Biology to a Physicist

Abiogenesis vs microRNA biogenesis

Summary: The pseudoscientific nonsense about abiogenesis that has been touted by Karo Michaelian and others like him has caused the unnecessary suffering and premature death of millions to billions of people by placing the pathogenic consequences of deregulated miRNAs into the context of ridiculous theories.
See for comparison: Structural diversity of supercoiled DNA and the parody from the same research group:
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Abiogenesis (2017)
Microscopic dissipative structuring and proliferation at the origin of life (Oct 13, 2017)

Some fundamental molecules of life are suggested to have been formed, proliferated, and evolved through photochemical microscopic dissipative structuring and autocatalytic proliferation under the UV-C/UV-B solar environment prevalent at Earth’s surface throughout the Archean. Evidence is given in the numerous salient characteristics of these, including their strong absorption in this spectral region and their rapid non-radiative excited state decay through inherent conical intersections. The examples of the dissipative structuring and dissipative proliferation of the purines and of single strand DNA are given. UV-C and UV-B-induced stationary state isomerizations and tautomerizations are shown to be crucial to the formation of the purines from hydrogen cyanide in an aqueous environment under UV-C light, while UV-C induced phosphorylation of nucleosides and denaturing of double helix RNA and DNA are similarly important to the production and proliferation of single strand DNA. This thermodynamic dissipation perspective provides a physical-chemical foundation for understanding the origin and evolution of life.

The suggestion is ridiculous. No serious scientist would claim that some fundamental molecules of life formed, proliferated, and evolved in the context of thermodynamic dissipation after the UV-C induced phosphorylation of nucleosides and denaturing of double helix RNA and DNA.
The functional structure of supercoiled DNA is energy-dependent.
All serious scientists start with the link from the sun’s anti-entropic virucidal energy on contact with water to the creation of ATP synthase; the creation of microRNAs; the creation of all other enzymes; the creation of all receptors; the creation of all hormones. That’s how serious scientists link microRNA biogenesis to all biophysically constrained food energy-dependent pheromone-controlled morphological and behavioral diversity on Earth.
MicroRNA biogenesis (2018)

The tipping point of 72,000 indexed published works that mention microRNAs was reached on 4/18/18
See: microRNA
Example: Arthropod viruses and small RNAs (2013)

Understanding the role of small RNAs in arthropod host-virus molecular interactions will facilitate manipulation of these pathways for both management of arthropod pests of agricultural and medical importance, and for protection of beneficial arthropods such as honey bees and shrimp. This review highlights recent research on the role of small RNAs in arthropod host-virus interactions with reference to other host-pathogen systems.

Example: MicroRNAs as mediators of insect host-pathogen interactions and immunity (2014)

In this review, we will discuss the latest developments in regards to the role of microRNA in insect host-pathogen interactions and provide some insights into this rapidly developing area of research.

Example: miRNA regulation of innate immunity (2018)

MicroRNAs (miRNAs) are small noncoding RNA and are pivotal posttranscriptional regulators of both innate and adaptive immunity. They act by regulating the expression of multiple immune genes, thus, are the important elements to the complex immune regulatory network. Deregulated expression of specific miRNAs can lead to potential autoimmunity, immune tolerance, hyper-inflammatory phenotype, and cancer initiation and progression. In this review, we discuss the contributory pathways and mechanisms by which several miRNAs influence the development of innate immunity and fine-tune immune response. Moreover, we discuss the consequence of deregulated miRNAs and their pathogenic implications.

The pseudoscientific nonsense touted by Karo Michaelian and others like him has caused the unnecessary suffering and premature death of millions to billions of people by placing the pathogenic consequences of deregulated miRNAs into the context of ridiculous theories.
See for comparison: Structural diversity of supercoiled DNA and the parody from the same research group:

See also: Michaelian K
and Retraction: Oligoarginine peptides slow strand annealing and assist non-enzymatic RNA replication (Nov 23, 2017)
The life’s works of all those who have ever touted their ridiculous claims about abiogenesis can now be placed into the context of the eternal significance of microRNAs. The energy dependent de novo creation of microRNA flanking sequences has repeatedly been linked from the physiology of pheromone-controlled reproduction to biophysically constrained viral latency and sympatric speciation in all living genera.
See: 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: Long-range coherence and energy storage in biological systems (1968)
See also: Cytosis (for ages 10+)

Players take turns placing workers on available organelles within a human cell in order to collect resources (such as Carbohydrates or ATP!) or take actions (such as purchasing Cell Component cards or translating mRNA into Proteins!)

Players use their resources to build Enzymes, Hormones, and Hormone Receptors and also to help detoxify the cell – all of which score health points. The player with the most health points at the end of the game wins!

See for comparison: DNA Denaturing through UV-C Photon Dissipation: A Possible Route to Archean Non-enzymatic Replication (2014)

Many of the fundamental molecules of life, those common to all three domains; bacteria, eukaryote, and archea, including RNA and DNA, amino acids, enzymes, vitamins, cofactors, and protoporphyrins, absorb photons in the UV-C 1. RNA or DNA in complexes with these molecules act as acceptor quenchers, providing the electronically excited pigment donor molecule with an extremely rapid (sub picosecond) non-radiative dexcitation channel, through internal conversion into vibrational energy of the nucleic acid and surrounding water molecules2.

On January 15, 2016 John Hewitt commented:  You have just described the founding principle and thermodynamic function of life
On April 17, 2018, I commented on the ridiculous claim this so-called science journalist made because he blocked me from seeing his tweets a few months ago.

5th-6th Sept 2018 Dublin, Ireland

2018 March for Science vs microRNAs (2)

The anti-entropic virucidal energy of sunlight on contact with water has been linked from the creation of ATP synthase to the creation of ATP and to the creation of RNA. Energy-dependent RNA-mediated DNA repair has been linked to biophysically constrained viral latency via the creation of microRNAs and feedback loops linked to the food energy-dependent microRNA-mediated physiology of reproduction. The physiology of energy-dependent pheromone-controlled reproduction biophysically constrains viral latency in the context of the creation of the innate immune system and autophagy.
See: miRNA regulation of innate immunity (4/14/18)
None of the facts about the energy-dependent creation of the microRNAs or the microRNA-mediated regulation of innate immunity are included in: The Transcription Factor Runx3 Establishes Chromatin Accessibility of cis-Regulatory Landscapes that Drive Memory Cytotoxic T Lymphocyte Formation (4/17/18)
The regulatory landscape that drive memory cytotoxic T lymphocyte formation might just as well be framed in the context of magic or in the equally ridiculous context of gene-centric theories.
See this report: Your immune system holds the line against repeat invaders, thanks to this molecule

Runx3’s control of T cell differentiation is important because when our bodies fight off viruses and cancers—and our T cells burst into action—the vast majority tend to become effector cells. These effector cells are short-lived and do not persist once the infection resolves.

The control of all cell type differentiation is energy-dependent, RNA-mediated and biophysically constrained by the physiology of reproduction in all living genera. The cell biology game “Cytosis” for ages 10+ teaches the facts that link Schrödinger (1944) What is Life? to Schrödinger at 75 – The Future of Biology – September 2018
In 1944, Schrödinger wrote:

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.)

See for comparison (this gene-centric pseudoscientific nonsense):
– Part I: FINDING THE CODE (Run time: 12:10
The race to sequence the human genome was also billed as a race to end disease. What happened?

