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.

5th-6th Sept 2018 Dublin, Ireland

Anti-entropic sunlight: Schrödinger’s Creationist Secret? (3)

Summary: Theorists and most science journalists have failed to link the anti-entropic energy of sunlight from physical constraints on the creation of new galaxies to the biophysical constraints of ultraviolet light on viral latency. Viral latency prevents mutation-driven evolution in the context of the energy-dependent creation of ATP, microRNAs, RNA and established links from base editing to microRNA editing and RNA editing. Every aspect of energy-dependent editing links alternative splicings of pre-mRNA (microRNAs) from light-activated endogenous substrates to the pheromone-controlled physiology of reproduction. Feedback loops link food odors and pheromones to all biodiversity via what has been known or suspected about biophysically constrained feedback for more than 50 years.
A whirling plane of satellite galaxies around Centaurus A challenges cold dark matter cosmology Feb 2, 2018
Reported as:

This is inconsistent with more than 99% of comparable galaxies in simulations. Centaurus A, the Milky Way, and Andromeda all have highly statistically unlikely satellite systems. This observational evidence suggests that something is wrong with standard cosmological simulations.Science, this issue p. 534; see also p. 520

See also: Synchronized Galactic Orbit Challenges Our Best Theory of How the Universe Works Feb 1, 2018
Thanks to Dan Winter for his comment.

“… kind of funny when they fail to recognize a simple picture of phase conjugate (opposing cones) doing ‘4 wave mixing’ – which is how gravity is stabilized- AND emerges into self organization (negentropy)-those who are basically clueless to why objects fall to the ground- have no hope of understanding that the phase conjugate cause of gravity- (www.fractalfield.com/conjugategravity ) is ITSELF the path out of the entropy (belief in inevitable chaos) those fatalists try to infect us with…”

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

This value is consistent with transmission statistics of the Lyα forest and with recent models of a UVB that is dominated by quasars.

Reported as: 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.

Theorists and most science journalists have failed to link the anti-entropic energy of sunlight from physical constraints on the creation of new galaxies to the biophysical constraints of ultraviolet light on viral latency. Viral latency prevents mutation-driven evolution in the context of the energy-dependent creation of ATP, microRNAs, RNA and established links from base editing to microRNA editing and RNA editing. Every aspect of energy-dependent editing links alternative splicings of pre-mRNA (microRNAs) from light-activated endogenous substrates to the pheromone-controlled physiology of reproduction. Feedback loops link food odors and pheromones to all biodiversity via what has been known or suspected about biophysically constrained feedback for more than 50 years.
Serious scientists are beginning to wonder when pseudoscientists and all science journalists will report findings in the context of top-down causation and energy-dependent constraints. Thankfully, we are about to see constraints placed on the amount of pseudoscientific nonsense reported.
See for examples: 
Co-author, John E. Walker is scheduled to present at Schrödinger at 75 – The Future of Biology – September 2018
Structure of the mitochondrial ATP synthase from Pichia angusta determined by electron cryo-microscopy

Living cells need fuel in the form of adenosine triphosphate, or ATP, to stay alive. This fuel is generated by a molecular machine made of two motors joined by a rotor. One generates rotation by using energy provided by oxidative metabolism or photosynthesis; the other uses energy transmitted by the rotor to make ATP molecules from its building blocks, adenosine diphosphate, or ADP, and inorganic phosphate. The structure has been determined of a fungal machine, isolated from its cellular power stations, the mitochondria, where the machine operates. It provides unsuspected details of the blueprint of the machine and how it works. The working principles of the fungal machine apply to similar machines in all species.

Permeability transition in human mitochondria persists in the absence of peripheral stalk subunits of ATP synthase

Mitochondria generate the cellular fuel ATP to sustain complex life. Production of ATP depends on the oxidation of energy-rich compounds to produce a chemical potential difference for hydrogen ions, the proton motive force (pmf), across the inner mitochondrial membrane (IMM). Disruption of the IMM, dissipation of the pmf, and cell death occur if the concentration of calcium ions inside mitochondria is sufficiently elevated to open a pore in the IMM. The identity of the pore is disputed. One proposal is that the pore is in the enzyme that makes ATP. Here, we show that proteins in the enzyme’s peripheral stalk are not involved in the formation or regulation of the pore.

Co-author, Susumu Tonegawa is scheduled to present at Schrödinger at 75 – The Future of Biology – September 2018

Tagging activated neurons with light

Two new protein tools translate neuronal activity into gene expression during a light-defined time window.

Co-author,Ada E. Yonath is scheduled to present at Schrödinger at 75 – The Future of Biology – September 2018

The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus

…we report the cryo-electron microscopy structure of the native 100S ribosome from S. aureus, revealing the molecular mechanism of its formation. The structure is distinct from previously reported analogs and relies on the HPF C-terminal extension forming the binding platform for the interactions between both of the small ribosomal subunits. The 100S dimer is formed through interactions between rRNA h26, h40, and protein uS2, involving conformational changes of the head as well as surface regions that could potentially prevent RNA polymerase from docking to the ribosome.

Co-author, John O’Keefe is scheduled to present at Schrödinger at 75 – The Future of Biology – September 2018

The honeycomb maze provides a novel test to study hippocampal-dependent spatial navigation

Rats learn rapidly and their choices are influenced by three factors: the angle between the two choice platforms, the distance from the goal, and the angle between the correct platform and the direction of the goal. Rats with hippocampal damage are impaired in learning and their performance is affected by all three factors.

Co-author, Linda Buck is scheduled to present at Schrödinger at 75 – The Future of Biology – September 2018
Feedback loops link odor and pheromone signaling with reproduction

These studies reveal a complex interplay between reproduction and other functions in which GnRH neurons appear to integrate information from multiple sources and modulate a variety of brain functions.

The levels of complexity include everything known to serious scientists about energy-dependent niche construction and changes in the fixation of RNA-mediated amino acid substitutions that differentiate the cell types of all individuals of all species.
See for example: Hypothalamic microRNAs flip the switch for fertility (2017); The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression (2014); and the section on molecular epigenetics from our 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior

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 (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

See for contrasting ignorance:Universal Alternative Splicing of Noncoding Exons (2018)

We propose that noncoding exons are functionally modular, with alternative splicing generating an enormous repertoire of potential regulatory RNAs and a rich transcriptional reservoir for gene evolution.

See also: (Co-author, Linda Partridge is scheduled to present at Schrödinger at 75 – The Future of Biology – September 2018)
Drosophila as a model for ageing

Drosophila melanogaster has been a key model in developing our current understanding of the molecular mechanisms of ageing. Of particular note is its role in establishing the evolutionary conservation of reduced insulin and IGF-1-like signaling in promoting healthy ageing.

