RNA central and RNA-mediated.com

By: James V. Kohl | Published on: November 6, 2015

What are lncRNAs?

Excerpt: 

There are many specialized lncRNA databases, which are organized and centralized through RNA central.
lncRNAs can be transcribed as whole or partial natural antisense transcripts (NAT) to coding genes, or located between genes or within introns. Some lncRNAs originate from pseudogenes (Milligan & Lipovich, 2015). lncRNAs may be classified into different subtypes (Antisense, Intergenic, Overlapping, Intronic, Bidirectional, and Processed) according to the position and direction of transcription in relation to other genes (Peschansky & Wahlestedt, 2014, Mattick & Rinn, 2015).

What are microRNAs?

Excerpt: 

MicroRNAs constitute a recently discovered class of non-coding RNAs that play key roles in the regulation of gene expression. Acting at the post-transcriptional level, these fascinating molecules may fine-tune the expression of as much as 30% of all mammalian protein-encoding genes. 

My comment: Here is the reason that most people do not know how microRNAs are linked to healthy longevity or to pathology.

Study Finds Nearly All Scientific Papers Controlled By Six Corporations

Excerpt:

People spend half of their lives taking classes, passing tests and filling out applications in hopes that one day they can become a scientist and cure a disease. After years of struggling to make the cut they realize that there is no funding for their charitable projects and if they dare step outside of the established guidelines they will be exiled from the scientific community.
Additionally, even when legitimate studies are done, they hardly ever reach the public or get taken seriously because most of the publishers that are considered “reputable” are controlled by just a few corporations that heavily censor the information that gets released.

For example, “Nature Publishing Group” group blocks my comments on articles. And, in the American Association for the Advancement of Science publication “Science,” my extended comments about a misrepresentation of how viruses could be linked to all pathology was replaced with this comment from the authors:

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

Here’s my comment that was published and replaced:

The idea of biophysical constraints seems antithetical to the idea of nature somehow selecting mutations that cause amino acid substitutions. However, I am not a biophysicist or evolutionary theorist.
The problem may be my focus on nutrient-dependent receptor-mediated amino acid substitutions in species from bacteria to humans (non-viral organisms). Since I am not a virologist or physicist, I’m not sure that the laws of physics apply to viruses and their replication.
If they do, natural selection for random mutations is not likely to result in amino acid substitutions because the thermodynamics of changes in organism-level thermoregulation preclude such randomness. Stability of protein biosynthesis and degradation that probably depends on protein folding must somehow be controlled. Besides, I don’t know how random mutations in viruses could be naturally selected for inclusion in the human virome (or in the virome of any organism capable of thermoregulating its thermodynamic intercellular signaling).
If the Second Law of Thermodynamics does not apply to viruses, which means the chemical bonds that enable the amino acid substitutions can form at random and somehow be naturally selected, the details of biophysical constraints in this article seems out of place, since I do not think in terms of constrained random mutations and natural selection in mutation-driven evolution.
Hopefully, someone with a background in biophysics will address my confusion in case others are confused. In addition, I wonder if the consequences of understanding the evolutionary mechanisms that govern viruses extend to consequences important to understanding the evolution of species from bacteria to humans via constrained random mutations and natural selection?

Sarcasm alert (from the comment above):
Excerpt:

I’m not sure that the laws of physics apply to viruses and their replication.

My comment: Sarcasm is sometimes effective. In this case, I think my sarcasm helped force the authors of Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution to think twice before ever again attributing nutrient-dependent antigenic changes to evolution of the influenza virus. Clearly, these authors are not alone among other academics who have been forced to report their findings in terms used by neo-Darwinian theorists who invented the “Modern Synthesis” at the beginning of the 20th century. The population geneticists based their theoretical approach on de Vries definition of “mutation” and assumptions about how long it would take for the accumulation of mutations to lead to the evolution of a new species. De Vries defined “mutation” in 1904.
Since the beginning of the 21st century, all serious scientists have learned that the mutation-driven evolution of a new species can never occur. However, Masatoshi Nei came to this ridiculous conclusion in his book Mutation-Driven Evolution

…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements (p. 199).

