulatory codes, which is very similar to someone claiming the proof for the origination of the genetic code itself. i.e. It is a very, very, fantastic claim which is backed up by ZERO empirical evidence other than their Darwinian belief that is must have happened by Darwinian processes since, by golly, there the novel regulatory code sits:

    notes:

    Researchers Crack ‘Splicing Code,’ Solve a Mystery Underlying Biological Complexity
    Excerpt: “For example, three neurexin genes can generate over 3,000 genetic messages that help control the wiring of the brain,” says Frey. “Previously, researchers couldn’t predict how the genetic messages would be rearranged, or spliced, within a living cell,” Frey said. “The splicing code that we discovered has been successfully used to predict how thousands of genetic messages are rearranged differently in many different tissues.
    http://www.sciencedaily.com/re.....133252.htm

    Nature Reports Discovery of “Second Genetic Code” But Misses Intelligent Design Implications – May 2010
    Excerpt: Rebutting those who claim that much of our genome is useless, the article reports that “95% of the human genome is alternatively spliced, and that changes in this process accompany many diseases.” ,,,, the complexity of this “splicing code” is mind-boggling:,,, A summary of this article also titled “Breaking the Second Genetic Code” in the print edition of Nature summarized this research thusly: “At face value, it all sounds simple: DNA makes RNA, which then makes protein. But the reality is much more complex.,,, So what we’re finding in biology are:

    # “beautiful” genetic codes that use a biochemical language;
    # Deeper layers of codes within codes showing an “expanding realm of complexity”;
    # Information processing systems that are far more complex than previously thought (and we already knew they were complex), including “the appearance of features deeper into introns than previously appreciated”
    http://www.evolutionnews.org/2.....of_se.html

    Canadian Team Develops Alternative Splicing Code from Mouse Tissue Data
    Excerpt: “Our method takes as an input a collection of exons and surrounding intron sequences and data profiling how those exons are spliced in different tissues,” Frey and his co-authors wrote. “The method assembles a code that can predict how a transcript will be spliced in different tissues.”
    http://www.genomeweb.com/infor.....issue-data

    further note:

    Venter vs. Dawkins on the Tree of Life – and Another Dawkins Whopper – March 2011
    Excerpt:,,, But first, let’s look at the reason Dawkins gives for why the code must be universal:
    “The reason is interesting. Any mutation in the genetic code itself (as opposed to mutations in the genes that it encodes) would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation…this would spell disaster.” (2009, p. 409-10)
    OK. Keep Dawkins’ claim of universality in mind, along with his argument for why the code must be universal, and then go here (linked site listing 23 variants of the genetic code).
    Simple counting question: does “one or two” equal 23? That’s the number of known variant genetic codes compiled by the National Center for Biotechnology Information. By any measure, Dawkins is off by an order of magnitude, times a factor of two.
    http://www.evolutionnews.org/2.....44681.html

    Shannon Information – Channel Capacity – Perry Marshall – video
    http://www.metacafe.com/watch/5457552/

    “Because of Shannon channel capacity that previous (first) codon alphabet had to be at least as complex as the current codon alphabet (DNA code), otherwise transferring the information from the simpler alphabet into the current alphabet would have been mathematically impossible”
    Donald E. Johnson – Bioinformatics: The Information in Life

    Further note:

    “In the last ten years, at least 20 different natural information codes were discovered in life, each operating to arbitrary conventions (not determined by law or physicality). Examples include protein address codes [Ber08B], acetylation codes [Kni06], RNA codes [Fai07], metabolic codes [Bru07], cytoskeleton codes [Gim08], histone codes [Jen01], and alternative splicing codes [Bar10].
    Donald E. Johnson – Programming of Life – pg.51 – 2010

    Ends and Means: More on Meyer and Nelson in BIO-Complexity – September 2011
    Excerpt: According to Garrett and Grisham’s Biochemistry, the aminoacyl tRNA snythetase is a “second genetic code” because it must discriminate among each of the twenty amino acids and then call out the proper tRNA for that amino acid: “Although the primary genetic code is key to understanding the central dogma of molecular biology on how DNA encodes proteins, the second genetic code is just as crucial to the fidelity of information transfer.”
    http://www.evolutionnews.org/2.....50391.html

  40. 40
    PaV says:

    It would appear that the de novo genes are found throughout the clusters; not in just one or two clusters. So the de novo origins are spread throughout the genome, marking many independent de novo origins.

    What is the likelihood of this happening by chance? 1 in 10^500,000? Any reasonable person would say that it could not have happened by chance mechanisms.

  41. 41
    PaV says:

    But it isn’t essential for all life-certainly not archaea, bacteria, and some fungi. The further you go from animals, the more divergent the sequence.

    Is this really an intellectually honest reply?

    You know full well that you’re venturing out into different kingdoms, the existence of which presents problems for Darwinism, as it exhibits a “bush-like” character, and not a “tree-like” character.

    Further, would you like to posit the way in which cytchrome C came about? Did it come from the archea, e.g.? But that would mean that one “kingdom” gave rise to another “kingdom”, thus making them part of only ONE “kingdom”.

    This is the kind of intellectual dishonesty that a predisposition to Darwinism brings about. This is pure rhetoric, and not worthy of scientific inquiry.

    PaV: “So, really, just ONE de novo gene is beyond Darwinian explanations.”

    DrREC:

    Why? There are several examples of de novo genes with tractable origins. A recombination of two genes, retrotransposition of an exon into a pseudogene, mutations at a transcribed, but non-translatable region, yielding a new ORF.

    “Examination of the gene structure and homology further revealed that these genes were generated by DNA-mediated duplication, RNA-mediated duplication (retroposition), and de novo origination (which created a protein without a parental locus) (Figure 3).”