– Part II: FIXING THE CODE (Run time: 13:07)
CRISPR — and the promise and pain of gene therapy that came before it. 

– Part III: SELLING THE CODE (Run time: 10:55)
Genetic testing has moved out of the labs into the masses. But even with your genome in hand, what can you believe?
The gene-centric pseudoscientific nonsense does not start with the creation of energy.  But every aspect of biophysically constrained life on Earth starts with the quantized energy-dependent creation of microRNAs. The epigenetically effected energy-dependent microRNA-mediated creation of the “Code” and the microRNA-mediated fixing of the “Code” is missing from the claims of biologically uninformed theorists who link beneficial mutations from natural selection to evolution. They have sold their gene-centric pseudoscientific nonsense to many people.
For example, some gene-centric biologically uninformed theorists share beliefs about abiogenesis for comparison to quantized energy-dependent microRNA biogenesis in articles like this: DNA Denaturing through UV-C Photon Dissipation: A Possible Route to Archean Non-enzymatic Replication
Conclusion:

Many of the fundamental molecules of life, those common to all three domains; bacteria, eukaryote, and archea, including RNA and DNA, amino acids, enzymes, vitamins, cofactors, and protoporphyrins, absorb photons in the UV-C 1. RNA or DNA in complexes with these molecules act as acceptor quenchers, providing the electronically excited pigment donor molecule with an extremely rapid (sub picosecond) non-radiative dexcitation channel, through internal conversion into vibrational energy of the nucleic acid and surrounding water molecules2.

See John Hewitt’s comment: You have just described the founding principle and thermodynamic function of life
In a classic example of human idiocy (See Feynman: food energy), biologically uninformed science idiots linked the dissipation of quantized energy to the origin of life via abiogenesis. The creation of biophysically constrained biophotonicaly based life in the context of the energy-dependent creation of microRNAs was reported in the context of photon dissipation and entropy as: Abiogenesis: A Theory on The Origins of Life

By now, we all know how evolution works. At least, most of us have a basic understanding of how it functions. At its most fundamental level, evolution is change over time. More specifically, it is changes within a biological population over successive generations.

Ultimately, biological complexity is one of the most important things to come out of evolution. Things started simple. Then genes mutated, cells interacted with their environment, mitochondria stopped being living organisms and started being part of a cell and—Tada—complex life.

A conflict arose between John Hewitt’s accurate representations of biophysically constrained life in The vibrational theory of olfaction for the win  and few months ago, Hewitt blocked me from seeing his tweets.

The same kinds of amino acid substitutions that control the separations and interactions of side chains in fluorescent proteins also play an essential role in tuning the proposed mechanism for vibration detection—inelastic electron tunneling. Life literally runs on electron tunneling through the respiratory chain complexes in mitochondria. These proteins employ complicated mechanisms including esoteric-soundings things like electron bifurcation and confurcation to pump protons across the mitochondrial inner membrane. When mitochondria go dark, cells can often continue to run for a short while, but it is only in the dim glow of the battery backup metabolism.

Here are some links to the reason for the conflict. Simply put, John Hewitt put everything known to serious scientists about energy-dependent microRNA biogenesis back into the context of abiogenesis.
2005 MicroRNA biogenesis: coordinated cropping and dicing
2015 Dysregulation of microRNA biogenesis and gene silencing in cancer
2015 RNA-mediated degradation of microRNAs: A widespread viral strategy?
Claims about abiogenesis exemplify what Richard Feynman referred to as human idiocy. So does John Hewitt and anyone else who believes in Michaelian’s pseudoscientific nonsense.
See other examples of Michaelian’s pseudoscientific nonsense and human idiocy by clicking here.
The energy-dependent creation of one domain of life links the physiology of reproduction in bacteria to biophysically constrained viral latency. The virus-driven degradation of messenger RNA is linked to the destruction of all life on Earth.
The degradation of messenger RNA links mutations to the creation of archaea and L-forms via entropy, which clearly links the weakening of the proton motive force to the elimination of the cell wall in L-forms (the last remnants of creation).
See also: Past 5,000 years prolific for changes to human genome
If you cannot link the miRNA regulation of innate immunity to all extant biodiversity via the physiology of pheromone-controlled reproduction and fixation of energy-dependent microRNA-mediated amino acid substitutions, thank a biologically uniformed science idiot.
 

An evolutionary theory killer

A reversible TCA cycle in a thermophile

Make no mistake, pseudoscientists have stolen the soul of science for more than 20 years, with their ridiculous claims about mutations and evolution.
For comparison, see:

“…considering that we have just 3 such round Nos ‘100’ ‘1000’ ‘10000’, its just three out of all realistic possibilities, no? Admit its looks cool just bec. we calc in Dec system. History books claims was invented by ancient societies; but I think its evolution: We have 10 fingers!”

My reply (SARCASM ALERT):

Thanks. The correlations are intriguing. Templeton funding might help you prove that the numbers game of evolution is true in the context of Cosmopsychism. With enough correlations, facts that link physics and chemistry to viral latency can be dismissed.

Thanks to the Ralser lab for bringing this to my attention with a claim about:
A reductive TCA cycle in a thermophile, which uses the same citrate synthase [enzyme] both for the oxidative and the reductive directionality.

“Every day it looks more likely that primoridial and modern metabolism look similar”

A link was provided to: A primordial and reversible TCA cycle in a facultatively chemolithoautotrophic thermophile

…raises the possibility of a facultatively chemolithomixotrophic origin of life.

Has anyone else considered that possibility?
I tried to look at it from the perspective of chemoorganoheterotrophic metabolism and electron-eating microbes that enzymatically (not automagically) create uranium isotopes, but I got side-tracked by the claims about mutations and evolution. I could not link those claims from the physiology of reproduction in microbes to claims that link the metabolism of food energy to pheromones that biophysically constrain viral latency in species from microbes to humans.

Now, the physiology of pheromone-controlled reproduction in electron-eating microbes that create uranium isotopes suggests the same thing that the Ralser lab suggested: SARCASM ALERT: “It’s turtles all the way down” (the infinite regress problem in cosmology).Unless, like the folks at the Ralser Lab,  you are a serious scientist.

The problem for pseudoscientists, theorists, and many so-called science journalists may be familiar to those at the Ralser lab. McEwen et al., (1964) reported “The synthesis of RNA in isolated thymus nuclei is ATP dependent.” All serious scientists know “ATP controls the crowd.

These findings suggest an additional way for cells to use ATP to maintain proteostasis in the crowded cytoplasm and also fine-tune the material properties of nonmembrane-bound organelles and the cell interior in general.

