From base editing to RNA editing (6)

By: James V. Kohl | Published on: December 27, 2017

Summary: Now that others have linked food energy to biophysically constrained pheromone-controlled RNA-mediated cell type differentiation and to the prevention and treatment of PTSD, help for veterans and others who might be contemplating suicide is one step closer to the reality of implementation.
But wait, first the NIH must fund another 26.2 million dollars worth of worthless research on “social epigenomics.”
See for comparison: A distinct hematopoietic stem cell population for rapid multilineage engraftment in nonhuman primates
Reported as: Subset of stem cells identified as source for all cells in blood and immune systems
The link from quantum physics to biophysically constrained feedback loops and the transgenerational epigenetic inheritance of food energy-dependent pheromone-controlled viral latency was included in Daev et al (2014): Chemosignals from isolated females have antimutagenic effect in dividing the cells of bone marrow from male mice of the CBA strain 

…specific, volatile, and zoosocial important chemosignals are a promising approach both to modeling posttraumatic stress disorders in humans [36] …

Daev et al (2014) cited our award-winning 2001 review: 

Humans also have various pheromone-induced physiological effects, especially those associated with reproduction [46, 47]. This suggests that the human olfactory system is still an effective pathway for influencing environmental factors on the human nervous system.

[46] is Kohl, J.V., Atzmueller, M., Fink, B., and Grammer, K., Human pheromones: integrating neuroendocrinology and ethology, Neuroendocrinol. Lett., 2001, vol. 22, pp. 309–321.
Now that others have linked food energy to biophysically constrained pheromone-controlled RNA-mediated cell type differentiation and to the prevention and treatment of PTSD, help for veterans and others who might be contemplating suicide is one step closer to the reality of implementation.
But wait, first the NIH must fund another 26.2 million dollars worth of worthless research to link “social epigenomics” (aka epigenetic effects of pheromones) from base editing to RNA editing and RNA-mediated cell type differentiation.

See: NIH Awards Grants Supporting Social Epigenomics Research

…funding to examine how socioeconomic/psychosocial conditions affect prenatal DNA methylation, miRNA expression, mRNA expression, and inflammation…

See also: Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation

Altogether, this systematic analysis of ribosome-associated mRNAs and lncRNAs demonstrates that nutrient availability and translational regulation controls protein and small peptide-encoding mRNAs as well as a diverse cadre of regulatory RNAs.

Arabidopsis thaliana is a small flowering plant that is widely used as a model organism in plant biology. The nutrient energy-dependent physiology of reproduction was linked to the food energy-dependent pheromone-controlled physiology of reproduction via the ribosome-associated mRNAs in the context of the ATP-dependent creation of the RNA and fixation of amino acid substitutions that stabilize the organized genomes of all living genera.

More than 68,000 indexed publications on PubMed link food energy-dependent changes in microRNAs from RNA-directed DNA methylation to mRNA expression in the context of the physiology of pheromone-controlled reproduction and transgenerational epigenetic inheritance of all phenotypes in species from microbes to humans. A search for microRNA and virus links 4782 published works from the virus-driven degradation of messenger RNA to all pathology.
The waste of money on more research should be perfectly clear in the context of this invited review of nutritional epigenetics:

For example, I linked the availability of sago palm-like leaves to endogenous levels of vitamin C in humans. That allowed me to detail how the pheromone-controlled physiology of reproduction in mice was linked to humans via one base pair change and a single amino acid substitution. Natural selection for energy-dependent codon optimality is all that’s required to link RNA-mediated DNA repair from sunlight to the creation of microRNAs in plants and the vitamin C-enhance stability of the organized genomes in a modern human population in Central China.

1) …access to endogenous vitamin C in human populations, supports efficient metabolism and ecological niche construction [17].

2) ..vitamin C appears to stimulate histone demethylases, which appear to alter the de novo creation of functional olfactory receptor genes [19-23].