    From: A Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions, Chuan-Yun Li, Yong Zhang, Zhanbo Wang, Yan Zhang, Chunmei Cao, Ping-Wu Zhang, Shu-Juan Lu, Xiao-Mo Li, Quan Yu, Xiaofeng Zheng, Quan Du, George R. Uhl, Qing-Rong Liu*, Liping Wei*, 2009:

    For decades, gene duplication, retrotranspositions and gene fusions were believed to be major ways to increase gene number. All involve “mother” genes as the “building blocks” for new genes. However, several recently identified “motherless” genes challenged the idea in that some proteins might have emerged de novo from ancestral non-coding DNAs.

    You seem to be a little bit behind the times, DrREC.

  42. 42
    PaV says:

    ThoughtSpark:

    Sometimes I don’t know who people are here. You haven’t blogged before. I presumed you were a Darwinist; but I reread your post from the vantage point of ID/Darwinian skepticism, and I think I realize your point now. Sorry (I was in a terrible hurry this morning)

  43. 43
    PaV says:

    Elizabeth:

    What makes you think that the new genes all arrived at once? The tree they give makes it fairly clear how new genes accumulate between branches.

    What makes me think that the new genes all arrived at once?

    The fact that a Darwinist claims that it takes 31.6 million years to fix two amino acid substitutions in a population, coupled to the fact that between the chimp and human lineages we’re looking at what, 15-20 million years. Would you like to propose a “gradualistic” mechanism explaining all of this?

    And, yes, the tree does give us a nice view of how new genes accumulate. But this exactly fits my point: They ALL look the same. That is, the proportion of “new genes” being upregulated as compared to the “old genes” is quite symmetrical; which dovetails with the point I was making above: i.e., what we see in the human/simian differentiation also likely took place at all other major evolutionary tree divergences.

    Liz Liddle:

    but it’s hard for me to imagine how anyone could read it and not find confirmatory evidence of common descent and the effects of natural selection! It even gives the genetic phylogeny!

    Confirmatory evidence of common descent? I don’t know about you, but it sure looks to me like there are discontinuities there. You can still run MS-DOS on many computers. Should we say that high-powered PCs are the “descendants” of the first, rather primitive ones? Be careful, Lizzie! 🙂

    There is no “mechanism” posited here, and you are not in fact positing one. For some reason you seem to have interpreted the finding as evidence for a single “macroevolutionary speciation event”. What, in the paper, leads you to think such an event occurred, and what “mechanism” for such an event do you see evidence for?

    Common sense tells me that if 10^20 replications are necessary to get a two amino acid substitution fixed in a population, then there is no way in hell that Darwinian mechanisms can account for 54 de novo genes—absolutely no way! So, something had to happen. And intelligent agency makes the most sense. And, if an intelligent agent intervenes once, why not take care of all 54 genes? Why intervene 54 times; or a hundred and fifty-four times?

    Now theistic evolutionists would say that God is nudging the process along. Well, there’s simply not enough time for that to happen. An intervention was needed.

    Again; common sense!

    We do not know why the chimp and human lineages originally diverged. It could simply originally have been some kind of physical separation of populations into non-interbreeding groups. At which point, the gradual accumulation of new genes would follow different paths in the two lineages, just as it seems to have done between orangs and champs, and between rhesus monkeys and orangs, and between marmosets and rhesus monkeys.

    As to your first two sentences, there is a study out today that challenges your stated view. How timely! 🙂

    As to your third sentence: when did this “physical separation” occur? 200 billion years ago? And even that amount of time is insufficient to account for Darwinian mechanisms arriving at the what is finally seen.

    However it does look as the there has been steady selection for genes that are beneficially expressed in PFC during development, and for regulatory genes that lead to such expression, not surprisingly, as it looks as though the associated PFC effects lead to greater intelligence, which is likely to have a reproductive advantage.

    What you’ve just stated is filled with Darwinian presuppositions. You talk about “selection”. Well, what does that mean? Nothing.

    Here’s how things really stand: genes for PFC are preferentially expressed during development. That’s all we KNOW. The rest is but fitting known facts into a Darwinian interpretation. IOW, a “just-so” story. No more. No less.

    So we see a steady accumulation along the homind lineage, from marmosets onwards, of genes that are expressed in the PFC, with various populations (rhesus, orang, chimp) getting of the bus a bit early.

    I don’t think you have any way of knowing whether what you just wrote is true or not. Yes, we see a “steady accumulation”. But is it “gradual”; or is it sudden? How do yo propose to distinguish these two, real possibilities?

  44. 44
    wd400 says:

    The fact that a Darwinist claims that it takes 31.6 million years to fix two amino acid substitutions in a population

    I really want to read this paper, will be fun to see how you’ve misconstrued this one 🙂

  45. 45
    DrREC says:

    “Is this really an intellectually honest reply?”

    Yes. PaV, you’re making some sort of argument that because cytochrome c is required for animal life, that what exactly? It isn’t required for all life. There isn’t any meat on this one.

    PaV: “So, really, just ONE de novo gene is beyond Darwinian explanations.”
    DrREC: There are several examples of de novo genes with tractable origins.

    PaV: Lists another example of a de novo gene with tractable origins.

    Are you familiar with the term ‘own-goal’ PaV?

    Contrast: “Cross-species analysis revealed interesting evolutionary paths of how this gene had originated from noncoding DNA sequences: insertion of repeat elements especially Alu contributed to the formation of the first coding exon and six standard splice junctions on the branch leading to humans and chimpanzees, and two subsequent substitutions in the human lineage escaped two stop codons and created an open reading frame of 194 amino acids.”

    With:
    PaV: “So, really, just ONE de novo gene is beyond Darwinian explanations.”

    Creation of new fCSI. Thanks for the example. And no, I’m not behind the times. I listed several mechanisms for de novo gene creation, including ones where no coding ORF existed. But thanks for the additional example!

  46. 46
    Acipenser says:

    I agree! Pav’s claim has me a bit confused on how s/he arrived at this conclusion. So how about a citation, Pav?

