Wednesday, July 13, 2011

Peak Fallacy: Proteins Evolved Because They Evolved

In spite of common sense and the scientific evidence, evolutionists have once again shown that evolution is a miracle worker. A new paper by evolutionists in the world’s leading journal argues that proteins evolved after all, despite just about every shred of evidence mandating otherwise. And just how did evolution do it again? It turns out proteins evolved because they evolved. If only I had thought of that—I could be an evolutionist too.

Not even wrong

The new paper acknowledges that molecular reality “severely restricts” the mutational changes a protein can undergo. Indeed, “the sparseness of functional protein sequences in sequence space and the ruggedness of the protein fitness landscape” make all but about 2% of the possible mutational changes unacceptable.

But since we know evolution is a fact, then proteins too must have evolved. One is tempted to say the research is wrong, but that would be a compliment. For it isn’t even wrong—it is downright ridiculous.

The fact that it found its way into the world’s leading scientific journal is a testament to how badly evolution has infected science. In the paper (details below), the evolutionists conclude that similar proteins are evolving away from each other faster than distant proteins are evolving away from each other. Just like Hubble’s receding galaxies right? Wrong. Once again evolutionists make a flawed analogy with physics, but that’s another story.

With their circular findings in hand, the evolutionists leap to a series of equally circular conclusions: (i) Rest assured, proteins are still busy evolving though sequence space for evolution has not reached its limit, (ii) All that evidence against protein evolution must be misleading, (iii) Proteins must be evolvable by the magic of epistasis, and (iv) The results are yet more evidence for evolution.

And you thought epistasis was a problem for protein evolution. After all, it makes for a rugged fitness landscape in the protein sequence space, greatly complicating any evolutionary search. Silly you—the evolutionists have turned it into a virtue. Yes it may appear that proteins cannot tolerate much change, but what if that tolerance is ever-changing in just the right way due to epistatic effects? Then the tiny amounts of tolerable change could be, themselves, ever changing. And so evolution can magically find a maze-like path to another protein. Just when you thought you had seen peak fallacy, the evolutionary speculation reaches new heights.

A self-refuting theory

And as usual, what little legitimate science there is in the paper easily refutes the very idea the evolutionists purport to confirm. What the evolutionists get right is that if evolution were true then protein evolution would take a long, long time. What they don’t get around to thinking about is that this undermines their silly thought experiment, which begins 3.5 billion years ago with all manner of proteins already fully formed. That leaves only a few million years for their origin, which isn’t enough time to create them from a warm little pond.

The details


For those who like to waste time probing junk science, here is an explanation of the evolutionary folly in this paper. The evolutionists begin by assuming evolution happened. Not a good start if you want to prove evolution. But moving beyond the usual petitio principii, they next compare similar proteins and find what they think is a curious pattern.

Imagine, for example, three proteins with very similar sequences. These are illustrated below as Proteins 1, 2 and 3. Next, imagine a fourth protein that is a bit more different. If the first three proteins are siblings, the fourth is a cousin.

Now in the first three protein sequences, there are very few differences. One difference highlighted in the notional example below at the third position is the tyrosine amino acid (Y) in Protein 1. It is different from the lysine (K) in Proteins 2 and 3.


But note that Protein 1’s tyrosine is also different from Protein 4, which also has a lysine at the third residue position. When one of the first three proteins differs from the other two, it will likely differ from Protein 4 as well because Protein 4 is fairly similar.

Now consider a second example illustrated below. In this case, Protein 4 is more distantly related. It shares fewer sequence matches with the first three proteins. Because Protein 4 is more distant, differences among the first three proteins, by definition, are less likely to differ from the Protein 4 sequence.

Or in other words, there is a better chance that a difference in one of the first three proteins might actually match the corresponding Protein 4 amino acid. This is illustrated below, as Protein 1’s tyrosine now matches the tyrosine in Protein 4. That would be much more unlikely if Protein 4 was more similar, as in the first example above.


There is nothing clever or profound here. As Protein 4 becomes increasing distant from the first three proteins, it simply follows that differences among the first three might not differ from the fourth sequence.

