5th-6th Sept 2018 Dublin, Ireland

The eternal significance of microRNAs (8)

Use of definitions in attempts to explain any aspect of species-specific biophysically constrained cell type differentiation and aging has been replaced by the use of model systems of biological processes.  Biological processes can be compared to so-called “evolutionary processes” to show that only biological processes need to be considered in the context of Darwin’s “conditions of life” or answers to the the question  What is Life? Schrödinger (1944).
K. L. Mettinger et al. (eds.), Exosomes, Stem Cells and MicroRNA, Advances in Experimental Medicine and Biology 1056, https://doi.org/10.1007/978-3-319-74470-4_6

This volume provides insight into the pivotal roles of stem cells, exosomes and other microvesicles in biofunction and molecular mechanisms and their therapeutic potential in translational nanomedicine. It further highlights evidence from recent studies as to how stem cell derived exosomes and microRNAs may restore and maintain tissue homeostasis, enable cells to recover critical cellular functions and begin repair regeneration.

Chapter 2 The Emerging Roles of microRNAs in Stem Cell Aging

involved in many biological processes such as developmental timing, differentiation, cell death, stem cell proliferation and differentiation, immune response, aging and cancer. Accumulating studies in recent years suggest that miRNAs play crucial roles in stem cell division and differentiation. In the present chapter, we present a brief overview of these studies and discuss their contributions toward our understanding of the importance of miRNAs in normal and aged stem cell function in various model systems.

Chapter 6  MicroRNAs, Regulatory Messengers Inside and Outside Cancer Cells

…like hormones, miRNAs can be secreted and regulate gene expression in recipient cells. Altered expression levels of miRNAs in cancer cells determine the acquisition of fundamental biological capabilities (hallmarks of cancer) responsible for the development and progression of the disease.

Model systems link the energy-dependent creation of microRNAs from microRNA biogenesis to the regulation of all cancer hallmarks. The virus-driven degradation of messenger RNA has been linked to all cancers and all other pathology in species from microbes to humans. Natural selection for energy-dependent codon optimality has been linked to healthy longevity.
See: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
See for comparison:  The Neutral Theory in Light of Natural Selection May 2, 2018

…50 years after its introduction by Kimura. We argue that the neutral theory was supported by unreliable theoretical and empirical evidence from the beginning, and that in light of modern, genome-scale data, we can firmly reject its universality. The ubiquity of adaptive variation both within and between species means that a more comprehensive theory of molecular evolution must be sought.

The ubiquity of adaptive variation attests to the facts about how the creation of quantized energy is linked to biophysically constrained viral latency. Adaptive variation links energy-dependent changes from angstroms to ecosystems in all living genera  via the physiology of their food energy-dependent pheromone-controlled reproduction.

For comparison to mRNA stability during the maternal-to-zygotic transition, see: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

The energy-dependent molecular mechanisms of recombination clearly link microRNA biogenesis to the stability of organized genomes during the life histories of all genera. Serious scientists object to the use of definitions in attempts to explain any aspect of species-specific biophysically constrained cell type differentiation.

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

…it is tiresome to raise the same objections repeatedly, wondering why researchers have not fulfilled some of the basic requirements for establishing the occurrence of an autophagic process.

 

Alternative splicing of pre-mRNA

Do not refute cherished theories

Synopsis:
All serious scientist know that pre-mRNAs (now known as microRNAs in more than 70,000 published works) do not create themselves.
For comparison, Ricki Lewis fails to mention how fertility is biophysically constrained by by the creation of the sun’s anti-entropic virucidal energy, the creation of enzymes (e.g, ATP synthase), the creation of ATP, the creation of microRNAs, and the RNA-mediated creation of hormones and receptors that link achiral glycine in position 6 of the GnRH decapeptide to all experience-dependent receptor mediated structures and function in all vertebrates with jaws.

8 Simple mistakes that can delay peer review (and how to avoid them) (2018)

Add: Do not refute neo-Darwinian pseudoscientific nonsense or Big Bang cosmology. If we publish your work, we will retract it.
See for instance: Biomechanical Characteristics of Hand Coordination in Grasping Activities of Daily Living (2016) [retracted]

Following publication, readers raised concerns about language in the article that makes references to a ‘Creator’, and about the overall rationale and findings of the study.

For comparison, there was no need to mention a “Creator’ in  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…

All serious scientist know that pre-mRNAs (now known as microRNAs in more than 70,000 published works) do not create themselves.
For comparison, Ricki Lewis fails to mention how fertility is biophysically constrained by by the creation of the sun’s anti-entropic virucidal energy, the creation of enzymes (e.g, ATP synthase), the creation of ATP, the creation of microRNAs, and the RNA-mediated creation of hormones and receptors that link achiral glycine in position 6 of the GnRH decapeptide to all experience-dependent receptor mediated structures and function in all vertebrates with jaws.
See: The Biology Behind the Fertility Clinic Meltdown

The spindle apparatus is among the most elegant structures in a cell, quickly self-assembling from microtubules and grabbing and aligning chromosomes so that equal sets separate into the two daughter cells that result from a division.

Self-assembling is a term often used by biologically uninformed theorists who do not understand what is known to serious scientists about cell type differentiation. See for an accurate representation of how fertility in all mammals is naturally biophysically constrained by FSH.
Regulation of FSH expression by differentially expressed miR-186-5p in rat anterior adenohypophyseal cells

Our results demonstrate that miR-186-5p regulates FSH secretion by directly targeting the FSHb 3′ UTR, providing additional functional evidence for the importance of miRNAs in the regulation of animal reproduction.

For more information about the virus-driven fertility meltdown that alters the structure and function of all mammalian genomes in every generation, see:
The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
and
Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
 

"Evolution of Man. - Undoubtedly there once lived upon the earth races of men who were much lower in their mental organization than the present inhabitants.

Natural selection for racism and all pathology

Why is natural selection hard to grasp? It is not what you think….

…human cognitive tendencies interfere more with deep understanding of how natural selection works.

Simply put, our intelligence and teleological reasoning interferes with the teaching of pseudoscientific nonsense. The nonsense does not place Darwin’s “conditions of life” before natural selection for reproductive fitness. Natural selection is food energy-dependent and pheromone-controlled in the context of biophysically constrained viral latency.
See for comparison: The vibrational theory of olfaction for the win

Darwin’s energy-dependent conditions of life link biophysically constrained viral latency to healthy longevity. Luca Turin’s works are among those that exposed the fraudulent claims of neo-Darwinian theorists.

See for example: Molecular recognition in olfaction

For physicists, maybe the single most important development that can be envisaged is the production of a high quality X-ray structure of a one or more olfactory receptors. This would open the door to large scale computer simulations that would help shed light on both the mechanical and electrical responses of olfactory receptors.

The X-ray structure of the virus that destroys olfactory receptors is more important. It can be viewed in the context of everything know to serious scientists who have linked quantum physics to quantum souls.
For example, see: Rosalind Franklin: The Hero Denied Her Due 

Franklin was also a brilliant chemist and a master of X-ray crystallography, an imaging technique that reveals the molecular structure of matter based on the pattern of scattered X-ray beams. Her early research into the microstructures of carbon and graphite are still cited, but her work with DNA was the most significant — and it may have won three men a Nobel.
Franklin left King’s in 1953 in a long-planned move to join J.D. Bernal’s lab at Birkbeck College, where she discovered the structure of the tobacco mosaic virus. But in 1956, in the prime of her career, she developed ovarian cancer — perhaps due to her extensive X-ray work. Franklin continued working in the lab until her death in 1958 at age 37.
“As a scientist, Miss Franklin was distinguished by extreme clarity and perfection in everything she undertook,” Bernal wrote in her obituary, published in Nature. Though it’s her achievements that close colleagues admired, most remember Franklin for how she was forgotten. — C.E.

