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Why Trump won't meet with some 2017 Nobel Laureates

Excerpt: Others have seen the latest experimental evidence on biophysically constrained energy storage coming, but they have remained relatively silent.

This is a deliberate attempt to increase the number of my tweet impressions to more than 80K since Christmas eve, during the same month that ~1000 more articles on microRNA-mediated energy storage were added to the PubMed database. On June 24, 2017,  I joked about the claims of science journalist Philip Ball. His pseudoscientific nonsense about quantum common sensee led to my Christmas eve-and-beyond efforts to establish the facts outside the context of the song: “Here Comes Santa Claus.”

I suggest you see: Mechanisms of Recombination conference and link what is known to all serious scientists about biophysically constrained viral latency from the anti-entropic virucidal of sunlight to the creation of RNA and cell type stability via phosphorylation. Cell type stability is energy-dependent and biophysically constrained by changes in the microRNA/messenger RNA balance, but now we see experimental evidence that the biophysical constraints are not linked to random events and the pseudoscientific nonsense touted by theorists.

Next, see: Phosphorylation-induced conformation of β2-adrenoceptor related to arrestin recruitment revealed by NMR

The phosphorylation-induced structures revealed in this study propose a conserved structural motif of GPCRs that enables β-arrestin to recognize dozens of GPCRs.

Link the energy-dependent creation of G protein-coupled receptors (GPCRs) to all biodiversity via the claims from 1964 in:

Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

Also, see the claims in: Long-range coherence and energy storage in biological systems

Others have seen the latest experimental evidence on biophysically constrained energy storage coming, but they have remained relatively silent.

See for example: Socially responsive effects of brain oxidative metabolism on aggression

…honey bee colony-level social manipulations that decrease individual aggression attenuated the effects of oxidative phosphorylation inhibition on aggression, demonstrating a specific effect of the social environment on brain function. Because decreased neuronal oxidative phosphorylation is usually associated with brain disease, these findings provide a powerful context for understanding brain metabolic plasticity and naturally occurring behavioral plasticity.

Reported as: Angry bees: Insect aggression boosted by altering brain metabolism

In the context of the honeybee model organism, Institute for Genomic Biology director Gene Robinson claimed that:

When he and his colleagues looked at brain gene activity in honey bees after they had faced down an intruder, the team found that some metabolic genes were suppressed. These genes play a key role in the most efficient type of energy generation in cells, a process called oxidative phosphorylation.

It seems that he then became confused because the findings on the conserved molecular mechanisms were placed into the context of 300 million years of evolution that supposedly separated fruit flies and honey bees. Simply put, nothing known about the food energy-dependent pheromone-controlled physiology of biophysically constrained RNA-mediated cell type differentiation made sense if only phosphorylation and the RNA-mediated protein folding chemistry are required to differentiate the cell types of the species in the context of their supercoiled DNA.

However, serious scientists no longer share all the views that Dozhansky (1973) expressed in Nothing in Biology Makes Any Sense Except in the Light of Evolution. 

It has become clear that the food energy-dependent RNA-mediated fixation of amino acid substitutions is linked from the pheromone-controlled physiology of reproduction in bacteria to biophysically constrained cell type differentiation via chromosomal rearrangements that protect organize genomes from the virus-driven degradation of messenger RNA that links mutations to all pathology.  Indeed, that fact may explain why the President of the United States did not meet with the 2017 Nobel Prize Winners. The President seems to known that some or all of them are still lying about what is known to other serious scientists about energy-dependent RNA-mediated biodiversity.

See:  Trump Won’t Meet With U.S. Nobel Prize Winners. They’re Pretty O.K. With That

Frank was among the 2017 Nobel Prize winners class for his work in chemistry, recognized for helping launch a medical imaging effort [cryo-EM] credited with making it easier to picture the biomolecular building blocks of life.

That picture became clearer in the context of works published by Michael Rosbash, who shared the 2017 Nobel Prize in Physiology or Medicine.

See: Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels (1990)

The conserved molecular mechanisms of food energy-dependent pheromone-controlled biophysically constrained RNA-mediated cell type differentiation began to be examined in the mid 1990’s by Rosbash and others, but any experimental evidence that refuted neo-Darwinian nonsense and “Big Bang” cosmology was ignored by Nobel Laureates like Joachim Frank. Why would President Donald Trump want to meet with scientists who are examples of human idiocy?

For example: Nobel Laureate, Richard P. Feynman placed nearly all physicists, chemists and biologists into his example of human idiocy. See: Food energy 

Some of the 2017 Nobel Laureates are ashamed that their ignorance has led to the unnecessary suffering and premature death of millions during the past two decades. They know that Trump realizes some Noble Prize winners are part of a “broken system” of science.

See: Science is broken

Perverse incentives and the misuse of quantitative metrics have undermined the integrity of scientific research

Trump’s priority is fixing the problems, not to welcome and/or  congratulate those who have caused the problems.

For a recent example, see:  Growing up on an Amish farm protects children against asthma by reprogramming immune cells (2016).

For comparison to what is known about immune system reprograming, all aspects of biophysically constrained RNA-mediated cell type differentiation, which protects all organized genomes from virus-driven entropy, were placed into the context of claims about evolved proteins in: A null mutation in SERPINE1 protects against biological aging in humans.