  47. 47
    DrREC says:

    PaV:

    “What is the likelihood of this happening by chance? 1 in 10^500,000? Any reasonable person would say that it could not have happened by chance mechanisms.”

    When in doubt, invent some big, big numbers.

  48. 48
    DrREC says:

    Also realize there are contrasting claims, like the fixation of four substitutions in 10
    HOURS.

    “… four apparently functional SNPs should fix in a population within 10 hours of exposure to antibiotic in our experiment. A detailed understanding of the order in which the SNPs occur is essential, but it is unlikely that the four SNPs emerged simultaneously; in all likelihood they are sequential (21–23). The device and data we have described here offer a template for exploring the rates at which antibiotic resistance arises in the complex fitness landscapes that prevail in the mammalian body. Furthermore, our study provides a framework for exploring rapid evolution in other contexts such as cancer (24).”

    Acceleration of Emergence of Bacterial Antibiotic Resistance in Connected Microenvironments” Qiucen Zhang, Guillaume Lambert, David Liao, Hyunsung Kim, Kristelle Robin, Chih-kuan Tung, Nader Pourmand, Robert H. Austin, Science 23 September 2011: Vol. 333 no. 6050 pp. 1764-1767

  49. 49
    bornagain77 says:

    When in doubt, invent some big, big numbers.

    Or when in science just falsify neo-Darwinism altogether using empirical evidence:

    Falsification Of Neo-Darwinism by Quantum Entanglement/Information
    https://docs.google.com/document/d/1p8AQgqFqiRQwyaF8t1_CKTPQ9duN8FHU9-pV4oBDOVs/edit?hl=en_US

  50. 50
    bornagain77 says:

    A Tale of Two Falsifications of Evolution – September 2011
    Excerpt: “Scientists were surprised at how fast bacteria developed resistance to the miracle antibiotic drugs when they were developed less than a century ago. Now scientists at McMaster University have found that resistance has been around for at least 30,000 years.”
    http://crev.info/content/11090....._evolution

    Antibiotic resistance is ancient – September 2011
    http://www.nature.com/nature/j.....E-20110922

    Evolution – Tested And Falsified – Don Patton – video
    http://www.metacafe.com/watch/4036803

    List Of Degraded Molecular Abilities Of Antibiotic Resistant Bacteria:
    http://www.trueorigin.org/bacteria01.asp

  51. 51
    bornagain77 says:

    suppose you want to claim they were random?

  52. 52

    Darwinism refutes Darwinism. It is an incoherent theory.

    It’s an extremely coherent theory. It simply says that if self-replicator replicate with differential variance in reproductive success, the best replicators will come to dominate the population, i.e. the population will evolve – aka adapt to its environment.

    How can this not be true?

    So the question is: does it apply to biological reproduction? And we find – yes: we have self-replication with differential variance in reproductive success, we have sources of variance, and we have evidence that it does actually work – populations adapt by the generation in the short term to cyclical changes in the environment, and track changes in the long term to long-term changes in the environment. Plus we also see interesting non-linear effects of drift.

    Isn’t it obvious why I highlighted the words in the post you’re responding to?

    No, it isn’t. Regulatory networks are just as evolvable by Darwinian process as protein coding genes. There’s no difference to the process.

    You objection just seems to be “It looks too much to me”. And the research suggests the opposite to your own conclusion, that wholesale batches of new genes with regulatory networks got plonked into the genomes of certain individuals at certain times. Do you envisage that one day an orang gave birth to a chimp, with a whole set of new genes, and then later a chimp gave birth to a human, with another new set?

    Or what do you envisage?

    The evidence suggests continuous evolution with the PFC genes and gene networks evolving along the whole lineage, probably from the fairly clearcut survival advantage in having a substantial PFC.

  53. 53
    Acipenser says:

    Antibiotic resistance is a very old story of competition. Antibiotics are chemical compounds that inhibit and/or prevent bacterial replication through a number of different mechanisms. That the first compounds with antibiotic properties were found in mold surprises no one today. What better way to protect a food source than to excrete a compound toxic to your competition…shades of hag fish slime by golly!

  54. 54
    Joseph says:

    Elizabeth,

    Larry Moran just posted that 99% of the variation is due to random genetic drift.

    And unfortunately there still isn’t any evidence that darwinian processes can create regulatory networks and there isn’t any evidence said processes can produce protein-coding genes!

  55. 55
    Petrushka says:

    Now scientists at McMaster University have found that resistance has been around for at least 30,000 years.”

    Do you actually think antibiotics are something new that humans invented?

  56. 56
    bornagain77 says:

    Waiting Longer for Two Mutations – Michael J. Behe
    Excerpt: Citing malaria literature sources (White 2004) I had noted that the de novo appearance of chloroquine resistance in Plasmodium falciparum was an event of probability of 1 in 10^20. I then wrote that ‘for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years’ (1 quadrillion years)(Behe 2007) (because that is the extrapolated time that it would take to produce 10^20 humans). Durrett and Schmidt (2008, p. 1507) retort that my number ‘is 5 million times larger than the calculation we have just given’ using their model (which nonetheless “using their model” gives a prohibitively long waiting time of 216 million years). Their criticism compares apples to oranges. My figure of 10^20 is an empirical statistic from the literature; it is not, as their calculation is, a theoretical estimate from a population genetics model.
    http://www.discovery.org/a/9461

    but hey if you disagree with these population geneticists you can always apply for the job at Oxford to ‘fix’ the fact that neo-Darwinism has no mathematical basis:

    Oxford University Admits Darwinism’s Shaky Math Foundation – May 2011
    Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. – On a 2011 Job Description for a Mathematician, at Oxford, to ‘fix’ the persistent mathematical problems with neo-Darwinism within two years.
    http://www.evolutionnews.org/2.....46351.html

    something tells me you won’t be able to lie your way out of this one guys (although I’m sure you will try!)