3) Researchers recently rediscovered a nutrient-dependent epigenetic variant that links vitamin C to what is probably a glucose and glucose dehydrogenase-dependent base pair change. The base pair change results in addition of a methyl group to a cytosine base, which takes on a hydroxyl group to form different 5-hydroxymethylcytosines (5hmCs). Different 5hmCs are associated with differences in cell types that have the same genetic backgrounds. Nutrient-dependent epigenetically-marked bases help to explain how hundreds of cell types in the human body and in the brain [24] are differentiated and how they maintain their glucose-dependent and other nutrient-dependent receptor-mediated identities [25].

Because vitamin C and other vitamins appear to epigenetically effect nutrient-dependent methylation at the level of single-base resolution in mammals, it has become more important to determine how base-pair changes alter intracellular interactions in embryonic stem cells or intercellular interactions in other cells that result in cascades of downstream intracellular and intercellular organizing interactions throughout life. Other vitamins, such as vitamin D, and metal ions such as calcium, iron, lead and manganese also appear to epigenetically alter these organizing interactions. Therefore, a biophysically constrained, nutrient-dependent, epigenetically-effected, receptor-mediated recognizable organized pattern of emergence can be viewed in the context of ecological variations and ecological adaptations.

4) Amino acid substitutions in humans are associated with loss of vitamin C synthesis and loss of uricase production at the advent of urate production as a substitute for vitamin C biosynthesis in primates.

Excerpt from the conclusion:

5) In mammals, for example, the explanatory power of a model of ecological variation and biophysically constrained nutrient-dependent pheromone-controlled ecological adaptations became clear with companion papers published in 2013. See for review [30].

The companion papers [162-163] told a new short story of ecological adaptations. In the context of climate change and changes in diet, the story began with what probably was a nutrient-dependent base pair change and a variant epiallele that arose in a human population in what is now central China.

Apparently, the effect of the epiallele was adaptive and it was manifested in the context of an effect on sweat, skin, hair, and teeth. In another mammal, such as the mouse, the effect on sweat, skin, hair, and teeth is probably due to a nutrient-dependent epigenetic effect on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. The pheromones appear to control the nutrient-dependent epigenetically-effected hormone-dependent organization and hormone-activation of reproductive sexual behavior in mammals such as mice and humans, but also in invertebrates and in microbes as previously indicated.

The ecological adaptations, which appear to be manifested in the human population are detailed in these two reports [162-163]. The ecological adaptations are likely to be nutrient-dependent and pheromone-controlled. If so, ecological variation probably leads to ecological, social, neurogenic, and socio-cognitive niche construction, which is manifested in increasing organismal complexity and species diversity. If not, there may be something as yet unknown about mutations and evolution that makes sense in the light of what is known about nutritional epigenetics and the molecular biology of species from microbes to man.

NIH funding for more research without first reviewing what is known to all serious scientists about energy-dependent RNA-mediated cell type differentiation is a horrid waste of money. If that fact is not perfectly clear, see any of these published works on microRNAs.

Two decades after Eugene Daev first linked pheromones to biophysically constrained viral latency, an article in Science asked the question: Do human pheromones actually exist?

…Wen Zhou, a behavioral psychologist at the Chinese Academy of Sciences in Beijing, contends that AND and EST may well be human pheromones. “My major concern with the experiments in this study is that they were not rigorously designed and conducted,” she wrote in an email to Science. Zhou, who in 2014 published a study finding that AND and EST do indeed influence whether participants judge walking dot figures with “genderless gaits” to be men or women, doubts the faces used were truly “gender neutral.”

See for comparison: Olfaction Warps Visual Time Perception
See also: The vibrational theory of olfaction for the win (John Hewitt)

…Turin also just published a much more sweeping treatise on molecular recognition in olfaction in the journal Advances in Physics: X. In it, he and his co-authors delve into more of the specifics of olfactory receptors, including particular amino acid motifs, metal binding capacities, and disulphide bridge redox status. It turns out that amino acid side chains alone frequently pull off some rather interesting electron transfer effects without the need for fancy co-enzymes or prosthetic groups.

The link from facts about amino acids in the context of vibrational theory to olfaction and receptor-mediated behaviors clearly extends from epigenetic effects on hormones to the unconscious affects of hormones on behavior.
Epigenetic effects on energy-dependent performance levels should also be reconsidered in the context of receptor-mediated biophysical constraints on amino acid substitutions that stabilize organized genomes, but in public/personal correspondence, John Hewitt professed his belief in evolution.  On 11/27/17 he wrote:

I think mutation and natural selection is a woefully weak force in the evolution of multicellular organisms, but I surely believe things evolve.