See for comparison the report: Amish gene mutation makes some live 10 years longer: study

The report in the journal Science Advances is the latest clue in a decade-plus search for the secrets to healthy aging in this traditional, Christian community that balks at most modern technology.

See also: What It Takes to Build a Hook for the Flagellum

…they are really talking about adaptation, not evolution. Nowhere do they describe how this extra-strong flagellum originated or how it evolved from another species.

Amino acid sequence variability in the central parts of FlgE proteins of C. jejuni strains was proposed to occur because of selection pressure during host invasion to generate variations in surface-exposed antigenic determinants. The variable regions do indeed correspond to the surface-exposed region of C. jejuni hook domains D3 and D4. The variability is tolerated because these regions are not essential for intra-molecular contacts that organize the hook.

Amino acid sequence variability ensures that fixation of nutrient energy-dependent RNA-mediated amino acid substitutions occurs in the context of the physiology of pheromone-controlled reproduction in all living genera.

In the context of attempts to discuss the weekend evolution of the bacterial flagellum on “The Battlefield” FB group, Larry Kisner Sr., and others realized that fluorescence was the obvious nutrient energy-dependent pheromone-controlled link from the molecular epigenetics of cell type differentiation in P. fluorescens to the fossil record via Mark Armitage‘s works.

I asked Mark Armitage to provide me with his slide(s), but realize how quickly others will stake their claim to the information. I explained that It links the nutrient energy-dependent pheromone-controlled physiology of reproduction in a bacteria to the energy-dependent fertilization that ultimately had to lead to lead to Christ’s energy-dependent weekend Resurrection to fulfill prophecy. I was banned before I could once again place energy as information into the context of everything known about physics, chemistry, and molecular biology. For example, it is obvious that nothing has changed since Biblical Genesis described the complexity of interactions in terms that people could understand thousands of years ago.
I fully expect that President Donald Trump has no interest in meeting with any Nobel Laureate who has helped to bastardize the works of all serious scientists since the years before Schrodinger’s claims were made in “What is Life?” (1944) and the subsequent claim by Roger Penrose (1991)
See also: Innate Immunity and Asthma Risk in Amish and Hutterite Farm Children
See also: Scents and Sensibility and Richard Axel’s 2005 Scents and Sensibility: A Molecular Logic of Olfactory Perception (Nobel Lecture) and Unraveling the sense of smell (Nobel lecture)
Keep in mind that food energy-dependent pheromone-controlled feedback loops are the only obvious source of ecological adaptation, because without food, organisms die. See for details: Feedback loops link odor and pheromone signaling with reproduction

The flip side of personal genomics: When a mutation doesn’t spell disease

…geneticists don’t have an accurate understanding of how mutations behave in people who are not obviously sick. “This is a fascinating flashpoint in the field right now,” says Robert Green, a geneticist at Brigham and Women’s Hospital in Boston, Massachusetts. “Many people are deeply concerned that widespread screening of ostensibly healthy people could actually lead to harm.”

How could academics allow this to happen. Millions of dollars have been spent and billions of lives have been altered by the ignorance of theorists who never learned the difference between an energy-dependent RNA-mediated amino acid substitution and a mutation caused by the virus-driven theft of quantized information.
 

The anti-entropic virucidal energy of sunlight is the obvious key to healthy longevity in all human populations. The link from a population in Central China to the Amish population in Berne, Indiana was placed into the context of this invited review of nutritional epigenetics.

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

Naturally occuring energy-dependent base editing, microRNA editing,  and RNA editing were linked from fixation of a single amino acid substitution in the mouse model to the physiology of pheromone-controlled reproduction and epigenetically effected homologous changes in human morphological phenotypes.

"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.

Two retractions of human idiocy

Excerpt: …she was interested in the PNAS research because it identified a potential inhibitor of the hepatitis C virus…

”Definitely embarrassing:” Nobel Laureate retracts non-reproducible paper in Nature journal

1)

This retraction marks the second in six months for Nature Chemistry after having none for eight years.

2)

In 2009, Szostak also retracted a 2008 paper in Proceedings of the National Academy of Sciences after an outside researcher could not replicate the results. The retraction notice credited Katherine Berry, then a doctoral student at the University of California, Berkeley, for bringing the issues to their attention. (Full disclosure: RW’s Victoria Stern and Berry were roommates freshman year of college).

Berry, who’s now an assistant professor of biochemistry at Mount Holyoke in South Hadley, Mass., told us that she was interested in the PNAS research because it identified a potential inhibitor of the hepatitis C virus…

Comment awaiting moderation

James V. Kohl December 7, 2017 at 4:35 am

The Science Behind the Game “Cytosis,” pits the collaborative efforts of 20 serious scientists against the pseudoscientific nonsense touted by theorists. The serious scientists know how energy-dependent RNA-mediated cell type differentiation occurs.

Resources (e.g., mRNA, ATP) are used to build enzymes, hormones, and/or receptors. Health points accumulate to show why food energy must be linked from the physiology of pheromone-controlled reproduction to biophysically constrained viral latency.

For comparison, Szostak and other theorists have been stuck with their ridiculous misrepresentations of emergence and neo-Darwinian evolution, which failed to consider Darwin’s “conditions of life.”