For comparison, these authors take the ball that Nesse and other theorists put into play, and these theorists run with it. They even pretend to be “biologically informed,” in response to my oft repeated claim that people like them are biologically uninformed science idiots.
The Future of Secularism: a Biologically Informed Theory Supplemented with Cross-Cultural Evidence

…earlier trends toward secularization (due to science education surrounding advancements in science) are currently being counter-balanced by genetic and reproductive forces. The authors also propose that the inverse association between intelligence and religiosity, and the inverse correlation between intelligence and fertility lead to predictions of a decline in secularism in the foreseeable future.

The agenda of at least two co-authors: Nyborg and Ellis, is clear. See: Race and Sex Differences in Intelligence and Personality: A Tribute to Richard Lynn at Eighty 

Nyborg and Lee Ellis promote the works of J. Phillipe Rushton who was reported to be among the top racists of the 20th century.

See: Do pigmentation and the melanocortin system modulate aggression and sexuality in humans as they do in other animals?

Pigmentation of the hair, skin, cuticle, feather and eye is one of the most salient and variable attributes of vertebrates. In many species, melanin-based coloration is found to be pleiotropically linked to behavior. We review animal studies that have found darker pigmented individuals average higher amounts of aggression and sexual activity than lighter pigmented individuals. We hypothesize that similar relationships between pigmentation, aggression, and sexuality occur in humans. We first review the literature on non-human animals and then review some of the correlates of melanin in people, including aggression and sexual activity. Both within human populations (e.g., siblings), and between populations (e.g., races, nations, states), studies find that darker pigmented people average higher levels of aggression and sexual activity (and also lower IQ). We conceptualize skin color as a multigenerational adaptation to differences in climate over the last 70,000 years as a result of “cold winters theory” and the “Out-of-Africa” model of human origins. We propose life history theory to explain the covariation found between human (and non-human) pigmentation and variables such as birth rate, infant mortality, longevity, rate of HIV/AIDS, and violent crime.

Pigmentation is food energy-dependent and RNA-directed DNA methylation links food odors to pheromones and the physiology of reproduction in all living genera. It would be interesting to hear what Jay R. Feierman thinks about this since I met him at a 1995 conference that Lee Ellis organized and J. Phillipe Rushton also attended (by invitation only).

All (~90) attendees should be familiar with works that extended the social science theories to “hate-mongering.” I have tried to stop the hate-mongering, but history may repeat itself with Feierman’s help, of course.
See for comparison: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

Natural selection for energy-dependent codon optimality has been linked via olfaction from quantum physics to all biologically based RNA-mediated cell type differentiation via amino acid substitutions in organized genomes. But Nesse and others like him want to keep their teaching positions and that requires them to deny everything known to serious scientists about physics, chemistry, and molecular epigenetics.
See for comparison: A Civic Biology: Presented in Problems (New York, 1914): pp. 193-196, 253-254, 261-263.
Social scientists ignored Darwin’s “conditions of life.” Most of them don’t seem to understand why I claim that their ignorance has caused the deaths of millions.
See for comparison:  The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…
Will history repeat itself? Will most of us return to the racism of Hunter (1914)?

In the review The Future of Secularism: a Biologically Informed Theory Supplemented with Cross-Cultural Evidence, they obfuscate the claim that Muslims are less intelligent and more fertile than Jews or Buddhists. What will happen when their claim is linked to this claim from Hunter: “A Civic Biology: Presented in Problems” pp. 195-196 

Evolution of Man. – Undoubtedly there once lived upon the earth races of men who were much lower in their mental organization than the present inhabitants. If we follow the early history of man upon the earth, we find that at first he must have been little better than one of the lower animals.
Any and all links from intelligence to fertility are claims that attempt to support the pseudoscientific nonsense touted by neo-Darwinian theorists. Their ridiculous theories are the cause of all pathology.

The Root Cause Of Cancer and Why it Has Been Kept a Secret!

…the root cause of cancer is too much acidity in the body, meaning that the pH in the body is below the normal level of 7.365, which constitutes an “acidic” state. Warburg investigated the metabolism of tumors and the respiration of cells and discovered that cancer cells maintain and thrive in a lower pH, as low as 6.0, due to lactic acid production and elevated CO2. He firmly believed that there was a direct relationship between pH and oxygen.
Anyone who ever performed a blood gas analysis could have helped to establish the fact that the virus-driven degradation of messenger RNA is the cause of all pathology. See for instance: 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.

That fact made it obvious to all serious scientists that energy-dependent RNA mediated DNA repair was required for healthy longevity. The anti-entropic virucidal energy of the sun was linked to the creation of ATP by Schrodinger (1944) in “What is Life?” The food energy-dependent pheromone-controlled physiology of reproduction in species from microbes to humans now links the creation of RNA to all biodiversity, and that links pheromones to biophysically constrained transgenerational epigenetic inheritance of healthy longevity via viral latency.

Nothing has been hidden. There was no reason to hide the facts after theorists made it possible to teach their pseudoscientific nonsense to students in high school via the Scopes Trial in Dayton, TN (1925). Sinclair Lewis published “Arrowsmith” in 1925 and since then, ATP-dependent biophysically constrained viral latency has been detailed in the context of the cell biology game “Cytosis” with its “Virus Expansion.”
 

Cytosis: A Cell Biology Board Game

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

For God and Country

Sci-Hub vs limits on the dissemination of information

The ideology of “Americanism” is not consistent with the tactics of academics and politicians that constrain release of accurate information about  biologically-based cause and effect.

Americanism is an ideology, or belief in devotion, loyalty, or allegiance to the United States of America, or to its flag, traditions, customs, culture, symbols, institutions, or form of government.[2] In the words of Theodore Roosevelt, “Americanism is a question of spirit, conviction, and purpose, not of creed or birthplace.”[3]

Americanism has two different meanings. It can refer to the defining characteristics of the United States and can also signify loyalty to the United States and a defense of American political ideals. These ideals include, but are not limited to self-government, equal opportunity, freedom of speech, and a belief in progress.

Scientific progress has been hindered by publishing companies whose corporate purpose is financial gain for stockholders, not the dissemination of freecinformation that is required to make scientific progress by serious scientists who are Combating Evolution to Fight Disease.
Rarely do the efforts of serious scientists get noticed because there is too much pseudoscientific nonsense that gets published in peer-reviewed journals. The nonsense overwhelms the ability to discern between facts and story-telling. Evolutionary theorists, for example, are story-tellers.
For an attempt to resolve the problem with theorists, see: Publishers’ Legal Action Advances Against Sci-Hub

Based on data from Google Trends, researchers found that the suits against Sci-Hub led to brief spikes in visits to the site.

