Finding Darwin in All the Wrong Places
Despite the fact that proponents of neo-Darwinian evolution claim to understand the origin of new genetic information, they obscure the fact that they lack explanations for such by making vague appeals to mechanisms such as "gene duplication," "rearrangement," and "natural selection." Such mechanisms are generally inferred from circumstantial evidence, i.e. similarities and differences between gene sequences, where a neo-Darwinian evolutionary history is assumed. More importantly, accounts that invoke such mechanisms almost never attempt to assess the likelihood of mutations producing the genetic changes in question. In this regard, important notes of caution must be observed when assessing evolutionary accounts of the origin of a gene.
A 2007 article by evolutionary biologist Michael Lynch in Proceedings of the National Academy of Sciences USA goes to the heart of some of the assumptions inherent in many claims of neo-Darwinian evolution. Lynch provides a list of myths promoted by biologists, and he calls it a "myth" to believe that "Characterization of interspecific differences at the molecular and/or cellular levels is tantamount to identifying the mechanisms of evolution."18
Of course, one of the typical "mechanisms of evolution" cited is natural selection, commonly invoked to account for how a gene duplicate acquires a new function. But what kind of evidence is sufficient to demonstrate that positive selection, or natural selection acting to preserve adaptive mutations, has occurred? Biologist Austin Hughes warns that most inferences of positive selection are based upon questionable statistical analyses of genes:
A major hindrance to progress has been confusion regarding the role of positive (Darwinian) selection, i.e., natural selection favoring adaptive mutations. In particular, problems have arisen from the widespread use of certain poorly conceived statistical methods to test for positive selection. 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. ... 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. ... In recent years the literature of evolutionary biology has been glutted with extravagant claims of positive selection on the basis of computational analyses alone ... This vast outpouring of pseudo-Darwinian hype has been genuinely harmful to the credibility of evolutionary biology as a science.19
In short, evolutionary biologists commonly assume that mutations that change protein sequence were fixed by natural selection, but this assumption may not hold true since many such mutations are neutral and confer no selective advantage.
Biochemist Michael Behe offers another reason not to infer neo-Darwinian mechanisms of change based upon mere evidence of sequence similarity:
Although useful for determining lines of descent ... comparing sequences cannot show how a complex biochemical system achieved its function--the question that most concerns us in this book. By way of analogy, the instruction manuals for two different models of computer put out by the same company might have many identical words, sentences, and even paragraphs, suggesting a common ancestry (perhaps the same author wrote both manuals), but comparing the sequences of letters in the instruction manuals will never tell us if a computer can be produced step-by-step starting from a typewriter. ... Like the sequence analysts, I believe the evidence strongly supports common descent. But the root question remains unanswered: What has caused complex systems to form? 20
[M]odern Darwinists point to evidence of common descent and erroneously assume it to be evidence of the power of random mutation. 21
Many scientific papers purporting to show the evolution of "new genetic information" do little more than identify molecular similarities and differences between existing genes and then tell evolutionary just-so stories of duplication, rearrangement, and subsequent divergence based upon vague appeals to "positive selection" that purport to explain how the gene arose. But exactly how the gene arose is never explained. In particular, whether chance mutations and unguided natural selection are sufficient to produce the relevant genetic changes is almost never assessed. 22 These scientific papers--especially the citation bluffs offered by the NCSE / Judge Jones / Ken Miller--play the Gene Evolution Game, an easy game to play which ultimately tells us little about the origin of new functional genetic information, as we'll see the next installment of this series.
[18.] Michael Lynch, "The frailty of adaptive hypotheses for the origins of organismal complexity," Proceedings of the National Academy of Sciences, Vol. 104:8597--8604 (May 15, 2007).
[19.] Austin L. Hughes, "The origin of adaptive phenotypes," Proceedings of the National Academy of Sciences USA, Vol. 105(36):13193--13194 (Sept. 9, 2008) (internal citations removed).
[20.] Michael J. Behe, Darwin's Black Box: The Biochemical Challenge to Evolution, pgs. 175-176 (Free Press, 1996).
[21.] Michael J. Behe, The Edge of Evolution: The Search for the Limits of Darwinism, pg. 95 (Free Press, 2007).
[22.] See for example, "Limits on Evolution" at http://ncseweb.org/creationism/analysis/extrapolations