Energy-dependent base editing and correction of mutations (2)

By: James V. Kohl | Published on: December 11, 2017

On 12/10/17, a long-term business partner called to tell me he was ending his efforts to sell human pheromone-enhanced fragrance products to those who understand how the products help to biophysically constrain viral latency in all mammals.
QuEBS workshop has established itself as an outstanding stage to present the research in the intersection of physics, chemistry and biology. […] discussion of notable scientists and pioneers of Quantum Biology… established excitons in biology as the “must-talk-language” when describing the quantum effects in biological light-harvesting systems.
Decades later, researchers reported on: Signatures of exciton condensation in a transition metal dichalcogenide. The mass media news representation is:  Physicists excited by discovery of new form of matter, excitonium.

…when an electron, seated at the edge of a crowded-with-electrons valence band in a semiconductor, gets excited and jumps over the energy gap to the otherwise empty conduction band, it leaves behind a “hole” in the valence band. That hole behaves as though it were a particle with positive charge, and it attracts the escaped electron. When the escaped electron with its negative charge, pairs up with the hole, the two remarkably form a composite particle, a boson—an exciton.


“An exciton is a bound state of an electron and an electron hole which are attracted to each other by the electrostatic Coulomb force. It is an electrically neutral quasiparticle that exists in insulators, semiconductors and in some liquids.”

If excitons are found in water, the speed of light on contact with water could be linked to the quantized energy-dependent de novo creation of all biodiversity on Earth via the pheromone-controlled physiology of reproduction in all living genera. That fact led me to find information that links thermodynamic cycles of energy-dependent RNA-mediated protein folding chemistry to hydrophobicity in supercoiled DNA.

The Water-Food-Energy Nexus: Processes, Technologies, and Challenges

The book is organized into 4 sections on water, food, energy, and the future of sustainability, highlighting the interplay among these topics. The first section emphasizes water desalination, water management, and wastewater treatment. The second section discusses cereal processing, sustainable food security, bioenergy in food production, water and energy consumption in food processing, and mathematical modeling for food undergoing phase changes. The third section discusses fossil fuels, biofuels, synthetic fuels, renewable energy, and carbon capture. Finally, the book concludes with a discussion of the future of sustainability, including coverage of the role of molecular thermodynamics…

See for comparison. There is no coverage of the role of molecular thermodynamics in the symbols used to represent different religions. It’s as if the differences exist outside the context of what is known about the creation of the sun’s anti-entropic virucidal energy.

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The role of molecular thermodynamics in energy-dependent RNA-mediated cell type differentiation was detailed in the context of: Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels (1990)

Energy-dependent changes in base pairs have since been linked from changes in the microRNA/messenger RNA balance and RNA editing to fixation of RNA-mediated amino acid substitutions that differentiate the cell types of all living genera. However, there appears to be no mention of how the virus-driven degradation of messenger RNA has been linked from mutations to all pathology in Guidelines for Genome-Scale Analysis of Biological Rhythms (2017).

Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods hold significant promise for future discovery, particularly when combined with computational modeling. However, genome-scale experiments are costly and laborious, yielding “big data” that are conceptually and statistically difficult to analyze. There is no obvious consensus regarding design or analysis. Here we discuss the relevant technical considerations to generate reproducible, statistically sound, and broadly useful genome-scale data. Rather than suggest a set of rigid rules, we aim to codify principles by which investigators, reviewers, and readers of the primary literature can evaluate the suitability of different experimental designs for measuring different aspects of biological rhythms.

Could ignoring this fact be a problem? See: Virus-mediated archaeal hecatomb in the deep seafloor

We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.

If the guidelines for linking the anti-entropic virucidal energy of sunlight to all biodiversity on earth via the physiology of pheromone-controlled reproduction in species from microbes to humans were applied, the guidelines could be extended to claims about the Molecular and cellular reorganization of neural circuits in the human lineage

…the dopaminergic interneurons found in the human neocortex were absent from the neocortex of nonhuman African apes. Such differences in neuronal transcriptional programs may underlie a variety of neurodevelopmental disorders.