Obviously, there are now several groups of serious scientists that can make fun of all the pseudoscientists and so-called science journalists who have failed to link physics and chemistry to biophysically constrained viral latency via energy-dependent changes in base pairs in species from thermophiles to those that create uranium isotopes. But Kudos to the first group, or one of the first, to do that:

12/10/14 All about that base and Structural diversity of supercoiled DNA 10/12/15

Sarcasm Alert: I hope that claims about the emergence of energy and mutation-driven evolution did not confuse others as much as they confused so-called science journalists such as John Hewitt, Philip C. Ball, Carl Zimmer, and many others.
When you see the facts reported by an intelligent science journalist, please tell others about the claims that link the creation of energy from the game “Subatomic” to biophysically constrained viral latency in “Cytosis.” Comparisons will be made. It will become clearer that pseudoscientists, theorists and many others have lost their games.
See for example: Attacked from All Sides: RNA Decay in Antiviral Defense

…RNA decay machinery plays important roles in antiviral defense. This can involve either direct effects on vRNA stability or indirect regulation of the intracellular milieu. Furthermore, an emerging theme suggests that many RNA binding proteins can be repurposed from their endogenous roles in the nucleus to antiviral roles in the cytoplasm. Future studies are necessary to further elucidate how these RNA binding…

…proteins recognize foreign RNAs and how they interface with the RNA decay machinery to restrict vRNA replication.”

Alternatively, everyone can simply accept the fact that food energy typically restricts the virus-driven degradation of messenger RNA, and tell all the pseudoscientists and so-called science journalists where to put their pseudoscientific nonsense (e.g., where the sun don’t shine).
For example: Is the Universe a conscious mind?

Cosmopsychism might seem crazy, but it provides a robust explanatory model for how the Universe became fine-tuned for life

For comparison: A Big Bang in spliceosome structural biology and Alternative splicing and the evolution of phenotypic novelty
But remember to link the claims about the evolution of phenotypic novelty to the missing claims about behavior, and see the claims made by Bruce McEwen and Martin Picard in:
Psychological Stress and Mitochondria: A Conceptual Framework (Part 1)

Mitochondria, a subcellular organelle with its own genome, produce the energy required for life and generate signals that enable stress adaptation. An emerging concept proposes that mitochondria sense, integrate, and transduce psychosocial and behavioral factors into cellular and molecular modifications. Mitochondrial signaling might in turn contribute to the biological embedding of psychological states.

Reported as: Cellular ‘powerhouses’ may explain health effects of stress
in the same context as Psychological Stress and Mitochondria: A Systematic Review (Part 2)

Evidence from metabolomic, proteomic, and transcriptomic studies also suggest additional layers of regulation by which stressful experiences may alter mitochondrial components among rodents. Although these metabolites, protein composition, and gene expression outcomes do not reflect the functionality of mitochondria, when assessed in parallel with functional outcomes, they will help explain and refine our understanding of the mechanisms by which stress influences mitochondrial function and health. In addition, whereas functional changes should be regarded as primary indicators of MAL (21), stress-induced molecular changes within mitochondria may also reflect compensatory mechanisms or recalibrations that contribute to long-term changes in mitochondrial function and to the accumulation of MAL. [mitochondrial allostatic load (MAL)]

Review: Subatomic
See also: Self-evident: Contrary to recent opinion, there is such a thing as the self, and it is empirically amenable to scientific investigation 
It has been investigated at every level of investigation that links quantum physics from quantum chemistry to quantum souls in the context of what is known to all serious scientists about biophysically constrained energy-dependent protein folding chemistry that protects supercoiled DNA from the virus-driven degradation of messenger RNA, which links mutations to all pathology.
Conclusion (from self-evident):

The multitudinous self mediates scientific explanations of the complexity of real people with and without mental disorders. It also provides resources for enhancing the moral agency that permits people to flourish. For me, flourishing is simply the development of a person’s psychological and social skills in engagement with herself and with others, in the face of the challenges triggered by her physical, social and psychological environment. If we know the characteristics of the self, we might be able to improve the lives of those whose self-experiences are not conducive to flourishing. The self is not an idle concept, either scientifically or ethically; it organises human experience and proliferates moral possibilities. So, yes, know thyself. Every single part.

See: 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).

Make no more mistakes, pseudoscientists have stolen the soul of science for more than 20 years, with their ridiculous claims about mutations and evolution.

5th-6th Sept 2018 Dublin, Ireland

A mental health problem at the highest level (3)

Summary: It has been 75 years since Erwin Schrödinger exposed the pseudoscientific nonsense of mutation-driven evolution in the lecture series that was published as What is Life? (1944)
The mental health of so-called science journalists must be addressed. Many of them seem to be pathological liars or, at best biologically uninformed science idiots who cannot link physics and chemistry from molecular epigenetics to all energy-dependent biodiversity on Earth.
The Biggest Myth In Quantum Physics by Ethan Siegel
Conclusion:

Take ourselves out of it, and all we have are the equations, the results, and the answers that the physical Universe gives. Physics cannot answer questions about “why” the Universe works the way it does; it can only explain how it works at all. If you’re interested in the fundamental nature of reality, ask the Universe questions about itself, and when it tells you its secrets, listen. Anything else that you layer atop it was put there by you, not by the Universe. Avoid that temptation, and you’ll never fall for the greatest myth about quantum physics: that it needs an interpretation at all.

The claim that quantum physics does not require a meaningful approach to explaining how energy is linked to all biodiversity in the context of interpretation of facts is ridiculous. Astrophysicist and author Ethan Siegel is the founder and primary writer of the blog “Starts With A Bang!” His books include Treknology and Beyond The Galaxy, Simply put, he is a biologically uniformed science idiot, like others who have failed to link their ridiculous theories to all biodiversity on Earth.
See for comparison: Refined control of cell stemness allowed animal evolution in the oxic realm
Reported as: Why animals diversified on Earth: Cancer research provides clues 

Just the presence of free oxygen is the result of some microbes finding a way of using sunlight to get energy. This was also a biological event.

The difference between how animals diversified and why they diversified is perfectly clear to all serious scientists. Energy is required!
McEwen et al (1964) linked the biological event from the creation of ATP to the creation of RNA and the creation of all biophysically constrained biodiversity. All other serious scientists have since followed his lead. Dobzhansky (1964) suggested that would happen.

The notion has gained some currency that the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists! I have heard a man whose official title happens to be Professor of Zoology declare to an assembly of his colleagues that “a good man cannot teach zoology. A good man can teach, of course, only molecular biology.

Such pronunciamentos can be dismissed as merely ridiculous. They are, however, caricatures of opinions entertained by some intelligent and reasonable people, whose views deserve an honest and careful consideration and analysis. Science must cope with new problems that arise and devise new approaches to old problems. Some lines of research become less profitable and less exciting and others more so.

The claims made in the fake news about Donald Trump’s mental state can now be linked to the mental heath of his antagonists who have never seen Dozhansky’s “light of evolution.”
Nothing in Biology Makes Any Sense Except in the Light of Evolution

For example, the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).”

The anti-entropic virucidal effect of sunlight was linked from ecological variation to ecological adaption in all living genera via the pheromone-controlled physiology of reproduction in soil bacteria in: What is Life? (1944)

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.)

Seventy-four years later we have this example of human idiocy: Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis
Reported as: Counting chromosomes: Plant scientists solve a century-old mystery about reproduction (2018)

Today, a team of geneticists reveals a remarkable mechanism that enables plants to count their chromosomes, solving a century-old mystery.

Molecular mechanisms are energy-dependent. That’s no mystery. See: How an RNA gene silences a whole chromosome (2015)
Most science journalists have refused to inform themselves. They have not linked sunlight on contact with water to all energy-dependent biodiversity via the physiology of reproduction. For example, John Hewitt wrote:

If anything we know the Sky Fathers totally forgot about selenium during most of the design phase and then had to write him in at the end as a walk-on.