Sense and antisense RNA are not toxic in Drosophila models of C9orf72-associated ALS/FTD

We confirmed that these RNA foci are capable of sequestering endogenous Drosophila RNA-binding proteins, and that the production of dipeptide proteins (poly-glycine-proline, and poly-glycine-arginine) is suppressed in our models. We find that neither cytoplasmic nor nuclear sense or antisense RNA are toxic when expressed in adult Drosophila neurons, suggesting they have a limited role in disease pathogenesis.

Schrödinger (1944) “What is LIfe?”  placed energy-dependent biophysical constraints on viral latency into the context of light-activated endogenous substrates and ecological adaptations via the physiology of reproduction in species from soil microbes to humans.

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: Mutation-Driven Evolution (2013) and my refutation of that pseudoscientific nonsense in Nutrient-dependent/pheromone-controlled adaptive evolution: a model, which was published on the same day.
See also for a brief video review: “What is life when it is not protected from virus driven entropy”

 

5th-6th Sept 2018 Dublin, Ireland

Anti-entropic sunlight: Schrödinger’s Creationist Secret? (2)

 

Arabidopsis mRNA decay landscape arises from specialized RNA decay substrates, decapping-mediated feedback, and redundancy

The decay of mRNA plays a vital role in modulating mRNA abundance, which, in turn, influences cellular and organismal processes. In plants and metazoans, three distinct pathways carry out the decay of most cytoplasmic mRNAs: The mRNA decapping complex, which requires the scaffold protein VARICOSE (VCS), removes a protective 5′ cap, allowing for 5′ to 3′ decay via EXORIBONUCLEASE4 (XRN4, XRN1 in metazoans and yeast), and both the exosome and SUPPRESSOR OF VCS (SOV)/DIS3L2 degrade RNAs in the 3′ to 5′ direction. However, the unique biological contributions of these three pathways, and whether they degrade specialized sets of transcripts, are unknown.

 
A claim like this could be used as cannon-fodder for any serious scientist who wanted to target a neo-Darwinian theorist. I will do what Daniel Dennet suggested and re-express my target’s position.
You should attempt to re-express your target’s position so clearly, vividly, and fairly that your target says, “Thanks, I wish I’d thought of putting it that way. — Daniel Dennett

Ready… Aim… Fire

Simply put, the target claims that the molecular mechanisms of energy-dependent microRNA-mediated cell type differentiation remove a protective 5′ cap, allowing for 5′ to 3′ decay. But, they place their claim into something that supposedly is unknown about how the biological contributions of three pathways prevent mRNA decay.
The problem with the target’s position: A one-sided attack on Schroedinger’s claims fails to link the epigenetic landscape to the physical landscape of supercoiled DNA in the context of energy-dependent feedback loops. The feedback loops link the physiology of reproduction from the creation of RNA to prevention of the decapping.
The energy-dependent creation of RNA is required to prevent the virus-driven theft of quantized energy that causes the decapping of the mRNA complex and link mutations to all pathology. For contrast, the food energy-dependent creation of microRNAs has repeatedly been linked from RNA-mediated DNA repair and the fixation of  amino acid substitutions to the stability of supercoiled DNA in the organized genomes of all living genera.
See: Evidence for Amino Acid Sequence Differences among Proteins Resembling the L-chain Subunits of Immunoglobulins (1965)

…we believe that this remarkable type of amino acid sequence variation reflects in part the mechanism by which specificity is conferred.

Note: The co-author, Lee E. Hood is scheduled to present at Schrödinger at 75 – The Future of Biology – September 2018 
Supercoiled DNA protects organized genomes from the virus-driven degradation of messenger RNA that the authors of the article on mRNA link to  specialized RNA decay substrates, decapping-mediated feedback, and redundancy without linking the energy-dependent feedback to healthy longevity via the fixation of RNA-mediated amino acid substitutions and DNA repair.
The article is paywalled, so you may need to take my word for the fact that they seem to be deliberately deceptive. The level of their obfuscation became clear to me in the context of their Figure 6.  They placed the role of energy-dependent RNA-mediated amino acid substitutions into the proper perspective of everything known to serious scientists about biophysically constrained viral latency.
Also, in the article text, they conclude that studies of oxidative phosphorylation attest to facts about prevention of mRNA decay components in response to nutrient stress or social stress, which they refer to as “osmotic stress.” They link the stress from changes in the mRNA half-life and suggest that energy-dependent regulation of the half-life could arise in the context of the direct modulation of mRNA decapping machinery.
The direct modulation is obviously energy-dependent but they place the modulation into some other context that seemingly involves upstream pathways and the creation of proteins. Simply put, they are swimming upstream at a time when all serious scientists are starting with energy-dependent top-down creation of microRNAs.
They conclude with a plea for funding of more pseudoscientific nonsense that fails to link the creation of the sun’s anti-entropic virucidal energy to healthy longevity via the creation of microRNAs that prevent the virus-driven degradation of messenger RNA, which serious scientist have linked from mutations to all pathology.  They claim that an important area of future research includes research that might lead to a better understanding of how stress is linked to pathology via conserved molecular mechanisms. I claim they are using correlations from the bottom-up to replace top-down causation and biophysically contrained cause and effect.
See for comparison: ORACLE: Options to Read in the Archive: Churchland Lab’s Experience
They highlight 7 comp/systems neuro papers to help others keep up with the amount of information that is being published in bioRxiv Neuroscience preprints.
For example: Human POMC processing in vitro and in vivo revealed by quantitative peptidomics

Human obesity can result from the aberrant production or processing of proopiomelanocortin (POMC) in hypothalamic neurons, but it is unclear which human POMC-derived peptides are most relevant to body weight regulation.

See also: Association of a lincRNA postmortem with suicide by violent means and in vivo with aggressive phenotypes

In a living cohort, carriers of the minor allele of a SNP associated with increased LINC01268 expression in brain scored higher on a lifetime aggression questionnaire and show diminished engagement of prefrontal cortex (BA10) when viewing angry faces during fMRI. WGCNA highlighted the immune response. Conclusions: These results suggest that LINC01268 influences emotional regulation, aggressive behavior and suicide by violent means; the underlying biological dynamics may include modulation of genes potentially engaged in the immune response.

See also: The behavioral and neurobiological effects of reduced Brd1 expression in mice are sex-biased and implicate gender dependent dysregulation of nuclear receptor mediated signaling in mental disorders

…we provide in vitro evidence that BRD1 modulates the transcriptional drive of a subset of nuclear receptors (e.g. the vitamin D and glucocorticoid receptors). Moreover, we demonstrate enrichment of psychiatric disorder risk in the target genes of nuclear receptors, sex-biased expression of several nuclear receptor genes in the adult brain of Brd1+/- mice, and that sex-biased genes in general are enriched with nuclear receptor genes particularly at the earliest developmental stage of the human brain. Overall, our data suggests that the spatio-temporal interaction between BRD1 and subsets of nuclear receptors in the brain is sex-biased and that hampered BRD1 mediated regulation of target genes governed by certain nuclear receptors may significantly contribute to sex differences in psychopathology.