The publishers contribute to the theft of information because most people do not care how they acquire it. People want the information on biologically based cause and effect for free, and many of them will use it to make scientific advances such as those that have linked energy-dependent changes in microRNAs to all pathology.
A PubMed search for “microRNA” reveals that nearly 65,000 indexed published works have already established facts that link virus-driven energy theft to all pathology. Most the publications are behind “pay walls.”
That means most researchers will be unable to access all of them. Anyone outside the specific discipline that is the focus of the article will not be likely to integrate the information across disciplines and accurately represent what is known about biophysically constrained biologically-based cause and effect.
For an example of the level of integration that is required, request a copy from the corresponding author and wait to see the information in this “pay-walled” publication: Olfaction Warps Visual Time Perception.
By the time you get it, there will probably be several hundred more publications that link the food energy-dependent physiology of pheromone-controlled reproduction in bacteria to our visual perception of energy and mass in the context of the space-time continuum.
See also:

Alternatively, see: Energy as information and constrained endogenous RNA interference
Cited works:
1) ATP hydrolysis by UPF1 is required for efficient translation termination at premature stop codons
2)  Evolutionary drivers of thermoadaptation in enzyme catalysis
3). Endogenous RNAi Pathways Are Required in Neurons for Dauer Formation in Caenorhabditis elegans
4) Nutrient-dependent/pheromone-controlled adaptive evolution: a model
5) Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
6) Metabolic theory predicts whole-ecosystem properties
7) The phylogenetic utility and functional constraint of microRNA flanking sequences
8) Impact of MicroRNA Levels, Target-Site Complementarity, and Cooperativity on Competing Endogenous RNA-Regulated Gene Expression
9) MicroRNA analysis in mouse neuro-2a cells after pseudorabies virus infection
10) microRNA-binding proteins: specificity and function
11) RNA in extracellular vesicles
12) Structural diversity of supercoiled DNA
13)  Communication between viruses guides lysis–lysogeny decisions
14) The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters
15) Prevalence and architecture of de novo mutations in developmental disorders
16) All about the base
17) Chemists know.
18) Dynamic control of chirality and self-assembly of double-stranded helicates with light
19) The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes
20) RNA-Guided Human Genome Engineering
21) What is Life?
22) Arginine 66 Controls Dark-State Formation in Green-to-Red Photoconvertible Fluorescent Proteins
23) Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor
24) A Big Bang in spliceosome structural biology
The works cited above have been placed into the context of the cell biology game “Cytosis.”

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

See for comparison: 2017 Royal Society Insight Investment Science Book Prize

The perfect science book marries scientific breakthrough with elegant, engaging communication. Reading these books side-by-side, we were struck by how creative and unique each voice was, and the varied ways these writers tackle their subjects, using metaphors and personal stories as much as scientific facts.

The perfect science book marries what is known about the creation of energy as information with the biophysically constrained physiology of pheromone-controlled reproduction, which prevents the virus-driven degradation of messenger RNA.

Biophysically constrained viral latency prevents all pathology. This year’s Prize winner linked testosterone to “gender” differences in behavior.

For comparison, see: The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences

Excerpt:

…this model incorporates a logical pathway that directly links sensory input from the social environmental to the development of sexual preferences and to the development of sexual behavior.

The five-step logical pathway that directly links sensory input from the social environment to the development of sexual preferences and sexual behavior is gene→cell→tissue→organ→organ system. Failure to incorporate any of the steps in this pathway makes it impossible to directly connect to sexual preferences and sexual behavior, a logical sequence of events that must somehow and somewhere begin with the effect of sensory input from the social environment.

See also: Intelligent Design – Science & Philosophy: discussion thread

Antagonist, Timothy Kershner wrote:

I have a PhD in Psychology and a minor degree in Microbiology and personally funded many Bacterial Consciousness studies between 2008 and 2012 and mentored directly under James Shapiro from 2009 to 2011.

Shapiro already is laughing at you and others as he tries to recover from teaching you to become biologically uninformed science idiots who believe in evolution outside the context of energy-dependent ecological adaptations that are biophysically constrained by the pheromone-controlled physiology of reproduction in all living genera.

See: Biological action in Read-Write genome evolution

Coincidentally, ‘non-coding’ RNAs rich in repetitive mobile DNA sequences function as key regulators of complex adaptive phenotypes, such as stem cell pluripotency. The intersections of cell fusion activities, horizontal DNA transfers and natural genetic engineering of Read-Write genomes provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.

Shapiro’s latest is part of a Theme issue ‘New trends in evolutionary biology: biological, philosophical and social science perspectives’ organized by Denis Noble, Nancy Cartwright, Patrick Bateson, John Dupré and Kevin Laland.

See for comparison: How life changes itself: The Read-Write (RW) genome

Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA.

See also: Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution

and UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair

All cell-mediated processes are energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans.

Energy dependent life does not change itself. RNA-mediated events must be linked to the stability of organized genomes. The organized genomes cannot come first. The details of energy-dependent cell-mediated RNA-directed DNA methylation clearly link the virucidal energy of sunlight from microRNAs in plants to the microRNAome of all mammals. All humans are included.

RNA interference occurs in plants, animals, and humans. It is of great importance for the regulation of gene expression, participates in defense against viral infections, and keeps jumping genes under control. RNA interference is already being widely used in basic science as a method to study the function of genes and it may lead to novel therapies in the future.

Naturally occurring endogenous RNA interference links what organisms eat from their physiology of pheromone-controlled reproduction to all energy-dependent biodiversity on Earth via biophysically constrained viral latency. For example, see:

The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

MicroRNA present in mature sperm appears to not only be left over from spermatogenic processes, but may actually serve important regulatory roles in fertilization and early developmental processes. Further, our results indicate the possibility that environmental changes may impact the expression of specific miRNA.

The Breadth of Viruses in Human Semen

The presence of viruses in semen is probably more widespread than currently appreciated, and the absence of virus in genital secretions should not be assumed for traditionally non–sexually transmitted viruses. The investigation of virus detection and persistence in semen across a range of viruses is useful for clinical and public health reasons, in particular for viruses that lead to high mortality or morbidity rates or to epidemics.

See for comparison: Alnylam’s rare disease drug shines in trial, paving way for a brand-new class of medicines

RNA interference, or RNAi, a technology that uses snippets of genetic code to shut down disease-causing genes. The scientists who invented RNAi were awarded the Nobel Prize for Medicine in 2006. Many years and more than $1 billion in research later, Alnylam is finally on the cusp of proving that RNAi can be transformed into a medicine that helps patients.

Scientists did not invent RNAi. They discovered that it links what organisms eat to their biophysically constrained pheromone-controlled physiology of reproduction. That fact links RNAi to all biodiversity without the pseudoscientific nonsense touted by evolutionary theorists. The cost of any RNAi drug that is approved will almost assuredly bankrupt the person who needs the drug and the cost will probably destroy the economy of the United States of America via the impact on the costs of Medicare and/or other insurance.
This is not Amercanism: Alnylam Data Puts a Nobel Discovery One Step Closer to Approved Drug

Shares of Alnylam soared more than 51 percent and closed at $113.84 apiece on Wednesday.

Alternative splicing of pre-mRNA

Methylation and the Innate Immune System

Free Webinar Training:

Methylation and the Innate Immune System

Please send your questions, comments and feedback to: support@qahomestudy.com

I sent these two questions in advance:

1) Does what organisms eat link food energy to RNA-directed DNA methylation and all healthy longevity via fixation of amino acid substitutions and transgenerational epigenetic inheritance in the context of the physiology of pheromone-controlled reproduction in species from microbes to humans?

2) Does the virus-driven theft of quantized energy link the loss of information from impaired methylation to all pathology?

——————————

See why I asked: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

The potential for sperm miRNA affecting zygote development has recently been reported in the literature [18] and has interesting implications for the use of sperm miRNA profiles as indicators of potential male fertility.