I was surprised by his sarcastic attack on religion and wrote:

Let’s not do this. See instead: A third of Americans don’t believe in evolution 

Those who do not believe in evolution understand that energy-dependent RNA-mediated amino acid substitutions must be linked from the physiology of reproduction to chromosomal rearrangements that biophysically constrain viral latency. If you can place your claim about selenium into the context of protection of all life on Earth from the virus-driven degradation of messenger RNA, we could discuss your claim. What is it?

John Hewitt wrote:

Sky Daddy likes cranberries so much he gave them sequence-level machinery for producing selenocysteine in their mitochondrial genome

I could not get  him to make sense. I wrote:

This is the type of cryptic sarcastic claim that kills people. Thousands  of them. Quit playing your silly games. Who are you calling “Sky  Daddy?”  Sequence-level molecular machinery does not exist outside the context of the creation of the sun’s anti-entropic virucidal energy. 

For comparison, Roger M. Pearlman wrote:

name one person you know that can explain Neo-Darwinian Theory (NDT) so it adds up, and how you know it adds up otherwise don’t knock the NDT adherents here as they are equally inept at making NDT add up as are the leading NDT scientists

How can anyone who wants to discuss NDT not know about this published work from 1973? Nothing in Biology Makes Any Sense Except in the Light of Evolution

… the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.

The differences in the amino acid sequences are Koonin’s proof of evolution. See: A universal trend of amino acid gain and loss in protein evolution

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

If the differences in the amino acid sequences are energy-dependent and RNA-mediated, NDT is the most ridiculous example of pseudoscientific nonsense that has every been touted by people who claim to be more intelligent than their primate ancestors.

Proof of that fact was published as: Modern diversification of the amino acid repertoire driven by oxygen

..we demonstrate an immediate survival benefit conferred by the enhanced redox reactivity of the modern amino acids tyrosine and tryptophan in oxidatively stressed cells. Our data indicate that in demanding building blocks with more versatile redox chemistry, biospheric molecular oxygen triggered the selective fixation of the last amino acids in the genetic code. Thus, functional rather than structural amino acid properties were decisive during the finalization of the universal genetic code.

Selective fixation of amino acid substitutions in organized genomes is energy-dependent and controlled by the physiology of reproduction.

That fact was reported as: Quantum Chemistry Solves The Question of Why Life Needs So Many Amino Acids 

If you were representing the amino acids as circles, they could be drawn as multiple concentric circles representing differing energy levels, rather than one single circle of the same chemical hardness and energy level – kind of like in the photo below.

Few people would make the connection from the amino acids as circles representing different energy levels to the claim that de Vries (1902) made when he invented the term mutation.

See:  What is Life? (1944)

But about forty years ago the Dutchman de Vries discovered that in the offspring even of thoroughly pure-bred stocks, a very small number of individuals, say two or three in tens of thousands, turn up with small but ‘jump-like’ changes, the expression ‘jump-like’ not meaning that the change is so very considerable, but that there is a discontinuity inasmuch as there are no intermediate forms between the unchanged and the few changed. De Vries called that a mutation. The significant fact is the discontinuity. It reminds a physicist of quantum theory -no intermediate energies occurring between two neighbouring energy levels. He would be inclined to call de Vries’s mutation theory, figuratively, the quantum theory of biology. We shall see later that this is much more than figurative. The mutations are actually due to quantum jumps in the gene molecule. But quantum theory was but two years old when de Vries first published his discovery, in 1902. Small wonder that it took another generation to discover the intimate connection!

It has been 75 years since Erwin Schrödinger exposed the pseudoscientific nonsense of mutation-driven evolution in the lecture series that was published as What is Life? (1944)

In the 1991 reprint edition, a forward by Roger Penrose who has co-authored with George F.R. Ellis, Stephen Hawking, Stuart Hameroff and others 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?

It is worth repeating the claim the food energy is required to link quantum physics from quantum chemistry to quantum biology and quantum souls until all pseudoscientists lean the difference between a mutation and an amino acid substitution. Until then, the mental health problem at the highest level will be maintained at the highest level by the highest level of human idiocy every known to have eliminated common sense from consideration in the context of biologically based cause and effect.

For example, Darwin’s claims were based on “conditions of life” that required all organisms to find food and reproduce. Nothing was known about mutations, and even then Darwin could not possibly have been foolish enough to put them first in the context of natural selection for mutation-driven pathology.

See also: Analysis of experience-regulated transcriptome and imprintome during critical periods of mouse visual system development reveals spatiotemporal dynamics

Visual system development is light-experience dependent, which strongly implicates epigenetic mechanisms in light-regulated maturation. Among many epigenetic processes, genomic imprinting is an epigenetic mechanism….

…through which monoallelic gene expression occurs in a parent-of-origin-specific manner.

See: An Epigenetic Signature for Monoallelic Olfactory Receptor Expression
This explains why John Hewitt claims I’m providing BS. He is a biologically uninformed science journalist who does not understand the facts about light energy-dependent changes in organized genomes.
Any journalist who publishes anything like The vibrational theory of olfaction for the win should prepare to defend his claims in the context of serious scientists who know how energy must be linked to the vibrations and how the vibrations link quantum physics from quantum chemistry to quantum souls via the physiology of pheromone-controlled reproduction and fixation of RNA-mediated amino acid substitutions.

http://nnjournal.net/article/viewFile/2354/1850/10234

A mental health problem at the highest level (2)

Biologically uninformed theorists and so-called science journalists have ignored their own mental health issues and focussed their attention on the mental health of serious scientists. Some of the serious scientists advise the President of the United States in attempts to help him make America great again by draining the political and academic swamps.
It is time to examine the personality disorders of theorists and biologically uninformed journalists for comparison to the mental health of serious scientists and the President of the United States of America.

The Eight Basic Qualities in All Personality Disorders

The theoretical underpinnings of interpersonal style fall into an approach popular in the mid-20th century postulating that “all interpersonal interactions reflects attempts to establish and maintain self-esteem or avoid anxiety” (p. 679). According to this view, you’re constantly trying to feel good about yourself in your relationships because to recognize weakness would make you feel anxious. At some level, the theory proposes, we’re always searching for approval and validation.

The theoretical underpinnings led pseudoscientists to claim:

The 8 traits identified [are] …. domineering, vindictive, cold, socially avoidant, nonassertive, exploitable, overly nurturant, and intrusive.

