RNA methylation, behavior, and disease

By: James V. Kohl | Published on: June 11, 2016

Epigenetics and Genetics of Viral Latency by Paul M. Lieberman (May 11, 2016)
My comment: Lieberman succinctly confirmed the fact that viral latency is responsible for life-long pathogenesis and mortality risk
His simplistic conclusion also attests to the fact that there is no defined boundary between epigenetics and genetics. Epigenetic effects on metabolic networks must be linked to genetic networks via the energy-dependent innate immune system. That’s how all serious scientists knew they would need to link angstroms to ecosystems in all genera via the physiology of reproduction, which led to the discovery that supercoiled DNA protects all organized genomes from virus-driven entropy. All serious scientists now know that all pathology arises in the context of virus-driven energy theft and immunological dysfunctions that clearly link the transgenerational epigenetic inheritance of DNA damage to birth defects, chronic inflammation, brain development, neuropathy, cardiovascular disease, and every preventable disease.
The diseases that link virus-damaged DNA and transgenerational epigenetic inheritance are not likely to be prevented or cured in any single generation. However, serious scientists also know how to control the molecular mechanisms that control virus-driven pathology by controlling the establishment, maintenance, and reactivation of complexity and further diversification of virus families, species, and strains. But prevention and cures require more than the collective knowledge of all serious scientists. Prevention and cures require the pseudoscientific nonsense touted by neo-Darwinian theorists to be eliminated from any further consideration whatsoever.
Fortunately, that fact is becoming clear to all theorists who are still touting their pseudoscientific nonsense, and some of them have stopped doing that.
See for example: Five years of Ferguson (May 2015)
and Genomic instability in human cancer: Molecular insights and opportunities for therapeutic attack and prevention through diet and nutrition (December 2015)
and Are We Eating Our Way to Prostate Cancer—A Hypothesis Based on the Evolution, Bioaccumulation, and Interspecific Transfer of miR-150 (April 2016)
Lynnette Ferguson co-authored and published The Interaction between Epigenetics, Nutrition and the Development of Cancer in January 2015. Until after the invited review she requested from me, I have found no indication that she knew anything more about RNA-mediated cell type differentiation than any neo-Darwinian theorist. See for example: Dietary influences on mutagenesis—Where is this field going? (December 2010).
For contrast, her publication history suggests that she and all her co-authors failed to learn anything about the role that energy-dependent microRNAs play in every aspect of healthy longevity or virus-driven pathology. Thus, Five years of Ferguson extends her works and the works of others back to the accumulated ignorance of biologically-based cause and effect that has been manifested in the publication histories of all others like her.
From 2000 to 2010 only a few thousand articles indexed on PubMed mentioned “microRNA.” Within the next 5 years ~25,000 more were published.
See also from June 10, 2016:  50,747
Five more years of publications by people like Ferguson are not likely to lead serious scientists to any additional information about the prevention of virus-driven pathology.
For comparison, see: MicroRNA regulation of neural plasticity and memory (2011) and The brain-specific microRNA miR-128b regulates the formation of fear-extinction memory (2011) or the series of published works that Timothy W. Bredy has published.
Since 2003, Bredy and his co-authors may have been the largest contributor of experimental evidence that links energy-dependent changes in the microRNA/messenger RNA balance from RNA methylation to behavior in all living genera.
See for example from 2012:
T. Bredy;
Queensland Brain Institute, The University of Queensland, St Lucia, AUSTRALIA.
6.07. The interplay between CBP and HDAC3 in regulating gene expression required for long-term memory processes
I’ve mentioned before that his November 2012 answer to my question after his Society for Neuroscience presentation in New Orleans, LA, led me to further examine what was known about the microRNA/messenger RNA balance. His answer suggested that changes in the balance could be linked to all downstream effects on morphological and all behavioral phenotypes in all living genera.
That fact has since been repeatedly confirmed in publications by Bredy’s group and publications by other individuals and other groups.  All facts about RNA-mediated cell type differentiation have now led from experimental evidence of biologically-based cause and effect to assumptions by serious scientists that link energy-dependent changes in the microRNA/messenger RNA balance to all healthy longevity and biodiversity, or to all virus-driven energy theft and all pathology.
See also: Creating a DNA Record with CRISPR
My comment to The Scientist (was promptly removed):

They appear to be linking energy-dependent hydrogen-atom transfer in DNA base pairs in solution from the innate immune system of microbes to RNA-mediated DNA repair and the physiology of reproduction. The physiology of reproduction is linked to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.