Teleology is a reason or explanation for something in function of its end, purpose, or goal.
Evolutionary theorists who continue to ignore explanations of biologically-based cause and effect that now clearly link atoms to ecosystems via RNA-mediated cell type differentiation must also ignore the fact that The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.
The ignorance of theorists continues to be revealed as others link the speed of light on contact with water from the virucidal effects of UV light to the de novo creation of receptors that allow nutrients to enter cells. Nutrient-dependent microRNAs are the link from quantum physics to RNA-mediated DNA repair of damage caused by the accumulation of viruses that links viral microRNAs to all pathology.  The fine-tuned microRNA/messenger RNA balance prevents nutrient-stress and/or social stress from causing virus-driven immune system suppression and all pathology. That fine-tuning is not being considered in the information most people get, which is censored by the six corporations that control the dissemination of that information at the same time they refuse to check the facts that academics provide to support their ridiculous conclusions about the evolution of species.
What should serious scientists do to ensure their voices are heard so that they can put a stop to the pseudoscientific nonsense about evolved species. Rupert Murdoch’s approach is a step forward in that direction.
See: Rupert Murdoch’s National Geographic Staff Cuts Are Attracting Huge Backlash
Excerpt:

Many of the staff being laid off from the publication’s prestigious nature magazine, which include photographers, designers, editors and fact-checkers, have won awards for their work at NatGeo.

My comment: First, you fire all the fact-checkers who have not checked for facts about how nutrient-dependent RNA-mediated cell type differentiation occurs. From that point forward, everyone will be forced to link the sun’s biological energy to cell type differentiation via what is currently known to serious scientists about biophysically constrained protein folding chemistry, which is perturbed by viruses that steal the energy from cells that is required for RNA-mediated DNA repair.
 
See also: From transcription to function: mapping brain networks

Excerpt:

These results agree with the initial functional networks found in adolescents. In addition, these findings validate the well-known involvement of ion channels as the molecular units driving transmission of information across neuronal networks and underscore the known involvement of ion channel-enriched networks in health and disease.

My comment: They place their findings into the concept of an atoms to ecosystems approach to RNA-mediated cell type differentiation that links biophysically constrained protein folding chemistry from ecological variation to ecological adaptation in all living genera via the nutrient-dependent physiology of reproduction. The ecological variation begins with the anti-entropic virucidal energy from the sun.

Again, see also: What are microRNAs? and my invited review of nutritional epigenetics, which was returned almost immediately WITHOUT REVIEW.

Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

Abstract excerpt: 

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man.

For comparison, see: The bioenergetic costs of a gene.
 

They “…eliminate the need to invoke an energetics barrier to genome complexity” and try to tell other biologically uninformed science idiots that “… variation in the power of random genetic drift has played a central role in the historical diversification of genome and possibly cellular architecture across the tree of life.”

Does anyone think that they can continue to link random genetic drift to the tree of life in an article with the title that suggests they will to address the bioenergetic costs of a gene? Neo-Darwinian theorists will continue their attempts to link random genetic drift to the tree of life despite the experimental evidence of biologically based cause and effect that links atoms to ecosystems across all biomass. Evolutionary biologists have no choice but to continue touting pseudoscientific nonsense because they have ignored facts about virus-driven genomic entropy that link nutrient-dependent cell type differentiation to pathology via the theft of energy required in the context of The bioenergetic costs of a gene. The bioenergetic costs are nutrient-dependent and RNA-mediated cell type differentiation is controlled by the physiology of reproduction in all living genera.
See also: APOE Stabilization by Exercise Prevents Aging Neurovascular Dysfunction and Complement Induction
Conclusion:

…data from human studies [4,9,23,84], point towards focusing efforts on understanding the impact of aging and lifestyle on neurovascular unit decline and neuroinflammation, particularly pericyte dysfunction and loss, and activation of innate immune responses. Understanding these processes will both help encourage a healthy lifestyle that where possible includes exercise and could lead to the development of improved treatments for AD and other neurodegenerative disorders.

See also the discussion at: Human brain created God and religions.
I vaguely recall learning that in Biblical times, male infants were not circumcised until they were 8 days old. I learned about the use of UV light therapy in newborns to help with development of the liver. When I learned about the virucidal effects of UV light, I decided to write a blog post about the transgenerational epigenetic inheritance of viruses and some unexplained devastating pathologies in infants, which might be treated with nutritional intervention, anti-viral therapy, or sun exposure — all of which could be linked to RNA-mediated cell type differentiation and potential cures, or more effective treatments of childhood pathology.


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