    Conservation of Information In Search – William Dembski and Robert Marks – Sept. 2009
    http://ieeexplore.ieee.org/xpl.....er=5204206

    The Capabilities of Chaos and Complexity: David L. Abel –
    Null Hypothesis For Information Generation – 2009
    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut:
    http://www.mdpi.com/1422-0067/10/1/247/pdf
    http://mdpi.com/1422-0067/10/1/247/ag

    “No human investigation can be called true science without passing through mathematical tests.”
    Leonardo Da Vinci

    Using Computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load:
    Excerpt: We apply a biologically realistic forward-time population genetics program to study human mutation accumulation under a wide-range of circumstances.,, Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space.
    http://bioinformatics.cau.edu......aproof.pdf
    MENDEL’S ACCOUNTANT: J. SANFORD†, J. BAUMGARDNER‡, W. BREWER§, P. GIBSON¶, AND W. REMINE
    http://mendelsaccount.sourceforge.net
    http://www.scpe.org/vols/vol08/no2/SCPE_8_2_02.pdf

    A comparative approach for the investigation of biological information processing: An examination of the structure and function of computer hard drives and DNA – David J D’Onofrio1, Gary An – Jan. 2010
    Excerpt: It is also important to note that attempting to reprogram a cell’s operations by manipulating its components (mutations) is akin to attempting to reprogram a computer by manipulating the bits on the hard drive without fully understanding the context of the operating system. (T)he idea of redirecting cellular behavior by manipulating molecular switches may be fundamentally flawed; that concept is predicated on a simplistic view of cellular computing and control. Rather, (it) may be more fruitful to attempt to manipulate cells by changing their external inputs: in general, the majority of daily functions of a computer are achieved not through reprogramming, but rather the varied inputs the computer receives through its user interface and connections to other machines.
    http://www.tbiomed.com/content/7/1/3

  57. 57
  58. 58
    Joseph says:

    linky, linky

    The explanation that best fits the data tells us that >99% of all evolutionary change is due to random genetic drift and not natural selection.

    But don’t worry I am told that remaining 1% is more than enough- 1% plus a whole lot of imagination and your position has all it needs.

  59. 59
    DrREC says:

    You still don’t get that realism in physics does not mean metaphysical realism do you?

    Another mad-lib argument, really. Toss words together, stir.

  60. 60
    bornagain77 says:

    DrREC, oh please do tell me of your imaginary concept of ultimate realism, I do need a good laugh! 🙂

  61. 61
    DrREC says:

    Define “ultimate realism.”

    And while your at it, why don’t you, in your own words, explain how quantum mechanics falsifies evolution?

    I really think even your peers who support you here probably are at a loss when it comes to your conception of quantum mechanics, and the fairy tale world of links you’ve built up around it.

  62. 62
    DrREC says:

    Just to follow up, PaV has provided us with a falsification of ID…the creation of fCSI by generation of a de novo gene by tractable mechanism, where no locus existed before.

    20^194 power exceeds the universal probability bound, does it not? My my….

    ““Cross-species analysis revealed interesting evolutionary paths of how this gene had originated from noncoding DNA sequences: insertion of repeat elements especially Alu contributed to the formation of the first coding exon and six standard splice junctions on the branch leading to humans and chimpanzees, and two subsequent substitutions in the human lineage escaped two stop codons and created an open reading frame of 194 amino acids.”

    Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions, Chuan-Yun Li, Yong Zhang, Zhanbo Wang, Yan Zhang, Chunmei Cao, Ping-Wu Zhang, Shu-Juan Lu, Xiao-Mo Li, Quan Yu, Xiaofeng Zheng, Quan Du, George R. Uhl, Qing-Rong Liu*, Liping Wei*, 2009:

  63. 63
    DrREC says:

    1 quadrillion years vs. 10 hours.

    Man, thats a margin of error.

    Doesn’t really convince me the design inference is valid. Hmm.

  64. 64
    junkdnaforlife says:

    DrRec: “I really think even your peers who support you here probably are at a loss when it comes to your conception of quantum mechanics,”

    Probably true for most that don’t understand QM. But first you have to understand that BA’s (if i’m wrong ba say so) arguments from QM are based on the Copenhagen interpretation, on the idea that an observer plays some role in collapsing wave function, but more specifically that consciousness causes collapse. Which is not that same as the Copenhagen interpretation in the sense that observer does not necessarily = consciousness. So based on this first premise, many of BA arguments do make sense. However, often he gets involved in debates whereas the differences are in the interpretation of wave-particle duality, (not the data), and whether or not wave-particle duality exists at all. Specifically, many of his opponents argue from the position of quantum decoherence, and that wave function collapse in an illusion. Differing interpretations (first premise) will naturally lead to different conclusions. This all comes down to which of the 14 or so interpretations of QM you accept. And it is impossible to know, at this stage of the game, which is the correct model.

  65. 65
    DrREC says:

    My objections are specifically:

    1) Proceeding from “local realism” to metaphysical realism in the same breath, which I doubt you can justify,

    2) Taking a complex and unresolved field, and concluding it falsifies evolution because???

    It is just BS. Sorry.

  66. 66
    junkdnaforlife says:

    You may conclude his interpretation is bs sure. But he does understand the data. And what is on the table is about 14 or so choices for QM models. All of which are no more correct than the next. So what BA does is collect the QM data and reviews the options. Then draws upon his Judeo-Christian theology/philosophy to shape which of the 14 or so flavors seems to make the most sense. Many atheist physicists, I believe prefer decoherence, for the same faith based, or lack of, reasons.
    What I think BA is doing absolutely correct is searching in the right places. The answers to many puzzles are probably nested somewhere in QM superpositions.

  67. 67
    DrREC says:

    junkdna,

    Please describe, then, in a few sentences:

    1) How quantum mechanics falsifies metaphysical realism.