For comparison, this was published on the same day: Evolutionary conserved neural signature of early life stress affects animal social competence
What do claims about evolutionary conserved neural signatures represent to serious scientists who understand the facts about energy-dependent top-down causation and biophysically constrained viral latency?

"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.

Enzyme-constrained interethnic biodiversity (6)

I think that I may be able to finish this series before the end of the month and use my tweets to expose more than 100,000  people to what is known about how the energy-dependent creation of microRNAs prevents all pathology.
See for one example of more than 68,000 published works:
MicroRNA-22 suppresses cell proliferation, migration and invasion in oral squamous cell carcinoma by targeting NLRP3
For an extensive review of biologically-based biophysically constrained viral latency, see:
Enzyme-constrained interethnic biodiversity (1)
Enzyme-constrained interethnic biodiversity (2)
Enzyme-constrained interethnic biodiversity (3)
Enzyme-constrained interethnic biodiversity (4)
Enzyme-constrained interethnic biodiversity (5)
Moving forward:

 
See: Celgene Near Acquisition of Impact Biomedicines

Chief Executive Officer Mark Alles has pledged to look outside Celgene’s own labs for new drugs to bolster its pipeline, telling investors in October that “we look for opportunity all the time.”

The CEOs of companies like this have been looking in all the wrong places for several decades. All of “Big Pharma” is dangerously close to collapse under the weight of evidence known to serious scientists who have linked physics and chemistry to the conserved molecular mechanisms of biophysically constrained RNA-mediated cell type differentiation that protect all living genera from the virus-driven degradation of messenger RNA.
The CEOs don’t want you to be freaked out by the price tag for medications that will bankrupt the economy of the United States of America. But, quite frankly, this freaks me out.
See also:  An $850,000 Price Tag on Gene Therapy Shouldn’t Freak You Out—Yet

Spark’s Luxturna was approved by the U.S. Food and Drug Administration in December for patients who have a genetic mutation in the RPE65 gene, which causes degenerative retinal disease.

The therapy, which is injected into the eye, contains millions of engineered virus particles containing correct copies of the gene. The treatment improves vision but doesn’t fully restore it.

The real test may come when Spark and other companies start winning approval to sell gene-replacement therapies for diseases like hemophilia and sickle-cell anemia, which affect tens of thousands of people in the U.S.

Spark’s inadvertently appears to claim gene-replacement therapies can prevent the virus-driven theft of messenger RNA that causes the mutation in the RPE65 gene. If so, the food energy-dependent pheromone-controlled hemoglobin S ecological adaptation will require treatment with enzymes or food supplements that increase the production of specific enzymes.
That might be the most effective treatment. However, sooner or later, people will learn that sickle-cell anemia is a food energy-dependent ecological adaptation that can be linked from one base pair change and one amino acid substitution to all other pathology. “Big Pharma” will then no longer control the economic success of the United States of America.
Indeed, this publication may drive the decline of the gene-editing component of the stock market:  Identification of Pre-Existing Adaptive Immunity to Cas9 Proteins in Humans
Pre-Existing Adaptive Immunity in Humans is RNA-mediated. The facts about interethnic variation in hemoglobin molecules link pre-existing humoral and cell-mediated adaptive immune responses from Cas9 to the RNA-mediated factors that must be taken into account before the CRISPR-Cas9 system moves forward into clinical trials. The CRISPR-Cas9 system damage to human DNA caused by gene editing could be prevented by something as relatively simple as enrolling more participants in studies like this one: Nevada Health Project Participants to Gain Access to Helix Genomics Marketplace
See for comparison: Exome Sequencing Data Links ADCY3 to Severe Obesity

Loss-of-function mutations in ADCY3 cause severe obesity, according to a series of new studies in Nature Genetics.

Exome sequencing yields much more data than genotyping does and the data conclusively shows that there is no such thing as a gain-of-function mutation. That is why food energy-dependent changes in SNPs have consistently been linked to interethnic biodiversity and to differences in longevity in modern human populations like the Amish.
See also:  Pfizer Ends Hunt for Drugs to Treat Alzheimer’s and Parkinson’s by Jonathan.Rockoff@wsj.com
The end of the hunt links Bruce McEwen’s works to the beginning of the search for effective treatments that must help to biophysically constrain viral latency if they are used to treat some neurodegenerative diseases.
Bruce McEwen’s works, link energy-dependent cell type differentiation from feedback loops that link olfaction to the pheromone-controlled physiology of reproduction.
Historical perspective: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” McEwen et al., (1964)

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

For a practical application of facts that McEwen’s life’s works have detailed since 1964, see:
Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis
The fact that human pheromones biophysically constrain the pathology of neurodegenerative diseases has been known to all serious scientists since the time that this was published in 1994.
Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)
The conserved molecular mechanisms of RNA-mediated cell type differentiation have not changed since the dawn of the energy-dependent creation of ATP and RNA.
 
That fact was indirectly represented in New Description of the Rostral Migratory Stream in Adult Mice Brains Delineating the Starter of the Stream as an Infundibulum: A New Described Limb, by H&E and Antidoublecortin Antibody 

Conclusion: The neuroblasts take different arrangement through their period of life from their site of origin to their final destination the olfactory bulb through the RMS.

The creation of the neuroblasts and their energy-dependent niche construction in the olfactory bulb is tractable to the niche creation of bacteria, which neo-Darwinian theorists seem to think occurs in the context of the evolution of functional structures such as the flagellum via a “quantum leap.”
See: Biologists Trace Evolution of Bacterial Flagellar Motors

This clear separation between primitive and sophisticated species represents a ‘quantum leap’ in evolution…

That claim represents a return to de Vries definition of mutation, which Schrodinger (1944) placed into the context of his organized thoughts about biophysically constrained biodiversity with my emphasis.

“…about forty years ago [in1902] the Dutchman de Vries discovered that… 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.

See for comparison: Evolution of higher torque in Campylobacter-type bacterial flagellar motors (January 8, 2018)

Phylogenetic inference was made using maximum-likelihood in GARLI (v2.01.1067)23, using Jones, Taylor and Thornton (JTT) amino acid substitution rates24.