This simplified explanation is not what the evolutionists did, but it gives a rough idea of the circuitous calculations the evolutionists used to try to confirm evolution. In the end, all they did was to prove a tautology. Below is their “key” result. The straight line illustrates the strong relationship between the distance between proteins and how the differences compare.


Only evolutionists could find this to be significant. As the graph not surprisingly shows, at short distances the differences in the protein sequences are more likely to show (as in the first example above). At greater distances, the differences are less likely to show (as in the second example above).

And given the degree of these differences, something must be slowing evolutionary progress. It must be epistatic effects which the evolutionists then enlist to contrive another one of evolution’s heroic just-so stories. In this case, the epistatic effects change as mutations accumulate so that mutations that once were not tolerable are now tolerable. And amazingly, these epistatic pathways just happen to lead to functional proteins that otherwise are so difficult to find in the protein sequence space.

If you don’t follow all this don’t worry. It is a silly, convoluted tautology that has no place in a scientific journal. Like a Rube Goldberg device that spits out A = A, the research is much ado about nothing.

And yet this is touted as new, novel evidence for protein evolution and common descent. As the evolutionists conclude:

Finally, our observation of receding protein sequences provides novel evidence of the common ancestry of life.

What an astonishing abuse of science. Yet here is how one professor responded to an earlier post of mine regarding protein evolution and this paper:

It's telling that he relies [especially in his point 4: Experiments show that proteins do not tolerate mutations very well] on his misunderstanding of a paper that he has cited repeatedly:

Sequence space and the ongoing expansion of the protein universe by Inna S. Povolotskaya & Fyodor A. Kondrashov, Nature 465, 922–926 (17 June 2010)

Would that I were the problem. Unfortunately evolutionary science—surely an oxymoron if there ever was one—is idiotic. To the uninitiated that may sound like hyperbole but it’s not. When something—like the idea that the universe and everything in it just happened to arise spontaneously—is idiotic, the best word to describe it is “idiotic.”

But when you point out the fallacies the evolutionists blame you. After all, evolution is a fact. Religion drives science and it matters.

22 comments:

  1. When something—like the idea that the universe and everything in it just happened to arise spontaneously—is idiotic, the best word to describe it is “idiotic.”

    Yes... I actually recently came to the conclusion that evolutionists are all crazy - they have a worldview that has no relationship to reality.

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  2. It's posts like this by CH that make me wonder if he has some sort of debilitating mental problems. They seem to be getting worse with time.

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  3. You know what is "idiotic?" Equating theory of evolution with "the universe and everything in it just happened to arise spontaneously." That's certainly idiotic.

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  4. Hunter:

    If you don’t follow all this don’t worry.

    I don't follow much of it; it's about as clear as mud.

    But I'm not worried, because I've learned that communicating a serious scientific critique is not the purpose of Dr Hunter's verbiage. His only aim on this blog is to rhetorically reassure himself and his acolytes (and possibly his employers) that science doesn't threaten their Creationist beliefs.

    It is a silly, convoluted tautology that has no place in a scientific journal. Like a Rube Goldberg device that spits out A = A, the research is much ado about nothing.

    If Dr Hunter seriously meant what he just said, he would apply his scientific expertise to a coherent scholarly analysis, suitable for publication. Surely, if his objections have merit, they could then be appreciated by a wider audience of scientifically literate people. Those people, including editors and reviewers, might then have good reason to re-evaluate their acceptance of the paper's conclusions.

    Nature, suitably chastened, might even retract the paper. Wouldn't that be delicious?

    At the very least, Hunter could post a comment exposing the flaws of the Povolotskaya & Kondrashov paper on the Nature Web site:

    http://www.nature.com/nature/journal/v465/n7300/full/nature09105.html

    Open the link to Comments on that page to see a comment that finds a flaw in the paper's claim that "only approximately 2% of amino-acid substitutions are tolerated at any given moment." (A claim that Dr Hunter has been repeatedly touting on this blog.)

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  5. CH: This simplified explanation is not what the evolutionists did, but it gives a rough idea of the circuitous calculations the evolutionists used to try to confirm evolution.

