The bug in the "holy grail" of evolution

Evolution Bug

by Richard William Nelson, October 1, 2015

In one of the largest invertebrate amino acid sequences studies to date, Young and Hebert, found highly variable patterns of amino acid sequences in the enzyme known as cytochrome C between species. None of Charles Darwin’s continuous “successive, slight” evolutionary changes in more than 4,000 species of arachnids studied were found. The paper, published in the highly respected journal PLoS ONE, August, 2015, demonstrates the persistent bug in the theory of evolution – no common ancestor.

My comment: This is an unparalleled accurate representation of facts that link nutrient-dependent RNA-mediated gene duplication and RNA-mediated amino acid substitutions to all cell type differentiation in all living genera via metabolic networks linked to genetic networks. See also: Clinically Actionable Genotypes Among 10,000 Patients With Preemptive Pharmacogenomic Testing. Pharmacogenomic testing links nutritional epigenetics via metabolism to energy-dependent protein folding via amino acid substitutions that stabilize organized genomes.
In the same context, McEwen et al (2015) Mechanisms of stress in the brain  can be compared to Bohacek & Mansuy (2015) Molecular insights into transgenerational non-genetic inheritance of acquired behaviours
McEwen et al (2015) eliminates evolutionary theory via focus on the conserved molecular mechanisms that link nutrient stress and/or social stress from ecological variation to ecological adaptations in all living genera. Bohacek & Mansuy (2015) try to put what is known about the nutrient-dependent innate immune system, cell type differentiation, and the physiology of reproduction into the context of evolutionary theory.
All serious scientists know the outcome of the conflict between McEwen et al (2015) and evolutionary theory. It is not possible to put what is known about RNA-mediated gene silencing or any other aspect of RNA-mediated epigenetic regulation of gene expression into the context of ridiculous theories. The conflict ends when all serious scientists link the “holy grail” of biophysically constrained nutrient-dependent RNA-mediated amino acid substitutions and protein folding to an end to the search for the “holy grail” of evolution.
Simply put, the search for the last universal common ancestor (LUCA) has ended badly for theorists. What is known about molecular epigenetics links ecological variation to ecological adaptation via RNA-mediated amino acid substitutions, without LUCA. Without LUCA, there is no neo-Darwinism; no Modern Synthesis; no evolution industry, and no big bang cosmology industry.
Ecological adaptation starts with the required response of the innate immune system to viruses, which perturb protein folding.

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

I wrote:

The idea of biophysical constraints seems antithetical to the idea of nature somehow selecting mutations that cause amino acid substitutions. However, I am not a biophysicist or evolutionary theorist.
The problem may be my focus on nutrient-dependent receptor-mediated amino acid substitutions in species from bacteria to humans (non-viral organisms). Since I am not a virologist or physicist, I’m not sure that the laws of physics apply to viruses and their replication.
If they do, natural selection for random mutations is not likely to result in amino acid substitutions because the thermodynamics of changes in organism-level thermoregulation preclude such randomness. Stability of protein biosynthesis and degradation that probably depends on protein folding must somehow be controlled. Besides, I don’t know how random mutations in viruses could be naturally selected for inclusion in the human virome (or in the virome of any organism capable of thermoregulating its thermodynamic intercellular signaling).
If the Second Law of Thermodynamics does not apply to viruses, which means the chemical bonds that enable the amino acid substitutions can form at random and somehow be naturally selected, the details of biophysical constraints in this article seems out of place, since I do not think in terms of constrained random mutations and natural selection in mutation-driven evolution.
Hopefully, someone with a background in biophysics will address my confusion in case others are confused. In addition, I wonder if the consequences of understanding the evolutionary mechanisms that govern viruses extend to consequences important to understanding the evolution of species from bacteria to humans via constrained random mutations and natural selection?

When my comment (above) was replaced by the author’s comment on Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution, the facts about evolution became perfectly clear.
Darwin claimed, “conditions of life” must come first. His conditions are nutrient-dependent and controlled by the physiology of reproduction. Top-down causation and the physiology of reproduction link ecological variation to ecological adaptations in all living genera via amino-acid substitutions the stabilize the organized genomes of all living genera.
See also: A universal trend of amino acid gain and loss in protein evolution

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.

My comment: If you have not yet grasped the fact that the claim above means there is no such thing as neo-Darwinian evolution, it is because the neo-Darwinists refuse to admit that they know the facts. (Alternatively, they may not know any.) Like Eugene Koonin, other neo-Darwinists are Riding the Evolution Paradigm Shift to its death. But most others have not admitted that:

The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…

That admission eliminates all the ridiculous claims made by neo-Darwinists who left more biological facts out of the “Modern Synthesis” than they included in the estimates of how long it might take for one species to evolve into another, which never happens. Ecological adaptations happen, not evolution of viruses, proteins, or people.
Patterns of Protein Evolution in Cytochrome c Oxidase 1 (COI) from the Class Arachnida

…cytochrome c oxidase 1 (COI) from more than 400,000 animal species…


…COI sequence data can provide an overview of patterns of amino acid evolution across both other groups of arthropods and animal life at large.

My comment: Animal life and plant life are linked to all biodiversity and all biomass by the conserved molecular mechanisms that link atoms to ecosystems via RNA-mediated epigenetic regulation of gene expression and RNA-mediated gene silencing.

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