See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
See also: Olfaction Warps Visual Time Perception



Alternative splicing of pre-mRNA

The Origin of Information (4)

Summary: Others have learned that the energy in a hydrogen atom must be linked to all biodiversity on Earth.
The question is: “Where did the energy in the hydrogen atom come from?
See: The Origin of Information (3)
Finally, someone is asking questions that can be summarized in one question (see below). Until now, on the International Society for Human Ethology’s Yahoo group, and elsewhere, the moderator: Jay R. Feierman has prevented the dissemination of accurate information on this topic. Now others have learned that the energy in a hydrogen atom must be linked to all biodiversity on Earth.
The question is: “Where did the energy in the hydrogen atom come from?
See the discussion attempt at: 88233 Re: DNA Begins As a Quantum Wave, According to New Science

Excerpt: Much of the information in this article came from The Synchronicity Key: The Hidden Intelligence Guiding The Universe and You

Conclusion: Clearly though, our view of the universe and life itself is changing as these concepts are understood by more people each day.

The fact that DNA begins as a quantum wave linked to biophysically constrained amino acid substitutions was addressed in the context of: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
Natural selection for quantized energy-dependent codon optimality and the stability of messenger RNA during transgenerational epigenetic inheritance has since been placed into the context of experimental evidence reported as Olfaction Warps Visual Time Perception.
See also the series of presentations at virtual conferences that began with: The Origin of Information: How to Solve It.
When I realized that people might not understand that the origin of information must be linked from quantum waves to RNA-mediated healthy longevity and from virus-driven energy theft to all pathology, I split the original presentation submission into two parts. The revised title was RNA mediated molecular epigenetics and virus driven entropy.
From hydrogen atom transfer in DNA base pairs to ecosystems was presented during the same virtual conference.
Several more presentations added information about top-down energy-dependent RNA-mediated biologically-based biodiversity. For example, this may be my final presentation at Labroots virtual conferences Energy as Information and Constrained Endogenous RNA Interference
The journalists from Labroots have ignored my presentations despite a series of my comments on their attempt to continue touting pseudoscientific nonsense about neo-Darwinian theories.  It seems unlikely that any science journalist will admit to their overwhelming ignorance.
See for comparison:168949 From the evolutionary psychology Yahoo group. Re: DNA Begins As a Quantum Wave, According to New Science
Jay R. Feierman admits:

This claim is above my level of expertise to refute. It comes from a peer reviewed article in The American Chemical Society’s Journal of Physical Chemistry B. See below, which is taken from https://phys.org/news/2008-01-genetic-telepathy-bizarre-property-dna.html.
“Scientists are reporting evidence that intact, double-stranded DNA has the “amazing” ability to recognize similarities in other DNA strands from a distance. And then like friends with similar interests, the bits of genetic material hangout or congregate together. The recognition — of similar sequences in DNA’s chemical subunits — occurs in a way once regarded as impossible, the researchers suggest in a study scheduled for the Jan. 31 issue of ACS’ Journal of Physical Chemistry B”.
Read more at: https://phys.org/news/2008-01-genetic-telepathy-bizarre-property-dna.html#jCp

There are many things in physics and physical chemistry that seem incredulous to me. That includes some of the claims of quantum mechanics. What about the Penrose Hameroff Theory of Quantum Consciousness. See http://www.quantumconsciousness.org/sites/default/files/1998%20Hameroff%20Quantum%20Computation%20in%20Brain%20Microtubules%20The%20Penrose%20Hameroff%20Orch%20OR%20model%20of%20consciousness%20-%20Royal%20Society_0.pdf.

On several occasions, Feierman has threatened to ban me from the Human Ethology Yahoo Group. Then, he simply fails to post my comments when they do not support his nonsense.
I’ve added some comments to this discussion because it seems to be progressing nicely at a time after Feierman has admitted he knows virtually nothing about biophysically constrained biologically based RNA-mediated cell type differentiation.
See: Discus for discussion of

How to teach evolution when students hold creationist views


Feierman, and others like him, have been teaching neo-Darwinian theories either directly or indirectly. But Feierman’s nonsense has consistently been the most offensive to me personally. After publication of my 2013 review, I attempted to discuss the refutation of neo-Darwinian nonsense he had been touting since I first met him at a conference in 1995.
His responses to Nutrient-dependent/pheromone-controlled adaptive evolution: a model include:
7/25/13
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.
7/26/13
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.
Now, he admits, albeit elsewhere, that he knows nothing about how food energy as quantized information must be linked to healthy longevity via the pheromone-controlled physiology of reproduction, or be linked from the virus-driven degradation of messenger RNA to mutations and all pathology.
See also this example of a false dichotomy: Scholars who believe nurture trumps nature also tend to doubt the scientific method

One group, made up of psychologists, economists, philosophers and political scientists believes more strongly in the genetic influences on behaviour, beliefs and culture. The other group, consisting sociologists, non-evolutionary anthropologists, women’s and gender studies scholars and all humanities scholars (except philosophy), believes in the primacy of environmental influences.

No Genetics without Epigenetics? No Biology without Systems Biology?

…there has never been a genetics without an epigenetics.

Energy-dependent changes link the epigenetic landscape to the physical landscape of supercoiled DNA, which protects all organized genomes from the virus-driven degradation of messenger RNA that all serious scientists have linked from mutations to all pathology in all living genera.
See: microRNA  for more than 63,000 examples of that fact.

Cytosis

Energy-dependent physical and biophysical constraints (1)

Summary: The hitchhiking, the epistasis, and the dynamics of adapting populations are energy-dependent and biophysically constrained in the context of RNA-mediated protein folding chemistry. The virus-driven degradation of messenger RNA links mutations to all pathology in all living genera.

An upper limit on the functional fraction of the human genome

For the human population to maintain a constant size from generation to generation, an increase in fertility must compensate for the reduction in the mean fitness of the population caused, among others, by deleterious mutations. The required increase in fertility due to this mutational load depends on the number of sites in the genome that are functional, the mutation rate, and the fraction of deleterious mutations among all mutations in functional regions. These dependencies and the fact that there exists a maximum tolerable replacement level fertility can be used to put an upper limit on the fraction of the human genome that can be functional. Mutational load considerations lead to the conclusion that the functional fraction within the human genome cannot exceed 25%, and is probably considerably lower.

Reported as: Most of Human Genome Nonfunctional: Study

If only a small bit of the genome is functional, then the odds of a mutation taking out an important sequence are smaller, and therefore fertility rates can be lower.

That conclusion makes sense in the context of natural selection for food energy-dependent codon optimality, which biophysically constrains RNA-mediated protein folding chemistry.  Feedback loops link the physiology of pheromone-controlled reproduction to protection from the virus-driven degradation of messenger RNA.
Simply put, the structure of functional DNA is food energy-dependent because what organisms eat prevents virus-driven entropy of their organized genomes in the context of reproduction.

I would like to think that most knowledgeable biologists who properly appreciate evolutionary theory and genomic diversity are well aware of the many problems with ENCODE’s claim.

Anyone who is not aware of the problems should search PubMed for the term “microRNA” before release of the cell biology game “Cytosis” forces them to learn what anyone more than ten years old can learn from playing the game.
Energy-dependent viral latency is biophysically constrained in organized genomes. Nutrient stress and social stress break the constraints and the stress-linked degradation of messenger RNA links viruses to all pathology.
All life on Earth is energy-dependent, which means that the energy must be biophysically “trapped” at least twice.
See also: Gamma-ray telescopes reveal a high-energy trap in our galaxy’s center

…suggests the center of our Milky Way contains a “trap” that concentrates some of the highest-energy cosmic rays, among the fastest particles in the galaxy.