Phylogenetic inferences still seem to be based on a definition of mutation from  1902. For comparison, all serious scientists have learned that the food energy-dependent pheromone-controlled physiology of reproduction links the fixation of RNA-mediated amino acid substitutions in the cell types of all individuals of all species from biophysically constrained viral latency to all biodiversity in all living genera.
I have placed the proof of concept for my model into a series of blog posts on “Interethnic Diversity” in an attempt to help biologically uninformed theorists join serious scientists from the 21st century who are Combating Evolution to Fight Disease
Recruits are required to take intelligence tests and compete basic training with an essay on top-down causation that links the sun’s anti-entropic virucidal energy from the physiology of reproduction to all biodiversity on Earth without mention of mutation or evolution.
Recommended reading includes a monograph from Bruce McEwen about his life’s works, and one recently published work that was co-authored by Bruce McEwen:
See: Redefining neuroendocrinology: Epigenetics of brain-body communication over the life course
The details of natural biological rhythms; “allostatic overload” (as a natural part of autophagy and limits on population density);
a natural molecule acetyl-L-carnitine (LAC);  our natural day-night rhythm; and natural cycles of protein biosynthesis and degradation are linked from a naturalistic rodent model to interethnic biodiversity. There is no mention of natural selection and only one mention of evolution and one mention of mutation.
See also: Loss of APOBEC1 RNA-editing function in microglia exacerbates age-related CNS pathophysiology
RNA interference links base editing from microRNA editing to the energy-dependent fixation of RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all living genera.

Bruce McEwen’s works and his advice: “Start with gene activation (in GnRH neurosecretory neurons)” led to publication of our 1996 Hormones and Behavior review of RNA-mediated cell type differentiation. We linked food energy to the pheromone-controlled physiology of reproduction and all biodiversity in species from yeasts to primates via alternative splicing of pre-mRNA.
From Fertilization to Adult Sexual Behavior

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…  That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

The fact that sex differences do not evolve has since been linked to all the other differences in cell types that did not evolve. The National Microbiome Initiative has been linked to the Precision Medicine Initiative and to refutations of all the pseudoscientific nonsense that has been touted by theorists during the past few decades of stalled scientific progress.
See for another example. Epigenetic supersimilarity of monozygotic twin pairs

…we identified genomic regions at which the epigenetic similarity of monozygotic twins is substantially greater than can be explained by their genetic identity. This “epigenetic supersimilarity” apparently results from locus-specific establishment of epigenotype prior to embryo cleavage during twinning. Epigenetically supersimilar loci exhibit systemic interindividual epigenetic variation and plasticity to periconceptional environment and are enriched in sub-telomeric regions. In case-control studies nested in a prospective cohort, blood DNA methylation at these loci years before diagnosis is associated with risk of developing several types of cancer.

Reported as: Identical twins can share more than identical genes: Molecular similarity

For decades, researchers have studied genetically identical twins to estimate what proportion of disease risk is determined by one’s genes. To the extent that epigenetic supersimilarity affects risk of disease, as our results indicate, genetic risk estimates based on twin studies have been inflated.

This is how sex researchers stalled scientific progress. They failed to recognize that all molecular similarities and differences are food energy-dependent and the transgenerational epigenetic inheritance of all similarities and differences must be links from the physiology of pheromone-controlled reproduction to the energy-dependent biodiversity that is displayed in all life on Earth.
Public health bodies such as the CDC are mandated to meet the needs of all people, in all their diversity.
All diversity is food energy-dependent and biophysically constrained in the context of the pheromone-controlled physiology of reproduction, which links autophagy to viral latency. The Trump administration is clearly making an attempt to ensure that the CDC does not obfuscate the language used by serious scientists. Serious scientists know how to link physics and chemistry from molecular epigenetics to biophysically constrained viral latency by one or more RNA-mediated amino acid substitutions. The amino acid substitutions are consistently referred to as mutations in examples of human idiocy:
See: Brief report: Geographic variation in EGFR mutation frequency in lung adenocarcinoma may be explained by interethnic genetic variation The full article can be downloaded from here: http://bit.ly/2z97l9b
EDAR V370A and ABCC11 G180A are the two energy-dependent RNA-mediated amino acid substitutions that the authors refer to as mutations, which they link to interethnic genetic variation in the context of de Vries 1902 definition of mutation and A Civic Biology: Presented in Problems (1914).
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.

p. 263

If such people were lower animals, we would probably kill them off to prevent them from spreading. Humanity will not allow this, but we do have the remedy of separating the sexes in asylums or other places and in various ways preventing intermarriage and the possibilities of perpetuating such a low and degenerate race. Remedies of this sort have been tried successfully in Europe and are now meeting with success in this country.

Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

Light activated error-free DNA repair (3)

The vibrational theory of olfaction for the win

…he and his co-authors delve into more of the specifics of olfactory receptors, including particular amino acid motifs, metal binding capacities, and disulphide bridge redox status. It turns out that amino acid side chains alone frequently pull off some rather interesting electron transfer effects without the need for fancy co-enzymes or prosthetic groups.

See for an example of what one enzyme can do:

Energy-dependent pumping in cytoplasm

High magnification of the slime mold Physarum polycephalum shows the cytoplasm pumping furiously through its huge single cell.

See also this example of how the energy-dependent creation of one enzyme can biophysically constrained viral latency
An example of biophysically constrained viral latency

This cytoplasmic streaming allows the slime mold to push forward toward nutrients and potentially carpet a surface.

For the logical extension of what is known to all serious scientists about how to link the sun’s anti-entropic virucidal energy to the creation of different enzymes and from quantum physics to quantum souls, see:

…to believe that you are, right now, thinking with anything other than a hive of independently living neurons is naive in the extreme…” — Robert Karl Stonjek

To believe that Robert Karl Stonjek does not understand the fact that every aspect of neo-Darwinian evolution has been refuted in its entirety by this model, makes you an example of human idiocy.

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

The honeybee model organism exemplifies what has been learned from the study of invertebrates (De Loof, Lindemans, Liu, De Groef, & Schoofs, ). This includes what has been learned about the epigenetic effects of nutrients and pheromones on juvenile hormone (JH). However, the molecular biology of cause and effect that is common to all species was left behind, and the epigenetic effects of human pheromones have not typically been considered in the same context as epigenetic effects of food odors and insect pheromones or the epigenetic effects of pheromones on other mammals.

To believe that Jay R. Feierman is not an example of human idiocy makes you an example of human idiocy.
On 11/20/17, Feierman wrote:
Science is about predicting, not post hoc explaining except under the conditions stated above.
I agree. That’s why this claim stands out as an example of pseudoscience.
Amino acid composition of proteins varies substantially between taxa and, thus, can evolve. –Jordan et al., (2005) A universal trend of amino acid gain and loss in protein evolution
The pervasive nature of pseudoscientific nonsense probably led to this claim:
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.

See also: Published on 19 Nov 2017

Excess alcohol caused a flare-up of diverticulitis that led to several days of hospitalization in ICU. The patient was the only person who ever asked me: “What is an amino acid?”
 
He learned from a horrid, almost deadly, experience that the energy-dependent creation of base pairs and the pheromone-controlled fixation of RNA-mediated amino acid substitutions protect all organized genomes from the virus-driven degradation of messenger RNA.
 
He learned enough to practice the concept of “everything in moderation”. He does not need to learn anything else about the links from mutations to all pathology in species from microbes to humans. But, he is back in the hospital for surgery to remove the part of his colon that is most inflamed (the part that contains the most bacteriophages (viruses in bacteria) that almost killed him.
 