All identified traits are based on social science and all social science is pseudoscience according to Richard P. Feynman.
See for comparison:  Epigenetic modifications poster
This poster covers

    • – Histone and DNA modifications
    • – Histone modifier enzymes
    • – Histone modification binding proteins

All epigenetic modifications are energy-dependent and biophysically constrained by the physiology of pheromone-controlled reproduction in species from microbes to humans. That fact has been known to all serious scientists since we included it in the context of our molecular epigenetics section from this 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior
See for comparison: The Future of Secularism: a Biologically Informed Theory Supplemented with Cross-Cultural Evidence
See the discussion attempt on the: Neuroscience Facebook group
Watch as participants from this group assert the claim that their theory about the intelligence and fertility of Muslims compared to Jews and Buddhists is “biologically informed.”
See for comparison: SIRT6-dependent cysteine monoubiquitination in the PRE-SET domain of Suv39h1 regulates the NF-κB pathway
Reported as: Researchers identify a new chromatin regulatory mechanism linked to SirT6

…suggests a regulatory landscape of these modifications much more complex than previously anticipated…

This suggests they failed to anticipate the link from the creation of anti-entropic virucidal energy of the sun by the entity that John Hewitt referred to as “Sky Daddy.” For comparison to his ignorant biologically uninformed approach to chromatin regulatory mechanisms, see:
Analysis of experience-regulated transcriptome and imprintome during critical periods of mouse visual system development reveals spatiotemporal dynamics (with my emphasis)

Visual system development is light-experience dependent, which strongly implicates epigenetic mechanisms in light-regulated maturation. Among many epigenetic processes, genomic imprinting is an epigenetic mechanism through which monoallelic gene expression occurs in a parent-of-origin-specific manner. It is unknown if genomic imprinting contributes to visual system development. We profiled the transcriptome and imprintome during critical periods of mouse visual system development under normal- and dark-rearing conditions using B6/CAST F1 hybrid mice. We identified experience-regulated, isoform-specific, and brain region-specific imprinted genes. We also found imprinted microRNAs were predominantly clustered into the Dlk1-Dio3 imprinted locus with light experience affecting some imprinted miRNA expression. Our findings provide the first comprehensive analysis of light-experience regulation of the transcriptome and imprintome during critical periods of visual system development. Our results may contribute to therapeutic strategies for visual impairments and circadian rhythm disorders resulting from a dysfunctional imprintome.

A broad-based approach to the failure of most science journalists to understand why energy must be linked to the creation of all biodiversity via the pheromone-controlled physiology of reproduction in all living genera can be viewed in the light of this 2017 published work: Olfaction Warps Visual Time Perception
Wen Zhou’s group linked the energy-dependent creation of the sense of smell in bacteria from the physiology of reproduction to our visual perception of energy and mass in the context of the biophysically constrained space-time continuum.
See for comparison: The vibrational theory of olfaction for the win
I hope that other serious scientists will forgive me for suggesting that John Hewitt could help others understand how the sun’s anti-entropic virucidal energy is used to link the side chains of the tripeptide Ser65-Tyr66-Gly67 to an intrinsic covalently-bonded chromophore.
Like most science journalists, John Hewitt failed to link the creation of energy as information from the sun’s anti-entropic virucidal effects on biophysically constrained viral latency to the creation of enzymes that metabolize food energy and to all pheromone-controlled biodiversity. Most science journalists seem to be united against those who are Combating Evolution to Fight Disease
For example, Ed Yong blocked me from following his tweets, Carl Zimmer blocked me from commenting elsewhere, and I now anticipate only more sarcasm from John Hewitt.  Perhaps I should have been less critical of Philip Ball at the end of this interview.

But, J.A. Parker laughed in the same context of this parody, which is a more technical representation of what all serious scientists know about energy-dependent cell type differentiation in the context of biophysically constrained mental and physical health.
All About that Base (Meghan Trainor Parody) 12/10/14
See: A mental health problem at the highest level (3)
 

For God and Country

Enzyme-constrained interethnic diversity (8)

I am intrigued by the fact that I detailed the energy-dependent links to interethnic diversity in this blog post on the same day that the so-called science journalist Ed Yong placed everything known to serious scientists back into the context of neo-Darwinian evolution.
See for comparison to Ed Yong’s nonsense: “Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!
Yong’s addendum:

*This article has been corrected to reflect the fact that Arc genes were co-opted by animals from a group of genes that also gave rise to retroviruses, and are not directly descended from retroviruses, as originally stated. We regret the error.

Retractions by Szostak reflect a similar theme.

In retrospect, we were totally blinded by our belief [in our findings]…we were not as careful or rigorous as we should have been (and as Tivoli was) in interpreting these experiments.

The food energy-dependent creation of Arc genes links the virus-driven theft of quantized energy to the creation of retroviruses, which are biophysically constrained by RNA-mediated amino acid substitutions in the context of the pheromone-controlled physiology of reproduction.
Something has gone horribly wrong in the context of respected scientist’s retractions and the addendums by science journalists who have failed to link ridiculous theories from top-down causation to biophysically constrained viral latency during the past two decades.
See for comparison:  The vibrational theory of olfaction for the win
John Hewitt will almost undoubtedly be the first science journalist to link the energy-dependent creation of enzymes from the sense of smell in bacteria to our visual perception of mass and energy.
Olfaction Warps Visual Time Perception will then be linked to “The Darwin Code: Intelligent Design without God” and interethnic biodiversity via food energy-dependent pheromone-controlled RNA-mediated amino acid substitutions.

IMG_3010

Enzyme-constrained interethnic diversity (7)

Summary:  I suspect that John Hewitt will soon publish an article on the energy-dependent creation of microRNAs and enzymes. He is most likely to link the virus-driven theft of quantized energy as information to all pathology without challenging pseudoscientists and other science journalists to revise their ridiculous claims about mutation-driven evolution.
Digital medicine, on its way to being just plain medicine

There are already nearly 30,000 peer-reviewed English-language scientific journals, producing an estimated 2.5 million articles a year.

Until recently, no published works linked the creation of the sun’s anti-entropic virucidal energy from ATP to the creation of RNA and biophysically constrained viral latency.
But see: EXD2 governs germ stem cell homeostasis and lifespan by promoting mitoribosome integrity and translation January 15, 2018

“Loss of EXD2 results in defective mitochondrial translation, impaired respiration, reduced ATP production…” and “…aberrant association of messenger RNAs with the mitochondrial ribosome.

Exonuclease 3′ –5′ domain-containing 2 (EXD2) is a mitochondrial ribonuclease. A ribonuclease is a type of nuclease that catalyzes the degradation of RNA into smaller components such as microRNAs. A nuclease is an enzyme capable of cleaving the phosphodiester bonds between monomers of nucleic acids. EXD2 is required for mitoribosome integrity and efficient mitochondrial translation.
See: The Excitable Mitochondria by John Hewitt, who brought the article on EXD2 to my attention in his tweets. The link from energy-dependent changes in EXD2 to homeostasis predicts the link from reduced ATP production to the virus-driven degradation of EXD2 to the aberrant associations that link mutations in messenger RNA to all pathology. I suspect that John Hewitt will soon publish an article on the energy-dependent creation of microRNAs and enzymes. He is most likely to link the virus-driven theft of quantized energy as information to all pathology without challenging pseudoscientists and other science journalists to revise their ridiculous claims about mutation-driven evolution. Challenging your peers leads to your elimination from consideration. Your peers cannot rise to the ocassion and meet the challenge, so they must ignore you.
As I finalize this series on enzyme-constrained interethnic diversity, I also offer information from my largely ignored FB posts on the anniversary dates indicated:
January 10, 2017

The scent of eros: mysteries of odor in human sexuality

“This is science at its best, with adventure, ideas, and lots of facts”. — Helen Fisher

“A treasure hunt through history, literature, and scientific data”. — Gina Ogden

On pages 160-162 of “The Scent of Eros” (1995/2002) we linked race and ethnicity to all biodiversity via the same model of biologically-based cause and effect. It is still the only valid model.

What exactly do people think was still being debated about the fact that all organisms must eat to reproduce, or that pheromones control the physiology of reproduction in all living genera?

