Evolutionary Biologist Drops Bombshell On Positive Selection

Austin L. Hughes, an evolutionary biologist at the University of South Carolina writes to the scientific community a bombshell about the evidence gathered for positive section. And it wasn’t pretty for evolutionists…

“Thousands of papers are published every year claiming evidence of adaptive evolution on the basis of computational analyses alone, with no evidence whatsoever regarding the phenotypic effects of allegedly adaptive mutations.”

I have been highly critical and skeptical of computational analyses and simulations of real life behavior…It’s not observational true science in my opinion, but just plain story telling based on many assumptions of unknowns. And it’s not only in biology either, it’s also in other fields of secular science as well. For example, outer space activity is simulated with computers and in one of the more recent attempts is the origin of the very first stars.

Hughes is actually correct in his assessment, evolution has no creditable evidence of “adaptive mutations” that changes one species into another…The vast majority of mutations are harmful to the cell which is why medical research has been focused on fighting the overwriting (mutations).

Hughes continues on with his bombshell of the current evidence for evolution (positive selection) as a major hindrance to progresswhich has been nothing more thanconfusion regarding the role of positive (Darwinian) selection, i.e., natural selection favoring adaptive mutations.”Thousands of papers Hughes writes are “poorly conceived statistical methods that fail to show how the genetic changes relate to adaptive benefits to the organism…” None of which Hughes writes are even on target, in fact he writes they are all 100 percent off target.

“Contrary to a widespread impression, natural selection does not leave any unambiguous “signature” on the genome, certainly not one that is still detectable after tens or hundreds of millions of years.  To biologists schooled in Neo-Darwinian thought processes, it is virtually axiomatic that any adaptive change must have been fixed as a result of natural selection.  But it is important to remember that reality can be more complicated than simplistic textbook scenarios.”

The origin of adaptive phenotypes (the bombshell) written by Austin L. Hughes an evolutionary biologist  and it’s damaging case against evolution cannot be overstated. This is not to say Hughes has now become a true creationist, by no means but hopefully he will someday, Lord willing.

Updated: 04-05-2009…It also interesting to note, some believe they are using positive selection (even though it’s not physically detectable on the genome) to identify the pathogenic mechanisms of HIV in humans which is one example, that has swayed evolutionary proponent Jerry Coyne who previously stated that evolutionary biology has little to do with medicine.

Hughes then concludes…

“In recent years the literature of evolutionary biology has been glutted with extravagant claims of positive selection on the basis of computational analyses alone, including both codon-based methods and other questionable methods such as the McDonald-Kreitman test.  This vast outpouring of pseudo-Darwinian hype has been genuinely harmful to the credibility of evolutionary biology as a science.”

“It is to be hoped that the work of Yokoyama et al. will help put an end to these distressing tendencies.  By incorporating experimental evidence regarding the phenotypic effects of reconstructed evolutionary changes, this study sets a new standard for studies of adaptive evolution at the molecular level.”

“In addition, by providing evidence that non-Darwinian and Darwinian processes are likely to be involved in the evolution of adaptive phenotypes, it points the way toward a new, more realistic appreciation of the evolutionary process.”

There is no physical evidence for positive selection. For further reading on the subject for you techical geeks and even for the average person…AIG has a paper on bacterial mutations which explains in more detail about positive selection, and natural selection in the smallest of animals.

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6 thoughts on “Evolutionary Biologist Drops Bombshell On Positive Selection

  1. I don’t suppose it bothers you in the least that you had to completely misrepresent the content of the cited article to make your point. But at this late date I don’t suppose it matters much because the people who will find this article are those who are searching for the PNAS article, and anyone who can read and comprehend it will simply laugh at your ridiculous and unfounded claims and then move on.

  2. Null,

    What is the drama with you? What are you afraid of, evolution being criticized? Tell me what do you think was misrepresented…

  3. Oh yes. You’ve got me. I’m trembling in terror of evolution being criticized. LMAO.

    And I think I made it clear what was misrepresented: Hughes’ entire article, which was a discussion of a research paper by Yokoyama et al. (2008) demonstrating the origin of adaptive mutations in rhodopsins. The Yokoyama et al. paper showed quite clearly that not only were adaptive mutations of rhodopsins possible, but also that they were common, and only a handful of amino acid substitutions were necessary for an adaptive effect on the phenotype. Twisting this paper in support of the thesis that no adaptive mutations have ever been shown to exist is the inverse of what Hughes was talking about. One can see that perfectly well by the way in which you took an aside that criticized the use of computer models to infer adaption absent any examination of function as a ‘bombshell’ that showed that there was no evidence of adaptive evolution at all. Even the title is a dead giveaway: it’s “The origin of adaptive phenotypes” and not “The absence of adaptive phenotypes”.

    Here’s Austin discussing the findings of the article:

    Their most remarkable finding was that 15 amino acid replacements at just 12 amino acid sites (Fig. 1) could account for the evolution of λmax values of most contemporary vertebrate rhodopsins (3). Moreover, certain of these functionally significant amino acid changes occurred multiple times over the course of evolution. For example, the replacement of alanine by serine at site 292 occurred nine times, and the replacement of aspartic acid by asparagine at position 83 occurred seven times (3). In addition, similar functional effects could be obtained in different ways. For example, they discovered three different combinations of mutations, involving entirely different residues, each of which has the effect of lowering λmax by 14–20 nm (3).

