MicroRNA-activated / RNA-mediated gene expression

By: James V. Kohl | Published on: March 15, 2018

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Summary:
All patterns exist only in the context of the de novo creation of enzymes and energy-dependent microRNAs that link light-activated endogenous substrates from what is known about particle physics to biophysically constrained viral latency in the cell biology game: Cytosis.
See also: miRNA activation is an endogenous gene expression pathway
Moving forward:
Few people are likely to ask about the origin (i.e., the de novo creation) of energy-dependent microRNAs. Fewer still will link the creation of quantized energy as information from the physiology of pheromone-controlled reproduction to viral latency via autophagy, which biophysically constrains the diversity of ecologically adapted life.
That fact provides the opportunity for Philip C. Ball, a British science writer, to take the information from my blog posts and present it in his book: “Beyond Weird.”
Excerpt from the description:

Over the past decade it has become clear that quantum physics is less a theory about particles and waves, uncertainty and fuzziness, than a theory about information and knowledge—about what can be known, and how we know it. Discoveries and experiments over the past few decades have called into question the meanings and limits of space and time, cause and effect, and, ultimately, of knowledge itself.

Kindle edition
Historical Perspective:
In the summer of 2017, I reported this claim from Philip C. Ball, and placed it into the context of childish beliefs about Santa Claus (video): To turn quantum to classical…

…we don’t need a conscious mind to measure or look; we just need an environment full of stuff. With or without us, the Universe is always looking.

By plagiarizing my life’s works on biophysically constrained energy-dependent RNA-mediated cell type differentiation, Philip C. Ball may now appear to have suddenly become a serious scientist. But he has already shown the world an unparalleled level of human idiocy. (See Feynman’s claim about Philip Ball’s idiocy).
See for comparison: Patterns in Nature: Why the Natural World Looks the Way It Does 1st Edition

By exploring similarities such as those between a snail shell and the swirling stars of a galaxy, or the branches of a tree and those of a river network, this spectacular visual tour conveys the wonder, beauty, and richness of natural pattern formation.

All patterns exist only in the context of the de novo creation of enzymes and energy-dependent microRNAs that link light-activated endogenous substrates from what is known about particle physics to biophysically constrained viral latency in the cell biology game: Cytosis.
See also: miRNA activation is an endogenous gene expression pathway

Transfection of small non-coding RNAs (sncRNAs) molecules has become a routine technique widely used for silencing gene expression by triggering post-transcriptional and transcriptional RNA interference (RNAi) pathways. Moreover, in the past decade, small activating (saRNA) sequences targeting promoter regions were also reported, thereby a RNA-based gene activation (RNAa) mechanism has been proposed. In this regard, Turner and colleagues recently discovered an endogenous microRNA (miRNA) which binds its promoter in order to upregulate its own expression. Interestingly, several miRNA-induced RNA activation (miRNAa) phenomena have since then been identified. My objective here is to introduce the reader into the emergent miRNAa research field, as well as bring together important discoveries about this unexplored transcriptional activation pathway.

The claim that this is an unexplored transcriptional activation pathway can be placed into the context of how the pathway links light-activated endogenous substrates in all cell types to biophysically constrained energy-dependent changes that link atoms to ecosystems.
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

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. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

See: Energy as information and constrained endogenous RNA interference (figshare, 2017) (video) (audio/visual narrative with citations to published works)
Abstract:

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy. The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection.

This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes. For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

The facts about the viral hecatomb link the virus-driven theft of quantized energy as information to all pathology. Science writers like Philip C. Ball have ignored that fact for several decades. Their ignorance has been the cause of unnecessary suffering and premature death, which could have been prevented if they had learned about the energy-dependent biophysically constrained ecological adaptations that link what is known about species from bacteria to humans. Simply put, food energy and the pheromone-controlled physiology of reproduction link what is known about microbes to all biodiversity on Earth.
That fact is not “Beyond Weird.” It is simply beyond the ability of Philip C. Ball to grasp.
See my book (with co-author, the late Robert T. Francoeur): The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002)

See his books for comparison:

Designing the Molecular World: Chemistry at the Frontier (1994)
Made to Measure: New Materials for the 21st Century (1997)
The Self-made Tapestry: Pattern Formation in Nature (1999)
H₂O: A Biography of Water (1999) (published in the U.S. as Life’s Matrix)
Stories of the Invisible: A Guided Tour of Molecules (2001), (republished as Molecules: A Very Short Introduction (2003)
Bright Earth: The Invention of Colour (2001)
The Ingredients: A Guided Tour of the Elements (2002) (republished as The Elements: A Very Short Introduction (2004)
Critical Mass: How One Thing Leads to Another (2004)
Elegant Solutions: Ten Beautiful Experiments in Chemistry (2005)
The Devil’s Doctor: Paracelsus and the World of Renaissance Magic and Science (2006)
The Sun and Moon Corrupted, a novel, Portobello Books Ltd, (2008)
Universe of Stone: A Biography of Chartres Cathedral (2008)
Shapes, Nature’s Patterns, a Tapestry in three Parts (2009)
Flow, Nature’s Patterns, a Tapestry in three Parts (2009)
Branches, Nature’s Patterns, a Tapestry in three Parts (2009)
The Music Instinct (2010)
Unnatural, The Heretical Idea of Making People (2011)
Why Society is a Complex Matter: Meeting Twenty-first Century Challenges with a New Kind of Science (2012)
Curiosity: How Science Became Interested in Everything (2013)
Serving the Reich: The Struggle for the Soul of Physics under Hitler (2014)
Invisible: The Dangerous Allure of the Unseen (2015), University of Chicago Press (2014), Random House
Patterns in Nature: Why the Natural World Looks the Way It Does (2016)
The Water Kingdom: A Secret History of China (2017)

Remember: Philip C. Ball and others like him failed to link the speed of light on contact with water to all biodiversity on Earth in the context of the energy-dependent creation of the enzyme ATP synthase, the creation of ATP, and the biophysically constrained creation of RNA, which links autophagy to the protection from the virus-driven degradation of messenger RNA in all living genera. Watch for reviews of his book by others who know nothing about biophysically constrained viral latency.
See for comparison: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

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

See also: Subatomic: An Atom Building Board Game (September, 2018)

A deck-building game where particle physics & chemistry collide! Use quarks to build subatomic particles & particles to build Atoms!