“Conditions of life” are energy-dependent. The energy is Schrodinger’s anti-entropic virucidal energy. It comes from sunlight and is epigenetically “trapped” in food via the physiology of reproduction.

Board Game:
Cytosis: A Cell Biology Game
Title:
Cytosis – The Science Behind the Game https://boardgamegeek.com/filepage/155090/cytosis-science-behind-game

Addendum: Naturally occurring base editing, microRNA editing, and RNA editing link the energy-dependent creation of microRNAs from natural selection for energy-dependent codon optimality to the physiology of pheromone-controlled reproduction, which biophysically constrains viral latency. Constraint breaking mutations have been linked to all pathology. The misrepresentations of Szostak and others like him have contributed to a history of unnecessary suffering and premature death. Richard Feynman helped to place their claims into this perspective:

 

 

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.

Energy-dependent base editing and correction of mutations (1)

Summary: Food energy-dependent base editing has been linked to biophysically constrained viral latency via microRNA editing, RNA editing and the pheromone-controlled fixation of RNA-mediated amino acid substitutions in species from microbes to humans.
Correction of β-thalassemia mutant by base editor in human embryos
Conclusion:

Intriguingly, we found that HBB −28 (A>G) mutation repairing efficiency was about 20% in the constructed cell line and primary skin fibroblast cells. Although 10.7% of the repaired skin fibroblast cells were heterozygous, it is still able to cure anemia (Dever et al., 2016). Whether base editors will be equally or more efficient in human hematopoietic stem cells is still under investigation. High repairing efficiency in human hematopoietic stem cells will lead to new therapeutics for β-thalassemia intermedia and β-thalassemia major patients with HBB −28 (A>G) mutation.

Reported as: Challenging Darwin: an ‘evolution machine’ for biomolecules

…genetically engineered phages infect different bacterial strains under selective stimuli, such as different growth conditions, and they respond and adapt to each change artificially introduced in the environment.

The food energy-dependent base editing has been linked to biophysically constrained viral latency via microRNA editing, RNA editing and the pheromone-controlled fixation of RNA-mediated amino acid substitutions in species from microbes to humans.
See for comparison: Molecular diversity through RNA editing: a balancing act

Alteration of amino acid codons, splice patterns, stability or localization of protein-coding transcripts, modulation of regulatory RNA biogenesis and function, as well as crosstalk of RNA editing with RNA processing and silencing pathways provides a rich resource for the generation of molecular diversity and for gene regulation. These findings also illustrate that we are only beginning to understand how RNA editing is integrated into the biological networks of gene expression, regulatory pathways and genome evolution.

All claims about “genome evolution” were based on mathematical models of how mutations might lead from natural selection the creation of new species. No serious scientists believed those claims. Feynman placed them into the context of “human idiocy.”

 
See also my comment to the Human Ethology Yahoo Group: My comment was divorced from the announcement of the article as Fwd: U. Warwick 2017 [ Challenging Darwin: an ‘evolution machine’ for biomolecules ]

Excerpt: “A new device produces desirable molecules by modifying the environments where virus and bacteria interact”

My comment: They are not challenging Darwin, whose “conditions of life” required the link from food odors to pheromone-controlled viral latency. They are challenging the neo-Darwinian pseudoscientific nonsense that linked the virus-driven degradation of messenger RNA from mutations to evolution, which was the most ignorant explanation of biologically-based cause and effect to ever reach acceptance among the suffering masses who have continued to suffer unnecessarily and die prematurely from the virus-driven theft of quantized energy as information that is required for survival of all species.

Conserved microRNA editing in mammalian evolution, development and disease

miRNAs are greatly overrepresented among conserved editing targets.

The claims about evolutionarily conserved site-specific microRNA (miRNA) editing and the diversity the increased functional diversity of mammalian miRNA transcriptomes do not link the anti-entropic virucidal energy of the sun from microRNA editing to claims about the integral and evolutionarily stable feature of mammalian transcriptomes.
See for comparison: RNA editing independently occurs at three mir-376a-1 sites and may compromise the stability of the microRNA hairpin

RNA editing is being recognized as an important post-transcriptional mechanism that may have crucial roles in introducing genetic variation and phenotypic diversity. Despite microRNA editing recurrence, defining its biological relevance is still under extended debate. To better understand microRNA editing function and regulation we performed an exhaustive characterization of the A-to-I site-specific patterns in mir-376a-1, a mammalian microRNA which RNA editing is involved in the regulation of development and in disease. Thorough an integrative approach based on high-throughput small RNA sequencing, Sanger sequencing and computer simulations we explored mir-376a-1 editing in samples from various individuals and primate species including human placenta and macaque, gorilla, chimpanzee and human brain cortex. We observed that mir-376a-1 editing is a common phenomenon in the mature and primary microRNA molecules and it is more frequently detected in brain than in placenta. Primary mir-376a-1 is edited at three positions, -1, +4 and +44. Editing frequency estimations and in silico simulations indicated that editing was not equally recurrent along the three mir-376a-1 sites, nevertheless no epistatic interactions among them were observed. Particularly, the +4 site, located in the seed region of the mature miR-376a-5p, reached the highest editing frequency in all samples. Secondary structure predictions revealed that the +4 position was the one that conferred the highest stability to the mir-376a-1 hairpin. We suggest that molecular stability might partially explain the editing recurrence observed in certain microRNAs and that editing events conferring new functional regulatory roles in particular tissues and species could have been conserved along evolution, as it might be the case of mir-376a-1 in primate brain cortex.