Small but distinct differences among species mark evolution of human brain

Researchers found one gene, ZP2, was active in only human cerebellum — a surprise, said the researchers, because the same gene had been linked to sperm selection by human ova.

That claim can be placed into the context of what we detailed about energy-dependent RNA-mediated cell type differentiation in the molecular epigenetics section of our 1996 Hormones and Behavior review.
See: From Fertilization to Adult Sexual Behavior (1996)

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…

The alternative splicings of pre-mRNA have since been place into the context of energy-dependent changes in microRNAs (aka pre-mRNAs), which have been linked to differentiation of all cell types in all individuals of all living genera.
See: Human GW182 Paralogs Are the Central Organizers for RNA-Mediated Control of Transcription

In the cytoplasm, small RNAs can control mammalian translation by regulating the stability of mRNA. In the nucleus, small RNAs can also control transcription and splicing. The mechanisms for RNA-mediated nuclear regulation are not understood and remain controversial, hindering the effective application of nuclear RNAi and investigation of its natural regulatory roles.

The tractable changes in organized genomes can be viewed in the context of The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression (2014)
The link to sperm selection by human ova establishes the role of quantized energy as information in the context of the physiology of reproduction, which protects all species from the virus-driven degradation of messenger RNA. 
The link from the dopaminergic neuronal system to feedback loops that biophysically constrain behavior have been placed into the context of the transition from adolescence to adulthood.
Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
The authors fail to mention that Val158Met function is known to be affected by a functional single nucleotide polymorphism (SNP) in COMT (G-to-A base-pair substitution) leading to a methionine (Met) valine (Val) substitution at codons 108/158 (COMT Val158Met). Carriers of the Met allele have been found to display a fourfold decrease in enzymatic activity compared to Val allele carriers going along with an increase of prefrontal DA activity (Lachman et al. 1996; Lotta et al. 1995).
The degrading enzyme catechol-O-methyltransferase (COMT), determines dopamine availability in the prefrontal cortex. Thermostablility and exploratory behavior link the difference in the valine allele and the methionine allele to difference in primate brain development and behavior. That fact links the Second Law of Thermodynamics to one energy-dependent base pair change and the creation of one enzyme to changes in the microRNA/messenger RNA balance that link natural selection for energy-dependent codon optimality to one amino acid substitution that differentiates the cell types of the brain in different species of primates.
Dobzhansky (1973) presciently placed that fact into this context:

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.

See also: Humans And Chimps Differ At Level Of Gene Splicing (2007)
See also: Tissue-specific alternative splicing remodels protein-protein interaction networks (2012)
Smocovitis (2006): Keeping up with Dobzhansky (link opens pdf):

The direction and speed of the evolution of any group of organisms at any given time is the resultant of the interaction of a series of reasonably well known factors and processes, both hereditary and environmental. The task of the evolutionist, therefore, is to seek out and evaluate all these factors and processes in respect to as many different organisms as possible, and from the specific information thus acquired construct such generalizations and hypotheses as he can. This requires the broadest possible knowledge of biology, which, if it cannot be acquired through direct contact with original research, must be built up vicariously through communication with biologists in different fields. — G. Ledyard Stebbins, Jr., ‘Preface’, Variation and Evolution in Plants, 1950.

Communication with biologists in different fields has revealed facts about the direction and speed of ecological adaptations linked to longevity.
See: The Secret to Long Life? It May Lurk in the DNA of the Oldest Among Us (2017)
The facts must be placed into the context of enzyme-dependent error-free DNA repair.
The secret to safe DNA repair (2015)

…if you don’t have this enzyme, then this error-free repair is stopped. You can’t do it. If you can’t do the error-free repair, among other things that happen is that you expect these cells to be cancer prone.

See for comparison: ”Definitely embarrassing:” Nobel Laureate retracts non-reproducible paper in Nature journal

In retrospect, we were totally blinded by our belief [in our findings]…we were not as careful or rigorous as we should have been (and as Tivoli was) in interpreting these experiments.

