Premise: Sunlight is the energy as information that is required to link endogenous RNA interference to healthy longevity

Counter claim:  The Quantum Thermodynamics Revolution: Information theory

Understanding entropy as a subjective measure allows the universe as a whole to evolve without ever losing information.

Precision Medicine virtual conference, Feburary 22-23, 2017

Title: Energy as information and constrained endogenous RNA interference

  •  James V. Kohl
  • RNA-mediated.com
  • jvkohl@bellsouth.net
  • Abstract describing the poster

 

Narrative: The term microRNA has been used in 58,000 indexed works. All the works support claims that link the anti-entropic virucidal energy of sunlight from endogenous RNA interference to biophysically constrained protein folding chemistry and cell type differentiation.

For comparison, news from last week reported: Physicists make the case that our brains’ learning is controlled by entropy.

On the same day, George Church spoke during the highest-profile lecture program at the NIH. His topic was “The future of genetic codes and BRAIN codes

But he failed to link energy-dependent endogenous RNA interference or exogenous RNA interference to the genetic codes or the brain codes.

For contrast, the systems complexity of energy-dependent top-down RNA-mediated causation is detailed here.

The details can be compared to claims that minimal mutational differences might link energy and/or entropy to the evolution of all morphological and behavioral diversity on Earth via DNA.

What I have done is to link Quantized Energy as Information from chirality and hydrophobicity to thermodynamic cycles of protein biosynthesis and degradation via the potential of hydrogen, which is referred to as pH.

pH links the sun’s anti-entropic virucidal energy from hydroxylation to the de novo creation of nucleic acids and hydrogen atom transfer in DNA base pairs in solution.

Photosynthesis links the creation of G protein-coupled receptor genes from the innate immune system to nutritional epigenetics and autophagy.

pH-taxis, chemotaxis, thermotaxis and phototaxis link microRNA biogenesis and microRNA flanking sequences from hydrogen energy-dependent changes in the microRNA/messenger RNA balance to autophagy.

Autophagy links everything currently known about nutritional epigenetics from alternative splicings of pre-messenger RNA to nutrient-dependent amino acid substitutions.

For example, feedback loops link odors and pheromones to the physiology of reproduction in all vertebrates via substitution of achiral glycine in position 6 of the gonadotropin releasing hormone decapeptide.

Simply put, endogenous RNA interference clearly links RNA-directed DNA methylation from DNA repair to supercoiled DNA and healthy longevity in all living genera via fixation of achiral glycine and/or fixation of other amino acid substitutions in all species.

For comparison, excess STRESS links reduced pH to virus-driven energy theft and genomic entropy via transgenerational epigenetic inheritance.

The cited works that support the details in this poster link epigenetically-effected changes in amino acid substitutions to cell type differentiation from archaea to Zika virus-damaged human DNA.

When that fact is considered in the context of the Precision Medicine Initiative it becomes clear that virus-driven energy theft links neural circuitry, odor hedonics, mood, memory, motivation, expressions of affect, cognitive behavioral state, and potentiating responses to other stimuli from nutritional and/or social stress to mutations and all pathology.

In the context of the Precision Medicine Initiative, prevention of pathology is achieved only in the context of nutritional epigenetics and the National Microbiome Initiative.

The National Microbiome Initiative links energy-dependent fixation of nutrient-dependent amino acid substitutions to supercoiled DNA, which protects all organized genomes from virus-driven entropy.

That fact helps to explain why exogenous RNA interference might sometimes be effective IF it restores nutrient-energy-dependent viral latency.

The failure to restore viral latency can now be placed into the context of three recent additions to the Merriam-Webster dictionary:

Phytoremediation,

Microbiome,

and CRISPR.

Taken together, the dictionary definition of these terms replaces ideas about evolved biodiversity that were based on de Vries 1902 definition of mutation. That definition led to the assumptions of population geneticists who never linked energy-dependent metabolic networks to genetic networks via endogenous RNA interference and the physiology of reproduction.

POSTER TEXT

Fact: The ribosome links the epigenetic landscape to the physical landscape of supercoiled DNA. The ribosome acts as a molecular decoder and as 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) ATP hydrolysis by UPF1 is required for efficient translation termination at premature stop codons

Alternative: Temperature-dependent biological processes could theoretically occur within a  range from –50°C, where cells vitrify or at +140°C when evolutionary theorists seem to think that nucleic acids spontaneously hydrolyze.

2)  Evolutionary drivers of thermoadaptation in enzyme catalysis

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 to 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 protects 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). Endogenous RNAi Pathways Are Required in Neurons for Dauer Formation in Caenorhabditis elegans

Example and summary: “….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-dependent/pheromone-controlled adaptive evolution: a model

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) Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

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) Metabolic theory predicts whole-ecosystem properties

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) 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

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. In the context of quorum sensing, viruses  decide how much energy to steal from cell types. Outside the context of quorum sensing in bacteria, the viruses must somehow 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)  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

In theory, until a specific cell type realizes that a change in chirality also indicates that energy is missing, the cell type does not decide to use autophagy to protect its supercoiled DNA from more energy theft. That theory links the 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 and what is known about energy-dependent changes in base pairs to biophysically constrained protein folding chemistry. 16) All about the base and 17) Chemists know.

The diagram represents what is known about the systems complexity of energy-dependent changes in base pairs, amino acid substitutions and RNA-mediated cell type differentiation, which has been placed into the context of RNAi.

Two recently published articles by co-authors who are 2016 Nobel Laureates, link chirality 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.

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

Until now, most researchers have failed to link light induced changes in chirality to the biophysically constrained structurel of supercoiled DNA. That fact makes the difference between metabolic theory and the arbitrium’ system clear. All metabolic approaches explicitly and quantitatively link the natural selection of food to the control 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 RNA interference, which links fixation of RNA 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) RNA-Guided Human Genome Engineering

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 using the technology think they can biophysically constrain virus-driven energy theft with directed virus-driven editing.

The current political climate in the USA indicates that a paradigm shift has already occurred. The National Microbiome Initiative and the Precision Medicine Initiative collectively appear to be blocking attempts to deliver an exogenous RNAi-based treatment. The treatment has been referred to as a “billion dollar baby.” The alternative to spending billions more dollars to perfect the treatment, which may cost more than what most people can afford, will require more 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 from ecological variation 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 other viruses.

For example, Roger Penrose inadvertently linked energy-dependent endogenous RNA interference to exogenous RNA interference: 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?”(Roger Penrose 8 August 1991) in 20) What is Life?

See also: 21) Arginine 66 Controls Dark-State Formation in Green-to-Red Photoconvertible Fluorescent Proteins

22) Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor

The photoconvertible fluorescent proteins link energy-dependent endogenous RNAi to the substitution of achiral glycine in position 6 of the GnRH decapeptide, 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 every detailed link from angstroms to ecosystems involves the energy-dependent protein folding chemistry that links what organisms eat to the functional structure of supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.

23) A Big Bang in spliceosome structural biology

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