    2) How quantum mechanics falsifies evolutionary biology,

    I call BS on you, too. What kind of moron say there are “14 or so flavors” in one field, and that since another idiot “draws upon his Judeo-Christian theology/philosophy to shape which of the 14 or so flavors seems to make the most sense” and concludes the poop that comes out to be the truth? Really?

  68. 68
    junkdnaforlife says:

    I never appealed to any truth. I was explaining why BA ends up at his conclusions. They are based on his interpretation of QM, (his first premise). And the reason he chooses that specific interpretation of QM and not another is based on his Christianity. I am of course, doing my best to explain what is in BA’s head. He may say something completely different. But again, this all based on interpretation. Some interpretations of QM are equally as spooky, one being that there are possibly an infinite amount of Drrecs operating online right now in some fashion, (not to be confused with the multi-verse).

    You keep asking me to argue for BA, that’s not my intention. I could not do his link carpet bomb’s justice. You said in the earlier post that most are at a loss when it comes to BA’s qm arguments. I was stating that I am not. I understand his arguments, and that they are based on a specific interpretation of QM.

    To your specifics:

    1.) Qm does not falsify this. However, the specific interpretation, the one BA accepts (consciousness causes collapse), if this were found to be the empirically true model, would seem to suggest that the mind is some separate immaterial thing. (Someone more familiar with that interpretation could answer that better. Buddhists I believe accept his interpretation also.)

    2.) I don’t see how any Qm interpretation would falsify evolution.

  69. 69
    bornagain77 says:

    Quantum entanglement falsifies local realism and thus finding quantum entanglement in molecular biology (on a massive scale) ONLY falsifies the atheistic/materialistic form of neo-Darwinian evolution since the atheistic/materialistic form of neo-Darwinian evolution is based upon ‘local realism’ (more specifically atheistic neo-Darwinism is based upon a reductive materialistic form of local realism). QM does not falsify the possibility of Theistic evolution! (Although I find theistic evolution implausible from many other lines of evidence) QM certainly makes ‘intellectually fulfilled’ atheism an impossibility, 🙂 .Local realism simply refers to the entire space-time, mass-energy, of the universe, and all causes inherent therein. Non-local realism refers to the fact that local realism is found to be insufficient to explain all phenomena inherent within the space-time mass-energy of the universe, specifically local realism is found to be insufficient to explain quantum entanglement (A. Aspect), and even quantum wave collapse (J. Wheeler), and even, most recently, found to be insufficient to explain the ‘local’ existence of mass-energy itself within space-time (A. Zeilinger) (i.e. mass-energy is found to be NOT self-sustaining but depends upon a non-local cause (beyond space-time matter-energy cause) to explain its continued existence with space-time). But even before Zeilinger’s recent formal experimental proof against self-sustaining ‘material’, Max Planck, the father of quantum mechanics, understood many years ago the need for a ‘non-local’ cause to explain material reality;

    “As a man who has devoted his whole life to the most clear headed science, to the study of matter, I can tell you as a result of my research about atoms this much: There is no matter as such. All matter originates and exists only by virtue of a force which brings the particle of an atom to vibration and holds this most minute solar system of the atom together. We must assume behind this force the existence of a conscious and intelligent mind. This mind is the matrix of all matter.” Max Planck – The Father Of Quantum Mechanics – Das Wesen der Materie [The Nature of Matter], speech at Florence, Italy (1944)

    etc.. etc.. etc..

  70. 70

    Thanks for the link. I rightly surmised that the 99% did not apply to this finding.

    As you were.

  71. 71
    PaV says:

    “Yes. PaV, you’re making some sort of argument that because cytochrome c is required for animal life, that what exactly? It isn’t required for all life. There isn’t any meat on this one.”

    And your argument is that cytochrome c is not required for other forms of life, so therefore, cytochrome c doesn’t matter? Does that make sense?

    You’ve just admitted: “It isn’t required for all life.” Thus, implicit in this comment is the admission that cytochrome c is necessary for life. And, yet, the probability of this one protein forming by chance mechanisms—remember, other forms of life don’t need it—are astronomical. So, how did it form? How did this huge probabilistic problem get overcome?

    Cross-species analysis revealed interesting evolutionary paths of how this gene had originated from noncoding DNA sequences: insertion of repeat elements especially Alu contributed to the formation of the first coding exon and six standard splice junctions on the branch leading to humans and chimpanzees, and two subsequent substitutions in the human lineage escaped two stop codons and created an open reading frame of 194 amino acids.

    Based on your subsequent comment, you consider this to be a Darwinian explanation. But it isn’t. It is a Darwinian description, of sorts. It is a description of what can be discerned, but utilizing a discernment process guided by Darwinian presumptions. No more.

    Take, for instance, this phrase: ” . . and two subsequent substitutions in the human lineage . . . ” What is the Darwinian explanation for this? How did it happen? What was the time frame?

    Per an article by evolutionary biologists wanting to refute Behe’s Edge of Evolution claims, they said that it would take 31.6 million years for two amino acids to become fixed. So, how do you square these two findings as a Darwinian? You can’t. Humans haven’t been around for 31.7 million years. So, there is no plausible Darwinian explanation. Shouldn’t we, then, seek a better explanation?

    Creation of new fCSI.

    We can be sure of two things here: (1) if it truly is fCSI, then an intelligent agent was involved, and (2) as I demonstrated above, there is no Darwinian explanation for fCSI.

  72. 72
    PaV says:

    It’s an extremely coherent theory. It simply says that if self-replicator replicate with differential variance in reproductive success, the best replicators will come to dominate the population, i.e. the population will evolve – aka adapt to its environment.

    How can this not be true?

    So the question is: does it apply to biological reproduction? And we find – yes: we have self-replication with differential variance in reproductive success, we have sources of variance, and we have evidence that it does actually work

    Let’s look at the moves you’ve made here.

    You set up a kind of generalized truth—- . . . self-replicators replicate . . . —and then go on to apply it to biology.