“Our results suggest that most of the cosmic rays populating the innermost region of our galaxy, and especially the most energetic ones, are produced in active regions beyond the galactic center and later slowed there through interactions with gas clouds…”

This appears to be another example of how ultraviolet light constrains the formation of new galaxies. Constraints on energy might be linked to quantum entanglement, which is something that theoretical physicists have not linked from quantum physics to quantum souls.
Should theoretical physicists be asked to include this new information in their theories so that their theories could be used to design experiments that link facts about sunlight as quantized energy to all energy dependent biodiversity on Earth via the physiology of reproduction?
Should theorists be asked about the facts included in these published works?
See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
See also: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

See also: Universe’s ultraviolet background could provide clues about missing galaxies

Simulations show that there should be more small galaxies in the Universe, but UV radiation essentially stopped them from developing by depriving them of the gas they need to form stars.

See also: World’s brightest laser sparks new behavior in light

The claim of new behavior linked from the light of a billion suns begins to make more sense. Now, a high energy trap links the diffuse glow of gamma rays reaching nearly 50 trillion electron volts can be compared to gamma-ray energies and the energy of visible light, which ranges from about 2 to 3 electron volts.

I am happy that we already presciently linked the differences in constrained energy from “…a change in the electron, which abandoned its usual up-and-down motion in favor of a figure-8 flight pattern.”

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

See: Olfaction Warps Visual Time Perception and this two-part video interview:
Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 1
Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 2

In the context of the solar analemma, Mobius strip, and the symbol for infinity, the report on the figure-8 “flight pattern” of electrons is consistent with representations of how the anti-entropic virucidal energy of sunlight is linked under ‘normal’ conditions to the collective energy of all scattered photons. That collective energy links energy as information to all biodiversity via the physiology of pheromone-controlled reproduction in the context of how quantum physics must be linked to quantum souls.

See also: Probabilistic epigenesis and A probabilistic classifier for olfactory receptor pseudogenes.

Everything known to serious scientists about the energy-dependent creation of receptors links the sense of smell in bacteria to our visual perception of mass and energy in the context of the space-time continuum via energy-dependent changes in the microRNA/messenger RNA balance

.For comparison see: Hitchhiking and epistasis give rise to cohort dynamics in adapting populations

Beneficial mutations are the driving force of adaptive evolution.

There is no such thing as a beneficial mutation. The virus-driven theft of quantized information is linked to increased virulence of viruses via a single amino acid substitution in the virus. The link from sunlight to food energy is the link to all ecological adaptations.

My comment: Reported on July 18, 2017 as Large-scale study of adaptation in yeast could help explain the evolution of cancer

See for comparison our 1996 Hormones and Behavior review of food energy-dependent RNA-mediated ecological adaptations that link sexual differentiation in yeasts to all biodiversity in all living genera in the context of our section on molecular epigenetics.
From Fertilization to Adult Sexual Behavior

The hitchhiking, the epistasis, and the dynamics of adapting populations are energy-dependent and biophysically constrained in the context of RNA-mediated protein folding chemistry. The virus-driven degradation of messenger RNA links mutations to all pathology in all living genera.

See also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

I used the term “adaptive evolution” instead of ecological adaptation to avoid problems with peer-review if the reviewers recognized that my review was a refutation of neo-Darwinian pseudoscientific nonsense.

Conclusion:

…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

rp_tumblr_ngykp0yfND1r5gzz6o1_500.jpg

Energy-dependent epigenetic translation to mRNA stability

Negative selection in humans and fruit flies involves synergistic epistasis

Negative selection against deleterious alleles produced by mutation influences within-population variation as the most pervasive form of natural selection.

Naturally occurring positive selection for energy-dependent codon optimality replaced every aspect of neo-Darwinian theories that linked natural selection from mutations to evolution of increasing organismal complexity. Positive selection for epigenetically-effected beneficial alleles links the epigenetic landscape to the physical landscape of supercoiled DNA via nutrient-dependent pheromone-controlled metabolic networks and genetic networks.
Everything from atoms to ecosystems was included in this invited review of nutritional epigenetics because all serious scientists know that organisms survive on food energy and that species exemplify the pheromone-controlled reproduction and chromosomal inheritance that ensures survival of all living genera.
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

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.

See also: Transcriptome-wide Discovery of microRNA Binding Sites in Human Brain

This interactome points to functional miRNA:target pairs across >3,000 genes and represents a valuable resource for accelerating our understanding of miRNA functions in brain. We demonstrate the utility of this map for exploring clinically relevant miRNA binding sites that may facilitate the translation of genetic studies of complex neuropsychiatric diseases into therapeutics.

See also: Connections Underlying Translation and mRNA Stability

…intimate connections between mRNA and the ribosome can drive biological regulation. In closing, we consider the likelihood that these connections between protein synthesis and mRNA stability are widespread or whether other modes of regulation dominate the mRNA stability landscape in higher organisms.

No experimental evidence of evolution includes biophysically constrained biologically-based cause and effect, which integrates the required link from ecological variation to the physics, chemistry, and molecular epigenetics of what Darwin presciently linked from his “conditions of life” to ecological adaption via energy-dependent changes in messenger RNA (mRNA).
See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition (with my emphasis)

…the ribosome interprets two codes within the mRNA: the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.

Natural selection for energy-dependent codon optimality conserves the amino acid substitutions in the context of the stability of supercoiled DNA. That stability protects all organized genomes from virus-driven energy theft and genomic entropy. Protection from viruses occurs via the pheromone-controlled biophysically constrained physiology of reproduction in all living genera. Experimental evidence of that fact was included in our section on molecular epigenetics from this 1996 Hormones and Behavior review.
From Fertilization to Adult Sexual Behavior

Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus (Runge and Zakian, 1996; Wu and Haber, 1995).

See for comparison: Tracing the Enterococci from Paleozoic Origins to the Hospital

Host energy-dependent speciation

Graphical abstract from “Tracing the Enterococci from Paleozoic Origins to the Hospital”

Reported as: Enterococci may have evolved antimicrobial resistance millions of years ago

…researchers have traced evidence of the bacteria’s evolutionary history back 425 million years and theorize that the same traits that allow the bacteria to thrive in hospitals likely emerged when they were carried onto land in the guts of the world’s first terrestrial animals. The study was funded in part by the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health.

The physiology of reproduction in bacteria and all other living genera is nutrient-dependent and pheromone-controlled. Researchers who think they have traced evidence back to the bacteria’s evolutionary history across 425 million years have not considered the weekend resurrection of the bacterial flagellum to be proof of their pseudoscientific nonsense. Instead, they report “Speciation: Host energy source driven” in their graphical abstract.
Where did the energy come from?
See: Evolutionary Rewiring
The nutrient-dependent pheromone-controlled physiology of reproduction in P. fliuorescens was linked to the weekend evolution of the bacterial flagellum.
See also for an invertebrate example of nutrient energy-dependent pheromone-controlled top-down causation: Inhibition of miR-274-3p increases BmCPV replication by regulating the expression of BmCPV NS5 gene in Bombyx mori  From: Virus Genes. 2017 May 10. doi: 10.1007/s11262-017-1466-7
See also: Two fatty acyl reductases involved in moth pheromone biosynthesis

Studies over the last two decades have pinpointed that the epigenetic effect of pheromone-driven adaptive evolution is one of the major factors driving the successful diversification of Lepidopteran insects10. In moths, a few substitutions in critical amino acids in the key pheromone biosynthetic enzymes are sufficient to create a novel pheromone component11,12.