Thank God, He’s alive!

 

Redox sensing controls DNA replication!

Schrodinger's answer to Schrodinger's question

There is no such thing as de novo control of electrons or self-assembly.

Answering Schrödinger’s question: A free-energy formulation

The free-energy principle (FEP) is a formal model of neuronal processes that is widely recognised in neuroscience as a unifying theory of the brain and biobehaviour. More recently, however, it has been extended beyond the brain to explain the dynamics of living systems, and their unique capacity to avoid decay.

They don’t understand the question that Schrodinger answered. He linked the anti-entropic virucidal energy of sunlight to the physiology of pheromone-controlled reproduction via what organisms eat. What they eat protects them from the virus-driven degradation of their messenger RNA. What they eat links food energy-dependent changes in base pairs from microRNA editing to RNA editing and fixation of RNA-mediated amino acid substitutions in organized genomes of all individuals of all living genera.

Schrodinger answered this question: What is life when it is not protected from virus driven entropy? (video 6:37) Published on 30 Mar 2016

Abstract:

The anti-entropic force of virucidal ultraviolet light links guanine–cytosine (G⋅C) Watson–Crick base pairing from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. For example, protection of DNA from permanent UV damage occurs in the context of photosynthesis and nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to DNA repair. In the context of thermodynamic cycles of protein biosynthesis and degradation, DNA repair enables the de novo creation of G protein coupled receptors (GPCRs). Olfactory receptor genes are GPCRs. The de novo creation of olfactory receptor genes links chemotaxis and phototaxis from foraging behavior to social behavior in species from microbes to humans. Foraging behavior links ecological variation to ecological adaptation in the context of this atoms to ecosystems model of biophysically constrained energy-dependent RNA-mediated protein folding chemistry. Protein folding chemistry links nutrient-dependent microRNAs from microRNA flanking sequences to energy transfer and cell type differentiation in the context of adhesion proteins, and supercoiled DNA that protects all organized genomes from virus-driven entropy.

Life that is not protected from the virus-driven degradation of messenger RNA links the reduced number of food energy-dependent microRNAs to activation of the death gene. See for example:

Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene 

The natural contribution of food energy is linked to the endogenous level of microRNA expression seen in neuronal cells in the context of limited cell death compared control glioblastoma cells. That fact was linked to the treatment of brain cancers.

For a review of how food energy-dependent microRNAs protect the organized genomes of all living genera from the virus-driven degradation of messenger RNA that links mutations to all pathology, see:

A Concise Review of MicroRNA Exploring the Insights of MicroRNA Regulations in Bacterial, Viral and Metabolic Diseases

For a example of how human idiocy has prevented the effective treatment of all pathology, see also:

Neuropathological and transcriptomic characteristics of the aged brain

Reported as: Researchers reveal new details on aged brain, Alzheimer’s and dementia

One factor that is not always taken into account when studying gene expression in the aged brain is the quality of the genetic material itself,” says Miller. “This variable is not necessarily related to any specific pathology or disease, but these results highlight the importance of properly controlling for RNA quality when studying the aged brain and indicate that degradation of genetic material may be an underappreciated feature of neurodegeneration or dementia.

 Re: degradation of genetic material may be an underappreciated feature of neurodegeneration or dementia.

See: Cytosis

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

Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

From base editing to RNA editing (5)

 
 
Please try to link the maturity molecule to the evolution of mental illness outside the context of food energy-dependent base editing, RNA editing, RNA-mediated amino acid substitutions and the pheromone-controlled physiology of reproduction that stabilizes the organized genomes of all living genera via chromosomal rearrangements.
 

Then see:Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

Dopamine-mediated behavioral are effected by COMT Val158Met function, which

“… is known to be affected by a functional single nucleotide polymorphism (SNP) in COMT (G-to-A base-pair substitution) leading to a methionine (Met) valine (Val) substitution at codons 108/158 (COMT Val158Met). Carriers of the Met allele have been found to display a fourfold decrease in enzymatic activity compared to Val allele carriers going along with an increase of prefrontal DA activity (Lachman et al. 1996; Lotta et al. 1995).”

The fact that one energy-dependent base-pair substitution and one RNA-mediated amino acid substitution can be linked to behavioral transitions via dopamine links epigenetics and genetics.

All serious scientists know that and some of them have been laughing at pseudoscientists for several decades. See from 10 December 2014:

See also: Structural diversity of supercoiled DNA

Tell the pseudoscientists and journalists who report ridiculous claims to stop treating us all as if we will always be biologically uninformed science idiots — unless that’s what you want to be when you grow up.

See for comparison: 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!

Alternative splicing of pre-mRNA

Evolutionary theories of epigenetic drift

Testing Two Evolutionary Theories of Human Aging with DNA Methylation Data
My summary: Outside the context of food energy-dependent biophysically constrained pheromone-controlled viral latency, mutation accumulation (MA) and disposable soma (DS) provide possible explanations for the existence of human aging. For example, age-differentially-methylated sites across the genome showed significant MA-consistent increases in heritability with age or significant DS-consistent decreases in heritability. Their results supposedly show that both MA and DS play a role in explaining aging and aging-related changes but their results do not link food energy-dependent RNA-directed DNA methylation to de novo gene creation or the virus-driven degradation of messenger RNA that serious scientists have linked from mutations to all pathology in all living genera.
See also: Caloric restriction delays age-related methylation drift

Epigenetic information encoded by DNA methylation is tightly regulated, but shows a striking drift associated with age that includes both gains and losses of DNA methylation at various sites.

Reported as: Researchers uncover mechanism behind calorie restriction and lengthened lifespan

Dr. Issa’s team made their discovery after first examining methylation patterns on DNA in blood collected from individuals of different ages for each of three species – mouse, monkey, and human.

Energy as information is epigenetically linked from the food that organisms eat to the physiology of pheromone-controlled reproduction in all living genera by RNA-directed DNA methylation and amino acid substitutions that differentiate all cell types in all individuals.
All serious scientists have linked RNA-mediated amino acid substitutions from the differentiation of cell types in yeasts to the differentiation of cell types in primates.
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.

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

In the mouse model, the diet of the mice determines their nutrient-dependent pheromone production and social interactions with other mice. The mouse model also reveals something that was not revealed in the context of dogs and wolves (Axelsson et al., ; Lord, ). The aversive human body odor associated with fish odor syndrome can be epigenetically controlled by reducing dietary choline intake. It can also be controlled through antibiotic use (citations in Li et al., ). This may be important in the context of chemical ecology and epigenetic effects of genetically predisposed nutrient-dependent pheromone-controlled human interactions (Martin et al., ; Preti & Leyden, ).