    But, please, Lizzie, where else, other than in biology, do you see “self-replicators”? Where do they exist?

    So you take an abstract concept that has biology as its basis of origin, and then you apply it to biology as a kind of analysis of what makes biology tick.

    And then you ask the question: How can this not be true?

    Well if self-replicators don’t replicate, then they can’t be self-replicators can they? So how can the statement that self-replicators replicate ever be wrong? Of course this is true. But you wouldn’t even be saying this unless life existed. So you’re simply looking at what life does and then saying this is true. Bravo.

    The rest of your “true” statement is simply a way of attempting to explain something else we see in the life around us: adaptation. And, so, this too is true—self-evidently true.

    But this was known long before Darwin’s Origin of Species. And the mechanism Darwin proposed was also proposed as an explanation for adaptation.

    Where all of this steers off the path of what is true is when Darwin posits the Law of Divergence, an absolute necessity if he is going to claim that adaptive mechanisms can also explain the progressive evolution of life forms.

    IOW, its a circular way of thinking. As is Darwinism. And that’s why it’s incoherent. But apparently, some people swoon over this kind of muddled thinking.

    Do you envisage that one day an orang gave birth to a chimp, with a whole set of new genes, and then later a chimp gave birth to a human, with another new set?

    Or what do you envisage?

    “Envisaging” is the problem, isn’t it? How did things happen?

    Well, if we look to the fossil record to help us, we don’t see true intermediate forms. And when we document what life can, or cannot do, in a highly detailed way, as is only now possible, we find that proposed Darwinian mechanisms can produce very little change. (cf Behe’s Edge of Evolution)

    So that means Darwin’s theory is out.

    What the fossil record does show, however, is that new forms “suddenly appear” and “suddenly disappear”. So this suggests a stochastic history of life, rather than a continuous one. We also seem to be finding, as we’re discussing here, the new appearance of genes, and, genes that provide a vital difference between one order of beings versus another.

    Now, should this all be attributable to genes? Hard to say. But we know that it has to be more than just genes since regulatory pathways seem to be of extreme importance.

    Now does this mean that “an orangutan gave birth to a chimp’? No. But whatever happened had to have looked more like this than anything Darwinism has to offer since there is no real evidence supporting any role for adaptive forces giving rise to macroevolution (Darwinism), and there is evidence for life evolving in a discontinuous fashion.

    IOW, how can this not be true?

  73. 73
    Joseph says:

    Elizabeth:
    blockquote>Thanks for the link. I rightly surmised that the 99% did not apply to this finding.

    What finding? I responded to your bald assertion.

  74. 74
    bornagain77 says:

    junkdnaforlife, you’ve pegged my position quite well! Save for I would have argued very strongly that Christian Theism is, by far, the best empirically supported position, not merely a choice, among many. In fact a ‘Christian’ interpretation offers a very plausible, empirically backed, reconciliation of General Relativity with Quantum Mechanics:

    First a little background:

    ,,, First I noticed that the earth demonstrates centrality in the universe in this video Dr. Dembski posted a while back;

    The Known Universe – Dec. 2009 – a very cool video (please note the centrality of the earth in the universe)
    http://www.youtube.com/watch?v=17jymDn0W6U

    ,,, for a while I tried to see if the 4-D space-time of General Relativity was sufficient to explain centrality we witness for the earth in the universe,,,

    Where is the centre of the universe?:
    Excerpt: The Big Bang should not be visualized as an ordinary explosion. The universe is not expanding out from a centre into space; rather, the whole universe is expanding and it is doing so equally at all places, as far as we can tell.
    http://math.ucr.edu/home/baez/.....entre.html

    Thus from a 3-dimensional (3D) perspective, any particular 3D spot in the universe is to be considered just as ‘center of the universe’ as any other particular spot in the universe is to be considered ‘center of the universe’. This centrality found for any 3D place in the universe is because the universe is a 4D expanding hypersphere, analogous in 3D to the surface of an expanding balloon. All points on the surface are moving away from each other, and every point is central, if that’s where you live.

    4-Dimensional Space-Time Of General Relativity – video
    http://www.metacafe.com/watch/3991873/

    ,,, yet I kept running into the same problem for establishing the sufficiency of General Relativity to explain our centrality in this universe, in that every time I would perform a ‘mental experiment’ of trying radically different points of observation in the universe, General Relativity would fail to maintain centrality for the radically different point of observation in the universe. The primary reason for this failure of General Relativity to maintain centrality, for different points of observation in the universe, is due to the fact that there are limited (10^80) material particles to work with. Though this failure of General Relativity was obvious to me, I needed more proof so as to establish it more rigorously, so i dug around a bit and found this;

    The Cauchy Problem In General Relativity – Igor Rodnianski
    Excerpt: 2.2 Large Data Problem In General Relativity – While the result of Choquet-Bruhat and its subsequent refinements guarantee the existence and uniqueness of a (maximal) Cauchy development, they provide no information about its geodesic completeness and thus, in the language of partial differential equations, constitutes a local existence. ,,, More generally, there are a number of conditions that will guarantee the space-time will be geodesically incomplete.,,, In the language of partial differential equations this means an impossibility of a large data global existence result for all initial data in General Relativity.
    http://www.icm2006.org/proceed.....l_3_22.pdf

    and also ‘serendipitously’ found this,,,

    THE GOD OF THE MATHEMATICIANS – DAVID P. GOLDMAN – August 2010
    Excerpt: Gödel’s personal God is under no obligation to behave in a predictable orderly fashion, and Gödel produced what may be the most damaging critique of general relativity. In a Festschrift, (a book honoring Einstein), for Einstein’s seventieth birthday in 1949, Gödel demonstrated the possibility of a special case in which, as Palle Yourgrau described the result, “the large-scale geometry of the world is so warped that there exist space-time curves that bend back on themselves so far that they close; that is, they return to their starting point.” This means that “a highly accelerated spaceship journey along such a closed path, or world line, could only be described as time travel.” In fact, “Gödel worked out the length and time for the journey, as well as the exact speed and fuel requirements.” Gödel, of course, did not actually believe in time travel, but he understood his paper to undermine the Einsteinian worldview from within.
    http://www.faqs.org/periodical.....27241.html