Facts about pheromones in species from microbes to humans have now been placed into their proper context.
Poor human olfaction is a 19th-century myth, which was reported as: “The human sense of smell: It’s stronger than we think” May 11, 2017
See for comparison: Human pheromones: integrating neuroendocrinology and ethology

The ‘affective primacy hypothesis’ [5] asserts that positive and negative affective reactions can be evoked with minimal stimulus input and virtually no cognitive processing. Olfactory signals seem to induce emotional reactions whether or not a chemical stimulus is consciously perceived. We theorize that the importance of human non-verbal signals is based upon information processing, which occurs in the limbic system, and without any cognitive (cortical) assessment. Affect thus does not require conscious interpretation of signal content. Underlying this fact is that affect dominates social interaction and it is the major currency in social interactions [6]. Affective reactions can occur without extensive perceptual and cognitive encoding. They are made with greater confidence than cognitive judgments, and can be made sooner [5, 7]. Olfactory input from the social environment is well adapted to fit such assertions. For example, chemical cues allow humans to select for, and to mate for, traits of reproductive fitness that cannot be assessed simply from visual cues.

See also: The RNA Age: A Primer
What is currently known about energy-dependent biophysically constrained RNA-mediated cell type differentiation refutes every aspect of neo-Darwinian evolution by placing natural selection for codon optimality and the pheromone-controlled physiology of reproduction first.
All published works and reviews of RNA-mediated events must be placed into the context of the paradigm shift that led to the development of this game.
Cytosis: A Cell Biology Game

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

Some researches may continue to ignore details about energy-dependent RNA-mediated protection from virus-driven energy theft; the degradation of messenger RNA; and the pathology that is linked from mutations to the loss of enzymes, hormones and receptors in all living genera.
Others will obfuscate what is known to serious scientists.
See for comparison: Ontological Systems In Cognition

There is investigated the possibility of cognition of everything that somehow and other is able to influence to the cognizer – its Existing, which exists for him and may be cognized by him. It is proved that all parts of the Existing are interconnected, it is closed and is the only one for all cognizers in it, and everything differed from the Existing is indistinguishable for the cognizer from non-Existing and cannot be cognized by him. It is shown that the surrounding world of the cognizer, understood as a collection of objects and interconnections identified by him, corresponds to the cognizer’s `nature’ – its ontology and are only a part of the Existing. Objects and interconnections of different ontology differ from each other on level of notions, so are uncertain, inconsistent and paradoxical in relation to each other, and corresponding systems of representations with definite ontology cannot be unified in frames of one system, so are irredundant with each other. There are found the correlations of physical objects of quantum theories, also as cosmological dark matter and dark energy with objects with different ontology. There are analyzed the methods of mathematical description of objects with different ontology, the so-called `correlation principle’ of physical theories in irredundant systems of representations, the `principle of freedom’ for formation of the universe understood as the surrounding world of the cognizer. There are considered the philosophical aspects of the existence of irredundant representations, the physical picture of the world, which this concept leads to. The surrounding worlds corresponding to irredundant representation systems, being parts of the one Existing, are closely interconnected, mutually complemented and form each other, without mixing and being different `by nature’, and contradictions between them stand as moving forces of their evolution.

All aspects of anything that has ever been linked to the “moving forces” of evolution have clearly been linked from food energy and movement to biodiversity and from stress-related virus-driven energy theft to mutations that link the lack of movement at the molecular level to all pathology.
See for instance: Valerie Horsley Gets Under Skin

The Yale University cell and molecular biologist is probing the deep mysteries of epidermal cells.

My comment:
See also: Brain on stress: How the social environment gets under the skin

The authors note that on page 17184, right column, first paragraph, line 4, “effect” should instead appear as “affect.”

The failure to provide a neurobiological framework for understanding natural selection for energy-dependent codon optimality, which is the basis for the biological embedding of epigenetically-effected positive health, positive affect, self-efficacy and self-esteem via effects on reactive alleles in the genome, continues to link all pathology from the virus-driven degradation of messenger RNA to the negative supercoiling of DNA.
No one asked me to establish that framework for healthy longevity or pathology, but I did it anyway after I was told to start with gene activation in GnRH neuroscrectory neurons by Bruce McEwen.
See also: Genome Digest

What researchers are learning as they sequence, map, and decode species’ genomes

The researchers found that genes involved in key survival functions, such as the removal of cellular toxins, the stabilization of proteins, and the activity of the innate immune system, were expanded in deep-sea mussels.

Anna Di Cosmo’s group presciently placed these finding into the context of General and Comparative Endocrinology in Role of olfaction in Octopus vulgaris reproduction
From the concluding paragraph:

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000). — p. 61

The fact that the energy-dependent stability of RNA-mediated protein folding chemistry links physics from autophagy to biophysically constrained viral latency went missing during the past 4 years, but is not likely to continue to be ignored.
See why: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Conclusion:

…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

There is still no other model for comparison, despite the publication of Mutation-Driven Evolution on the same day my 2013 review was published.

(1) Mutation is the source of all genetic variation on which any form of evolution is dependent. Mutation is the change of genomic structure and includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc. (2) Natural selection is for saving advantageous mutations and eliminating harmful mutations. Selective advantage of the mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation.

That claim differentiates ridiculous theories from my model of biophysically constrained biologically-based cause and effect. The differences were noted in 1991 when Roger Penrose wrote:

How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy? – From What is Life? (reprint edition)

See also: The Latest Discovery In Quantum Physics Shows Reality Is Not What It Seems

New experiments and studies conducted in laboratories such as CERN seem to suggest that everything is actually composed of energy rather than material particles, including human beings.
Biology to a Physicist

Energy as information and constrained endogenous RNA interference (4)

Premise: Sunlight is the energy as information that is required to link endogenous RNA interference to healthy longevity
Counter claim:  The Quantum Thermodynamics Revolution: Information theory

Understanding entropy as a subjective measure allows the universe as a whole to evolve without ever losing information.

Precision Medicine virtual conference, Feburary 22-23, 2017

Title: Energy as information and constrained endogenous RNA interference

  •  James V. Kohl
  • RNA-mediated.com
  • jvkohl@bellsouth.net
  • Abstract describing the poster

 

