Codon optimality vs systemic fraud (1)

By: James V. Kohl | Published on: June 5, 2022

Two summaries of neo-Darwinian evolutionary theory:

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

…yeast receptors trigger activation of heterotrimeric G proteins just as mammalian receptors do, this conserved signaling pathway must have been present in the common ancestor of yeast and humans.

Unless you are a biologically uninformed theorist, see first Epistemic corruption (10)

Watch for my next 10-part series on Codon optimality vs systemic fraud. I will link it to the fraudulent representations in the special issue of Science Magazine published on 5/27/22 as “The Systemic Microbiome” and the molecular epigenetics section of our 1996 Hormones and Behavior review of energy-dependent microRNA-mediated stem cell creation and differentiation: From Fertilization to Adult Sexual Behavior

Neo-Darwinian theorists have since bastardized everything known to serious scientists about biophysically constrained viral endemicity across kingdoms.

See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system” 2/27/15 was reported as

and linked from
3) the end of the 1918 Spanish influenza via A two-amino acid change in the hemagglutinin of the 1918 influenza virus abolishes transmission 2/3/07 to former President Trump’s 4/23/20 claim that
The fact that sunlight and humidity protect all organized genomes from the virus-driven degradation of messenger RNA and all virus-driven pathology has been placed into the context of this historical perspective from 5/31/22.
Molecular phylogenies map to biogeography better than morphological ones

…molecular trees provide a better fit to biogeographic data than their morphological counterparts and that biogeographic congruence increases over research time. We find no significant differences in stratigraphic congruence between morphological and molecular trees.

The congruence of morphological and molecular trees has consistently been placed by intelligent serious scientists into the context of sympatric speciation.
A Google search for sympatric speciation suggests that it occurs when there are no physical barriers preventing any members of a species from mating with another, and all members are in close proximity to one another. A new species, perhaps based on a different food source or characteristic, seems to develop spontaneously.

If a different food source is required, there is no support for the claim that new species develop spontaneously. For comparison to the magic of spontaneous sympatric speciation, Thomas Hunt Morgan (1910) presciently linked nutrient-dependent pheromone-regulated genetic processes of reproduction from chromosomal rearrangements in flies to sympatric speciation across kingdoms via natural selection for energy-dependent codon optimality and fixation of amino acid substitutions in organized genomes.

The facts were subsequently placed into the context of prevention of all mental and physical pathology in “Puberty: ontogeny, neuroendocrinology, physiology, and disorders.” (1992) Williams Textbook of Endocrinology.

“noradrenergic, dopaminergic, serotoninergic, and opiotergic pathways; inhibitory neurotransmitters (e.g., gamma aminobutyric acid) and excitatory amino acids (e.g., glutamic and aspartic acids); and other brain peptides including pineal secretions (melatonin) and corticotrophin releasing hormone, and the complex interactions among them are subtle but functional species-specific influences on the electrochemical transmission of neuronal signals that the hypothalamus translates to the chemical signal GnRH. (p. 1164).

The claim about the chemical signalling pathways was cited in: Molecular Mechanisms of Hormone Actions on Behavior Anne M. Etgen, ‎Donald W. Pfaff – 2010 Neuroendocrine Regulation of Puberty
See also: Williams Textbook of Endocrinology, 12th Edition, which bastardized the claims of all intelligent serious who understand the molecular mechanisms of behavior by placing them into the context of: THE EVOLUTIONARY PERSPECTIVE

Hormones can be defined as chemical signals secreted into the bloodstream that act on distant tissues, usually in a regulatory fashion. Hormonal signaling represents a special case of the more general process of signaling between cells. Even unicellular organisms, such as baker’s yeast, Saccharomyces cerevisiae, secrete short peptide mating factors that act on receptors of other yeast cells to trigger mating between the two cells. These receptors resemble the ubiquitous family of mammalian seven-transmembrane spanning receptors that respond to ligands as diverse as photons and glycoprotein hormones. Because these yeast receptors trigger activation of heterotrimeric G proteins just as mammalian receptors do, this conserved signaling pathway must have been present in the common ancestor of yeast and humans. Signals from one cell to adjacent cells—so-called paracrine signals—often trigger cellular responses that use the same molecular pathways used by hormonal signals.

No experimental evidence of biologically based cause and effect is linked to a common ancestor of yeast and humans. Thank God, my mentor, Bruce S. McEwen, told me I needed to link the claims of Robert L. Moss about c-fos activation in GnRH neurons to biophysically constrained ATP-dependent RNA-mediated protein folding chemistry via God’s Creation of RNA.
See for comparison: The extent of codon usage bias in human RNA viruses and its evolutionary origin (2003)

…the strong correlation between base and dinucleotide composition and codon usage bias suggested that mutation pressure rather than natural (translational) selection is the most important determinant of the codon bias observed.