    But if General Relativity is insufficient to explain the centrality we witness for ourselves in the universe, what else is? Universal Quantum wave collapse to each unique point of observation! To prove this point I dug around a bit and found this experiment,,,

    This following experiment extended the double slit experiment to show that the ‘spooky actions’, for instantaneous quantum wave collapse, happen regardless of any considerations for time or distance i.e. The following experiment shows that quantum actions are ‘universal and instantaneous’ for each observer:

    Wheeler’s Classic Delayed Choice Experiment:
    Excerpt: Now, for many billions of years the photon is in transit in region 3. Yet we can choose (many billions of years later) which experimental set up to employ – the single wide-focus, or the two narrowly focused instruments. We have chosen whether to know which side of the galaxy the photon passed by (by choosing whether to use the two-telescope set up or not, which are the instruments that would give us the information about which side of the galaxy the photon passed). We have delayed this choice until a time long after the particles “have passed by one side of the galaxy, or the other side of the galaxy, or both sides of the galaxy,” so to speak. Yet, it seems paradoxically that our later choice of whether to obtain this information determines which side of the galaxy the light passed, so to speak, billions of years ago. So it seems that time has nothing to do with effects of quantum mechanics. And, indeed, the original thought experiment was not based on any analysis of how particles evolve and behave over time – it was based on the mathematics. This is what the mathematics predicted for a result, and this is exactly the result obtained in the laboratory.
    http://www.bottomlayer.com/bot.....choice.htm

    Genesis, Quantum Physics and Reality
    Excerpt: Simply put, an experiment on Earth can be made in such a way that it determines if one photon comes along either on the right or the left side or if it comes (as a wave) along both sides of the gravitational lens (of the galaxy) at the same time. However, how could the photons have known billions of years ago that someday there would be an earth with inhabitants on it, making just this experiment? ,,, This is big trouble for the multi-universe theory and for the “hidden-variables” approach.
    http://www.asa3.org/ASA/PSCF/2.....r.html.ori

    Shoot there is even a experiment that shows the preceding quantum experiments will never be overturned by another ‘future’ theory;

    An experimental test of all theories with predictive power beyond quantum theory – May 2011
    Excerpt: Hence, we can immediately refute any already considered or yet-to-be-proposed alternative model with more predictive power than this (quantum theory).
    http://arxiv.org/abs/1105.0133

    ,, and to make universal quantum Wave collapse much more ‘personal’ I found this,,,

    “It was not possible to formulate the laws (of quantum theory) in a fully consistent way without reference to consciousness.” Eugene Wigner (1902 -1995) from his collection of essays “Symmetries and Reflections – Scientific Essays”; Eugene Wigner laid the foundation for the theory of symmetries in quantum mechanics, for which he received the Nobel Prize in Physics in 1963.

    Here is the key experiment that led Wigner to his Nobel Prize winning work on quantum symmetries:

    Eugene Wigner
    Excerpt: To express this basic experience in a more direct way: the world does not have a privileged center, there is no absolute rest, preferred direction, unique origin of calendar time, even left and right seem to be rather symmetric. The interference of electrons, photons, neutrons has indicated that the state of a particle can be described by a vector possessing a certain number of components. As the observer is replaced by another observer (working elsewhere, looking at a different direction, using another clock, perhaps being left-handed), the state of the very same particle is described by another vector, obtained from the previous vector by multiplying it with a matrix. This matrix transfers from one observer to another.
    http://www.reak.bme.hu/Wigner_.....io/wb1.htm

    i.e. In the experiment the ‘world’ (i.e. the universe) does not have a ‘privileged center’. Yet strangely, the conscious observer does exhibit a ‘privileged center’. This is since the ‘matrix’, which determines which vector will be used to describe the particle in the experiment, is ‘observer-centric’ in its origination! Thus explaining Wigner’s dramatic statement, “It was not possible to formulate the laws (of quantum theory) in a fully consistent way without reference to consciousness.”

    I find it extremely interesting, and strange, that quantum mechanics tells us that instantaneous quantum wave collapse to its ‘uncertain’ 3-D state is centered on each individual observer in the universe, whereas, 4-D space-time cosmology (General Relativity) tells us each 3-D point in the universe is central to the expansion of the universe. These findings of modern science are pretty much exactly what we would expect to see if this universe were indeed created, and sustained, from a higher dimension by a omniscient, omnipotent, omnipresent, eternal Being who knows everything that is happening everywhere in the universe at the same time. These findings certainly seem to go to the very heart of the age old question asked of many parents by their children, “How can God hear everybody’s prayers at the same time?”,,, i.e. Why should the expansion of the universe, or the quantum wave collapse of the entire universe, even care that you or I, or anyone else, should exist? Only Theism offers a rational explanation as to why you or I, or anyone else, should have such undeserved significance in such a vast universe:

    Psalm 33:13-15
    The LORD looks from heaven; He sees all the sons of men. From the place of His dwelling He looks on all the inhabitants of the earth; He fashions their hearts individually; He considers all their works.

  75. 75
    bornagain77 says:

    continued:

    The expansion of every 3D point in the universe, and the quantum wave collapse of the entire universe to each point of conscious observation in the universe, is obviously a very interesting congruence in science between the very large (relativity) and the very small (quantum mechanics). A congruence that Physicists, and Mathematicians, seem to be having a extremely difficult time ‘unifying’ into a ‘theory of everything’.(Einstein, Penrose).

