My model links the biophysically constrained fixation of nutrient-dependent RNA-mediated amino acid substitutions to the stability of organized genomes. Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
Nutrient-dependent pheromone-controlled stability of organized genomes has since been placed into the context of anti-aging medicine, as I did in presentations from 1994 and 1995.
See: Repression of the Heat Shock Response Is a Programmed Event at the Onset of Reproduction, which was reported as:
It’s a big jump from worms to human beings of course, but the two researchers behind these experiments say there are enough common biological links to suggest that the same technique could be applied to other animals.
My comment: The heat shock response and thermodynamic cycles of protein biosynthesis and degradation are linked to longevity and biodiversity via DNA repair in nematodes and all other organisms. No experimental evidence of biologically-based cause and effect suggests that proteins evolve. Misrepresentations of protein evolution are based on the failure to include what is currently known about virus-perturbed protein folding that prevents amino acids from building functional proteins.
–Eugene Koonin (2015)
See for example:
Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites
… thermodynamic stability provides a wealth of insight into important aspects of protein evolution, such as the evolution of mutational robustness (Bloom et al. 2007), the origin of epistatic interactions (Bershtein et al. 2006, Gong et al. 2013), lethal mutagenesis (Chen & Shakhnovich 2009), determinants of evolutionary rate at protein level (Drummond & Wilke 2008, Serohijos et al. 2012), the evolution of novel function (Bloom et al. 2006, Tokuriki et al. 2008), and the expected equilibrium distributions of stability and the explanation of marginal stability (Taverna & Goldstein 2002, Goldstein 2011, Wylie & Shakhnovich 2011). Moreover, some studies suggest that G-based models are useful to study site-specic constraints. For example, Bloom & Glassman (2009) have shown that changes in stability upon mutation ( G values) are intimately linked to the patterns of amino-acid substitutions observed over evolutionary divergence, to the extent that G values can actually be inferred with accuracy comparable to state-of-the art structure-based methods solely from an alignment of diverged protein sequences. More recently, Arenas et al. (2013) have used stability-based models to predict site-specic amino acid distributions.
Two external factors cause changes in amino acid compositions of proteins in all genera that lead to biodiversity via mortality of individuals. The external factors are nutrient uptake and the pheromone-controlled physiology of reproduction. Together, they link the epigenetic landscape to the physical landscape of DNA in organized genomes via the bio-physically constrained chemistry of protein folding. That is how protein folding can be linked to the conserved molecular mechanisms of ecological adaptations in all species via amino acid substitutions.
Excerpt from a comment by Julian Echave:
The paper that initiated this discussion, deals with evolution at the level of single proteins, without considering epistatic interactions at levels higher than the single-protein level (e.g. protein-protein interactions, co-participation on metabolic networks, etc).
Summary: Anyone who thinks that proteins evolve will be forced to limit discussion to the thermodynamic cycles of protein biosynthesis and degradation that do not extend to organism-level thermoregulation.
Attempts to extend what is known about thermodynamics and organism-level thermoregulation in the context of healthy longevity must continue to ignore virus-perturbed protein folding. Reasearchers ignore the role of viruses because only nutrient-dependent RNA-mediated amino acid substitutions can restore the stability of organized genomes. That stability links ecological variation to ecological adaptations without the evolution of proteins, because the stability of protein folding is nutrient-dependent. Nutrient-dependent organism-level thermoregulation is achieved by suppression or repair of the DNA damage caused by the accumulation of viral microRNAs.
If you eliminate the damage caused by the accumulation of viral microRNAs you cannot link nutrient-dependent microRNAs to organism-level thermoregulation and can therefore claim that it evolved.