How could race and ethnicity not be aspects of a valid model of biologically-based cause and effect unless pseudoscientists convinced you to believe in mutation-driven evolution?

January 10, 2016

This serves as a reminder to all sex researchers. Most of them understand nothing about how RNA-mediated sex differences in cell types are linked to sex differences in #behavior by nutrient-dependent amino acid substitutions.
They refused to accept the fact that the pheromone-controlled physiology of reproduction and chromosomal rearrangements link the molecular epigenetics of cell type differentiation in all cell types of all individuals of all species from microbes to humans.

Xistential crisis: Discovery shows there’s more to the story in silencing X chromosomes
Xist is widely believed to be both necessary and sufficient for X silencing,” … “We for the first time show that it’s not sufficient, that there have to be other factors, on the X-chromosome itself, that activate Xist and then cooperate with Xist RNA to silence the X-chromosome.
An example of how 20 years of ignorance about RNA-mediated cell type differentiation leads to “NEW” discoveries.
From Fertilization to Adult Sexual Behavior 1996
Genomic-imprinting is also manifest in specific parts of the X-inactivation region’s related XIST gene. Here male- and female-specific methyl-group patterns participate in X-inactivation in females and also in the preferential inactivation of the paternal X in human placentae of female concepti (Harrison, 1989; Monk, 1995). This process indicates that tissues of the early conceptus can sense and react differentially to epigenetic sexual dimorphisms on the female conceptus’ own two X chromosomes. Furthermore, variations of X-inactivation patterns often account for traits discordance in monozygotic twin females. In other words, they are often found to have nonidentical patterns of X-inactivation, yielding differing expression of noticeable X-linked traits (Machin, 1996).
January 10, 2017

The anniversary of an attack on science.

Odious Christianity
Ray Comfort

Professor PZ Myers hates Christianity. Nor is he a big fan of my good friend, Ken Ham.
In writing about his hatred, PZ unwittingly showed his hand when he said,

“I reject his notion of sin — the idea that there is some kind of divine law against which we can transgress — but humanists do not deny that we can do wrong and we can do harm. We think we should do better, not to appease some vengeful deity, but because it improves our lives and helps make those around us happier and better able to live up to their potential. We certainly do accept that death is inevitable, but not because we are wicked — the wicked often seem to flourish while the good may die young. Are we to measure the virtue of human beings by their longevity? Charles Manson is 82, and surely destined to join the saints in heaven, while every infant death must open a chute directly to hell for its wicked soul.”
His hatred is perfectly in line with the Bible:
“Because the carnal mind is enmity against God; for it is not subject to the law of God, nor indeed can be” (Romans 8:7).
PZ is unashamedly godless (a state the Bible refers to as “carnal”), and so his mind is at “enmity” against God. That means he is in a continual state of hostility towards his Creator. That certainly is true. Even though he doesn’t believe that He exists, but he contemptuously hates the very thought of “a god.”
But look at the pinpoint accuracy of the Scriptures:
“…for it [our carnal mind] is not subject to the law of God, nor indeed can be.”
His hatred is directed at the “law of God,”–the moral Law (the Ten Commandments).
PZ is like a criminal who hates the police, not because of who they are individually, but because of what they represent. They stand for the law–that which is right and good, and that is offensive to someone who loves and lives for crime.
PZ’s railings about his loved ones dying is tragic, but peripheral. They are not the main reason why he is angry.
His anger is primarily at God and His Law, because he doesn’t like being told what to do. Like you and I before we came to Christ, he loves his sin, and he who loves the darkness hates the light.
I’m not sure why PZ called Charles Manson “wicked,” when his atheistic worldview doesn’t allow for anyone to be “wicked.”
Or could it simply be that Manson transgressed the moral Law, which says “You shall not kill,” and PZ intuitively knows that, because of his God-given knowledge of right and wrong (see Romans 2:15).
It’s actually heartening to see him using his moral compass. If he would put down his weapons and study how God’s moral compass is infinitely higher, he may rethink his rejection of “The soul who sins, shall die.”
This is because every death is sobering evidence of the truth of that verse.
You can see PZ in action in our movie “Evolution vs God” (over 2 million views) at www.FullyFreeFilms.com
P.S. PZ hates the movie.

January 10, 2017

How Your Toxic Boss Is Hurting Your Mental Health

Get out before the DNA damage is irreparable.


I do not have a boss. But the stress of attempting to interest others in what is known about how biologically-based cause and effect must be linked to interethnic similarities and differences may prevent some further attempts to explain how DNA damage is biophysically constrained in the context of naturally occurring RNA interference and viral latency.
November 27, 2017 See: Damage-induced lncRNAs control the DNA damage response through interaction with DDRNAs at individual double-strand breaks
Reported on November 29, 2017 as: RNA takes over control of DNA break repair

Now, a study shows that following the formation of DNA double-strand breaks, bidirectional transcription events adjacent to the break generate small RNAs that trigger the DNA damage response by local RNA:RNA interactions.

The RNA:RNA interactions are energy-dependent and they link the creation of microRNAs to the creation of enzymes, receptors, and hormones that protect organized genomes from virus-driven energy theft and all pathology.  But they are not just RNA:RNA interactions. The interactions among microRNAs and messenger RNA link food energy and the pheromone-controlled physiology of reproduction to all biodiversity on Earth without the pseudoscientific nonsense touted by biologically uninformed theorists and science journalists such as Ed Yong and Carl Zimmer.

 
Cytosis

From E. coli to monkeys and mankind: Theories vs models (4)

More Complexity with Tau

Tagging and un tagging occurs at Ser214, Thr231 and Ser262 at least in order to attach to microtubules in good neurons along the axon highways. Interactions of these affect the PSD as well such as Ser212/Thr214, Ser202/Thr205, and Thr231 by altering the tau interaction with the PSD.

Tau is called a “microtubule associated protein”, one of many stabilizing and regulating the vast amount of shapes that microtubules form. The gene that makes tau is called MAPT for microtubule-associated protein tau gene.

Tau is also important in the nucleus. It binds to RNA by electro chemical interactions and it may also help stabilize RNA and DNA structures in the nucleus, as well as microtubules. It is possible that this interaction with RNA is part of the problem that forms aggregates of abnormal tau. One of the tau variants (4R) is better at helping microtubules.

J.A. Parker and John Hewitt are among the others who will recognize the degree of plagiarism in this blog post by Jon Lieff. Both journalists have reported either directly, or indirectly, on the link from virus-driven energy theft to pathology. For example J.A. Parker specifically linked the virus-driven damage to energy-dependent changes in microtubules and damage to quantum souls.

That fact forces all plagiarists to reinvent their ridiculous theories at the same time they try to include obvious facts about how nutrient energy-dependent RNA-mediated amino acid substitutions in supercoiled DNA protect all organized genomes from the virus-driven degradation of messenger RNA.

Jon Lieff writes about tagging and untagging, which occurs at Ser214, Thr231, and Ser262 to obfuscate the fact that “tagging” is energy-dependent and RNA-mediated. The tagging is RNA-directed DNA methylation and untagging is linked from virus-driven energy theft to the degradation of messenger RNA in all organized genomes. When viruses steal the energy that links amino acid substitutions to cell type differentiation, the degradation of messenger RNA links mutations to all pathology.

