More than another year has passed, but here is a new attempt to present old information on biophysically constrained viral latency as if the information was new.
Pervasive Strong Selection at the Level of Codon Usage Bias in Drosophila melanogaster 12/23/19 (senior author, Dmitri Petrov)
Our findings support a new model of CUB [codon usage bias] and indicate that the functional importance of CUB, as well as synonymous sites in general, have been underestimated.
Throughout his career, Dmitri Petrov underestimated the functional importance of CUB in species from yeasts to primates.
See for example: Hidden Complexity of Yeast Adaptation under Simple Evolutionary Conditions 2/8/18
These results reveal hidden complexities of the adaptive process even under ostensibly simple evolutionary conditions, in which fitness gains can accrue during time spent in a growth phase with little cell division, and reveal that the memory of those gains can be realized in the subsequent growth cycle.
We revealed the hidden complexities of nutrient-dependent pheromone-controlled ecological adaptations to viruses in species from yeasts to primates in our 1996 Hormones & Behavior review of RNA-mediated cell type differentiation.
See our section on molecular epigenetics in From Fertilization to Adult Sexual Behavior.
Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.
Thank God, Greg Bear accurately represented our claims from 1996 and other claims about food energy and pheromones from The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002).
For example, Dmitri Petrov bastardized our claims in Viruses are a dominant driver of protein adaptation in mammals 5/17/16
When an environmental change occurs, species are able to adapt in response due to mutations in their DNA. Although these mutations occur randomly, by chance some of them make the organism better suited to their new environment. These are known as adaptive mutations.
Biophysically constrained energy-dependent RNA-mediated fixation of amino acid substitutions in organized genomes is adaptive. Adaptive mutations exist only in the context of ridiculous theories.
See Dmitri Petrov’s continuation of pseudoscientific nonsense in Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans 10/4/18
Reported as: Modern humans inherited viral defenses from Neanderthals 10/4/18 and on 10/5/18 as Neanderthal liaisons bestowed virus-fighting genes on humans
The facts about viruses have been virtually ignored for 92 years.
Ariel Bazzini and others have tried to correct the errors of theorists with publications like this:
Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition 7/19/16 and in on-demand video presentations like this: Genome-Wide Study Reveals a Novel Regulatory Pathway: Translation Affects mRNA Stability in a Codon-Dependent Manner 6/26/19
It has become clearer, however, that biologically uninformed theorists will continue to tout their theories until everyone learns that the patent for microRNA-mediated effective treatment and/or prevent of all cancers convinces all intelligent people that the theorists are fools.