Energy as information and constrained endogenous RNA interference

By: James V. Kohl | Published on: January 31, 2017

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On January 30, 2017 Jon Lieff published this article to his blog site. The First Virus Communication Signals
He recapitulated the works I have published during the past two decades without citing any supporting evidence for his claims.
This is the draft copy of a poster presentation I was preparing to submit for consideration at Precision Medicine (2017). I am posting it to my blog site to show that those who do not support their claims with citations to experimental evidence will continue to have an advantage over serious scientists.
Simply put, they can also take all the works cited in this forthcoming presentation and pretend that they always knew how to link the sun’s anti-entropic virucidal energy to all biodiversity via the conserved molecular mechanisms that have been detailed by serious scientists.

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Fact: The ribosome links the epigenetic landscape to the physical landscape of supercoiled DNA. The ribosome acts as a molecular decoder and a sensor that couples changes in the efficiency of messenger RNA (mRNA) translation to its biophysically constrained stability, which is regulated by energy-dependent stop codons. (1)
Alternative: Temperature-dependent biological processes could occur within a range from –50°C, where cells vitrify, to +140°C if, in theory, nucleic acids spontaneously hydrolyze. (2)
Elaboration: The speed of light on contact with water links adenosine triphosphate (ATP) from energy-dependent changes in chirality and hydrolysis to phosphorylation. The anti-entropic virucidal effects of sunlight link the energy-dependent creation of RNA to the innate immune system. For example, the de novo creation of G protein-coupled receptors (GPCRs) is energy-dependent.
Feedback loops link odor and pheromone signaling from ATP to the physiology of reproduction via GPCRs and nutrient energy-dependent phosphorylation. The innate immune system links chirality and autophagy to biophysically constrained RNA-mediated protein folding chemistry in all living genera. Nutrient energy-dependent fixed RNA-mediated amino acid substitutions in supercoiled DNA protect all organized genomes from virus-driven energy theft.
For example, nutrient energy-dependent endogenous RNA interference (RNAi) has been linked to cell type differentiation and species diversity via nutritional epigenetics and the pheromone-controlled physiology of reproduction in nematodes. (3)
Summary and example: “….the epigenetic effects of food odors and pheromones are involved in neurogenic niche construction as exemplified in nematodes…” See Bumbarger et al., (2013) as cited in Kohl (2013). (4)
Nutrient energy-dependent pheromone-controlled quorum sensing links codon identity to the biophysically constrained stability of mRNA. Natural selection for energy-dependent codon optimality appears to be the link from Darwin’s “conditions of life” to endogenous RNAi and all biodiversity via conserved molecular mechanisms in all living genera. (5)
The ATP-dependent creation of RNA links energy from endogenous RNAi to the stability of mRNA and healthy longevity. That fact underlies every aspect of metabolic theory, which predicts how nutrient energy-dependent changes are linked from angstroms to ecosystems via genetic networks in all living genera. (6)
RNAi pathways appear to link ATP from hydrogen atom transfer in DNA base pairs in solution to microRNA flanking sequences and to all morphological phenotypes and behavioral phenotypes via the transgenerational epigenetic inheritance of healthy longevity. (7-12)
Alternative facts and the ‘arbitrium’ system link communication among viruses and bacteria to all biodiversity on Earth inside and outside the context of quorum sensing. Inside the context of quorum sensing, viruses must decide how much energy to steal from cell types. Outside the context of quorum sensing in bacteria, the viruses tell each other exactly how much energy to use to link RNA-mediated amino acid substitutions to the stability of their organized genomes via minimal mutational distances and/or de novo mutations. (13-15)
In theory, when a specific cell type realizes that energy is missing, the cell type somehow links chirality and autophagy to protect its supercoiled DNA from more damage. That theory links alternative facts about the ‘arbitrium’ system from de novo mutations to evolution.
Theories of mutation-driven evolution fail to explain any aspect of what is known to those who have linked energy-dependent changes from angstroms to ecosystems in all living genera via the physiology of reproduction. Two song parodies link the difference in theory to what is known about energy-dependent changes in base pairs and biophysically constrained protein folding chemistry. (16-17)
Two recently published articles by co-authors who are 2016 Nobel Laureates, link chirality (18) to autophagy and endogenous RNAi. The current understanding of RNAi surpasses all understanding of systems complexity that was placed into the context of RNA-mediated DNA methylation. (19)
