pH-dependent viral latency (1)

By: James V. Kohl | Published on: May 22, 2020

Four back-to-back articles in Science Magazine on May 15, 2020 attest to facts about how God’s Creation of energy-as-information was linked to all biodiversity on Earth via President Donald J. Trump’s claim about UV light and facts about light activated microRNA biogenesis, which biophysically constrains viral latency via the pH-dependent physiology of reproduction.

1) Modeling infectious disease dynamics

The current pandemic has no parallel…, but the new virus is following rules common to other pathogens.

The so-called “rules” are Darwin’s “conditions of life.”

Pandemics end when human populations ecologically adapt to viruses. See this 2007 report from researchers at the CDC: A Two-Amino Acid Change in the Hemagglutinin of the 1918 Influenza Virus Abolishes Transmission

2) Microclimate shifts in a dynamic world

Re: A better understanding of microclimate change… and the biodiversity crisis…

For the current understanding climate change and biodiversity, see: Spindle-shaped viruses infect marine ammonia-oxidizing thaumarchaea

…viral predation has a profound impact on thaumarchaeal functioning and mortality, thereby regulating global biogeochemical cycles.

Global biogeochemical cycles of protein biosynthesis are biophysically constrained by  hydrogen-atom transfer in DNA base pairs in solution.

See: Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution  and UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair

3) Freeman Dyson (1923–2020)

“Dyson…showed how to derive Feynman’s rules from Dirac’s theory mathematically…” [and] “… proved that quantum mechanics explains the stability of matter.”

Feynman linked food energy to coherently organized biology, which explains the stability of cell types:

4) Incompatibilities between emerging species 

Dobzhansky-Muller incompatibilities are food energy-dependent. Pheromones regulate the genetic processes of microRNA-mediated sympatric speciation via fixation of amino acid substitutions, which link RNA interference to biophysically constrained viral latency in species from microbes to humans.

See: [Pheromonal Regulation of Genetic Processes: Research on the House Mouse (Mus Musculus L.)] (1994)

See also: Nutrient-dependent/pheromone-controlled Adaptive Evolution: A Model (6/14/13)

The model from 2013 was extended from physics and chemistry to pH-dependent molecular epigenetics across all levels of biological organization in 2018.

See: Nutrient-dependent Pheromone-Controlled Ecological Adaptations: From Angstroms to Ecosystems 4/18/18

The model of pH-dependent microRNA-mediated ecological adaptations was recapitulated in Optimal Nutritional Status for a Well-Functioning Immune System Is an Important Factor to Protect against Viral Infections (4/23/20)

See also: Unified rational protein engineering with sequence-based deep representation learning 10/21/19

Rational protein engineering requires a holistic understanding of protein function. Here, we apply deep learning to unlabeled amino-acid sequences to distill the fundamental features of a protein into a statistical representation that is semantically rich and structurally, evolutionarily and biophysically grounded.

Energy-dependent biophysical constraints comparisons between the hecatombic evolution of pathology and the polycombic ecological adaptations that link the patent for naturally occurring light-activated RNA interference.
See: RNA-Guided Human Genome Engineering (2015)

5. Repetitive elements or endogenous viral elements can be targeted with engineered Cas+gRNA systems in microbes, plants, animals, or human cells to reduce deleterious transposition or to aid in sequencing or other analytic genomic/transcriptomic/proteomic/diagnostic tools (in which nearly identical copies can be problematic).

Link biophysically constrained RNA interference to the prevention of all virus-driven pathology via quantum biology.
See: Photoactivated biological processes as quantum measurements (2015)

We outline a framework for describing photoactivated biological reactions as generalized quantum measurements of external fields, for which the biological system takes on the role of a quantum meter.

Using coherence to enhance function in chemical and biophysical systems (2017)

Here we survey the state of recent discoveries, present viewpoints that suggest that coherence can be used in complex chemical systems, and discuss the role of coherence as a design element in realizing function.

Molecular Mechanics Simulations and Improved Tight-Binding Hamiltonians for Artificial Light Harvesting Systems: Predicting Geometric Distributions, Disorder, and Spectroscopy of Chromophores in a Protein Environment (2018)

We present molecular mechanics and spectroscopic calculations on prototype artificial light harvesting systems consisting of chromophores attached to a tobacco mosaic virus (TMV) protein scaffold.

Modern Approaches to Exact Diagonalization and Selected Configuration Interaction with the Adaptive Sampling CI Method (2020)

The largest of these calculations is Si2H6 which is a simulation of 34 electrons in 152 orbitals. We also present some preliminary results for fast deterministic perturbation theory simulations…

For comparison, see: Mutation-driven evolution (6/14/13) and ask a theorist how the mutations are biophysically constrained to prevent the virus-driven degradation of messenger RNA that serious scientists have linked to all virus-driven pathology across kingdoms.

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