See also the section on “An epigenetic continuum of nutrient-dependent / pheromone-controlled adaptive evolution”

Nematodes

Differences in the behavior of nematodes are determined by nutrient-dependent rewiring of their primitive nervous system…

Insects

The honeybee is currently an accepted model organism of nutrient-dependent pheromone-controlled adaptive evolution of the brain and behavior that is consistent with what is known about neurogenic niche construction in nematodes…

Mammals

Species-specific health and reproductive fitness is associated with nutrient-dependent amino acid substitutions and with pheromone-controlled reproduction. Disease is associated with mutations exemplified in cancer where perturbations of the glucose-dependent thermodynamic/thermoregulatory equilibrium are equally clear (Locasale, ).

Humans

Two additional recent reports link substitution of the amino acid alanine for the amino acid valine (Grossman et al., ) to nutrient-dependent pheromone-controlled adaptive evolution. The alanine substitution for valine does not appear to be under any selection pressure in mice. The cause-and-effect relationship was established in mice by comparing the effects of the alanine, which is under selection pressure in humans, via its substitution for valine in mice (Kamberov et al., ).

See for comparison: Feynman on social science
See also:

 

Cytosis

Host-derived creation of all pathology (2 of 2)

Summary: All serious scientists know that all epigenetic diversity is food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction.

See for comparison: 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.”

A Bacterial Messenger Molecule Extends Healthspan

…indole, a molecule produced by commensal bacteria, extends “healthspan” not only in mice but in the nematode worm Caenorhabditis elegans and in fruit flies as well. Taking away the bacterial production of the molecule ablated these anti-aging gains.

Does anyone need to repeatedly be reminded that food energy is required for the production of any molecule associated with nutrient-dependent pheromone-controlled anti-aging gains? The epigenetically effected gains are consistently manifested in the survival of species via the physiology of reproduction.
The food energy-dependent production of indole is the obvious link from nutrient-dependent pheromone-controlled feedback loops to biophysically constrained viral latency and ecological adaptation in all living genera. Testing for indole is used to determine the ability of an organism to split (deaminate) the amino acid tryptophan.  Indole contributes to fecal odor and it is a chemical messenger that has been indirectly or directly included in detailed representations of biologically-based pheromone-controlled energy-dependent cause and effect like these.
See: Feedback loops link odor and pheromone signaling with reproduction (2005)
There is a model for that! See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013)
The food energy-dependent pheromone-controlled physiology of reproduction in species from microbes to humans biophysically constrains the virus-driven degradation of messenger RNA. That fact links constraint-breaking mutations to all pathology in all living genera. A test protocol established that fact in the context of this book chapter, which links the test for indole to differences in the microRNA/messenger RNA balance in humans.

For example, the test protocol links the creation of energy as information to all biodiversity via the physiology of reproduction and links the virus-driven degradation of messenger RNA to all pathology. The complexity of the testing can be reduced via the focus on the energy-dependent creation of microRNAs.

See the abstract:

Disease research and treatment development have turned to the impact and utility of microRNA. The dynamic and highly specific expression of these molecular regulators can be used to predict and monitor disease progression as well as therapeutic treatment efficacy and safety…

MicroRNAs are identified and monitored through the use of locked nucleic acid (LNA)™-based detection probes. The LNA™ technology enhances the sensitivity and specificity of target binding for short, highly similar, microRNA sequences, which help to differentiate cell types in the context of everything known to serious scientists about how to link physics and chemistry from molecular epigenetics to all biodiversity via fixation of RNA-mediated amino acid substitutions.

The availability of this testing was predicted in: Energy as information and constrained endogenous RNA interference (7-min video)

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy.

The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection.

This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes.

For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

See also: The phylogenetic utility and functional constraint of microRNA flanking sequences
See also: From Fertilization to Adult Sexual Behavior (1996)
See for comparison: Metabolic, Epigenetic, and Transgenerational Effects of Gut Bacterial Choline Consumption (2017)

There is no such thing as transgenerational epigenetic inheritance of morphological or behavioral phenotypes outside the context of feedback loops that link food odors from the metabolism to pheromones and biophysically constrained viral latency. The consumption of choline by bacteria links food energy to protection from viral latency via the test for indole. The virus-driven theft of quantized energy can be linked from reduced amount of choline that link viruses in the bacteria to their ability to overwhelm the immune system. The effects of virus-driven energy theft link the CRISPR-Cas9 technology of gene-editing to DNA repair via exogenous RNA-interference because energy-dependent endogenous RNA-interference protects all organized genomes from virus-driven entropy.
Corporate America is not willing to tell the truth about that. You will probably suffer unnecessarily and die prematurely because the goal of every corporation is to make more money.

See also: Americans Are Dying Younger, Saving Corporations Billions

Absent a war or an epidemic, it’s unusual and alarming for life expectancies in developed countries to stop improving, let alone to worsen. “Mortality is sort of the tip of the iceberg,” says Laudan Aron, a demographer and senior fellow at the Urban Institute. “It really is a reflection of a lot of underlying conditions of life.”

Darwin’s “conditions of life” were food energy-dependent. Serious scientists have since learned that all “conditions of life” also are fixed in the organized genomes of all living genera via the physiology of reproduction. Without the link from ecological variation to ecological adaptation via fixation of amino acid substitutions in supercoiled DNA, natural selection for energy-dependent codon optimality would link mutations to evolution instead of linking mutations to all pathology.

Instead, the reality of cell type differentiation was reported as: Microbes compete for nutrients, affect metabolism, development in mice

 …new research that shows mice that harbor high levels of microbes that eat choline are deprived of this essential nutrient.
 

I placed that fact into the context of this excerpt from my 2013 review: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

Sex-dependent production of a mouse ‘chemosignal’ with incentive salience appears to have arisen de novo via coincident adaptive evolution that involves an obvious two-step synergy between commensal bacteria and a sex-dependent liver enzyme that metabolizes the nutrient chemical choline.

The result of this synergy is (1) a liver enzyme that oxidizes trimethylamine to (2) an odor that causes (3) species-specific behaviors. Thus, the complex systems that biology required to get from nutrient acquisition and nutrient metabolism to species-specific odor-controlled behavior is exemplified by adaptive evolution of an attractive odor to mice that repels rats (see for review Li et al., 2013).

Addendum: Fish odor syndrome is the link from the virus-driven theft of quantized energy. The odor links ecological variation to failed ecological adaptation and all pathology when there is insufficient food energy. Any scientist who does not already know that based on the facts known to every medical laboratory scientist is an example of “human idiocy” (Feynman) or a biologically uninformed science idiot (Kohl).

Serious scientists have begun to effectively use energy-dependent microRNAs to the prevention of all virus-driven pathology. That fact is being reported in the context of gene therapy using ‘junk DNA’  at a time when all serious scientists realize there is no such thing as ‘junk DNA.’

Gene therapy using ‘junk DNA’ could lower risk for heart disease

The LeXis gene belongs to a unique group of genes that until recently were considered “junk DNA” because scientists believed they served little purpose. However, evidence from the human genome project led to the discovery that genes like LeXis are actually active. The study of these genes, now referred to as long noncoding ribonucleic acids, or lncRNAs, is a rapidly evolving area in biology.