See for comparison from December 2007:
Sex and Smell: Molecular Biology of Pheromone Perception (Catherine Dulac)
Talk Overview

Pheromones have evolved to signal the sex and the dominance status of animals and to promote social and mating rituals.

No experimental evidence of biologically-based cause and effect supports that claim that pheromones evolved to do anything. All experimental evidence provided by serious scientists who use it to support their claims attests to this fact from December 2012:
The activity-dependent histone variant H2BE modulates the life span of olfactory neurons (co-authored by Catherine Dulac)
An experience-dependent epigenetic trap stabilizes the organized genomes of all living genera. See: An Epigenetic Trap Stabilizes Singular Olfactory Receptor Expression.
The “epigenetic trap” links the speed of light on contact with water to all food energy-dependent biodiversity via olfaction and the pheromone-controlled physiology of reproduction.
Dynamic control of chirality and self-assembly of double-stranded helicates with light
Senior author Ben L. Feringa won the 2016 Nobel Prize in Chemistry for works that link the anti-entopic virucidal energy of sunlight on contact with water from the creation of microRNAs to experience-dependent changes in electrons to ecosystems via changes in the microRNA/messenger RNA balance.
Something has gone horribly wrong. In the iBiology alert I received this morning, ‘Tis the Season to be Sensing, this claim was made:

While you take off time for a holiday vacation, not everyone will be taking a break. Your body’s cells will be clocking overtime to ensure you can enjoy all of the festivities. They are responsible for everything from hearing the chatter of loved ones and the tasting of delicious food to seeing all of the bright and colorful decor. Consider taking some time this holiday to learn about all the hard work your cells are doing to help you enjoy the holiday cheer!

Hearing, seeing and tasting occur only in the context of experience-dependent epigenetic effects that link feedback loops to all biodiversity via the sense of smell. See: Feedback loops link odor and pheromone signaling with reproduction
See also: Evolution Flipped Course

Fundamentals such as Darwinian evolution, genetic variation and natural selection are covered. In addition, leading scientists present their research in areas as diverse as the evolution of multicellularity, the discovery a fossil intermediate between fish and tetrapods, the co-evolution of plants and predators, and how viruses constantly evolve to “outsmart” their hosts.

Session 10: Viral Evolution

In this session, Drs. Turner and Malik focus on the ability of viruses to rapidly evolve and adapt to changing environments. Turner explains how some viruses have evolved to infect many hosts while others infect a single cell type. He also uses experimental evolution to study the ability of a virus to survive under different environmental conditions versus its ability to effectively reproduce.

They obfuscate the difference between mutations and amino acid substitutions because the food energy-dependent RNA-mediated fixation of amino acid substitutions prevents all virus-driven pathology. Only theorists continue to tout their pseudoscientific nonsense.
Serious scientists make claims like this (although some must be forced to do it):
The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.
See also: Mitochondrial pyruvate metabolism controls neuronal function and excitotoxic death

…we show that glutamate is readily used as a metabolic substrate in cortical neurons in response to mitochondrial pyruvate carrier (MPC) inhibition. Reductions in mitochondrial pyruvate uptake do not compromise viability or energy metabolism, but rather rewire mitochondria to increase reliance on glutamate to fuel anaplerosis and ATP production.

The ATP-dependent rewiring is energy-dependent and RNA-mediated. Food energy is required for error-free DNA repair and that fact was first accurately represented in 1964:
Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

Antagonist Jay R. Feierman has done more than anyone to prevent people from learning the facts about how food energy and pheromones protect all organized genomes from the virus-driven degradation of messenger RNA.
For a historical record of his ignorance, see: 90689 Re: [evol-psych] Re: [human-ethology] Phenotype, Form, and Function

…it is doubtful if such constructive criticism will change anyone’s views on this subject, as the views regarding psychological paradigms are held together in many people with the same emotional glue that hold political and religious views together. The next generation will think differently. 

See also his constructive criticisms of my model: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Jay R. Feierman: Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.

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