The magnitude of deception that continues to link the plagiarism to failed efforts to prevent or effectively treat all pathology is increasing. That suggests the plagiarists recognize the facts, which is why they must continue to obfuscate them for as long as is humanly possible.

In a few more months, we will see the the plagiarist’s time has run out. The cell biology game Cytosis will eliminate all the games played by theorists because their games do not start with the creation of energy-dependent microRNAs. Until then, follow the scientific progress here.

See: The Excitable Mitochondria

Current approaches to the neurosciences are naïve and often misguided. Contemporary researchers are hopelessly enthusiastic about computer simulations, wiring diagrams or connectomes, and brain activity maps.

See also: CRISPR gene editing can cause hundreds of unintended mutations

…the genomes of two independent gene therapy recipients had sustained more than 1,500 single-nucleotide mutations and more than 100 larger deletions and insertions. None of these DNA mutations were predicted by computer algorithms that are widely used by researchers to look for off-target effects.

See for comparison: Physicists Claim the Soul Exists in a Quantum State After Death
Richard P. Feynman presciently predicted that theoretical physicists would be surprised to learn how quantized energy is linked to quantum souls in the context of how supercoiled DNA is created and maintained during times of ecological variation that must be linked from amino acid substitutions to ecological adaptations.

See also: Quantum Souls youtube channel

Light-induced-conformer-intercoversion-of-hydrogen-bond

Open Science: Closed to facts about microRNAs

See my 5-part series on: The tipping point? 50, 000 publications

Imagine how we could accelerate innovation, stimulate economic growth and all the solutions we need to live on a healthy and sustainable planet, if we were to open up our science fully and allow a free flow of scientific knowledge.” says Kamila Markram, a neuroscientist and the CEO of Frontiers, one of the largest Open Access science publishers in the world and a leader in the Open Science movement.

Talk is cheap. See: Understanding and accounting for relational context is critical for social neuroscience
I wrote:

New data on how genetic predispositions are epigenetically linked to phenotypically distinct neuroanatomy and behaviors is provided in the honeybee model. Across-species comparisons from insects to vertebrates clearly show that the epigenetic influence of food odors and pheromones continues throughout the life of organisms that collectively survive whereas individuals do not. These comparisons also attest to the relative salience of sensory input from the rearing environment. For example, when viewed from the consistency of animal models and conditioned behaviors, food odors are obviously more important to food selection than is our visual perception of food. Animal models affirm that food odor makes food either appealing or unappealing. Animal models reaffirm that it is the pheromones of other animals that makes them either appealing or unappealing.

Socioaffective neuroscience and psychology may progress more quickly by keeping these apparent facts in mind: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).

— Kohl, JV (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors Socioaffective Neuroscience & Psychology 2012

Open access publication in Frontiers has not led to any discussion of facts represented since 2005 in articles like this and this one which was co-authored by 2004 Nobel Laureate, Linda Buck. Feedback loops link odor and pheromone signaling with reproduction.
See for comparison, the validation of my model and its importance in the context of integrating disparate disciplines.
George F R Ellis wrote:

“This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics. This is explored here [Top-down causation Organized by George F. R. Ellis, Denis Noble and Timothy O’Connor]: http://rsfs.royalsocietypublishing.org/content/2/1.toc ” 25 Apr 2014 at 07:49am

See also, my comment posted to YouTube:

Talk is cheap. I am a medical laboratory scientist whose efforts to use open access publication have not led to any discussion of facts about energy-dependent biophysically constrained RNA-mediated cell type differentiation or facts about how virus-driven energy theft can be linked from the degradation of messenger RNA to mutations and all pathology in all living genera. See: Energy as information and constrained endogenous RNA interference https://www.youtube.com/watch?v=cdtsfweO5SQ

Q: What happened to the facts about energy as information?

See: A different tack for Alzheimer’s research

“Despite observations that link mitochondrial dysfunction and sporadic neurodegenerative disease, there hasn’t been a robust hypothesis that could explain the origin of mitochondrial stress associated with human aging and able to account for neurological disease observed across the entire human population,” Larsen continues. “The ‘Alu neurodegeneration hypothesis’ provides this link. Alus belong to a class of retrotransposons or mobile elements. They get the name ‘jumping gene’ because they can move about the genome and insert themselves into new locations. Alus are found only in primates, and they are abundant in the human genome (approximately 11 percent of human DNA). For a long time, they were considered junk DNA because their function was largely unknown. Only recently has the scientific community begun to appreciate how much Alu elements have influenced human evolution.”

A: The assumption that humans evolved has influenced the interpretation of any facts based on experimental evidence of energy-dependent de novo creation and/or maintenance of organized genomes. The facts have repeatedly showed that supercoiled DNA protects organized genomes from virus driven degradation of messenger RNA and that the degradation of messenger RNA links mutations to all pathology. The facts also links natural selection for energy-dependent codon optimality to the transgenerational epigenetic inheritance of all biophysically constrained biodiversity.

See also:  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 (Ikemura, 1982; Akashi, 1994; Akashi & Gojobori, 2002; Drummond & Wilke, 2008; Kudla et al, 2009; Novoa & Ribas de Pouplana, 2012). The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

See also: The Excitable Mitochondria by science journalist, John Hewitt.

…the brain’s logical architecture may, in the end, be familiar to us. We do not, after all, have that many models for computation.

Also, there is only one model that links what organisms eat from food energy to the biophysically constrained brain development of humans. Nutrient-dependent/pheromone-controlled adaptive evolution: a model

…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. The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, 2012; Duvarci, Nader, & LeDoux, 2008; Griggs et al., 2013; Monahan & Lomvardas, 2012) in adaptive evolution will certainly be discussed in published works that will follow.

See also: MicroRNA Items: 1 to 20 of 59836

What can be said about researchers who fail to use any model of biophysically constrained biologically-based cause and effect to link energy to supercoiled DNA and virus-driven energy theft to all pathology?

See for example: Mutation-Driven Evolution

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.

See also and combination of these search terms for articles that have been published about clear links to energy-dependent increasing organismal complexity and how virus-driven energy theft contributes to all pathology.

microRNA; miRNA; virus; viruses; psychiatric disorders; autism spectrum disorder; biomarkers; genetic variation; expression profiling; animal studies

Location, Location, Location

Since first proposing that a cell’s function and biology depend on its surroundings, Mina Bissell continues to probe the role of the extracellular matrix.

Virus-driven energy theft prevents the typical interactions that link the function of the extracellular matrix to healthy longevity. As predictably occurs at the time of completion for any paradigm shift, Mina Bissell and others like her will claim that they have known about the role of viruses in cell type differentiation for several decades.

Revealing literature gaps. At UCB, Bissell became interested in cell culture techniques and how viral transformation changes metabolism, working with virus-transformed chicken cells to study how glucose metabolism differs from that of normal cells in culture. She began to read the literature on the Warburg effect—the observation that cancer cells produce energy by aerobic glycolysis and lactic acid fermentation rather than through the typical ATP-producing oxidative phosphorylation cycle.

Bissell’s lab again confirmed that transformed cells rely more heavily on aerobic glycolysis for energy, but that the switch to this energy pathway did not result from the impairment of the hydrogen-transfer pathway. The results, says Bissell, went against the other half of Warburg’s hypothesis: that the reason for the increased glycolysis is impaired hydrogen transfer.