    The conflict of reconciling General Relativity and Quantum Mechanics appears to arise from the inability of either theory to successfully deal with the Zero/Infinity problem that crops up in different places of each theory:

    THE MYSTERIOUS ZERO/INFINITY
    Excerpt: The biggest challenge to today’s physicists is how to reconcile general relativity and quantum mechanics. However, these two pillars of modern science were bound to be incompatible. “The universe of general relativity is a smooth rubber sheet. It is continuous and flowing, never sharp, never pointy. Quantum mechanics, on the other hand, describes a jerky and discontinuous universe. What the two theories have in common – and what they clash over – is zero.”,, “The infinite zero of a black hole — mass crammed into zero space, curving space infinitely — punches a hole in the smooth rubber sheet. The equations of general relativity cannot deal with the sharpness of zero. In a black hole, space and time are meaningless.”,, “Quantum mechanics has a similar problem, a problem related to the zero-point energy. The laws of quantum mechanics treat particles such as the electron as points; that is, they take up no space at all. The electron is a zero-dimensional object,,, According to the rules of quantum mechanics, the zero-dimensional electron has infinite mass and infinite charge.
    http://www.fmbr.org/editoral/e....._mar02.htm

    Quantum Mechanics and Relativity – The Collapse Of Physics? – video – with notes as to plausible reconciliation that is missed by materialists (Please note; the ‘infinity problem’ is focused primarily in black holes)
    http://www.metacafe.com/watch/6597379/

    Yet, the unification, into a ‘theory of everything’, between what is in essence the ‘infinite Theistic world of Quantum Mechanics’ and the ‘finite Materialistic world of the 4-D space-time of General Relativity’ seems to be directly related to what Jesus apparently joined together with His resurrection, i.e. related to the unification of infinite God with finite man. Dr. William Dembski in this following comment, though not directly addressing the Zero/Infinity conflict in General Relativity and Quantum Mechanics, offers insight into this ‘unification’ of the infinite and the finite:

    The End Of Christianity – Finding a Good God in an Evil World – Pg.31
    William Dembski PhD. Mathematics
    Excerpt: “In mathematics there are two ways to go to infinity. One is to grow large without measure. The other is to form a fraction in which the denominator goes to zero. The Cross is a path of humility in which the infinite God becomes finite and then contracts to zero, only to resurrect and thereby unite a finite humanity within a newfound infinity.”
    http://www.designinference.com.....of_xty.pdf

    Also of related interest to this ‘Zero/Infinity conflict of reconciliation’, between General Relativity and Quantum Mechanics, is the fact that a ‘uncollapsed’ photon, in its quantum wave state, is mathematically defined as ‘infinite’ information:

    Wave function
    Excerpt “wave functions form an abstract vector space”,,, This vector space is infinite-dimensional, because there is no finite set of functions which can be added together in various combinations to create every possible function.

    Quantum Computing – Stanford Encyclopedia
    Excerpt: Theoretically, a single (photon) qubit can store an infinite amount of information, yet when measured (and thus collapsing the Quantum Wave state) it yields only the classical result (0 or 1),,,
    http://plato.stanford.edu/entr.....tcomp/#2.1

    Moreover there actually is physical evidence that lends strong support to the position that the ‘Zero/Infinity conflict’, we find between General Relativity and Quantum Mechanics, was successfully dealt with by Christ:

    THE EVENT HORIZON (Space-Time Singularity) OF THE SHROUD OF TURIN. – Isabel Piczek – Particle Physicist
    Excerpt: We have stated before that the images on the Shroud firmly indicate the total absence of Gravity. Yet they also firmly indicate the presence of the Event Horizon. These two seemingly contradict each other and they necessitate the past presence of something more powerful than Gravity that had the capacity to solve the above paradox.
    http://shroud3d.com/findings/i.....-formation

    The Center Of The Universe Is Life – General Relativity, Quantum Mechanics, Entropy and The Shroud Of Turin – video
    http://www.metacafe.com/w/5070355

    Turin Shroud Enters 3D Age – Holographic Pictures, Articles and Videos
    https://docs.google.com/document/pub?id=1gDY4CJkoFedewMG94gdUk1Z1jexestdy5fh87RwWAfg

    “Miracles do not happen in contradiction to nature, but only in contradiction to that which is known to us of nature.”
    St. Augustine

    While I agree with a criticism, from a Christian, that was leveled against the preceding Shroud of Turin video, that God indeed needed no help from the universe in the resurrection event of Christ since all things are possible with God, I am none-the-less very happy to see that what is considered the number one problem of Physicists and Mathematicians in physics today, of a ‘unification into a theory of everything’ for what is in essence the finite world of General Relativity and the infinite world of Quantum Mechanics, does in fact seem to find a successful resolution for ‘unification’ within the resurrection event of Jesus Christ Himself. It seems almost overwhelmingly apparent to me from the ‘scientific evidence’ we now have in hand that Christ literally ripped a hole in the finite entropic space-time of this universe to reunite infinite God with finite man. That modern science would even offer such a almost tangible glimpse into the mechanics of
    what happened in the tomb of Christ should be a source of great wonder and comfort for the Christian heart.

    Psalms 16:10
    because you will not abandon me to the grave, nor will you let your Holy One see decay.

    Matthew 28:18
    And Jesus came up and spoke to them, saying, “All authority has been given to Me in heaven and upon earth.”

    Achieved Is The Glorious Work
    http://www.youtube.com/watch?v=StTFG2KJf9M

    further note: It should also be pointed out that Special and General Relativity reveal two very, very different ‘eternalities of time’ within space-time. The ‘eternality of time’ revealed for black holes is rather disturbing for those of us of spiritual persuasion:

    On The Mystery of Time:
    https://docs.google.com/document/d/1FFKL3FeyebpNNyal1DQ64y20zlplVrjkaLXrM0P5ES4/edit?hl=en_US

  76. 76

    Which “bald assertion” of mine did you think it was a response to?

  77. 77
    junkdnaforlife says:

    BA: “you’ve pegged my position quite well!”

    ok good, I thought I was close.

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