Narrative: The term microRNA has been used in 58,000 indexed works. All the works support claims that link the anti-entropic virucidal energy of sunlight from endogenous RNA interference to biophysically constrained protein folding chemistry and cell type differentiation.
For comparison, news from last week reported: Physicists make the case that our brains’ learning is controlled by entropy.
On the same day, George Church spoke during the highest-profile lecture program at the NIH. His topic was “The future of genetic codes and BRAIN codes
But he failed to link energy-dependent endogenous RNA interference or exogenous RNA interference to the genetic codes or the brain codes.
For contrast, the systems complexity of energy-dependent top-down RNA-mediated causation is detailed here.
The details can be compared to claims that minimal mutational differences might link energy and/or entropy to the evolution of all morphological and behavioral diversity on Earth via DNA.
What I have done is to link Quantized Energy as Information from chirality and hydrophobicity to thermodynamic cycles of protein biosynthesis and degradation via the potential of hydrogen, which is referred to as pH.
pH links the sun’s anti-entropic virucidal energy from hydroxylation to the de novo creation of nucleic acids and hydrogen atom transfer in DNA base pairs in solution.
Photosynthesis links the creation of G protein-coupled receptor genes from the innate immune system to nutritional epigenetics and autophagy.
pH-taxis, chemotaxis, thermotaxis and phototaxis link microRNA biogenesis and microRNA flanking sequences from hydrogen energy-dependent changes in the microRNA/messenger RNA balance to autophagy.
Autophagy links everything currently known about nutritional epigenetics from alternative splicings of pre-messenger RNA to nutrient-dependent amino acid substitutions.
For example, feedback loops link odors and pheromones to the physiology of reproduction in all vertebrates via substitution of achiral glycine in position 6 of the gonadotropin releasing hormone decapeptide.
Simply put, endogenous RNA interference clearly links RNA-directed DNA methylation from DNA repair to supercoiled DNA and healthy longevity in all living genera via fixation of achiral glycine and/or fixation of other amino acid substitutions in all species.
For comparison, excess STRESS links reduced pH to virus-driven energy theft and genomic entropy via transgenerational epigenetic inheritance.
The cited works that support the details in this poster link epigenetically-effected changes in amino acid substitutions to cell type differentiation from archaea to Zika virus-damaged human DNA.
When that fact is considered in the context of the Precision Medicine Initiative it becomes clear that virus-driven energy theft links neural circuitry, odor hedonics, mood, memory, motivation, expressions of affect, cognitive behavioral state, and potentiating responses to other stimuli from nutritional and/or social stress to mutations and all pathology.
In the context of the Precision Medicine Initiative, prevention of pathology is achieved only in the context of nutritional epigenetics and the National Microbiome Initiative.
The National Microbiome Initiative links energy-dependent fixation of nutrient-dependent amino acid substitutions to supercoiled DNA, which protects all organized genomes from virus-driven entropy.
That fact helps to explain why exogenous RNA interference might sometimes be effective IF it restores nutrient-energy-dependent viral latency.
The failure to restore viral latency can now be placed into the context of three recent additions to the Merriam-Webster dictionary:
Phytoremediation,
Microbiome,
and CRISPR.
Taken together, the dictionary definition of these terms replaces ideas about evolved biodiversity that were based on de Vries 1902 definition of mutation. That definition led to the assumptions of population geneticists who never linked energy-dependent metabolic networks to genetic networks via endogenous RNA interference and the physiology of reproduction.
POSTER TEXT
Fact: The ribosome links the epigenetic landscape to the physical landscape of supercoiled DNA. The ribosome acts as a molecular decoder and as sensor that couples changes in the efficiency of messenger RNA (mRNA) translation to its biophysically constrained stability, which is regulated by energy-dependent stop codons.
1) ATP hydrolysis by UPF1 is required for efficient translation termination at premature stop codons
Alternative: Temperature-dependent biological processes could theoretically occur within a  range from –50°C, where cells vitrify or at +140°C when evolutionary theorists seem to think that nucleic acids spontaneously hydrolyze.
2)  Evolutionary drivers of thermoadaptation in enzyme catalysis
Elaboration: The speed of light on contact with water links adenosine triphosphate  (ATP) from energy-dependent changes in chirality and hydrolysis to phosphorylation. The anti-entropic virucidal effects of sunlight  link the energy-dependent creation of RNA to the innate immune system. For example, the de novo creation of G protein-coupled receptors (GPCRs) is energy dependent. Feedback loops link odor and pheromone signaling from ATP to the physiology of reproduction via GPCRs and nutrient energy-dependent phosphorylation.
The innate immune system links chirality to autophagy to biophysically constrained RNA-mediated protein folding chemistry in all living genera. Nutrient energy-dependent fixed RNA-mediated amino acid substitutions in supercoiled DNA protects all organized genomes from virus-driven energy theft.
For example, nutrient energy-dependent endogenous RNA interference (RNAi) has been linked to cell type differentiation and species diversity via nutritional epigenetics and the pheromone-controlled physiology of reproduction in nematodes.
3). Endogenous RNAi Pathways Are Required in Neurons for Dauer Formation in Caenorhabditis elegans
Example and summary: “….the epigenetic effects of food odors and pheromones are involved in neurogenic niche construction as exemplified in nematodes…”  See Bumbarger et al., (2013) as cited in Kohl (2013)
4) Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Nutrient energy-dependent pheromone-controlled quorum sensing links codon identity to the biophysically constrained stability of  mRNA. Natural selection for energy-dependent codon optimality appears to be the link from Darwin’s “conditions of life” to endogenous RNAi and all biodiversity via conserved molecular mechanisms in all living genera.
5) Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
The ATP-dependent creation of RNA links energy from endogenous RNAi to the stability of mRNA and  healthy longevity. That fact underlies every aspect of metabolic theory, which predicts how nutrient energy-dependent changes are linked from angstroms to ecosystems via genetic networks in all living genera.
6) Metabolic theory predicts whole-ecosystem properties
RNAi pathways appear to link ATP from hydrogen atom transfer in DNA base pairs in solution to microRNA flanking sequences and to all morphological phenotypes and behavioral phenotypes via the transgenerational epigenetic inheritance of healthy longevity.
7) The phylogenetic utility and functional constraint of microRNA flanking sequences
8) Impact of MicroRNA Levels, Target-Site Complementarity, and Cooperativity on Competing Endogenous RNA-Regulated Gene Expression
9) MicroRNA analysis in mouse neuro-2a cells after pseudorabies virus infection
10) microRNA-binding proteins: specificity and function
11) RNA in extracellular vesicles
12) Structural diversity of supercoiled DNA
Alternative facts and the ‘arbitrium’ system link communication among viruses and bacteria to all biodiversity on Earth inside and outside the context of quorum sensing. In the context of quorum sensing, viruses  decide how much energy to steal from cell types. Outside the context of quorum sensing in bacteria, the viruses must somehow tell each other exactly how much energy to use to link RNA-mediated amino acid substitutions to the stability of their organized genomes via minimal mutational distances and/or de novo mutations.
13)  Communication between viruses guides lysis–lysogeny decisions
14) The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters
15) Prevalence and architecture of de novo mutations in developmental disorders
In theory, until a specific cell type realizes that a change in chirality also indicates that energy is missing, the cell type does not decide to use autophagy to protect its supercoiled DNA from more energy theft. That theory links the alternative facts about the ‘arbitrium’ system from de novo mutations to evolution.
Theories of mutation-driven evolution fail to explain any aspect of what is known to those who have linked energy-dependent changes from angstroms to ecosystems in all living genera via the physiology of reproduction. Two song parodies link the difference in theory and what is known about energy-dependent changes in base pairs to biophysically constrained protein folding chemistry. 16) All about the base and 17) Chemists know.
The diagram represents what is known about the systems complexity of energy-dependent changes in base pairs, amino acid substitutions and RNA-mediated cell type differentiation, which has been placed into the context of RNAi.
Two recently published articles by co-authors who are 2016 Nobel Laureates, link chirality to autophagy and endogenous RNAi. The current understanding of RNAi surpasses all understanding of systems complexity that was placed into the context of RNA-mediated DNA methylation.
18) Dynamic control of chirality and self-assembly of double-stranded helicates with light
19) The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes
Until now, most researchers have failed to link light induced changes in chirality to the biophysically constrained structurel of supercoiled DNA. That fact makes the difference between metabolic theory and the arbitrium’ system clear. All metabolic approaches explicitly and quantitatively link the natural selection of food to the control the carbon cycle at every level of examination that is required to link what organisms eat to supercoiled DNA via the physiology of reproduction. No alternative facts or theories are required. Supercoiled DNA links everything known about cell type differentiation in all  individuals of all species to energy-dependent ecosystems and the Earth’s biosphere.
Energy-dependent links from angstroms to ecosystem are clearly manifested in endogenous RNA interference, which links fixation of RNA amino acid substitutions in all differentiated cell types to the Precision Medicine Initiative. For comparison, links from virus-driven energy theft and gene-editing via the CRISPR-Cas9 technology are included in this proposal for the treatment of pathology. 20) RNA-Guided Human Genome Engineering
In the context of human genome engineering: “Repetitive elements or endogenous viral elements can be targeted with engineered Cas+gRNA systems in microbes, plants, animals, or human cells to reduce deleterious transposition or to aid in sequencing or other analytic genomic/transcriptomic/proteomic/diagnostic tools (in which nearly identical copies can be problematic).”
Simply put, viruses are used to edit DNA in genomes that are damaged by virus-driven energy theft. Researchers using the technology think they can biophysically constrain virus-driven energy theft with directed virus-driven editing.
The current political climate in the USA indicates that a paradigm shift has already occurred. The National Microbiome Initiative and the Precision Medicine Initiative collectively appear to be blocking attempts to deliver an exogenous RNAi-based treatment. The treatment has been referred to as a “billion dollar baby.” The alternative to spending billions more dollars to perfect the treatment, which may cost more than what most people can afford, will require more scientists to learn what is known about how the microbiome and metabolic networks are linked to precision medicine by  genetic networks.
In the context of precision medicine, learning more about how ecological variation and endogenous RNAi link metabolism from ecological variation to energy-dependent  ecological adaptation  in species form microbes to humans may make more sense than learning more about the use of viruses to repair DNA damage caused by other viruses.
For example, Roger Penrose inadvertently linked energy-dependent endogenous RNA interference to exogenous RNA interference: How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?”(Roger Penrose 8 August 1991) in 20) What is Life?
See also: 21) Arginine 66 Controls Dark-State Formation in Green-to-Red Photoconvertible Fluorescent Proteins
22) Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor
The photoconvertible fluorescent proteins link energy-dependent endogenous RNAi to the substitution of achiral glycine in position 6 of the GnRH decapeptide, which links the pheromone-controlled physiology of reproduction in all vertebrates to the conserved molecular mechanisms of RNA-mediated protein folding chemistry in all living genera. Every aspect of every detailed link from angstroms to ecosystems involves the energy-dependent protein folding chemistry that links what organisms eat to the functional structure of supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.
23) A Big Bang in spliceosome structural biology