The truth about natural selection for energy-dependent codon optimality can be linked to every indexed publication that mentions microRNAs and allostery. For instance, Domino effect in allosteric signaling of peptide binding 5/28/22 links Peptide synthesis at the origin of life 11/13/20 from Footprints of a Singular 22-Nucleotide RNA Ring at the Origin of Life 4/25/20 to more than 200 patents for therapeutic solutions that link stem cells to prevention of virus-driven pathology. Please revisit any model that links the energy-dependent architecture of RNA-peptide interactions at the origin of life to viral endemicity and healthy longevity across kingdomss.
For instance, light-activated microRNA biogenesis has been linked from quantum coherence to coherently organized biology via Translation affects mRNA stability in a codon-dependent manner in human cells (2019) and what is known about the chemistry-to-biology (CTB) transition.
The transition links light-activated carbon fixation in cyanobacteria to microRNA-mediated protein folding chemistry via the pH-dependent physiology of pheromone-regulated genetic processes of reproduction and the patented cure for all virus-driven pathology held by George M. Church et al.
RNA-Guided Human Genome Engineering  7/2/15
Details of these all encompassing works on natural selection for codon optimality and protection from viruses were included in the STEM toy “Genotype” for ages 14+ Note, however, it is not legal to patent a naturally occurring process that links God’s Creation of sunlight and humidity from photosynthesis to protection from viruses across kingdoms.
See also: Distinct responses to rare codons in select Drosophila tissues 5/6/22. Reported as: Fly researchers find another layer hiding in the code of life 5/19/22

A decade after solving the structure of DNA as a double helix of the bases A,C, T and G, Francis Crick went on to decode the intermediate step by which three of these letters are translated into a “codon,” the recipe for a single amino acid, the building block of protein.

That fact casts doubt on this claim from A universal trend of amino acid gain and loss in protein evolution 1/19/05

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

See for comparison:  How life could have arisen on an ‘RNA world’ 5/11/22

At the moment, the ribosome simply falls from the heavens,” says Thomas Carell, a chemist at Ludwig Maximilian University of Munich.

See for comparison: MicroRNAs affect GPCR and Ion channel genes needed for influenza replication 11/17/21
There is no mention of amino acids in the context of viral replication. But wait!
Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon 5/20/22

This shows that there exists a dependence between codon identity and backbone torsion of the translated amino acid.

See for comparison: A microRNA or messenger RNA point of departure estimates an apical endpoint point of departure in a rat developmental toxicity model 5/21/22
With no mention of the fact that amino acid substitutions determine the energy-dependent endpoint compared to the virus-driven degradation of mRNA, which links mutations to all diseases, the context of the microRNA/messenger RNA (mRNA) balance goes missing, and facts become theories.
On 6/26/19, a friend and I stopped at the Scopes Museum in Dayton, Tennessee to make sure I could view this presentation of facts on my laptop computer via a hotspot wi-fi connection.
See: Genome-Wide Study Reveals a Novel Regulatory Pathway: Translation Affects mRNA Stability in a Codon-Dependent Manner 6/26/19 (available for free on demand with registration).
I may try to find my on-location video to show that, as predicted, the presentation put an end to all the nonsense about natural selection for beneficial mutations and evolved biodiversity during billions to millions of years. That pseudoscientific nonsense has been touted since it began, a few decades after the time of the Scopes Trial in 1925.
On 6/26/19, Ariel Bazzini presciently established that God’s ATP-dependent Creation of RNA links microRNA-mediated pH-dependent fixation of amino acid substitutions from quantum coherence to coherently organized biology via microRNA-mediated stem cell creation.
See: MicroRNAs organize intrinsic variation into stem cell states 3/5/20

…naturally arising cell-to-cell variation, sometimes described as stochastic fluctuation, is in fact coherently organized biology.

See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition 7/9/16

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

See for comparison to Bazzini’s works: Exploring evolutionary immunogenomics: Lessons from our ancestors and past pandemics 4/20/22
It’s a theory-based killer of men, women, and children.

During this webinar, viewers will:

Gain insight into how past pandemics, such as Yersinia pestis, the agent of the Black Death, led to the evolution of the human immune system

Discover how the unique immunogenetic variation in present-day populations has impacted population differences in immune response to pathogens and susceptibility to immune-related disorders

Learn how cutting-edge techniques, such as RNA sequencing (RNA-seq), are used in evolutionary immunogenomics

SARCASM ALERT:  Someone else may want to link the pseudoscientific nonsense about mutations and evolutionary immunogenomics to unnecessary suffering and premature death. No wait! They already have. It seems like only yesterday. This is when it happened.
See: Codon optimality-mediated mRNA degradation: Linking translational elongation to mRNA stability 4/21/22

…transient pauses induce a unique ribosome conformational state that is probed by the deadenylase complex, thereby inducing an orchestrated set of events that enhance both poly(A) shortening and cap removal. Together, these data imply that the coding region of an mRNA not only encodes for protein content but also impacts protein levels through determining the transcript’s fate.

See also: and learn more about how to prevent virus-driven existential threats at as this 10-part series continues.

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