    Huh? I would seem that Cornelius fancies himself a modern day Shaman who interprets earthly realities in a way that does not conflict with core fundamental Christian theology.

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  6. CH: Only evolutionists could find this to be significant. As the graph not surprisingly shows, at short distances the differences in the protein sequences are more likely to show (as in the first example above). At greater distances, the differences are less likely to show (as in the second example above).

    As Thorton essentially pointed out on another thread, you're disagreeing with us in practice, but not in principle…

    To again, quote David Deutsch…

    This is exactly analogous to why, as I argued, [a single] fossil rabbit in the Jurassic stratum would not refute the theory of evolution: experimental testing is useless in the absence of a good explanation.

    This applies to all experimental testing, not just biological experimental teasing. Yet we do not see you waving your hands about other scientific conclusions.

    Why is this?

    In fact, Deutsch points out that it's impossible to interpret observations without first putting them in some sort of explanatory framework by referencing Bertrand Russell's chicken.

    So, again, it would seem you're objections to evolutionary theory are due to the fact that it cannot meet a criteria that is not only impossible for evolution, but for all fields of science. Nor does it claim to meet said criteria in the first place.

    Furthermore, you have continually failed to answer direct questions which are relative to this very issue. In case you forgot…..

    - AIs there a solution to the problem of induction? If so, what is it?

    - As a confessed Christian, where do you put divine revelation in the traditional hierarchy of deduction, induction and philosophy?

    I'm guessing you cannot disclose your position on this issues as it would reveal the underlying reasons for your selective objections to to evolutionary theory, but not science in general.

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  7. A Few Hundred Thousand Computers vs. A Single Protein Molecule – video
    http://www.metacafe.com/watch/4018233

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

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  8. Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe:
    Excerpt: The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences.
    http://www.ncbi.nlm.nih.gov/pubmed/15321723

    further notes:
    http://www.uncommondescent.com/intelligent-design/peak-fallacy-proteins-evolved-because-they-evolved/#comment-390040

    ReplyDelete
  9. bornagain77,

    your non-stop spamming of threads with the same old videos and links to creationist sites must have caused enough scrolling to power a small city for a year. Are you on Exxon's payroll?

    ReplyDelete
  10. Another excellent post. This science is fascinating.

    I can see that getting the truth out is deeply disturbing your vacuous religious critics. They humorously think that their volume of empty postings can rebut the truth, and that anyone would actually believe them. What a joke they are.

    Any evolutionary scientist, truly an oxymoron, but unfortunately the best description, that can say 'rapid evolution' proves how great a length they will go to defend a false religion.

    .

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  11. This comment has been removed by the author.

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  12. Peter: Another excellent post. This science is fascinating.

    Perhaps you missed the part where even Cornelius admitted...

    CH: This simplified explanation is not what the evolutionists did, but it gives a rough idea of the circuitous calculations the evolutionists used to try to confirm evolution.

    So, you're not even getting "the science."

    While ancient shaman claimed to communicate and act as mediators with the mysterious spirit world, Cornelius plays the role of a modern-day shaman, interpreting and mediating between the mysterious "realm" of scientific observations and the theological beliefs of his fundamental Christian audience.

    After all, Cornelius has gone as far as to claim evolutionary thinking could represent thoughts corrupted by sin.

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  13. It's posts like this by CH that make me wonder if he has some sort of debilitating mental problems. They seem to be getting worse with time.

    I don't know if you're joking or not, but I for one am beginning to genuinely wonder. I don't mean it as a joke or as a roundabout way of insulting him. I am genuinely worried for him.

    The posts since his hiatus earlier this year have continually gotten more and more simplistic. He hasn't directly answered a single comment since his return, and all of the "Response to Comments" posts have had very little to do with the comments that he's supposedly responding to.

    My hope is that the posts since his hiatus are a reaction to a bout of cognitive dissonance brought about by his frequent interactions with the commenters on his blog and a brief shining moment when evolution actually made perfect sense to him. That would mean his recent posts are less about convincing anyone else that he's right, and more about convincing himself that he's been right all along. In that case, who cares about the quality of the posts as long as they reinforce the truth that he still desperately wants to believe.