 
 

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

Summary: The same set of microRNAs controls expression of the genes for rate-limiting enzymes, which control differences in the hormone production of different hormones in insects and crustaceans. That fact led to this claim in: The secret to safe DNA repair.

…if you don’t have this enzyme, then this error-free repair is stopped. You can’t do it. If you can’t do the error-free repair, among other things that happen is that you expect these cells to be cancer prone.

The Secret to Long Life? It May Lurk in the DNA of the Oldest Among Us

If unusual patterns in their three billion pairs of A’s, C’s, G’s and T’s — the nucleobases that make up all genomes — can be shown to have prolonged their lives and protected their health, the logic goes, it is conceivable that a drug or gene therapy could be devised to replicate the effects in the rest of us.

The unusual patterns exist only in the context of error-free RNA-directed DNA repair. DNA repair is linked from the energy-dependent creation of one enzyme and the metabolism of food to species-specific pheromones.
The secret to safe DNA repair.

…if you don’t have this enzyme, then this error-free repair is stopped. You can’t do it. If you can’t do the error-free repair, among other things that happen is that you expect these cells to be cancer prone.

The pheromones control the physiology of reproduction. In the mouse model, pheromones have repeatedly been linked to epigenetic effects on gene regulation.
See: [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)] 1994

A study of the influence of pheromone stressor(s) on proliferating germ and somatic cells was performed on laboratory lines of house mouse in the context of the physiological hypothesis of mutation process, proposed by M.E. Lobashev in 1947. Data from experiments are presented, and results obtained during last 10-15 years are discussed. The adaptive role of cytogenetic and other observed pheromonal effects is considered. The possible existence of interorganism systems of genetic regulation is discussed, the search for and study of which may help in more complete understanding of the regularities of functioning of genetic material.
 

The virus-driven degradation of messenger RNA has since been linked to all pathology. Food odors and pheromones biophysically constrain the transgenerational epigenetic inheritance of viral latency via the creation of amino acid substitutions that differentiate all the cell types of all individuals of all individuals of all species.
When all serious scientists fully disclose what is known about the biophysically constrained energy-dependent links from 1) base editing and 2) microRNA editing to 3) RNA editing and RNA-mediated DNA repair, pseudoscientists will be put out of the business of drug development. Medical practice will be based on what is known about Precision Medicine, which specifically links the food energy-dependent creation of enzymes to healthy longevity and to the metabolism of the drugs that often do more harm than good.
1)
Base Editing Now Able to Convert Adenine-Thymine to Guanine-Cytosine

“Nature conveniently provides us with cytosine deaminase enzymes that operate on DNA,” Liu tells The Scientist.

The creation of quantized energy in sunlight links energy as information from electrons to ecosystems via the physiology of reproduction in all living genera. The claim that “Nature” provides us with cytosine deaminase enzymes makes it seem that the enzymes emerged and automagically evolved to become purposeful and meaningful in the context of ridiculous theories about mutation-driven evolution.
2)
Conserved microRNA editing in mammalian evolution, development and disease
MicroRNA (miRNA) editing is a site-specific conserved mechanism that links ecological variation to energy-dependent ecological adaptations via the physiology of pheromone-controlled reproduction, which increases the functional diversity of mammalian miRNA transcriptomes. These authors place microRNA editing into the context of an “evolutionarily stable feature” without explaining how the energy-dependent stability was linked to biophysically constrained viral latency.
3)
RNA Editing Possible with CRISPR-Cas13
Serious scientists moved forward by calling pre-mRNAs “microRNAs.” They linked energy-dependent alternative splicings to all biodiversity via fixation of amino acid substitutions in the context of the pheromone-controlled physiology of reproduction. Now, Zhang and others make the claim that’s akin to saying they rediscovered the innate immune system, which biophysically constrains viral latency.
The so-called secret to the three-step recognition of the pattern linked to longevity may be as simple as this: Learn how anything you eat or drink may be beneficial and do not take drugs that will kill you by stealing the quantized energy as information that McEwen et al. (1964) linked the light-activated creation of ATP to the food energy-dependent creation of RNA.
Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

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

See also: Dobzhansky (1964): Biology, molecular and organismic

Ingram and others found that hemoglobin S differs from A in the substitution of just a single amino acid, valine in place of glutamic acid in the beta chain of the hemoglobin molecule.

See also: Dobzhansky (1973) 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.