achiral-glycine

Energy-dependent microRNA biogenesis

Published May 3, 2017 Genetic variation and RNA structure regulate microRNA biogenesis

…primary sequence determinants and RNA structure are key regulators of miRNA biogenesis.

Genetic variation aka primary sequence determinants are energy-dependent and RNA-mediated. Energy-dependent RNA methylation is an experience-dependent link from natural selection for energy-dependent codon optimality. Natural selection for energy-dependent codon optimality links ATP-dependent microRNA biogenesis to RNA biosynthesis.
Ridiculous attempts to portray energy-dependent top-down causation as if genetic variation came first may continue for another 52 years. But see this report from 1964 to help you recognize how much pseudoscientific nonsense has been touted since then.
See: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

Isolated thymus nuclei transport amino acids into an intranuclear pool by a process which seems to depend on energy from nuclear ATP synthesis (20).

If any experimental evidence of biophysically constrained RNA-mediated cell type differentiation was not linked from an anti-entropic energy source to nuclear ATP synthesis that experimental evidence might support the claims of pseudoscientists who think that mutations link natural selection to evolution of different species.
See for comparison: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The bias between codons or amino acids, and mRNA expression levels has been previously recognized across species and is thought to result from selection for efficient, accurate translation, and folding of highly expressed genes…

My translation: Natural selection for energy-dependent and energy-efficient protein folding chemistry links what organisms eat to the energy that they require for reproduction via the accurate translation and folding of highly expressed genes.
Alternatively, virus-driven energy theft links the degradation of messenger RNA to all pathology via conserved molecular mechanisms in all living genera. Simply put, the molecular mechanisms of healthy longevity and biodiversity are nutrient energy-dependent and pheromone-controlled.

The fact that population geneticists have ignored what us known to all serious scientists about the controlled molecular mechanisms that link metabolic networks to genetic networks has led to the unnecessary suffering and premature death of millions to billions of people. If you are not willing to join those who are Combating Evolution to Fight Disease, you probably will be asked why you decide to ignore everything known about the energy-dependent de novo creation of genes. If you did not recognize your ignorance, try to find experimental evidence in the works of evolutionary theorists who did not start after the energy-dependent de novo creation of genes.

So far as I know, all pseudoscientists still consistently place the facts about de novo gene creation, which refute their nonsense about mutation-driven evolution, into the context of their published works. Those works will continue to cause the unnecessary suffering and premature death of millions to billions of people.

The fact that experience-dependent genetic variation does not create itself is a thorn in the side of all theorists who now recognize and must ignore the facts about RNA-mediated cell type differentiation. The facts link the energy-dependent RNA-mediated fixation of amino acid substitutions to all biodiversity.

The facts also link mutations to all pathology, which means the facts have always been evolutionary theory killers. The facts haven’t changed since Thomas Hunt Morgan presciently linked them to chromosomal inheritance and Schrodinger presciently linked the anti-entropic virucidal energy of sunlight to RNA-mediated DNA repair.

See also: Exiqon “Genome Web” This link opens the pdf for microRNA target identification by RNA pull down with biotinylated microRNA mimics

Approximately one in five microRNA interactions with mRNAs occur through non-canonical binding sites. Although of functional relevance these microRNA targets are not predicted by bioinformatics tools. Improved RNA pull-down techniques with biotinylated microRNA mimics open new possibilities to identify microRNA targets experimentally.

Download the tech note

My  comment: Although I have repeatedly mentioned works that link energy-dependent changes in the microRNA/messenger RNA balance to cell type differentiation and healthy longevity, I had not seen any mention of biotinylation, until today.

In biochemistry, biotinylation is the process of covalently attaching biotin to a protein, nucleic acid or other molecule. Biotinylation is rapid, specific and is unlikely to perturb the natural function of the molecule…

I do not know any theorists who are biochemists and suspect that all the ridiculous theories of pseudoscientists include nothing that is known about biotinylation. That may be why I did not hear the term mentioned, until today. What would happen if I heard it and failed to learn what it meant? God forbid, I might still be a biologically uninformed theorist
See for example: The landscape of sex-differential transcriptome and its consequent selection in human adults

This work provides a comprehensive overview of the sex-differential transcriptome and its importance to human evolution and human physiology in health and in disease.

Reported as: Researchers identify 6,500 genes that are expressed differently in men and women

The detailed map of these genes, reported in BMC Biology, provides evidence that males and females undergo a sort of separate, but interconnected evolution.

I thank God, for not allowing me to believe that males and females are different mutants of the same species.
See for comparison: We are all mutants

Darwin is a god in evolution, so you can’t criticize Darwin. If you do, you’re branded as arrogant.

But any time a scientific theory is treated like dogma, you have to question it. The dogma of natural selection has existed a long time. Most people have not questioned it. Most textbooks still state this is so. Most students are educated with these books.

You have to question dogma. Use common sense. You have to think for yourself, without preconceptions. That is what’s important in science.

Common sense? Masatoshi Nei’s textbook Mutation-Driven Evolution was published on the same day as my 2013 review: Nutrient-dependent/pheromone-controlled adaptive evolution: a model, which is a refutation of mutation-driven evolution.

Excerpt:

…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution.

Conclusion:

…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

See for comparison: John Deely, from the Point of View of Biosemiotics

Conclusion:

….his unlimited but judiciously applied enthusiasm, his sterling example as  a scholar, and his inspirational support of semiotic colleagues, institutions, and the ongoing investigation into the reality of sign process at every level of life have been and will remain a force that both inspires and that sets the standard by which our colleagues continue with their important work.

My comment: The reality of sign process at every level of life is that it is energy-dependent, RNA-mediated, and biophysically constrained by the physiology of reproduction in species from archaea to humans.