Darwinians Find Positive Selection

Yesterday we broadcast seven episodes of the Darwin Fail comedy show. Today, we let some evolutionists claim success for positive natural selection.

Gimme Your Best Shot

Genetic stock speculation. Another paper in Nature Communications does mention “positive selection” along with “purifying selection” (a kind of natural selection that weeds out bad things). Indeed, the authors, including evolutionary free-thinker Eugene Koonin (see ENV), talk about “vertical evolution” and “novel phenotypic traits.” Whoopee! Darwinians should be thrilled—that is, until they look into the details. The paper is about “the evolution of repeats in proteins,” which is like making photocopies of existing information. Repeating random sentences in a book might make the book larger, but it won’t add information. Look at the kind of vertical evolution and positive selection they describe:

To analyse the evolution of repeats and maximize the likelihood that evolutionary rates can be estimated, we develop a rigorous method to extract repeats with conserved length and significant sequence similarity from protein sequences. We validate it and apply it to systematically compare the horizontal and vertical evolution of repeats in diverse groups of organisms. We show that repeats are highly conserved between species, while horizontally propagating and diverging. Thus, each fixed repeat appears to be functionally important in itself and hence subject to purifying selection, whereas in the initial phase of the evolution of repetitive regions, a combination of strongly relaxed purifying selection and positive selection drives fast horizontal divergence of the repeat sequences, presumably yielding new functions. Because variation of repeats plays a crucial role in human disease, in particular neurodegeneration and cancer, the methodology employed here provides means to study somatic horizontal evolution of repeats, and could contribute to the identification of disease drivers associated with this mutational class.

Let’s understand what they just said. They found horizontal evolution, which is like repeating sentences in a book. They only imagine that it might create some kind of benefit: “presumably yielding new functions.” Presumably? Any examples? Yes! Cancer! Neurodegeneration! The Darwin celebration suddenly looks like a disaster.

Now, they do observe that lower organisms have fewer repeats, and that repeats in higher organisms are often associated with important functions, like “chromatin, nucleosome and cellular organization; DNA metabolism; nucleoside phosphate binding; nucleotide and RNA binding; and various metabolic functions.” But to claim those functions arose because of the repeats by “positive selection” begs the question of Darwinian evolution. Do they ever show that a repeat somehow led to a useful new structure, like an eye or a wing, that didn’t exist before? No; it’s all circular reasoning, based on the belief that species must have evolved vertically somehow. If an organism seems more advanced, they assume that it was positively selected. But the evidence is all circumstantial. They don’t tie a repeat to a new recognizable function. Look for that word “presumably” again, and try to find something that Darwinians can rest their faith on:

These findings reveal a dramatic difference between the selection regimes of horizontal and vertical evolution indicating that, although in most of the comparisons dN/dS<1 [indicating negative selection], horizontal evolution of repeats seems to drive them apart, leading to substantial divergence of repeat copies within individual proteins. This divergence contrasts the strong vertical conservation across species, suggesting that not only is purifying selection strongly relaxed once new repeats are generated, but that many repeats are positively selected during evolution following their generation, presumably with functional consequences (Discussion). After a period of strongly relaxed purifying selection (and/or positive selection), the unique functions of the individual repeats appear to be fixed causing a substantial slowdown of vertical evolution.

This is sad. Most of what they observe is “accelerated horizontal evolution,” something young-earth creationists would not find objectionable. In their concluding Discussion, Darwinian evolution falls apart completely, rescued only by imagination. Their use of “scenario” and “suggests” and other storytelling words shows they are only whistling in the dark.

Repeats in protein-coding genes are often viewed as a major source of new raw genetic material, which rapidly evolves and facilitates the acquisition of new functions and complex phenotypic traits. Under this view, a new copy is assumed to be free of selective constraints, such that a new function can emerge rapidly, minimizing the risk of deleterious effects. However, the global conservation of repeats across species puts into question the concept of rapid evolution and the above neofunctionalization scenario. In other words, analogously to the fate of duplicated genes, these observations reflect Ohno’s dilemma, which projects here to paralogous elements within proteins: if repeats are subject to strong purifying selection to maintain a function, how can they rapidly diverge?

In the end, the only thing they appear confident about is that repeats can cause disease.

The results of the present analysis emphasize the potential importance of the evolution of protein repeats in human disease, where horizontal expansion of repeats could play an adaptive role. In particular, cancer is marked by genomic instabilities, which can lead to duplications at all scales, from runs of amino acids to whole-genome duplications, and there is increasing evidence for the existence of a wide spectrum of complex insertion or deletions. These instabilities generate inter- and intra-tumour heterogeneity, which enhances the capacity of cancers to progress, invade and metastasize.

Darwin is not smiling.

If you took out all instances of assuming evolution through imagination, suggestion and speculation, the evidence for Darwinian evolution would collapse in a heap. Everything could just as well fit the worldview of the staunchest young-earth creationist: God designed animals to diversify so that they can survive in changing environments. That’s horizontal evolution of existing information. None of it is due to “positive selection” on random variations by blind, unguided processes. If Koonin’s best example of positive selection is cancer, let’s tell that to the world and see if it drives up the price of Darwin stock.