Long Noncoding RNA Facilitated Gene Therapy Reduces Atherosclerosis in a Murine Model of Familial Hypercholesterolemia

Long noncoding (lnc) RNAs form the vast majority of transcriptionally active regions and are arbitrary defined as transcripts >200 bps that biochemically resemble mRNA and yet do not template protein.2

Diet and drug-induced changes in LeXis link energy as information to liver X receptor activation of genes via the “promoter binding of RNA-binding proteins.” That fact supports the claim that a transcriptional coactivator for genetically predisposed cholesterol biosynthesis in the mouse liver links promoters, enhancers, quantitative trait loci, et al., to the transciptional coactivator referred to as “Rally” without mention of energy-dependent changes in the microRNA/messenger RNA balance.
If you believe that the long noncoding ribonucleic acids (RNAs) are genes, you may be convinced that mutations in RNA are the same as mutations in genes. But mutations are the cause of all pathology. Linking mutations in RNA to pathology outside the  context of energy-dependent healthy longevity allows others with no expertise in laboratory testing to continue to believe that mutation-driven evolution is the link from natural selection to the origin of new species. That belief is probably common among others who believe that the Universe itself may be conscious.

See for comparison: Scientists Now Believe the Universe Itself May Be Conscious

For the behavior of subatomic particles and the systems they constitute promises to be fully explained by physics and the other physical sciences.

 See for comparison: Subatomic

Subatomic is a deck building game where players are competing to build a number of available atoms. Each player starts with the same small deck of cards that consist of Proton Cards, Neutron Cards, Electron Cards and Energy Cards and a beginning hand limit of 5 cards. They use these cards to build upon their current Atom, in an attempt to construct one of the available Atom Cards, and/or use their hand of cards to purchase more powerful atom building cards for later use, or increase their hand limit. The deck building cards are simple and clean, but offer a number of interesting combinations. Players also have an energy track that allows them to store energy, which introduces a “push-their-luck” type of mechanic enabling players to pay energy to shuffle through their deck quicker, or to offset the cost of more powerful deck building cards.

We don’t need a conscious mind to measure or look. With or without us, the Universe is always looking
 

The question arises: “Who needs this kind of nonsense?” Does anyone at any level of examination believe that “the Universe is always looking” is the best representation of what we can expect from a “Conscious Universe?”

See for comparison: 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!

 Chromogenic In Situ Hybridization Methods for microRNA Biomarker Monitoring of Drug Safety and Efficacy was reported on the Exiqon FB page. Exiqon is a biotechnology company that specializes in RNA products and services. I recommend that they purchase this domain (RNA-mediated.com) in an attempt to promote their products, which obviously link energy-dependent healthy longevity to all biodiversity and also link virus-driven energy theft to all pathology via changes in the microRNA/messenger RNA balance.

See also: ‘Chromatin modifiers and remodellers in DNA repair and signalling’ The fact that food energy as information must be linked from ecological variation to ecological adaptation via the pheromone-controlled physiology of reproduction in all living genera appears to be the focus of this Theme issue.

But wait: Here is one of the articles from  the Theme issue:

Nucleosome remodelling, DNA repair and transcriptional regulation build negative feedback loops in cancer and cellular ageing

Nucleosome remodelling (NR) regulates transcription in an ATP-dependent manner, and influences gene expression required for development and cellular functions, including those involved in anti-cancer and anti-ageing processes. ATP-utilizing chromatin assembly and remodelling factor (ACF) and Brahma-associated factor (BAF) complexes, belonging to the ISWI and SWI/SNF families, respectively, are involved in various types of DNA repair.

See for comparison, from 1964: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

McEwen et al., knew that “The synthesis of RNA in isolated thymus nuclei is ATP dependent.” That statement of fact was the beginning of the abstract from 1964. When he told me my model could not be validated unless I started with energy-dependent gene activation in gonadotropin releasing hormone (GnRH) neurons, I had no reason to doubt him. When I learned that Robert L. Moss had already linked pheromones to energy-dependent gene activation in GnRH neurons, I continued to pursue top-down causation as if it was energy-dependent — because it obviously is energy-dependent.

I never considered that my model of food energy-dependent pheromone-controlled biophysically constrained gene activation would not be accepted by theorists. See for comparison:

Induction of FOS immunoreactivity in central accessory olfactory structures of the female rat following exposure to conspecific males (1992)

See also: Gonadotropin releasing hormone and human sexual behavior (1991) in Neuropeptides and Psychiatric Disorders (1991)

Is anyone else interested in linking the facts from our 1996 Hormones and Behavior review From Fertilization to Adult Sexual Behavior or from any other works I have published before Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013) to what is known about all biophysically constrained biologically- based cause and effect?
If so, see: Worldwide patterns of human epigenetic variation

We found that population-specific DNA methylation mirrors genetic variation, and has greater local genetic control than mRNA levels. We estimated the rate of epigenetic divergence between populations, which indicates far greater evolutionary stability of DNA methylation in humans than has been observed in plants. This study provides a deeper understanding of worldwide patterns of human epigenetic diversity…

All serious scientists know that all epigenetic diversity is food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction.
See for comparison: 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.
See for comparison: Quantum Biology: An Introduction (video) by Philip Ball and Quantum common sense

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

See also these restricted and unrestricted articles: ARTICLES 

Cytosis

God vs host-derived creation of virus-driven pathology

Summary: The virus-driven theft of quantized energy forces cells to compete for nutrient energy-dependent RNA-mediated reprogramming in the context of the structure of photons, one-carbon metabolism, autophagy, and the physiology of reproduction, which links energy-dependent changes in chirality from base pairs to RNA-mediated amino acid substitutions.

Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton (with my emphasis)

Viruses often carry genes acquired from their host. In the present work, we show that a virus of a marine alga carries a gene encoding a transporter protein that mediates nutrient uptake. We confirm that the viral transporter protein is expressed during infection and show that the protein functions to take up sources of nitrogen. This is important because acquisition of nutrients often determines the ecological success of phytoplankton populations. This work demonstrates how a virus can amend host–viral dynamics by modulating acquisition of nutrients from the environment.

Reported as: Virus reprograms ocean plankton

The virus has stolen a gene from the phytoplankton, which has the surprising effect of making the infected plankton better at absorbing certain nutrients for a period – before the virus kills them.

Much of the planet’s carbon is stored in the sea by a process of algae dying and sinking to the ocean floor, and this research shows a new feature of that process.

“Availability of vitamins and nutrients determine how these phytoplankton function,” said Professor Thomas Richards, of the University of Exeter.

“We have shown that this virus reprogrammes how the phytoplankton obtain nutrients, which affects how they grow and is likely to affect how they absorb carbon dioxide.

“Cells that have the virus are more competitive in the short-term.