    Thus the adaptive changes are 1) common, 2) simple to produce, and 3) can be produced in multiple ways. Does this really sound to you like Austin is drawing the curtain on the possibility of ever discovering adaptive changes? Actually, don’t answer that: I can guess what the answer would be, and also can guess the extremely long odds that the answer would be based on actually understanding the papers in question.

    Yokoyama, S. et al. (2008) “Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates.”
    PNAS 105(36): 13480-13485.

  4. Null,

    Here is what Austin also says, “This vast outpouring of pseudo-Darwinian hype has been genuinely harmful to the credibility of evolutionary
    biology as a science.”

    He is trying to fix a major problem with Darwinian research. It is not surprising to see thousands upon thousands of papers being produced with the claim of positive selection through a computer program rather than an actual signature in the genome where he says hasn’t been detected in present day animals. Assumption vs. Observation.

    “Contrary to a widespread impression, natural selection does not leave any unambiguous “signature” on the genome, certainly not one that is still detectable after tens or hundreds of millions of years. To biologists schooled in Neo-Darwinian thought processes, it is virtually axiomatic that any adaptive change must have been fixed as a result of natural selection. But it is important to remember that reality can be more complicated than simplistic textbook scenarios.”

    You say, “The Yokoyama et al. paper showed quite clearly that not only were adaptive mutations of rhodopsins possible, but also that they were common…”

    I bet since this paper has been published, there are still many papers produced the same way before Austin’s bombshell of Darwinian research was published. I bet many of them remain unconvinced even though they both believe in mutations being able to do certain things required by evolutionary thought. So which side are you on, really? Darwinian’s evolution interpretation of evolution or Austin’s? Nowhere did I mislead anything but pointed to the fact that there is no direct evidence in Darwinian evolution as pointed out by Austin.

  5. He is trying to fix a major problem with Darwinian research.

    This is, at most, only a minor problem with research in evolutionary biology. By the way, why is it that you cannot use the correct terminology for things? “Darwinian research” is meaningless in the context of evolutionary biology, although it has some currency among historians of science for research into Darwin’s writings, life, and times.

    It is not surprising to see thousands upon thousands of papers being produced with the claim of positive selection through a computer program rather than an actual signature in the genome where he says hasn’t been detected in present day animals.

    He is saying both more and less than that. The problem, as Hughes sees it, is not that there might evidence of adaptive evolution in the genome that we haven’t found yet, but the whole idea of an adaptive signature in the genome is a mistake. So it’s not a matter of not having the evidence in hand, but that you can’t get the evidence. Here I think he’s overstating the case. There have been cases where positive selection has first been detected in the ratio of non-synonymous substitutions to synonymous substitutions and it has led in productive directions, e.g. the discovery of a site critical for retroviral resistance (Sawyer et al. 2004). However, he does have a point about researchers who do the statistical analysis and then publish, without tying the analysis to an analysis of function. Yokoyama et al. DID demonstrate the adaptive nature of the non-synonymous substitutions, which is why Hughes is singling out their paper for praise.

    I bet since this paper has been published, there are still many papers produced the same way before Austin’s bombshell of Darwinian research was published.

    And what way do you think papers were produced prior to Hughes’ review article? (And that’s all it is—it’s just a review article.) Have you ever read a scientific paper directly, unmediated by the distorting lens of lying creationist websites?

    I bet many of them remain unconvinced even though they both believe in mutations being able to do certain things required by evolutionary thought.

    Yeah, I bet many people remain unconvinced by Hughes’ criticisms too. I’m one of them. As I said above, he overstates the case, and there is certainly a role for SNAP (synonymous non-synonymous analysis program) analysis of genomes. But his point is well-taken when he says that such statistical analysis must be tied to an examination of function. If what you are claiming he said was actually what he said, then this warning would be moot because there would be no possible way of inferring adaptive function on the evidence, since the evidence wouldn’t be there. So either you are right about what Hughes said or Hughes is right about what Hughes said, and—since you’re so fond of a “bet”—I know which one I’d put my money on.

    Nowhere did I mislead anything but pointed to the fact that there is no direct evidence in Darwinian evolution as pointed out by Austin.

    Look, this is a lie. Period. Hughes’ criticism is of indirect inference of adaptive evolution from statistical analysis alone. He is not claiming that there is no direct evidence of adaptive evolution. In fact, his whole thesis relies on the fact that Yokoyama et al. did marshal that evidence for adaptive changes in the phenotype. If they hadn’t, then Hughes pointing out that the statistical analysis, unaided by functional analysis, yielded false positives would not have the force it did: how would he know the positives were false unless he had the true positives provided by Yokoyama et al.’s analysis to compare it against? I doubt you have read the paper even by now, but are simply going by what other creationist sites quote mined in their articles. I have read the review paper and the original research paper upon which Hughes was reviewing. In fact, that’s what I was looking for originally when I found this site. I am therefore not going to be impressed by you simply restating the same things I know are false from having read the paper in question. Nor am I going to find it compelling when you snip relevant quotes I have provided and do not reference them in your reply. Do you have anything to say to the fact that Yokoyama et al. discovered that these adaptive mutations were common, simple to produce, and could be produced in multiple ways? Don’t you think that has some relevance to your claim?

  6. Meant to include the full cite:
    Sawyer SL, et al. (2005) “Positive selection of primate TRIM5α identifies a critical species-specific retroviral restriction domain.” PNAS 102(8): 2832-37.

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