Among the phrases most likely to get my attention but least likely to get the attention of an evolutionary theorist is “bacterial proteins evolve.” See for example (with my emphasis): To provide insight into how bacterial proteins evolve to adapt to cold environment….
Most people would assume that evolution led to the ecological adaptation so that these bacteria could survive in a cold environment. In fact, many people must have made that assumption along with all the other assumptions they made when they invented the neo-Darwinian theory of evolution.
“[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. The anglophone tradition was taught. I was taught, and so were my contemporaries, and so were the younger scientists. Evolution was defined as “changes in gene frequencies in natural populations.” The accumulation of genetic mutations was touted to be enough to change one species to another…. No, it wasn’t dishonesty. I think it was wish fulfillment and social momentum. Assumptions, made but not verified, were taught as fact.” Replace the Modern Synthesis (Neo-Darwinism): An Interview With Denis Noble
Given the difficulty of inventing a theory from scratch, the de novo creation of neo-Darwinism was required to start from the evolution of proteins that had already somehow adapted. Moving forward, the population geneticist/creators of evolutionary theory decided that changes in the gene frequencies caused by the evolution of proteins created new species. Others have since noted that “The repertoire of proteins and nucleic acids in the living world is determined by evolution; their properties are determined by the laws of physics and chemistry.” However, in their accurate representation of how physics and chemistry limit the ability of bacterial proteins to evolve into humans, these authors noted that the properties of proteins are determined by the laws of physics. That changes everything!
Everything taught about evolution neglected to mention that the laws of physics made it impossible for functional proteins to evolve. The invention of neo-Darwinism left out physics and physicists accepted their fate.
No one ever understood what physicists talked about, anyway. The popularity of neo-Darwinism let them enter discussions of how species evolved via protein evolution. For example, “As proteins evolve, they follow trajectories along edges through the genotype–phenotype space.” Finally, physicists could discuss the evolution of morphological and behavioral phenotypes in the context of natural selection instead of the Laws of Physics. The question arose: Does selection against misfolding and aggregation due to translational errors explain why certain codons for the same amino acid are observed more frequently than others54–56?
The answer was: Who cares? What’s an amino acid? Natural selection somehow selects, who cares how it selects whatever it selects?
Answering these questions requires evaluating the role of an evolutionary force — natural selection in this case — on physical properties, so an approach that synthesizes the two modes of analysis is necessary.
The prevention of misfolding and aggregation by the nutrient-dependent thermodynamics of amino acids substitutions and protein folding that stabilizes DNA in the organized genomes of species from microbes to man was eliminated from any further consideration by physicists or evolutionary theorists. They have continued to invent more theories about protein evolution via natural selection. They never tried to teach anyone about biophysical constraints that prevent increasing organismal complexity from arising due to perturbed protein folding. Those biophysical constraints enable nutrient-dependent amino acid substitutions to facilitate the epigenetically-effected link from ecological variation to ecological adaptions in species from microbes to man. See for examples:
“Recent studies have also offered detailed information about the composition of specific populations from around the world, revealing how [their RNA-mediated] history has shaped their genetic makeup.”