Her lab could not have confirmed anything associated with Warburg’s hypothesis (in 1976). The differences in the energy of photons had not yet been linked from hydrogen-atom transfer in DNA base pairs in solution to the biophysically constrained physiology of reproduction and all biodiversity via changes in base pairs and fixation of amino acid substitutions in supercoiled DNA that protect all organized genomes from virus-driven energy theft and genomic entropy. Since then, the Nobel Prize-winning works of Thomas Hunt Morgan (1933 Physiology or Medicine) and Schrodinger/Dirac (1933 Physics) have linked changes in atomic energy from chirality (Ben Feringa, Chemistry 2016) to autophagy (Yoshinori Ohsumi, 2016 Physiology or Medicine and chromosomal inheritance via the pheromone-controlled physiology of nutrient energy-dependent reproduction in species from microbes to humans.

According to Bissell’s ‘dynamic reciprocity’ model, signals from the ECM traveled through transmembrane receptors to a cell’s interior and nucleus, altering its gene expression.

According to my model of biophysically constrained biologically-based cause and effect Bissell’s ‘dynamic reciprocity’ model fits into the context of neo-Darwinian pseudoscientific nonsense instead of into the context of established facts.

See: Feedback loops link odor and pheromone signaling with reproduction

See for comparison:

Universe's ultraviolet background could provide clues about missing galaxies

Life in your UV light-constrained galaxy

A measurement of the z = 0 UV background from Hα fluorescence

Despite the substantial systematic uncertainty that affects our measurement, our work has demonstrated the potential that future MUSE observations have in constraining the intensity of the UVB in the local Universe.

This is a report on the Multi Unit Spectroscopic Explorer (MUSE) instrument. The preposterous claim is not supported with experimental evidence that observations made in the context of the instrument somehow constrain the intensity of UV light.
That unsupported claim is worth placing into the context of other preposterous claims about the mutation-driven evolution of all biodiversity on Earth.  See: Mutation-Driven Evolution
The picture below represents facts about UV light that link energy-dependent changes from angstroms to ecosystems in all living genera via the physiology of reproduction.
Universe's ultraviolet background could provide clues about missing galaxies
Galaxy UGC 7321 is surrounded by hydrogen gas, and as this gas is irradiated with UV radiation, it emits a diffuse red glow through a process known as fluorescence. This image shows the light emitted by stars inside the galaxy, surrounded by a red ring that represents the fluorescent emission induced by the UV radiation. Credit: M. Fumagalli/T. Theuns/S. Berry

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.

I saw no mention of the missing galaxies until 3/21/17. I only knew that the anti-entropic virucidal energy of ultraviolet light biophysically constrains all life on Earth via nutrient energy-dependent endogenous RNA interference and the physiology of pheromone-controlled reproduction.
Now that information on the missing galaxies has been presented in the context of observations, those observations can be correlated with evidence from observations of individual bones, which exist only in the context of the observable fossil record evidence.
Observers tell us those bones come from species that became extinct millions to billions of years ago.  Dobzhansky (1964) told us about those observers.

“The notion has gained some currency that the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists! I have heard a man whose official title happens to be Professor of Zoology declare to an assembly of his colleagues that “a good man cannot teach zoology. A good man can teach, of course, only molecular biology.

Such pronunciamentos can be dismissed as merely ridiculous. They are, however, caricatures of opinions entertained by some intelligent and reasonable people, whose views deserve an honest and careful consideration and analysis. Science must cope with new problems that arise and devise new approaches to old problems. Some lines of research become less profitable and less exciting and others more so.”

Indeed, it would be hard to miss the fact that current lines of research are expected to be much more profitable that the observations of theorists. For example, RNA-mediated amino acid substitutions in supercoiled DNA link energy-dependent changes in angstroms to ecosystems. Clearly, if organisms within an ecosystem cannot find food, they will not have the energy to reproduce.
The pheromone-controlled physiology of reproduction will no longer prevent the transgenerational epigenetic inheritance of virus-driven energy theft, and all individuals of the species may eventually become extinct. Observable evidence that some individuals died led observers to claim that many species became extinct during millions of years of evolution. No experimental evidence of biologically-based cause and effect supports those claims. Instead, facts about how quickly virus-driven energy theft continues to degrade their messenger RNA suggests that the fossil record of bones exemplifies how quickly ossification occurs in the absence of sunlight.
For comparison, anti-entropic virucidal UV light still appears to be the source of all biodiversity because all biodiversity appears to be energy-dependent and biophysically constrained.
See: Nerve Dependence: From Regeneration to Cancer
Reported as: How the nervous system controls tumor growth

At the dawn of cell differentiation, mitochondria from a particular donor cell may have been the only source of some particular proteins for a new host cell that could no longer make them.

John Hewitt made this fact perfectly clear. Cell type differentiation has always been energy-dependent and biophysically constrained by the physiology of pheromone-controlled reproduction.
Observers claims that fossilized bacteria could be used as evidence to support millions to billions of years of evolution were replaced when chemists provided experimental evidence that the observers were wrong.
Fossil or inorganic structure? Scientists dig into early life forms

Oliver Steinbock and Professor Juan Manuel Garcia-Ruiz of the Consejo Superior de Investigaciones Cientificas (Spanish National Research Council) in Granada, Spain published an article in Wednesday’s edition of Science Advances that shows fossil-like objects grew in natural spring water abundant in the early stages of the planet. But they were inorganic materials that resulted from simple chemical reactions.

See also: A Post Mortem Case Study: Diffuse Pulmonary Ossification and Sudden Death 
Immunotherapeutic targeting of LIGHT/LTβR/HVEM pathway fully recapitulates the reduced cytotoxic phenotype of LIGHT-deficient T cells.
LIGHT (TNFSF14) Increases the Survival and Proliferation of Human Bone Marrow-Derived Mesenchymal Stem Cells
Tumor Necrosis Factor Superfamily Member 14 (TNFSF14)
LIGHT stands for:
“homologous to lymphotoxin, exhibits inducible expression and competes with HSV glycoprotein D for binding to herpesvirus entry mediator, a receptor expressed on T lymphocytes”.
If you do not know that all cell type differentiation is energy dependent and receptor-mediated, you are not likely to link LIGHT to viral latency and all biophysically constrained biodiversity on Earth via the herpesvirus entry mediator or any other receptor that protects organized genomes from virus-driven energy theft and genomic entropy.
However, you could still link LIGHT to Dobzhansky’s claims about the light of evolution. Nothing in Biology Makes Any Sense Except in the Light of Evolution

For example, the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).

Obviously, he was joking about 10 billion years of evolution when he made this claim:

I am a creationist and an evolutionist. Evolution is God’s, or Nature’s, method of Creation.

Anyone who ever linked sunlight to energy-dependent biodiversity on Earth via endogenous RNA interference and the physiology of reproduction knows the difference between jokes about evolution and facts about cell type differentiation. For example, biophysically constrained cell type differentiation is energy-dependent and viruses steal the energy for replication. That’s why all serious scientists have linked  supercoiled DNA to viral latency without making claims about mutations, natural selection, and/or evolution. Serious scientists do not simply link observations from intruments, such as the Multi Unit Spectroscopic Explorer (MUSE) instrument, to missing galaxies. Serious scientists link facts about virus-driven energy theft from mutations to all pathology.
See for example: The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.