    The alternative is that the decline in quality is a reflection of a decline in his cognitive abilities for whatever reason. I truly hope this is not the case.

    And who knows...maybe I'm just reading way too much into it. Maybe he just has some major new project in his life and he simply doesn't have time to craft posts with the same rhetorical density as he used to. If this is the case, then more power to you, CH.

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  14. Venture Free said...

    I don't know if you're joking or not, but I for one am beginning to genuinely wonder. I don't mean it as a joke or as a roundabout way of insulting him. I am genuinely worried for him.


    Me too. Despite his comical way over the top anti-science rantings I kinda like the guy. I am always reminded that he allows free uncensored posts from scientifically knowledgeable folks here, which makes him virtually unique among the incestuous Creationist wingnut crowd.

    CH may be a wackaloon, but he's our wackaloon, and I wish him well.

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  15. Thorton is right

    "I am always reminded that he allows free uncensored posts"

    I respect CH for that. While I may disagree with some posters here but I like they have freedom to comment what they think. Compare that to moderation policies on UD.

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  16. Peter: "Another excellent post. This science is fascinating."

    I honestly don't see any science on CH's part here. All here is doing is critiquing some findings from other scientists. and doing it a rather hand-waving fashion without any real details on what his objections are (other than the usual and repetitive polemics).

    He doesn't offer any alternative explanations, or do anything to add to our understanding of protein evolution, or indeed any insight as to how we might even get more knowledge. Doing science adds to the body of knowledge. I have yet to see CH do this yet.

    Whatever it is that CH is doing, it is certainly not science in any generally accepted use of the word. As others have pointed out, there's nothing stopping CH from submitting to journals, writing letters, or many other avenues, but so far his "publishing" seems to be confined to a rather obscure blog with a small audience (and no offense to anybody here but seems to be visited mostly by amateurs rather than professional scientists, although there are of course some that do stop by).

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  17. Ritchie and others,

    For information regarding Doug Axe's research on the probability issues with protein evolution, the links are provided here.

    The first one is regarding his article in the journal of molecular biology. The link for the journal article is at the bottom of the summary article link here (but you need password access to the journal).

    http://biologicinstitute.org/2011/05/04/correcting-four-misconceptions-about-my-2004-article-in-jmb/#more-69


    The link provided here is to other articles regarding similar issues with protein evolution. The links to the articles in pdf format are at the bottom of this link so you can follow the article down to the bottom and click on his references...

    http://biologicinstitute.org/2011/04/16/when-theory-and-experiment-collide/#more-66

    Have a nice weekend.

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  18. An evolutionist said:

    "Whatever it is that CH is doing..."

    Very humourous. He has a PhD in biology critiquing current scientific findings, all a part of the review process which makes science credible in the first place.

    No wonder evolutionists have trouble following the difficult stuff if they can understand the elementary review process.

    .

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  19. Peter: "Very humourous. He has a PhD in biology critiquing current scientific findings, all a part of the review process which makes science credible in the first place. "

    Maybe CH did good work for his PhD, but why now has he essentially dropped out of the scientific community and his only output appears to be this blog? If what he has to say is so vital to the future of science, shouldn't he be making every effort to get his message out in as many ways as possible?

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  20. Neal Tedford said...

    Ritchie and others,

    For information regarding Doug Axe's research on the probability issues with protein evolution, the links are provided here.


    Here is a good overview of Axe's sole paper that appeared in Journal of Molecular Biology.

    Axe (2004) and the evolution of enzyme function

    The review explains in detail what Axe actually calculated, how he once again picked unrealistic example to come up with basically meaningless probability numbers that he can tout as disproving ToE.

    Axe is another religiously driven loose cannon who has set out to confirm his theological beliefs that GAWD did it. To that end he designs experiments (like his evolving one enzyme into another) that while not being outright fraudulent are certainly conceived to produce the low probability numbers he wants as ammo for his religious cause.

    More on Axe's Creationism pushing

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  21. I thought you might appreciate this article Dr. Hunter about the way we interpret data. http://online.wsj.com/article/SB10001424052702303936704576397771567839728.html?mod=wsj_share_twitter

    ReplyDelete
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