For example, see the authors’ comment here:

Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

If not for energy-dependent RNA-mediated DNA repair, viruses might already have stolen the energy of life that Schrodinger (1944) claimed could be linked from the anti-entropic effects of sunlight to all biodiversity. Subsequently, Dobzhansky (1973) mused that what was known could be placed into context of fixed amino acid substitutions for comparison to what might be expected by theorists to happen during millions of years of accumulated mutations and/or evolution.

Last year, a report on the Structural diversity of supercoiled DNA left litte doubt about the fact reported last month by Paul M. Lieberman in Epigenetics and Genetics of Viral Latency.

 …viral latency is responsible for life-long pathogenesis and mortality risk…

That claim confirms Dobzhansky’s claims that presciently linked RNA methylation from RNA-directed DNA methylation to RNA-mediated amino acid substitutions and all biodiversity. If Lieberman is correct, his claim also refutes many, if not all, claims about mutation-driven evolution

Indeed, what is currently known about the energy-dependent links from angstroms to ecosystems in all living genera appears to also confirm the claims in Nutrient-dependent/pheromone-controlled adaptive evolution: a model.

For an example of what others may not want you to know about how RNA methylation is linked to the physics and biophysically constrained molecular mechanisms of protein folding chemistry see:

A New Biomarker for Nerve Cell Damage

COMT Val158Met and BDNF Val66Met already exemplify the links across species from energy-dependent changes in angstroms to ecosystems manifested during life history transitions in mammalian models of virus-driven energy theft and pathology. The COMT Val158Met findings were based on a population size of 10,000 that rapidly grew at the onset of the Precision Medicine Initiative.
See also: Irreproducible biology research costs put at $28 billion per year and this attempt to discuss the differences between theories and experimental evidence that support fact about RNA-mediated cell type differentiation.
This is from the miRNA and siRNA FB group, which is supposed to be for discussion of “anything related to RNAi: microRNAs and non-coding RNAs, latest discoveries, trends, questions on RNAi in vitro/in vivo protocols, discussions re basic research, what happens in the diagnostics space, progress with miRNA and siRNA-based therapeutics, latest product launches for miRNA analysis, new siRNA tools, delivery reagents, etc”
I had hoped others would discuss this OP:  Second layer of information in DNA confirmed

You could keep citing works that will lead to the end of Darwinian theories after November 2016, or acknowledge the fact that my works have already ended all the claims by pseudoscientist. See for example: https://journal.frontiersin.org/article/10.3389/fnhum.2014.00127/full
See the comments by George FR Ellis, who as everyone knows has co-authored with Denis Noble and with Stephen Hawking, among others:
“This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics. This is explored here: https://rsfs.royalsocietypublishing.org/content/2/1.toc”
See also: George F R Ellis “Great links, thanks. I’m intrigued by your work on pheromones. It is just possible it might relate to the issue of primordial emotional systems, see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3540967/”
https://science.sciencemag.org/content/early/2016/06/08/science.aaf1175 They make it impossible to link what is known about the energy-dependent innate immune system from metabolic networks and genetic networks to cell type differentiation in any model organism. They make no claims that could vaguely be put into the context of what is currently known about biophysically constrained protein folding and virus-driven energy theft, which is linked to all pathology.
This presents a “red flag” to all serious scientists via the patent application #20160002670 filed by Church et al.
“RNA-Guided Human Genome Engineering”
Each time they invent a new term and/or use acronyms without definition, or fail to place the acronym into the context of what is known about biophysically constrained protein folding chemistry, the level of deception becomes clearer. The arrogance also becomes clear.
They are so self-assured that no one can see through their claims, that the claims become more bizarre and can only be placed into the context of ridiculous neo-Darwinian theories. But what about virus-driven energy theft, George Church? Why do you intend to use RNA-guided genome engineering? Doesn’t supercoiled DNA protect all organized genomes from the virus-driven energy theft that causes the problem with mutations that you are attempting to address outside the context of quantized energy as information?

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