Sept 5, 2008 — Erase all that evidence for positive natural selection in the genes you’ve read about.  It’s all misleading confusion based on “certain poorly conceived statistical methods,” argues Austin L. Hughes, an evolutionary biologist at the University of South Carolina.  Writing a commentary in PNAS, he accused, “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.”…

Hughes described how the typical paper uses an “unwarranted generalization” from one classic case in which relative frequencies of synonymous and nonsynonymous mutations seemed to be related to the forces of positive selection.  Since then, evolutionists have recklessly applied instances of dN > dS as evidence of positive selection.  This assumption is “demonstrably false,” Hughes argued, because due to the stochastic nature of mutations, such inequalities are just as likely to occur by chance, without any adaptive value.  “Yet, despite their shaky foundations, numerous publications have used these methods as the basis for claims of positive selection at the molecular level.”  In fact, using the Yokoyama et al paper to test the codon-based methods and Bayesian methods so often used in the literature, Hughes found them to be “100% off-target.”  The mutations putatively showing positive selection, in other words, bore no relation to the ones Yokoyama et al found to be adaptive.  “These results support the theoretical prediction that, because of the faulty logic in their underlying assumptions, codon-based focus mainly on statistical artifacts rather than true cases of positive selection.”  Has Hughes just falsified thousands of papers published each year?…

Hughes is merciless in his conclusion:

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.

More… (source)

Advertisements