All serious scientists know that the creation of the sun’s anti-entropic virucidal energy must be linked from ecological variation to ecological adaptations, whether or not they refer to light in the context of evolution. Nothing makes sense when theorists fail to link the speed of light on contact with water from the creation of enzymes to the metabolism of food. And nothing else about food energy makes sense when pseudoscientists fail to link it to the physiology of pheromone-controlled reproduction, which biophysically constrains viral latency.
See: The phylogenetic utility and functional constraint of microRNA flanking sequences (2015)
Reported as:‘Junk DNA’ Used To Sort Species and also as: All in the (bigger) family with my comment:

The 2015 Society for Integrative and Comparative Biology (SICB) presenters may not recognize how much progress has been made since the 2013 ecological epigenetics symposium. For example, since then authors claimed “…ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.” http://dx.doi.org/10.1038/nature13400
Six months later, other authors traced signaling factors found in vertebrates to the origin of nerve cell centralization via the diffuse nerve net of animals like the sea anemone. http://dx.doi.org/10.1038/ncomms6536 That fact suggests ecological variation is linked to ecological adaptations in morphological and behavioral phenotypes via signaling protein concentrations that differentiate various cell types in body axes and the central nervous system.
Links across species from the epigenetic landscape to the physical landscape of DNA in organized genomes appear to have their origins in the conserved molecular mechanisms of RNA-directed DNA methylation and RNA-mediated protein folding. Two weeks after the publication that refuted ideas about independently evolved neural systems or muscle specification — and perhaps refuted the independent evolution of anything else, SICB presenters linked crustaceans to insects.
Apparently, they’ve learned that the same set of microRNAs controls expression of the genes for rate-limiting enzymes that control the hormone production of different hormones in insects and crustaceans.
Why were they left with any questions about how crustaceans and insects could all be part of one big family? They linked RNA-mediated cell type differentiation to what we described in our section on molecular epigenetics in our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior

 

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

From base editing to RNA editing (4)

Summary: To claim evolution, Koonin must link food energy from the pheromone-controlled physiology of reproduction to fixation of a beneficial mutation in the organized genome of one species that evolved into another species.
Search Results for “base editing” = 82 blog posts starting with Cell-type differentiation on February 7, 2014
Search Results for “RNA editing” = 95 blog posts starting with In theory, or supported by experimental evidence? October 22, 2014
See for comparison PubMed: “base editing” (33 citations) and “RNA editing” (4222 citations)
The failure to link energy-dependent base editing to RNA editing and RNA-mediated cell type differentiation in all publications about healthy longevity compared to pathology can be attributed to the pseudoscientific nonsense touted by theorists. In their ridiculous mathematical models, they claimed the emergence of energy could be linked to the evolution of all biodiversity. Their lack of experimental evidence, which is required to link biologically-based cause and effect to biodiversity, was placed into the context of “human idiocy” by Richard P. Feynman.

See Richard P. Feynman’s lecture on: Food energy. See for comparison see: Energy as information and constrained endogenous RNA interference.

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

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

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

The failure to link energy-dependent base editing and energy-dependent RNA editing to healthy longevity predicted the failure to link the virus-driven degradation of messenger RNA to all pathology. See for instance: The Science of Personalized Nutrition

A single nucleotide polymorphism (SNP) or change occurs in nearly 1 in 1,000 base pairs and accounts for much of an individual’s uniqueness. Research on SNPs and other genetic variations like deletions, inversions, duplications and copy number variations (CNV), which represent up to 9.5 percent of the human genome, have changed the face of human nutrition and validated the concept that nutrition could and should be personalized. (Mullally, 2007)

A single nucleotide polymorphism (SNP) is a single base-pair difference in the DNA sequence of individual members of a species. SNPs in genes may lead to variations in the amino acid sequence, but SNPs can also occur in noncoding regions of DNA. Base editing of A•T to G•C in genomic DNA was linked from RNA editing to the physiology of pheromone-controlled reproduction and fixation of amino acid substitutions in organized genomes. The amino acid substitutions differentiate all cell types in all individuals of all living genera.
See: Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage
Reported as: Base Editing Now Able to Convert Adenine-Thymine to Guanine-Cytosine

Bioengineer Feng Zhang of MIT’S Broad Institute notes in an email that the team employed “a comprehensive and creative approach” to achieve such precision. “As a field, we have been looking for ways to precisely rewrite parts of the genetic code,” writes Feng, whose own, CRISPR-based method to edit single bases in RNA was published today in Science. “Base editors move us closer to this goal.”

The CRISPR-based editing of single base pairs in RNA links the energy-dependent function of the innate immune system to all biophysically constrained biodiversity via the pheromone-controlled physiology of reproduction, which biophysically constrains viral latency. Natural selection for energy-dependent codon optimality, links the editing of single base pairs in RNA to every aspect of healthy longevity via RNA editing.
See: RNA editing with CRISPR-Cas13
Reported as: RNA Editing Possible with CRISPR-Cas13

“This work is an impressive study from a highly productive research group that suggests the possibility of editing RNA transcripts to alter their coding potential in a programmable manner,” David Liu…[who] has a report out today in Nature describing specific nucleotide editing of DNA by a similar method.

Feng Zhang (base editing) gives a pat on the back to David Liu (RNA editing), and Liu reciprocated, or vice versa. Taken together, they are making face-saving attempts that ignore everything known to serious scientists about biophysically constrained viral latency.

The tool itself could be further developed, adds computational biologist Eugene Koonin of the National Center for Biotechnology Information who also was not involved in the study. “This paper is not the end of the road,” he says. It’s possible that Cas13b could be fused to a variety of editing enzymes that would allow a range of different sequence changes. The possibilities are numerous, Koonin says, and “the best is still to come.”

