Lawless evolution: No physics

By: James V. Kohl | Published on: August 29, 2016

New leader of NIH’s research watchdog faces staff revolt

Partin may be looking to NSF for ideas about how to handle charges of plagiarism. Although 81% of NSF’s research misconduct findings involve plagiarism, ORI has left most plagiarism allegations to institutions to handle.

Plagiarism was so widespread more than 20 years ago that the co-author of my book said to ignore it. The continuation of the problem for two decades has left pseudoscientists in charge and put the claims serious scientists have made in the background.

For example:  Roger Penrose wrote:”How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?

See also: Riding the Evolution Paradigm Shift With Eugene Koonin

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…

A Multicomponent Animal Virus Isolated from Mosquitoes

…average levels of amino acid divergence among the Jingmenviruses… include genome segments with distinct coding strategies and no measurable homology…  On the basis of the extensive sequence-level and structural genomic diversity, this clade of segmented flavi-like viruses appears to be quite old, and it likely includes substantial viral diversity that has yet to be described.

Reported as: New Virus Breaks The Rules Of Infection

“There’s so much we don’t know about viruses…  We should always expect the unexpected,” he says.
“It’s the most bizarre thing,” says Edward Holmes,* a virologist…. It’s like the virus is dismembered, he says.

Professor Edward Holmes studies the evolution and emergence of infectious diseases, particularly the mechanisms by which pathogens jump species boundaries to emerge in humans. Claims about “emergence” fail to link virus-driven energy theft to all pathology and instead tend to link mutations to evolution.
How can the “dismemberment” of the amino acid sequences be linked from recombination to evolution of anything? Who will accept the expert’s claims about the dismemberment of a virus and its emergence during its evolution?
People like Edward Holmes do not seem to have any answers to questions about how ecological variation is linked to ecological adaptation in all living genera. They are puzzled about the origins of viruses
See also: Molecular Clocks and the Puzzle of RNA Virus Origins (2003) by Edward Holmes

… it is clear that we need new models of sequence evolution that incorporate the idiosyncrasies of RNA virus evolution. There are a number of areas where improvements could be made. First, more sophisticated models of nonsynonymous evolution are required, specifically those that allow a limited number of sites to accumulate the vast majority of changes, as may be true of viruses in nature, as well as those that take account of RNA and protein secondary structure (15).

The amino acid sequences of viruses do not “evolve.” Experimental evidence of biologically-based cause and effect links energy-dependent changes in angstroms to ecosystems,  but Holmes assumes that RNA viruses can somehow “evolve” their sequences.
See also:  Edward C. Holmes is co-author of Quantifying influenza virus diversity and transmission in humans.
Reported as: Scientists find minor flu strains pack bigger punch

What was surprising was how readily these variants were transmitted across the studied individuals.  “What stood out was also how these mixes of major and minor strains were being transmitted across the population during the 2009 pandemic—to the point where minor strains became dominant.

Holmes is co-author of the report and also: Faculty Member, Marie Bashir Institute for Infectious Diseases and Biosecurity. All experimental evidence of biologically-based cause and effect links the theft of the sun’s anti-entropic virucidal quantised energy from the amino acid divergence to differences in viruses. His comments link evolutionary forces to all biodiversity. How can he remain so horribly uninformed?
My comment on: The Quest to End the Flu

See also: “Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution”

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?

See the author’s response to my comment:

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

Viral diversity has yet to be described in terms of energy-dependent changes in amino acid substitutions that differentiate all cell types in all individuals of all living genera. Differentiation starts with energy-dependent hydrogen-atom transfer in DNA base pairs in solution. Differentiation is biophysically constrained by the physiology of reproduction.
Viral replication occurs outside the context of the physiology of reproduction, which means the laws of physics must be removed from consideration in the context of neo-Darwinian theory.
See for comparison: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

See also: Epigenetics and Genetics of Viral Latency

… viral latency is responsible for life-long pathogenesis and mortality risk…

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