Viruses, proteins, and gut metagenomes do not evolve

A new family of hybrid virophages from an animal gut metagenome
Excerpt from their conclusion: “These findings further highlight recombination and module shuffling as the central theme in the evolution of viruses and other selfish genetic elements [27]. More specifically, these results indicate that the evolutionary trajectories of Polintons (polintoviruses) and virophages have repeatedly crossed beyond the original, ancestral relationship. Conceivably, the recombination that gave rise to the RVPs involved a virophage and a viral form of a Polinton [23] (polintovirus) within a giant virus-infected amoeba which is known as a “melting pot” for the evolution of diverse selfish elements [28].”
My comment: Viruses adapt to ecological variation via amino acid substitutions. The substitutions have been directly linked from virulence and/or maintenance of viruses in organized genomes to biodiversity via the biophysically constrained anti-entropic chemistry of nutrient-dependent RNA-mediated protein folding in species from microbes to man.
Elsewhere, for example, senior author Eugene Koonin (with others) has stated:
“We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms.” See: Military combat training to fight disease (2)
This observed universal intrinsic trend, which predates the emergence of the last universal common ancestor of all extant organisms is linked to the light-induced de novo creation of amino acids via the experimental evidence reviewed here: On the Origins of Life with my comments about the Virus-driven origin of life.

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