They touted their belief in the emergence and the evolution of all biodiversity on Earth.

As I was preparing this post, a long-term business partner called to tell me he was ending his efforts to sell human pheromone-enhanced fragrance products to those who understand how the products help to biophysically constrain viral latency in all mammals. Not enough people understand biologically-based cause and effect, which limits the market for anything that protects the organized genomes of people from the virus-driven degradation of messenger RNA.

See: [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)]

A study of the influence of pheromone stressor(s) on proliferating germ and somatic cells was performed on laboratory lines of house mouse in the context of the physiological hypothesis of mutation process, proposed by M.E. Lobashev in 1947. Data from experiments are presented, and results obtained during last 10-15 years are discussed. The adaptive role of cytogenetic and other observed pheromonal effects is considered. The possible existence of interorganism systems of genetic regulation is discussed, the search for and study of which may help in more complete understanding of the regularities of functioning of genetic material.

My business partner and I discussed the obvious fact that most people do not want to learn anything about preventative medicine or effective treatments for all pathology, and that most are willing to accept what they are told by “pill-pushing” medical practitioners. The medical practitioners will not tell them that feedback loops link food odors and pheromones to the biophysically constrained pathways of healthy longevity. The medical practitioners will not tell people that vaccines and drug therapies alter the feedback loops. The vaccines and drug therapies act on the energy-dependent creation of the same enzymes linked from the creation of sunlight to all biodiversity on Earth.

In mammals, this is manifested in links from what offspring ingest to their food energy-dependent pheromone-controlled survival. See for example: MicroRNAs: Milk’s epigenetic regulators

The deficiency of exosomal miRNAs in infant formula and the persistent uptake of milk miRNAs after the nursing period via consumption of cow’s milk are two epigenetic aberrations that may induce adverse long-term effects on human health.

It has been more that two decades since publication of The Scent of Eros: Mysteries of Odor in Human Sexuality. We linked the pheromones from mother’s milk to the mother-infant bond and to adult behaviors. I am disappointed to admit that all experimental evidence of biologically-based cause and effect has been ignored by theorists who tout emergence and mutation-driven evolution.
Apparently, Nothing can stop them! They do not seem to realize that Dobzhansky’s “light of evolution” was sunlight and it linked ecological variation to ecological adaptation in all living genera via the pheromone-controlled physiology of reproduction.

Nothing in Biology Makes Any Sense Except in the Light of Evolution (1973)

For example, the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).

See for comparison: Cytosis – The Science Behind the Game (free pdf download)

This is the four page booklet that explains the science in Cytosis. It was written and edited collaboratively by 20 PhD’s and Doctors through the world.
Please take some time to learn what happens to biologically uninformed theorists when serious scientists collaborate.
The collaborators achieved their common goal. The link from the creation of the sun’s anti-entropic virucidal energy to ATP and the creation of RNA is clear to players 10y/o +. The link from the virus-driven degradation of messenger RNA to all pathology in species from microbes to humans is equally clear..
Simply put 1) What organisms eat links the pheromone-controlled physiology of reproduction to biophysically constrained viral latency.
Simply put 2) Food odors and species-specific pheromones biophysically constrain viral latency.
Simply put 3) Feedback loops typically prevent the hecatombic evolution of pathology that starts with viruses in seawater or the viruses in bacteria that eat electrons and produce uranium isotopes.

You may not believe that the sun was created and may not think that electrons were created to be eaten. Winners of this game will not care what losers believe. Losers can compare what they believe about the evolution of hydrogen and all biodiversity to the facts known to serious scientists who helped to create this game.

See also:

A rendering of how changes in an electron’s motion (bottom view) alter the scattering of light (top view), as measured in a new experiment that scattered more than 500 photons of light from a single electron. Previous experiments had managed to scatter no more than a few photons at a time. Credit: Extreme Light Laboratory|University of Nebraska-Lincoln

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