The virus-driven theft of quantized energy forces cells to compete for nutrient energy-dependent RNA-mediated reprogramming in the context of the structure of photons, quantum entanglement, one-carbon metabolism, autophagy, and the physiology of reproduction, which links energy-dependent changes in chirality from base pairs to RNA-mediated amino acid substitutions. The amino acid substitutions stabilize the organized genomes of all living genera. Virus-driven energy theft links amino acid substitutions to the stability of viruses at the expense of the stability of organized genomes in all living genera.
The significance of Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton can be viewed in the context of prescient predictions made by young earth creationists and other serious scientists. Unfortunately, most of them failed to link energy-dependent RNA-mediated cell type differentiation to all biophysically constrained biodiversity via viral latency.

Pseudoscientists did not mention the likelihood that viruses cause the mutations, which all serious scientists have linked to all pathology. That may be the most recognizable difference between a pseudoscientist and a serious scientist.
See for information reported by serious scientists: Who rules the waves? – Viruses might just be bit players in the drama of the seas. Then again, they could be major actors (1996)

Most consider viruses to be a legion of cripples, sterilised by ultraviolet radiation and rendered impotent by hosts that are largely immune to their threat. But a few researchers take the opposite view. And if they turn out to be right, viruses could radically alter the balance of life in the oceans, ripping away huge parts of the food web that supports whales, sea birds and the fisheries on which many people rely.

See also: 1999 Did God Make Pathogenic Viruses? (1999)
See also: Where do viruses come from? (2004)

“…when virus-infected bacterial cells burst, their energy-rich cell contents spill into the water for other bacteria to scavenge. ‘Viruses tend to keep nutrients away from the big stuff and keep them going around in the little stuff,’ says Fuhrman. If so, viruses have shaped the entire structure of the ecosystem.”

See also: Viral Genome Junk Is Bunk (2015)

So, where do viruses come from that essentially share the same sequences as those found in their host genomes? Perhaps the evolutionists have placed the cart before the horse on this issue, as proposed by several creationist scientists.4,6 In fact, in an ironic twist, the evidence mentioned above indicates that viruses likely arose from their hosts and not the other way around. As molecular biologist and biochemist Peter Borger notes, “The most parsimonious answer is: the RNA viruses got their genes from their hosts.”6

See for comparison from 2017:
Overthrowing the Hegemony of the Culture of Margulis?
Asgard archaea illuminate the origin of eukaryotic cellular complexity
Mitochondria are not captive bacteria

Carl Woese failed to place his ideas about the three domains of life into the context of how biophysically constrained viral latency links the anti-entropic virucidal energy of sunlight from the physiology of pheromone controlled reproduction to all biodiversity. Woese was wrong about everything. There is one domain of life. In all living genera, the pheromone-controlled physiology of reproduction is energy-dependent and RNA-directed DNA methylation links amino acid substitutions in supercoiled DNA to all biodiversity.

See for comparison this example of human idiocy, On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires

Only neo-Darwinian theorists insist on playing word games to link what they refer to as “enigmatic spacer repertoires” to biodiversity outside the context of energy-dependent changes in the microRNA/messenger RNA balance that link electrons to ecosystems via hydrogen-atom transfer in DNA base pairs in solution.

“Human idiocy” was the term used by Feynman before Roger Penrose reminded us that all organisms must eat. See: “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?” (1991)

For comparison see: Fink et al., (2017) Cross-Cultural Investigation of Male Gait Perception in Relation to Physical Strength and Speed Fink also is a co-author of the award-winning review: Human pheromones: integrating neuroendocrinology and ethology (2001)
See for comparison: A BRIEF ESSAY ON HOW COMPARATIVE PSYCHOLOGY BECAME AN ENDANGERED SPECIES (link opens pdf)

Rather than continue to link food energy from the pheromone-controlled physiology of reproduction to all biodiversity in all living genera, Fink joined the pseudoscientists. He appears to be following the lead of people like Jay R. Feierman. As moderator of the International Society for Human Ethology’s Yahoo Group, Feierman has inadvertently eliminated all works of human ethologists from any further consideration, and he admits it.

See: 8/21/17 [HUMAN ETHOLOGY MODERATOR NOTE: I could write a similar essay on why human ethology is an endangered species but the causes would be different.  I’m old enough to have seen many academic disciplines disappear and new ones take their place. It is rather easy to put this process into a cultural evolution model. Academic disciplines are like species, most of the ones who have ever lived are now extinct. New species are born and old species die…. jrf]

On July 25, 2013, Feierman [jrf] wrote: 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.
Four years later, the concept of “new species are born and old species die” is divorced from the claims Jay R. Feierman made.
See for comparison: Linking mental health and the gut microbiome

The main idea of our review is that there is strong communication between the gastrointestinal tract and the brain, and that changes to the microbiome-gut-brain axis could be associated with the etiology of different neuropsychiatric disorders such as depression…

Food energy-dependent changes in the microbiome-gut-brain axis link nutrient stress and social stress from the de novo creation of microRNAs in plants to changes in the microRNA/messenger RNA balance of animals via links from food odors to pheromone-controlled ecological adaptations in species from microbes to humans.
See: Feedback loops link odor and pheromone signaling with reproduction
See for comparison: “I Am I and My Bacterial Circumstances”: Linking Gut Microbiome, Neurodevelopment, and Depression

A better perception of the significance of the MGB axis in the etiology of depression will help us to obtain a better understanding about the pathophysiology of this syndrome. Also, it opens the possibility to offer better treatment strategies to our patients. This will be possible only if we accomplish to decipher the genetic, anatomical, functional, and behavioral characteristics of the human microbiota. The most important limitation in the area of the MGB axis’ research lies in the fact that there is very little knowledge about the gut microbiome.

The claim that there is very little knowledge about the gut microbiome can be compared to what is known about the link from the virus-driven degradation of messenger RNA in soil bacteria to all pathology in all living genera. Everything known to serious scientists was detailed in the context of this report: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression The changes in the microRNAome included the link to the transgenerational epigenetic inheritance of all pathology in all living genera. The links from the transgenerational epigenetic inheritance of cancer and the transgenerational epigenetic inheritance of behavioral disorders were place into the context of links from quantum physics to quantum souls.
See: Quantum Souls and Welcome to the official YouTube Channel of Quantum Souls.
Video interview about the death of Robin Williams
Superbugs, Bacteriophages and Phage Therapy: An Interview with James Kohl
Food Energy-Dependent Cell Type Differentiation Refutes Theory of Evolution
How to Treat Cancer as a Disorder of Energy Transfer
Charles Darwin Taught Conditions of Life, Not Mutations
Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 1
Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 2
When you next see someone claim that “…there is very little knowledge about the gut microbiome” you may associate that claim with the ignorance touted by neo-Darwinian theorists and compare it to what anyone 10 years-old or older will learn when they play the cell biology game “Cystosis.”

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