Evolution: a different view with loss of traits; not Behe (Introduction)

by David Turell , Thursday, February 18, 2021, 01:53 (1374 days ago) @ David Turell

A new Darwinist paper that supports Behe:

https://www.nature.com/articles/s41437-021-00403-2

Abstract:

"Discoveries of adaptive gene knockouts and widespread losses of complete genes have in recent years led to a major rethink of the early view that loss-of-function alleles are almost always deleterious. Today, surveys of population genomic diversity are revealing extensive loss-of-function and gene content variation, yet the adaptive significance of much of this variation remains unknown. Here we examine the evolutionary dynamics of adaptive loss of function through the lens of population genomics and consider the challenges and opportunities of studying adaptive loss-of-function alleles using population genetics models. We discuss how the theoretically expected existence of allelic heterogeneity, defined as multiple functionally analogous mutations at the same locus, has proven consistent with empirical evidence and why this impedes both the detection of selection and causal relationships with phenotypes. We then review technical progress towards new functionally explicit population genomic tools and genotype-phenotype methods to overcome these limitations. More broadly, we discuss how the challenges of studying adaptive loss of function highlight the value of classifying genomic variation in a way consistent with the functional concept of an allele from classical population genetics.

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"Only relatively recently, through discoveries enabled by the availability of molecular sequence data, were alternative views of adaptive loss-of-function alleles formalized, most notably with the “less is more” ideas proposed by Olson (1999). Classical paradigms of molecular evolution had by that time been challenged, for example, by evidence that natural loss-of-function variants of CCR5 lead to reduced HIV susceptibility in humans (Libert et al. 1998). Discoveries during the subsequent two decades have continued to support the idea that loss of function contributes to adaptation (Murray 2020), with cases of adaptive or beneficial loss of function being discovered across diverse organisms, genes, traits, and environments.

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"Comparisons of gene content between distantly related species have revealed considerable evidence for adaptation via complete deletion of genes or even entire sets of functionally related genes (Wang et al. 2006; Blomme et al. 2006; Will et al. 2010; McLean et al. 2011; Griesmann et al. 2018; van Velzen et al. 2018; Sharma et al. 2018; Huelsmann et al. 2019; McGowen et al. 2020; Baggs et al. 2020).

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"First principles and empirical evidence indicate that many types of mutations can have effects that are equivalent to total gene loss, and for the purposes of this review, we employ this definition of complete gene losses being functionally equivalent to other loss-of-function mutations such as premature stop codons. However, there is the practical difficulty that these different types of mutations vary in how easily they can be detected and correctly annotated as loss-of-function alleles."

Comment: This is a Darwinist article in Nature!!! (Actually, Nature Heredity) Devolution does exist and is recognized by folks not at all related to ID. Much of the article discusses the difficulties in identifying the devolutionary mutations. Many articles are referenced in this review article. So, Behe's theory is well known outside ID.