Koonin is a biologically uninformed science idiot who has followed in the footsteps of others like him. Their computations link mutations to evolution across millions of years. The computational biologists are evolutionary biologists who have failed to link food energy from the creation of enzymes and the the RNA-mediated editing of the enzymes, which is required to link differences in sequence changes from fixation of RNA-mediated amino acid substitutions in organized genomes to the prevention of virus-driven messenger RNA degradation. All serious scientists have linked the virus-driven degradation of messenger RNA from mutations to all pathology. Koonin’s claim that “the best is still to come” is moronic.
Every link to energy-dependent RNA-mediated cell type differentiation via the pheromone-controlled fixation of amino acid substitutions has been detailed in the context of experimental evidence. But, Koonin (2016) made this ridiculous claim:

The proper question is: how has this sequence evolved? And the proper null hypothesis posits that it is a result of neutral evolution: that is, it survives by sheer chance provided that it is not deleterious enough to be efficiently purged by purifying selection. To claim adaptation, the neutral null has to be falsified.

To claim evolution, Koonin must link food energy from the pheromone-controlled physiology of reproduction to fixation of a beneficial mutation in the organized genome of one species that evolved into another species.
If Koonin and others like him cannot provide an example of how biologically-based evolution occurs, there is only the pseudoscientific nonsense of their mathematical models for comparison to facts about: How flu shot manufacturing forces influenza to mutate

“Now we can explain — at an atomic level — why egg-based vaccine production is causing problems,” said TSRI Research Associate Nicholas Wu, Ph.D., first author of the study, published recently in the journal PLOS Pathogens.

Clearly, an explanation — at the atomic level — of how viruses adapt to the cell types of one species during the production of an egg-based vaccine must be linked from atoms to ecosystems in all living genera via adaptations in the host.
See for example: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

The genesis of variation is manifested in ecological variation, which confers the ability to adapt via nutrient-dependent epigenetically-effected pheromone-controlled ecological, social, neurogenic, and socio-cognitive niche construction. Niche construction is manifested in organismal complexity. Everything about ecological adaptation appears to make sense in the light of what is currently known about molecular biology. What is currently known about the conserved molecular mechanisms that link the epigenetic landscape to the physical landscape of DNA can now be compared to any forthcoming explanations that attempt to make sense of how mutation-driven evolution might occur.

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 (3)

Summary: Claims about spontaneous deamination fail to link energy-dependent changes from base editing to RNA-mediated DNA repair of damage caused by the virus-driven degradation of messenger RNA.
Highly efficient RNA-guided base editing in mouse embryos 27 February 2017
They reported the use of RNA-programmable deaminases to make various animal models with single amino-acid substitutions.They linked the single amino acid substitutions from the correction of nonsense mutations in the future to the correction of genetic defects in human embryos.
Reported as: An Efficient Single-Nucleotide-Editing CRISPR

“We showed here for the first time that programmable deaminases efficiently induced base substitutions in animal embryos, producing mutant mice with disease phenotypes,” remarked senior study investigator Jin-Soo Kim, Ph.D., director of the Center for Genome Engineering at IBS. “This is a proof-of-principle experiment. The next goal is to correct a genetic defect in animals. Ultimately, this technique may allow gene correction in human embryos.”

Their technique linked base editing to naturally occurring energy-dependent gene editing in human embyos.  These researchers also inadvertently linked what is known about the pheromone-controlled physiology of reproduction from microbes to human populations outside the context of mutation-driven evolution.
They helped force other researchers to place their findings back into the context of “evolved” biodiversity after first linking evolution to the spontaneous deamination of cytosine. Claims about spontaneous deamination fail to link energy-dependent changes from base editing to RNA-mediated DNA repair of damage caused by the virus-driven degradation of messenger RNA.
Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

The spontaneous deamination of cytosine is a major source of C•G to T•A transitions, which account for half of known human pathogenic point mutations. The ability to efficiently convert target A•T base pairs to G•C could therefore advance the study and treatment of genetic diseases. While the deamination of adenine yields inosine, which is treated as guanine by polymerases, no enzymes are known to deaminate adenine in DNA. Here we report adenine base editors (ABEs) that mediate conversion of A•T to G•C in genomic DNA. We evolved a tRNA adenosine deaminase to operate on DNA when fused to a catalytically impaired CRISPR-Cas9. Extensive directed evolution and protein engineering resulted in seventh-generation ABEs (e.g., ABE7.10), that convert target A•T to G•C base pairs efficiently (~50% in human cells) with very high product purity (typically ≥ 99.9%) and very low rates of indels (typically ≤ 0.1%). ABEs introduce point mutations more efficiently and cleanly than a current Cas9 nuclease-based method, induce less off-target genome modification than Cas9, and can install disease-correcting or disease-suppressing mutations in human cells. Together with our previous base editors, ABEs advance genome editing by enabling the direct, programmable introduction of all four transition mutations without double-stranded DNA cleavage.

After a brief look at what they attribute to spontaneous deamination, please see: How flu shot manufacturing forces influenza to mutate

“Now we can explain — at an atomic level — why egg-based vaccine production is causing problems,” said TSRI Research Associate Nicholas Wu, Ph.D., first author of the study, published recently in the journal PLOS Pathogens.

In this 2014 invited review of nutritional epigenetics I linked energy-dependent changes from atoms to ecosystems in all living genera via food energy and the pheromone-controlled physiology of reproduction.

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

The plausibility and ecological validity of Kohl’s Laws [of Biology] in the context of Darwin’s ‘conditions of life’ can be compared to theories about biologically-based cause and effect in the context of species diversity. In mammals, for example, the explanatory power of a model of ecological variation and biophysically constrained nutrient-dependent pheromone-controlled ecological adaptations became clear with companion papers published in 2013. See for review [30].

The companion papers [162-163] told a new short story of ecological adaptations. In the context of climate change and changes in diet, the story began with what probably was a nutrient-dependent base pair change and a variant epiallele [amino acid substitution] that arose in a human population in what is now central China.

30) Kohl, J. V., Nutrient–dependent / pheromone–controlled adaptive evolution: a model. Socioaffective Neuroscience & Psychology 2013, 3. doi: 10.3402/snp.v3i0.20553
162) Kamberov, Yana G.; Wang, S.; Tan, J.; Gerbault, P.; Wark, A.; Tan, L.; Yang, Y.; Li, S.; Tang, K.; Chen, H., et al., Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant. Cell 2013, 152 (4), 691-702. doi: 10.1016/j.cell.2013.01.016
163) Grossman, Sharon R.; Andersen, Kristian G.; Shlyakhter, I.; Tabrizi, S.; Winnicki, S.; Yen, A.; Park, Daniel J.; Griesemer, D.; Karlsson, Elinor K.; Wong, Sunny H., et al., Identifying Recent Adaptations in Large-Scale Genomic Data. Cell 2013, 152 (4), 703-713. doi: 10.1016/j.cell.2013.01.035
See again: How flu shot manufacturing forces influenza to mutate

The researchers say further studies are needed to investigate replacing the egg-based system. “Other methods are now being used and explored for production of vaccines in mammalian cells using cell-based methods and recombinant HA protein vaccines,” said Wilson.

“There’s a huge need for flu vaccine research,” added Wu.

There is a huge need for biologically uninformed theorists to address the fact that the flu virus does not mutate and evolve.
See: Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

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

The energy-dependent physiology of pheromone-controlled reproduction in species from microbes to humans prevents the virus-driven degradation of messenger RNA that links mutations to all pathology. Only RNA-mediated amino acid substitutions have been linked from ecological variation to ecological adaptations. Claims that anything mutates and evolved are not based on the facts about cell type differentiation that are known to all serious scientists.
Those facts are included in the rules of this game: 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!

 

Cytosis

From base editing to RNA editing (2)

Summary: The link from the creation of the sun’s anti-entropic virucidal energy and the physiology of pheromone-controlled reproduction to fixation of RNA-mediated amino acid substitutions in the organized genomes of all living genera is all that is required to claim adaptation for comparison to Koonin’s moronic assertion that the amino acid composition of proteins varies because the composition evolved.
Digital reconstruction of the Ceprano calvarium (Italy), and implications for its interpretation

A “fresh” (i.e., not yet “fossil”) bone can be plastically deformed before it breaks because it is still rich in collagen and because the calcium crystals that constitute large part of the bony matrix are not yet substituted by other minerals, as happens during the process of mineralization34. Such a diagenetic process may occur in environments that are rich in water, like a riverbed or a perilacustrine paleosol; the latter was probably the case in the Ceprano area5.

The virus-driven degradation of messenger RNA links the diagenetic process in living tissue links to the fossil record via changes that appear to have occurred during the past 5-10,000 years.
See for instance: MicroRNA-32 promotes calcification in vascular smooth muscle cells: Implications as a novel marker for coronary artery calcification
The increased level of calcification in smooth muscle cells, which is associated with increased rates of coronary artery calcification is a clear indicator that the proliferation of viruses in organized genomes causes the negative supercoiling of DNA, which serious scientists have linked to all pathology.
See also: A Post Mortem Case Study: Diffuse Pulmonary Ossification and Sudden Death
Case studies have no explanatory power outside the context of models that link electrons to ecosystems in all living genera. In this case study, it is clear that the pulmonary ossification and sudden death can be placed into the context of my model of nutritional epigenetics.
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

Attempts to support theories about random mutations and evolution have failed miserably and have largely been replaced with facts about energy-dependent RNA-mediated cell type differentiation.
See: RNA Editing Possible with CRISPR-Cas13

The tool itself could be further developed, adds computational biologist Eugene Koonin of the National Center for Biotechnology Information who also was not involved in the study. “This paper is not the end of the road,” he says. It’s possible that Cas13b could be fused to a variety of editing enzymes that would allow a range of different sequence changes. The possibilities are numerous, Koonin says, and “the best is still to come.”

This paper is the end of the road for pseudoscientists and biologically uninformed theorists, like Eugene Koonin, who made this ridiculous claim in 2005:
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
See for comparison: The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis… (2015) — Eugene Koonin
See also Koonin’s attack on all models of ecological adaptation: Splendor and misery of adaptation, or the importance of neutral null for understanding evolution (2016)

…population genetic theory, combined with the data of comparative genomics, clearly indicates that such a “pan-adaptationist” approach is a fallacy. The proper question is: how has this sequence evolved? And the proper null hypothesis posits that it is a result of neutral evolution: that is, it survives by sheer chance provided that it is not deleterious enough to be efficiently purged by purifying selection. To claim adaptation, the neutral null has to be falsified.

The link from the creation of the sun’s anti-entropic virucidal energy and the physiology of pheromone-controlled reproduction to fixation of RNA-mediated amino acid substitutions in the organized genomes of all living genera is all that is required to claim adaptation for comparison to Koonin’s moronic assertion that the amino acid composition of proteins varies because the composition evolved.
Each time a new claim attests to the facts about energy-dependent RNA-mediated biophysically constrained cause and effect, remember how long those facts have been placed on hold by people like Eugene Koonin and Jay R. Fiereman, who is the moderator of the International Society for Human Ethology’s Yahoo Group.
See this attempt to discuss mysterious DNA changes with Jay R. Feierman who on 7/25/13 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.

All DNA modifications are energy-dependent and RNA-mediated. Publications in Science and Nature attest to the foolishness of those who have tried to link base editing and RNA editing to human cell type differentiation without starting with the fact that RNA-mediated amino acid substitutions are food energy-dependent.
Clearly there are no mysterious stress-linked DNA modifications. Nutrient stress and/or social stress cause the proliferation of viruses. Typically the proliferation of viruses is biophysically constrained by food energy and the pheromone-controlled physiology of reproduction in species from microbes to humans.
See “Cytosis” for the game-ending details that placed the nonsense about neutral null falsification back into the historical perspective of the “Dark Ages.”
See also: Tempo and mode of genome evolution in a 50,000-generation experiment (with my emphasis)

Evidence for beneficial mutations

We sought to understand what proportion of the genomic changes in the non-mutator populations was adaptive, and how that proportion changed over time. One line of evidence derives from the expectation that synonymous substitutions—point mutations in protein-coding genes that do not affect the amino-acid sequence—are neutral and should therefore accumulate at a rate equal to the underlying mutation rate20,35. This expectation is not strictly true owing to selection on codon usage, RNA folding, and other effects, but it is generally thought that such selection is extremely weak, affects only a small fraction of sites at risk for synonymous mutations, or both 36,37.

RNA-mediated protein folding chemistry is biophysically constrained. It is nutrient energy-dependent and biodiversity is controlled by the energy-dependent physiology of reproduction. In 2015, Lenski’s group admitted to their lie about the beneficial mutations, with the claim “This expectation is not strictly true owing to selection on codon usage…”
No beneficial mutations have been found by serious scientists. But Lenski’s group clearly indicated they would continue to lie about all aspects of energy-dependent biodiversity. They hoped to make it appear that all energy-dependent biodiversity emerged and then automagically evolved. If they could do that, they knew that their idiot minions were not likely to examine selection for energy-dependent codon usage. But then,
See for comparison: The dynamics of molecular evolution over 60,000 generations
After 10,000 more generations, Lenski’s group reported that standard models of mutation-driven evolution has not been supported by their experimental evidence. Instead, they placed their results into the context of natural selection for energy-dependent codon usage and long-term adaptation, which obviously occurred outside the context of mutation–selection balance and neutral mutation accumulation.
They clearly indicated that the complexity of ecological variation and energy-dependent ecological adaptation must be considered before reporting anything in the context of natural genetic variation. Simply put, they refuted all the pseudoscientific nonsense their past claims caused to be touted by other biologically uninformed theorists. They reported that ecological adaptation occurs outside the context of the mutations and evolution.
But see: Molecular evolution: No escape from the tangled bank

Ecological interactions emerge spontaneously in an experimental study of bacterial populations cultured for 60,000 generations, and sustain rapid evolution by natural selection.

The claim that there is no escape from the tangled bank is true. Joshua B. Plotkin took Lenki’s group’s refutation of mutation-driven evolution and placed it back into the context of the spontaneous emergence of energy-dependent ecological interactions. And then, he again touted the nonsense about evolution by natural selection.
See also: Rapid and Inexpensive Evaluation of Nonstandard Amino Acid Incorporation in Escherichia coli (2017)

…we developed a toolkit for characterizing any Escherichia coli OTS that reassigns the amber stop codon (TAG). It assesses OTS performance by comparing how the fluorescence of strains carrying plasmids encoding a fused RFP-GFP reading frame, either with or without an intervening TAG codon, depends on the presence of the nsAA. We used this kit to (1) examine nsAA incorporation by seven different OTSs, (2) optimize nsAA concentration in growth media, (3) define the polyspecificity of an OTS, and (4) characterize evolved variants of amberless E. coli with improved growth rates.

Even with the tools available, which have refuted all ridiculous theories of mutation-driven evolution, the claims that variants “evolved” continues to plague all serious scientists. It seems that placing the claims that variants evolved into the context of natural selection for energy-dependent codon optimality and the physiology of pheromone-controlled reproduction in all living genera serves no purpose. However, even if biologically uninformed science idiots are not willing to admit that top-down causation requires first consideration for the energy source, there is hope for the future. Most people intuitively understand that the food energy from what organisms eat must be linked to the metabolism of food and the metabolism of food to species-specific pheromones is the only known link from the physiology of reproduction to all biophysically constrained biodiversity in the context of viral latency.
Epigenetic effects must be linked to affects on behavior and the difference between an effect on hormones and an affect of hormones on behavior must be considered in the context of how food odors and pheromones are linked to the physiology of human reproduction by serious scientists.
For example, see: Feedback loops link odor and pheromone signaling with reproduction