Until now, most researchers have failed to link light-induced changes in chirality to the biophysically constrained structure of supercoiled DNA. That fact makes the difference between metabolic theory and the arbitrium’ system clear. Metabolism explicitly and quantitatively links the natural selection of food to the control of the carbon cycle at every level of examination that is required to link what organisms eat to supercoiled DNA via the physiology of reproduction. No alternative facts or theories are required. Supercoiled DNA links everything known about cell type differentiation in all individuals of all species to energy-dependent ecosystems and the Earth’s biosphere.
Energy-dependent links from angstroms to ecosystem are clearly manifested in endogenous RNAi, which links fixation of RNA-mediated amino acid substitutions in all differentiated cell types to the Precision Medicine Initiative. For comparison, links from virus-driven energy theft and gene-editing via the CRISPR-Cas9 technology are included in this proposal for the treatment of pathology. (20)
In the context of human genome engineering: 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).
Simply put, viruses are used to edit DNA in genomes that are damaged by virus-driven energy theft. Researchers who use this technology think they can biophysically constrain virus-driven energy theft with directed virus-driven editing.
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The current political climate in the USA indicates that a paradigm shift has occurred. The National Microbiome Initiative and the Precision Medicine Initiative collectively may block attempts to deliver an exogenous RNAi-based treatment. The treatment has been referred to as a “billion dollar baby.”
The alternative to spending billions to perfect the treatment, which may cost more than what most people can afford, will require all scientists to learn what is known about how the microbiome and metabolic networks are linked to precision medicine by genetic networks.
In the context of precision medicine, learning more about how ecological variation and endogenous RNAi link metabolism to energy-dependent ecological adaptation in species form microbes to humans may make more sense than learning more about the use of viruses to repair DNA damage caused by virus-driven energy theft.
For example, Roger Penrose inadvertently linked energy-dependent endogenous RNAi to exogenous RNAi when he 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?“(8 August 1991) in (21)
Also, photoconvertible fluorescent proteins link energy-dependent endogenous RNAi (22) to the substitution of achiral glycine in position 6 of the GnRH decapeptide, (23) which links the pheromone-controlled physiology of reproduction in all vertebrates to the conserved molecular mechanisms of RNA-mediated protein folding chemistry in all living genera.
Every aspect of detailed top-down causation appears to link angstroms to ecosystems via energy-dependent RNA-mediated protein folding chemistry. The energy links what organisms eat to the receptor-mediated functional structure of supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy. (24)
Cell type differentiation is energy-dependent and RNA-mediated via G protein-coupled receptors and amino acid substitutions in supercoiled DNA
1) ATP hydrolysis by UPF1 is required for efficient translation termination at premature stop codons
2) Evolutionary drivers of thermoadaptation in enzyme catalysis
3) Endogenous RNAi Pathways Are Required in Neurons for Dauer Formation in Caenorhabditis elegans
4) Nutrient-dependent/pheromone-controlled adaptive evolution: a model
5) Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
6) Metabolic theory predicts whole-ecosystem properties
7) The phylogenetic utility and functional constraint of microRNA flanking sequences
8) Impact of MicroRNA Levels, Target-Site Complementarity , and Cooperativity on Competing Endogenous RNA-Regulated Gene Expression
9) MicroRNA analysis in mouse neuro-2a cells after pseudorabies virus infection
10) microRNA-binding proteins: specificity and function
11) RNA in extracellular vesicles
12) Structural diversity of supercoiled DNA
13) Communication between viruses guides lysis–lysogeny decisions
14) The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters
15) Prevalence and architecture of de novo mutations in developmental disorders
16) All about the base
17) Chemists know
18) Dynamic control of chirality and self-assembly of double-stranded helicates with light
19) The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes
20) RNA-Guided Human Genome Engineering
21) What is Life?
22) Arginine 66 Controls Dark-State Formation in Green-to-Red Photoconvertible Fluorescent Proteins
23) Evolution of gonadotropin -releasing hormone (GnRH) structure and its receptor
24) A Big Bang in spliceosome structural biology
See also:
Deep Sequencing of the Human Retinae Reveals the Expression of Odorant Receptors
Functional Characterization of the Odorant Receptor 51E2 in Human Melanocytes
The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression