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.

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The MicroRNAome Strikes Back: A Sokalian hoax (8)

Defeating Diseases with Energy (January 9, 2018) is a thinly disguised attempt to help corporate giants continue to promote ridiculous neo-Darwinian theories. It features the works of Douglas C. Wallace, who failed to link the virus-driven degradation of messenger RNA to all pathology since he published: Neoplastic transformation is associated with coordinate induction of nuclear and cytoplasmic oxidative phosphorylation genes (1990).

Similar analysis of a cervical carcinoma (HeLa), fibrosarcoma (HT1080), and an Epstein-Barr virus (EBV)-transformed lymphoblastoid line (EBV-L) revealed that all three ANT isoforms were also expressed in these cells. Hence, changes in the expression of OXPHOS genes may be a common feature of transformed cells.

Did he not recognize the significance of the energy-dependent transformation of adenine (in the context of the adenine nucleotide translocator) and oxidative phosphorylation (OXPHOS) genes?
Did Douglas C. Wallace introduce the world to the pervasive nature of the first biologically-based Sokalian hoax, which was subsequently used to bastardize everything known to serious scientists about molecular epigenetics?
Is that how you become a corporate “Champion of Science?”
See for comparison: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)
Why isn’t Bruce McEwen a corporate “Champion of Science” in the context of his claims about the food energy-dependent creation of RNA via a type of “oxidative phosphorylation?”
When will so-called science journalists realize the difference between a serious scientist like Bruce McEwen and a pseudoscientist like Douglas C. Wallace?
Simply put, the difference is in their approach to explaining how biophysically constrained energy-dependent changes in base pairs are linked from fixation of RNA-mediated amino acid substitutions to the differentiation of all cell types. In all living genera, fixation of RNA-mediated amino acid substitutions occurs in the context of the physiology of pheromone-controlled reproduction, which links feedback loops to all biodiversity.
People like Douglas C. Wallace claim that “evolution did it.” Serious scientists put his ridiculous claim into the context of experimental evidence of biophysically constrained energy storage.
See: Long-range coherence and energy storage in biological systems  (1968)
Energy storage begins with the creation of energy and ends with the virus-driven degradation of messenger RNA that links mutations to all pathology. How many more victims of Sokalian hoaxes will there be? Who will help to prevent the next viral apocalypse? Will it be the “Trump Administration?”
I think that fact is obvious.
See: Double-layered protein nanoparticles induce broad protection against divergent influenza A viruses

The amino acid sequence of influenza matrix protein 2 ectodomain (M2e) is highly conserved among human seasonal influenza A viruses20.

Reported as: Researchers Develop Universal Vaccine To Protect Against Influenza A Viruses

“Vaccination is the most effective way to prevent deaths from influenza virus, but the virus changes very fast and you have to receive a new vaccination each year,”

See also: Lung-derived exosomal miR-483-3p regulates the innate immune response to influenza virus infection

Exosomes regulate cell-cell communication by transferring functional proteins and RNAs between cells. Here, to clarify the function of exosomes during influenza virus infection, we characterized lung-derived exosomal microRNAs (miRNAs).

For comparison see this Sokalian hoax: Comparison of miRNA evolution and function in plants and animals

MicroRNAs (miRNAs), as a major player in post-transcriptional regulation of gene expression, have been reported to regulate a broad variety of key biological processes, including growth, development and stress responses in both plants and animals. While the biogenesis and regulatory abilities of miRNAs have been extensively studied, the evolutionary history of miRNAs still needs more exploration. So far, several models explain the origination of plant and animal MIRNA (MIR) genes. Both inter-species and intra-species conservation and divergence of miRNAs exhibits functional adaptation to changing environments in evolution. Here we summarize recent progress in how these similarities and differences contribute to the characteristic features of miRNA evolution in the two kingdoms.

MicroRNAs do not have an evolutionary history. They link the creation of the sun to the creation of ATP to the creation of RNA. ATP did not evolve. RNA did not evolve. Amino acids did not evolve. Viruses do not evolve.
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.

See the NIH report: Flu infection study increases understanding of natural immunity
Natural immunity did not evolve!
For a historical perspective on the ridiculous claims about evolution, see: Neo-Darwinism has failed as an evolutionary theory (May, 1995) by Brian Goodwin

To understand why organisms look the way they do we need models that involve physical forces as well as biological variables, organised to produce organisms with specific morphologies, as described in my book, How the Leopard Changed its Spots.

See: Brian Goodwin:

In a critical review, biologist Catherine S. C. Price noted that although he had succeeded in providing an alternative to mutation as the only source of variation, he failed to provide an alternative to natural selection as a mechanism of adaptation.[7]

That claim has been echoed in the literature published by pseudoscients and so-called science journalists for more than two decades. Natural selection for food energy-dependent codon optimality has repeatedly been linked from the pheromone-controlled physiology of reproduction to all biophysically constrained biodiversity and ecological adaptation since the time we published The Scent of Eros: Mysteries of Odor in Human Sexuality (first published in May, 1995)
Helen Fisher said this about The scent of eros: mysteries of odor in human sexuality (by Kohl and Francoeur 1995): “This is science at its best, with adventure, ideas, and lots of facts.”
Reviewed by Mark Sergeant
Reviewed by Ralph Underwager, Institute for Psychological Therapies
Reviewed by Jan Peregrine
See also: 6 Amazon.com customer reviews
No experimental evidence of biologically-based cause and effect supports the ridiculous claims that Catherine S. C. Price, and others like her, seem to think link mutations to the molecular mechanisms of adaptation via natural selection. That fact explains why theorists must invent new theories and claim to be reconceptualizing their past pseudoscientific nonsense.
See: Theme issue ‘Re-conceptualizing the origins of life’ compiled and edited by Sara Walker and George Cody
For example: Review article: Exploring astrobiology using in silico molecular structure generation
See for comparison: Jerry Fodor Held High Ground to Evolution’s Militant Fundamentalists

Astrobiology doesn’t exist. What are its laws?

See also: The First Virus Communication Signals

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.

The tipping point (revisited): 68,000 publications

MicroRNA  Items: 1 to 20 of 68011 (earlier today, on 12/21/17)

See for example: In Vitro Validation of miRNA-Mediated Gene Expression Linked to Drug Metabolism 12/20/17

The approaches described can be employed broadly for the validation of miRNA-mediated negative regulation of any gene. Determining miRNA-mediated regulation of enzymes and transporters affecting drug metabolism is a critical step in designing personalized therapy and for understanding the mechanisms responsible for variations in the responses to therapeutic agents.

The “…miRNA-mediated regulation of enzymes and transporters affecting drug metabolism…” links the National Microbiome Initiative to the Precision Medicine Initiative and to all healthy longevity or to all virus-driven pathology in all living genera via differences in energy as information.
For review, 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.

For a historical perspective on what is known about energy-dependent RNA-mediated (aka microRNA-mediated) cell type differentiation, see:
The quantum / classical RNA-mediated ‘tipping point’ 3/26/15
The tipping point? 50, 000 publications 5/16/16
The tipping point? 50, 000 publications (2) 5/16/16
The tipping point? 50,000 publications (3) 5/17/16
The tipping point? 50,000 publications (4) 5/26/16
The tipping point? 50,000 publications (5) 7/27/16
The tipping point (revisited): 60,000 4/20/17
By May 16, 2016, the innate antiphage defense strategy was linked from quantum physics to classical physics by 50,000 publications that mentioned microRNAs. Nineteen months later, every aspect of the microRNA-mediated gene expression that had already been linked to drug metabolism attests to the fact that not all scientists have followed the extant literature.
Many scientists are still among the pseudoscientists who who failed to notice the most obvious links from the antiphage defense strategy to healthy longevity. Perhaps they were also too busy to notice the most obvious links from the virus-driven degradation of messenger RNA to the need for drug therapies.
If so, that may explain why the drug therapies have been largely ineffective. The drug therapies may be like vaccinations. They appear to link the virus-driven degradation of messenger RNA to more mutations, which clearly link the virus-driven theft of quantized energy to all pathology.
With more than 18,000 published works in the past 19 months, (8,000 in the past 8 months) it is time to again address the tipping point between quantum physics and classical physics in the context of food energy-dependent pheromone-controlled microRNA-mediated cell type differentiation via what is known about autophagy.
In the context of drug metabolism, the energy-dependent microRNA-mediated creation of enzymes was linked from the metabolism of food to all biodiversity on Earth via pheromone-controlled physiology of reproduction.
See for example page 19 of the sample report from Alpha Genomix that you can download as a pdf here. The food energy-dependent creation of the CYP enzymes protects our organized genome by biophysically constraining viral latency.

See for comparison: Our Top 17 in ’17: The Year in Science at PLOSBLOGS 

…the far-reaching war on science being conducted by the Trump administration, an assault on facts which, as several of our bloggers have noted, constitutes a removal of scientific evidence from the formation and discussion of public policy and an evisceration of funding and communication of vital research in medical research and regulation, public health, climate, energy, agriculture and education.

The only war on science that I know about, is the one in which serious scientists are Combating Evolution to Fight Disease. To place that claim into the context of what has happened during 2017, see the retraction of this article.
Biomechanical Characteristics of Hand Coordination in Grasping Activities of Daily Living [retracted]
It was retracted because the authors mentioned the creator of the hand. The creation of the hand occurs only in the context of biophysically constrained viral latency.

See for comparison: Retraction Watch

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

Where else besides PLOS have you seen a retraction for the mention of a creator? Where did PLOS report on the retraction for misrepresentations in “Nature Chemistry?” Who still believes that microRNA and messenger RNAs created each other so that they could automagically constrain viral latency?
Who else besides PLOS is waging a far-reaching war on science?
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems 4/10/14

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.

Obama Advisers Urge Action Against CRISPR Bioterror Threat 11/17/16

Scientific advisers to President Obama warn that the U.S. urgently needs a new biodefense strategy and should regularly brief President-elect Donald Trump on the dangers posed by new technologies like CRISPR, gene therapy, and synthetic DNA, which they say could be coöpted by terrorists.

See for comparison:  2017 Global Infectious Diseases Threats to the United States 12/22/16

Flu.  Influenza remains one of the greatest threats to the US population killing on average 3,000-49,000 Americans annually.  People at the greatest risk of severe flu and death are pregnant women, residents of long-term care facilities, the very old (adults over the age of 65), the very young (children less than 2), Native American populations, and those with underlying chronic conditions such as asthma, COPD, heart disease, obesity, and other conditions.  Timely vaccination remains the most proven and effective way to avoid serious injury from influenza.

The new Trump Administration will face a formidable array of global and indigenous infectious disease threats in 2017.  A Global Health Security Agenda will help provide a framework for tackling some of these tough issues, but enhanced efforts will be needed to prevent new epidemics, especially from vector-borne and zoonotic neglected tropical diseases, measles, and the ever-constant threats from AMR and flu.

The biggest threat that the Trump administration has faced in the first year is the fake news. The most recent example accused him of censorship at the CDC for his director’s efforts to biophysically constrain energy-dependent viral latency. The CDC director’s efforts to help others with budget concerns were linked to censorship, and the President of the United States was compared to Hitler. Wake up and “Remember the Alamo.”
SARCASM ALERT: No, that was a different war. Wake up and remember the Manhattan Project, which also linked censorship about energy to the winning of a war.

diseases-disorders

Your indifference is killing you and others

Summary: Coherence-inducing mechanisms is double-speak for mechanisms that are nutrient-dependent and pheromone-controlled.
Feedback loops link odor and pheromone signaling with reproduction has been presented in double-speak as Looplessness in networks is linked to trophic coherence

We are currently studying the entropy of the coherence ensemble we defined for this work. “In general, higher trophic coherence would be associated with lower entropy states, which means that if networks are more coherent than the random expectation there must indeed be some kind of negentropic process at work.” Johnson notes that the impact in this case relative to trophic coherence would be found in quantifying the extent to which different empirical networks have been driven from their maximum entropy state. “This might be the best way of discovering when there are coherence-inducing mechanisms at work, how much energy must be involved, and ultimately identifying the nature of such processes.”

Feedback loops link the sun’s anti-entropic virucidal energy from the food that organisms eat to the physiology of pheromone-controlled reproduction in all living genera. The virucidal effect of ultraviolet light biophysically constrains viral latency. Energy-dependent RNA-mediated amino acid substitutions in supercoiled DNA are fixed in organized genomes via the physiology of reproduction and supercoiled DNA protects all organized genomes from the virus-driven degradation of messenger RNA that links mutations to all pathology.
Coherence-inducing mechanisms is double-speak for nutrient-dependent and pheromone-controlled in the context of Nutrient-dependent/pheromone-controlled adaptive evolution: a model. 
Despite the validity of the model, it has not been accepted by neo-Darwinian theorists or “Big Bang” cosmologists. Ridiculous beliefs about emergence and evolution are pervasive and the pseudoscientific nonsense of their theories leads to claims about coherence-inducing mechanisms.
That is why I changed the FB page description at RNA-mediated after a series of posts (see below).

It took 20 years for others to realize that all life on Earth is food energy-dependent. Now, most people are indifferent to that fact. They refuse to learn anything about where the food energy comes from.

Differences in the energy of photons have been linked to quantized energy-dependent fixation of RNA-mediated amino acid substitutions. The substitutions biophysically constrain supercoiled DNA via the physiology of pheromone-controlled reproduction.

Virus-driven energy theft links the degradation of messenger RNA to mutations via amino acid substitutions in viruses. The substitutions in the viruses have been linked to all pathology via changes in the energy-dependent microRNA/messenger RNA balance.

For comparison, the pseudoscientific nonsense of neo-Darwinian theories links mutations from natural selection to the evolution of new species. In reality, light energy is quantized information. The information links physics, chemistry, and molecular epigenetics from the speed of light on contact with water and hydrogen-atom transfer in DNA base pairs in solution to learning, memory, and behavior via RNA-mediated events such as the energy-dependent creation of enzymes and the the de novo creation of G protein-coupled receptors such as olfactory receptor genes.

Top-down causation and de novo gene creation are exemplified by energy-dependent differences in the microRNA/messenger RNA balance that link natural selection for codon optimality to amino acid substitutions that link the physiology of reproduction to supercoiled DNA. Supercoiled DNA protects all organized genomes from virus-driven energy theft. That fact supports the beliefs of young earth creationists, which may be the only existing basis for discussion of quantum biology and refutations of neo-Darwinian theories that have linked olfaction to quantum souls. If there is another basis for the link from quantum physics to quantum souls, no one has detailed in in the context of top-down causation, which must include information about the creation of genes.

Most people seem unwilling to accept experimental evidence that attests to how genes are created or information that shows how virus-driven energy theft is linked to all pathology. Discussion of the energy-dependent paradigm shift would lead others away from pseudoscientific nonsense about emergence and/or beneficial mutations and evolution.

Only via discussion of facts about the paradigm shift will others learn what is currently known to serious scientists about the biophysically constrained nutrient energy-dependent chemistry of RNA-methylation and all biophysically constrained RNA-mediated protein folding chemistry. Simply put, the protein folding chemistry must be linked to all biodiversity by the physiology of energy-dependent pheromone-controlled reproduction in all living genera.

Your indifference to that fact is killing people.

See for comparison: Looplessness in networks is linked to trophic coherence (May 16, 2017)

Our theory correctly classifies a variety of networks-including those derived from genes, metabolites, species, neurons, words, computers, and trading nations-into two distinct regimes of high and low feedback and provides a null model to gauge the significance of related magnitudes. Because trophic coherence suppresses feedback, whereas an absence of feedback alone does not lead to coherence, our work suggests that the reasons for “looplessness” in nature should be sought in coherence-inducing mechanisms.

Reported August 14, 2017 as Trophic coherence explains why networks have few feedback loops and high stability

The researchers are also investigating whether negentropy – the opposite of entropy, and in which a physical, thermodynamic or biological process creates order – are affected by trophic coherence. “The modern concept of entropy,” Johnson points out, “comes from statistical physics and is a property of ensembles, as described above – that is, the entropy of an ensemble is simply a function of the number of elements it contains.” Moreover, he adds, graph ensemble entropy has proven to be a powerful tool for understanding various network properties. We are currently studying the entropy of the coherence ensemble we defined for this work. “In general, higher trophic coherence would be associated with lower entropy states, which means that if networks are more coherent than the random expectation there must indeed be some kind of negentropic process at work.” Johnson notes that the impact in this case relative to trophic coherence would be found in quantifying the extent to which different empirical networks have been driven from their maximum entropy state. “This might be the best way of discovering when there are coherence-inducing mechanisms at work, how much energy must be involved, and ultimately identifying the nature of such processes.”

See for comparison: Feedback loops link odor and pheromone signaling with reproduction

These studies also indicate that GnRH neurons are likely to influence numerous brain functions. They appear to transmit signals to as many as 30,000 or more neurons in 34 brain areas, consistent with previous studies showing GnRH+ fibers and GnRH receptors in multiple brain regions (Badr and Pelletier, 1987; Jennes et al., 1988; Jennes et al., 1997). BL+ neurons likely to receive synaptic input from GnRH neurons were seen in areas associated with numerous different functions, including odor and pheromone processing, sexual behavior, appetite, defensive behavior, motor programs, and the relay of information to higher cortical areas. These results may reflect a strategy wherein GnRH neurons can modify diverse functions in order to coordinate the internal state of the animal and its behavior with reproduction in order to optimize reproductive success.

See my posts on Discovering Vismodegib in the Fight Against Skin Cancer: The First Approved Inhibitor of the Hedgehog Pathway
No one I know is likely to understand this link from the anti-entropic virucidal energy of sunlight to prevention of all pathology because they must first understand the fact that proteins do not create themselves. There is no need for this inhibitor of the Hedgehog pathway or inhibition of any other pathway if cancer is prevented. But most people are not willing to learn about prevention because they think they can rely on medical practitioners to effectively treat their diseases. Do you think that your physician knows anything about light scattering characterization of glycoproteins and their interactions with other proteins and antibodies?
Absolute Characterization of Glycoproteins and their Interactions with Proteins and Antibodies by Light Scattering
Light scattering can now be linked to the characterization of glycoproteins and their immune system interactions in all species on Earth. That suggests the speed of light on contact with water links energy as information to the de novo creation of the glycoproteins,
If so, the physiology of reproduction links pheromones to biophysical constraints on the creation of more glycoproteins in the context of morphological and behavioral differences in species from microbes to humans. That suggests the refutation of neo-Darwinism is complete, since the virus-driven degradation of messenger RNA has been linked to all pathology in bacteria that become archaea before virus-driven energy theft causes them to become L-forms.
Simply put, Carl Woese was wrong. There is only one domain of life and virus-driven energy theft is what destroys all life on Earth.

 

A rendering of how changes in an electron's motion (bottom view) alter the scattering of light (top view), as measured in a new experiment that scattered more than 500 photons of light from a single electron. Previous experiments had managed to scatter no more than a few photons at a time. Credit: Extreme Light Laboratory|University of Nebraska-Lincoln

Energy-dependent physical and biophysical constraints (10)

Summary: 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…— Eugene Koonin
My comment: Viruses are not life forms. They steal the quantized energy that links sunlight to viral latency in the context of everything known to all serious scientists about the fact that Feedback loops link odor and pheromone signaling with reproduction
See for comparison: Olfaction Warps Visual Time Perception Energy as information links the sense of smell in bacteria to our visual perception of energy and mass in the context of the space-time continuum and food odors that link the physiology of reproduction in bacteria to the pheromone-controlled physiology of reproduction and biophysically constrained viral latency in all living genera.
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Energy-dependent physical and biophysical constraints (9)

2010 A single amino acid substitution confers enhanced methylation activity of mammalian Dnmt3b on chromatin DNA

…the I662N substitution in mammalian Dnmt3b conferred enhanced chromatin DNA methylation activity and contributed to functional adaptation in the epigenetic system.

Energy-dependent amino acid substitutions link what organisms eat to their pheromone-controlled physiology of reproduction and chromosomal rearrangements that have been linked to all biodiversity via the sense of smell in bacteria and quorum sensing.
2013 Nutrient-dependent/pheromone-controlled adaptive evolution: a model

CONCLUSION:

An environmental drive evolved from that of nutrient ingestion in unicellular organisms to that of pheromone-controlled socialization in insects. In mammals, food odors and pheromones cause changes in hormones such as LH, which has developmental affects on pheromone-controlled sexual behavior in nutrient-dependent reproductively fit individuals across species of vertebrates.

2013 The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.
2017 Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention

There are at least four sources of R mutations in normal cells: quantum effects on base pairing (30), mistakes made by polymerases (31), hydrolytic deamination of bases (32), and damage by endogenously produced reactive oxygen species or other metabolites (33).

2015 Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes

…their covalently bonded 13C/15N nuclei were assigned using heteronuclear single/multiple quantum coherence correlation experiments (HSQC or HMQC).

2017 Nature does not rely on long-lived electronic quantum coherence for photosynthetic energy transfer

…/the observed extremely fast decoherence should be viewed as general, bringing to question any significant quantum coherent transport contributions to photosynthesis.

2017 Recent progress on the effects of microRNAs and natural products on tumor epithelial-mesenchymal transition
My summary: Two researches in NATURE denied the role that microRNAs play epithelial-mesenchymal transition in tumors and their denial of everything known about food energy-dependent biophysically constrained pheromone-contolled biodiversity is discussed in this review. See for comparison the section on Regulation of miRNA on EMT in tumors
The role of miRNA/ZEB in head and neck squamous cell carcinoma, in breast cancer, in lung cancer, in pancreatic cancer and in bladder cancer was anticipated in reports by serious scientists such as the late Eshel Ben-Jacob. See: MicroRNA-based regulation of epithelial–hybrid–mesenchymal fate determination, which was reported as:

They found that there is a molecular “on” and “off” switch that cancer cells use to determine their fate. Evidently, there is an on or off state for metastasis (migration), but also a third possibility, according to this recently-discovered molecular data.

The researchers discovered that there was an intermediate function, which is termed a “ternary,” or three-way switch. This function relates to the fact that ZEB has the ability to turn itself on due to a positive feedback system. This allows a cell to keep intermediate levels of all four proteins required for the switch. Ben-Jacob notes that the hybrid, or partially on-off state, also supports cancer metastasis by enabling collective cell migration and by imparting stem-cell properties that help migrating cancer cells evade the immune system and anticancer therapies.

See also: Stability of the hybrid epithelial/mesenchymal phenotype

Our results suggest that partial EMT, i.e. a hybrid E/M phenotype, need not be ‘metastable’, and strengthen the emerging notion that partial EMT, but not necessarily a complete EMT, is associated with aggressive tumor progression.

The food energy-dependent stability of the hybrid epithelial/mesenchymal phenotype has been linked from photosynthesis to the creation of energy-dependent microRNAs in plants and in animals via what has been known to all serious scientists about the physiology of pheromone-controlled reproduction in bacteria.
See:
2003 Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment
2006 Seeking the foundations of cognition in bacteria: From Schrödinger’s negative entropy to latent information
2009 Learning from Bacteria about Natural Information Processing with my emphasis

Focusing on the energy, matter, and thermodynamic imbalances provided by the environment, Schrodinger proposed that life required the consumption of negative entropy, that is, the use of thermodynamic imbalances in the environment. From the perspective of thermodynamics, each bacterium can be viewed as a complex system that is composed of an “engine” that uses imbalances in the environment to do work, and a “machine” that uses this energy (to act against the natural course of entropy increase) for the synthesis of organic substances.13 A third information-processing system is also needed for the coordination and synchronization of the functioning of the engine and the machine. Namely, a living cell is analogous to a complex man-made cybernetic system, or a “chimera,” composed of information processing systems and of at least two thermodynamic elements. In addition, using the outer membrane, cells sense the environment.

We proposed that, besides “negative entropy,” organisms sense the environment to extract latent embedded information.13 By latent information we refer to data embedded in the environment that, once processed cognitively, initiates change in the organism’s function or behavior. Information induces changes; hence it can be used to generate an internal condensed description (model or usable information) of the environment, which guides the organism’s functioning.

Conclusion: Olfaction Warps Visual Time Perception Energy as information links the sense of smell in bacteria to our visual perception of energy and mass in the context of the space-time continuum and food odors that link the physiology of reproduction in bacteria to the pheromone-controlled physiology of reproduction in all living genera.
See for comparison (Koonin is a co-author): On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires
…another cause of the lack of detectable protospacers is likely to be the existence of a virtually untapped pool of mobile genetic elements that, at any given time, are not represented in a given environment (10). This paucity of spacer matches is conceivably explained by the vastness and diversity of viromes…
Biologically uninformed evolutionary theorists have failed to link the anti-entropic virucidal energy of the sun to all biodiversity and failed to link the virus-driven degradation of messenger RNA to all pathology via changes in the microRNA/messenger RNA balance. The release of the game “Cytosis” in September (2017) will make all theorists appear to be among the biologically uninformed science idiots who invented ridiculous theories in attempts to explain away Darwin’s “conditions of life.”
See: 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!
See also the comments on: Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention
For example:  2017 Jul 28 06:45 a.m. (research profile) challenges the “bad luck” theory of cancer.

Cancer etiology: assumptions lead to erroneous conclusion

The authors claim that cancer is caused and driven by mutations, and that two-thirds of the mutations required for cancer are caused by unavoidable errors arising during DNA replication. The first claim is based on the somatic mutation theory. The second claim is based on a highly positive correlation between the lifetime number of stem cell divisions in a tissue and the risk of cancer in that tissue, and on their method for estimating the proportion of mutations that result from heredity (H mutations), environmental factors (E mutations) and unavoidable errors arising during DNA replication (R mutations). These claims raise several questions:

1. Sequencing studies have found zero mutations in the genes of a variable proportion of different cancer types (see, e.g., https://dx.doi.org/10.1093/jnci/dju405 and references therein). If cancer is caused by mutations in driver genes, could the authors explain what causes these cancers with zero mutations? Could the authors use their method for estimating the proportion of cancer risk that is preventable and unpreventable in people with tumors lacking driver gene mutations?

2. Environmental factors are known to affect stem cell division rates. According to IARC, drinking very hot beverages probably causes esophageal cancer (Group 2A). If you drink something hot enough to severely damage the cells lining the esophagus, the stem cells located in deeper layers have to divide to produce new cells to replace the damaged cells. These stem cell divisions, triggered by an environmental factor, will lead to mutations arising during DNA replication. However, these mutations are avoidable if you do not drink very hot beverages. Should these mutations be counted as environmental mutations (H mutations) or as unavoidable mutations arising during DNA replication (R mutations)?

3. The authors’ work is based on the somatic mutation theory. This theory is primarily supported by the idea that cancer incidence increases exponentially with age. Since our cells are known to accumulate mutations throughout life, the accumulation of driver gene mutations in our cells would perfectly explain why the risk of cancer increases until death. However, it is now well established that cancer incidence does not increase exponentially with age for some cancers (acute lymphoblastic leukemia, testicular cancer, cervical cancer, Hodgkin lymphoma, thyroid cancer, bone cancer, etc). It is also well known that cancer incidence decreases late in life for many cancer types (lung cancer, breast cancer, prostate cancer, etc). For example, according to SEER cancer statistics review, 1975-2014, men in their 80s have approximately half the risk of developing prostate cancer than men in their 70s. The somatic mutation theory, which is the basis for this article, does not explain why the lifetime accumulation of driver gene mutations in the cells of many tissues is not translated into an increase in cancer incidence throughout life. Are the authors’ conclusions applicable to all cancers or only to those few cancers in which incidence increases exponentially with age until death?

4. The authors estimate that 23% of the mutations required for the development of pancreatic cancer are associated with environmental and hereditary factors; the rest (77%) are mutations arising during DNA replication. However, Notta et al. recently found that 65.4% of pancreatic tumors develop catastrophic mitotic events that lead to mutations associated with massive genomic rearrangements (https://doi.org/10.1038/nature19823). In other words, Notta et al. demonstrate that cell division not only leads to mutations arising during DNA replication, but also to mutations arising during mitosis. For this cancer type, the authors could introduce a fourth source of mutations, and estimate the proportion of mutations arising during mitosis (M mutations) and re-estimate those arising during DNA replication (R mutations). Alternatively, they could reanalyze their raw data without assuming that the parameters “stem cell divisions” and ”DNA replication mutations” are interchangeable. Cell division, process by which a cell copies and separates its cellular components to finally split into two cells, can lead to mutations occurring during DNA replication, but also to other cancer-promoting errors, such as chromosome aberrations arising during mitosis, errors in the distribution of cell-fate determinants between the daughter cells, and failures to restore physical interactions with other tissue components. Would the authors’ conclusions stand without assuming that the parameters “stem cell divisions” and ”DNA replication mutations” are interchangeable?

5. The authors report a striking correlation between the number of stem cell divisions in a tissue and the risk of cancer in that tissue. They do not report any correlation between the number of mutations in a tissue and the risk of cancer in that tissue; in fact, these parameters are not correlated (see. e.g., https://doi.org/10.1038/nature19768). In addition, the authors discuss that most of the mutations required for cancer are a consequence, not a cause, of the division of stem cells. So, why do the authors use their correlation to say that cancer is caused by the accumulation of mutations in driver genes instead of saying that cancer is caused by the accumulation of cell divisions in stem cells?

For references and additional information see: Comment on ‘Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention’ DOI: 10.13140/RG.2.2.28889.21602 https://www.researchgate.net/publication/318744904; also https://www.preprints.org/manuscript/201707.0074/v1/download

See also: Miguel Lopez-Lazaro
My comment: Like him, others from a new generation of researchers, will no longer tolerate the pseudoscienitfic nonsense touted by evolutionary theorists and “Big Bang” cosmologists who know nothing about natural selection for energy-dependent codon optimality, which links the physiology of reproduction to biophysically constrained viral latency.

A rendering of how changes in an electron's motion (bottom view) alter the scattering of light (top view), as measured in a new experiment that scattered more than 500 photons of light from a single electron. Previous experiments had managed to scatter no more than a few photons at a time. Credit: Extreme Light Laboratory|University of Nebraska-Lincoln

Epigenetic effects of stress by Bruce McEwen (1)

A rendering of how changes in an electron’s motion (bottom view) alter the scattering of light (top view), as measured in a new experiment that scattered more than 500 photons of light from a single electron. Previous experiments had managed to scatter no more than a few photons at a time. Credit: Extreme Light Laboratory|University of Nebraska-Lincoln
Summary:

In the early 1990’s, Bruce McEwen inspired my life’s works, which link the epigenetic effects of nutrient-stress and/or social stress to the fact that RNA biosynthesis is ATP-dependent. That fact helped all serious scientists link the virus-driven energy theft of quantized energy to the degradation of messenger RNA, which links mutations to all pathology.

Pseudoscientists refuse to accept that fact.

When is stress good for you? by Bruce McEwen

The subtle flows and toxic hits of stress get under the skin, making and breaking the body and brain over a lifetime

Excerpt:

We now understand that epigenetics is the means by which stress acts on the body, the genome, and the brain.

My life’s work has helped me to tell the story of stress, starting with the mentors for my dissertation, completed in 1964.

See McEwen et al., (1964): Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

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

In the early 1990’s, Bruce McEwen inspired my life’s works, which link the epigenetic effects of nutrient-stress and/or social stress to the fact that RNA biosynthesis is ATP-dependent. That fact helped all serious scientists link the virus-driven energy theft of quantized energy to the degradation of messenger RNA, which links mutations to all pathology.

Pseudoscientists refuse to accept that fact.

See for example: Quantum Physics News

Robert Karl Stonjek claims and asks (with my emphasis):Where did all that energy come from?

Big Bang and Quantum Physics

As we well know, there are some huge difficulties for the Big Bang model. There is the problem of the missing antimatter, the failure to come up with the required unification theory of matter, the requirement for Dark Matter which has never been directly observed and Dark Energy for which there is no description of what it actually is, at least when we ask QM questions about it.

Other problems include the general picture that says that the universe began with spacetime expansion and not a ballistic explosion and that spacetime expansion has slowed ever since. But spacetime expansion was later shown to be increasing, not decreasing, and there is no indication that spacetime expansion was ever explosively fast. Then there is inflation on top of that, an explanation, given without any evidence whatsoever, simply because it makes a preconceived model work.

In other words the model comes first and then we search for evidence, which is what religionists have been doing for millennia. Science differentiated itself from religion by starting with observation and experiment before structuring mathematical models based on what was already established empirically.

There are other problems with the Big Bang that Quantum Physicists should be concerned with. There is not only the thermal entropy, which Roger Penrose rightly points out is at maximum (not minimum) at the Big Bang and for some time after (gravitational entropy is at a minimum) but the idea that the initial condition was extremely hot.

I question how this can be. Sure, if you compress matter it will heat up, but the initial configuration of matter was not a result of compression. Further, and most importantly, the particles of matter were maximally compressed so that they could not possibly move before expansion began. If a particle can not move then it can neither emit or absorb energy, a photon, and so is at absolute zero Kelvin.

In fact this is how we define zero Kelvin, and in Black Holes the temperature is at zero Kelvin. One might argue that the energy is in the form of a halo of photons and other bosons, which is more or less the Lamartre model which was overtaken by Gamow’s hot big bang (as it came to be known).

So, how can a compressed matter taking up a zero or near zero volume that is in that configuration not as a result of compression suddenly acquire a high temperature? Where did all that energy come from?

Researchers simply plug the temperature in, easy to do with the math, but I question where this energy came from and in what form it was in before expansion began to occur. Sure, Bosons can all occupy the same space, but a photon can not be at rest and so can not exist for any interval before expansion.

It seems to me that the first era of the Big Bang, up to the emission of the CMB, is a ‘just so’ story based entirely on the wishes and imagining of a few theorists and entirely devoid of evidence of any kind. There is, however, abundant evidence that the Big Bang did not occur: almost no anti-matter, high thermal entropy, no evidence of the near infinite number of additional universes postulated by inflation theory, no observational or experimental evidence for inflation, no unification of gravity, strong and electroweak forces and so on.

See for comparison: Quantum common sense

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

See also: Aeon Archive. During my vacation from June 26 until July 7, I commented on posts to Aeon because I did not have access to my bibliography of ~8000 published works. I’ve included all past comments to Aeon because Bruce McEwen has again helped to clarify the role of epigenetic effects on energy-dependent RNA-mediated cell type differentiation.

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terrarium-eco-system

The emergence of light as energy from a life-giving star

The Sun – our steady, reliable companion – tells a very different story up close

“…a mesmerising, perspective-shaking glimpse at Earth’s life-giving star.” (video)

Questions:
1) Did the energy in this life-giving star create itself?
2) How is hydrogen-atom transfer in DNA base pairs in solution biophysically constrained.
3) Who created the feedback loops that link the solar analemma from the time-space continuum to representations of biophysically constrained life and free will in the Mobius strip.
4) Was Linda Buck the first Nobel Laureate to establish the link from the food energy-dependent pheromone-controlled physiology of reproduction to biodiversity in all living genera?
5) Are biologically uninformed theorists capable of answering any questions about the energy of life or how virus-driven energy theft causes the degradation of messenger RNA that links constraint-breaking mutations to all pathology?
The Mobius strip and the solar analemma exemplifie biophysical constraints on life history events.

The Mobius strip (above) is a visual aid for those who do not understand the concept of how free will is connected to the conserved molecular mechanisms of biophysically constrained energy-dependent RNA-mediated cell type differentiation in all living genera. If you cannot answer all 5 questions about energy in the context of the visual aid, which links the solar analemma to choices between quantized energy-dependent life and death, please search for microRNA on PubMed. The sun’s anti-entropic virucidal energy is biophysically constrained in microRNAs at every level of examination from angstroms to ecosystems.
If you cannot find the answers to any of the five questions about energy, ask a theorist to answer the first question. Alternatively, see: Computational identification of mutually homologous Zika virus miRNAs that target microcephaly genes

…ZIKV may modulate the action of various miRNAs, and miR-1304 in particular, resulting in microcephaly.

ZIKV – driven degradation of messenger RNA is linked to microcephaly. See also: Absolute Biophysical Characterization with Multi-Angle and Dynamic Light Scattering

A SEC-MALS-RI or UV with DLS system extends the characterization range of biomolecules to glycoproteins, PEGylated proteins, hydrophobic proteins, biopolymers, and other biomolecules.

My summary: The “Brownian” motion of molecules links dynamic light-scattering (DLS) from ecological variation to ecological adaptations via Ultraviolet-visible (UV-Vis) spectroscopy. Detection of energy as information has been placed into the context of virucidal light as energy.

Dynamic light scattering [DLS]

Dynamic light scattering (DLS) is a technique in physics that can be used to determine the size distribution profile of small particles in suspension or polymers in solution.[1] In the scope of DLS, temporal fluctuations are usually analyzed by means of the intensity or photon auto-correlation function (also known as photon correlation spectroscopy or quasi-elastic light scattering).

See also: Detection Limits of DLS and UV-Vis Spectroscopy in Characterization of Polydisperse Nanoparticles Colloids
My summary: Ultraviolet-visible (UV-Vis) spectroscopy links the the food energy-dependent pheromone-controlled physiology of reproduction to the weekend resurrection of the bacterial flagellum in P. fluorescens, which responds to the light-activated chemistry of life with fluorescence even after the “knock-out” of the gene for its mobility, which was resurrected over the weekend as reported in: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
The resurrection in this organism, links its fluorescence to quantized energy-dependent exosome-delivered microRNAs, which have been reported to be Ultraconserved Elements in the Human Genome. When theorists use terms like ultraconserved elements outside the context of the conserved energy in microRNAs, it is clear that theorists are attempting to obfuscate this fact: The energy-dependent de novo creation of microRNAs has been linked to all biodiversity in all living genera via the physiology of pheromone-controlled reproduction.
See for example: All in the (bigger) family I wrote:

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

See for comparison: Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

The interactions of these small noncoding RNAs in such primitive species have wide-reaching effects, from increasing viral and bacterial proliferation, better responses to stress, increased virulence, to manipulation of host immune responses…

The small non-coding RNAs are energy-dependent microRNAs, which are the same thing as Ultraconserved Elements in the Human Genome..
Here’s a way to make that fact perfectly clear. When it becomes available, play 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!

Stop playing the ridiculous games of theorists who have failed to link the Creation of the sun’s quantized energy to all biodiversity on Earth. Theorists also failed to link the virus-driven degradation of messenger RNA from mutations to all pathology. Instead, they have used definitions of terms and definitions of species that are not limited to that fact that all organisms on Earth must eat or they fail to reproduce.
See for examples of pseudoscientific nonsense: New Research Problem of Species Definitions

Darwin first noted that there is no one definition of species, and not much has changed since then.

All species-specific behavior is food energy-dependent and RNA-mediated cell type differentiation biophysically constrains it in the context of the physiology of pheromone-controlled reproduction in all living genera. Darwin presciently included that fact in his “conditions of life.” He warned others that they could not start with natural selection, but many others have consistently ignored Darwin’s warnings. They also ignore the consistency of biological facts that link what organisms eat to the survival of all species via the pheromone-controlled physiology of reproduction. That forces them to ignore the consequences of virus-driven energy theft.
See: Virus-mediated archaeal hecatomb in the deep seafloor

We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.

See for support of the fact that virus-archaea interactions play a central role in global biogeochemical cycles: Feedback loops link odor and pheromone signaling with reproduction
The feedback loops link natural selection for energy dependent codon optimality from RNA-mediated amino acid substitutions in supercoiled DNA to all biodiversity on Earth via the exosome-mediated delivery of microRNAs.
See also: The phylogenetic utility and functional constraint of microRNA flanking sequences

…the clear identity and easy alignment of these sequences makes them good candidates for estimating phylogeny, and they can reliably be found and identified across all members of a clade of interest. Their relatively slow evolution [3] also means that they can easily be identified in de novo assemblies of genomes.

The assembly of all organized genomes is food energy-dependent. Without food energy there is no energy for assembly of anything. Exosomes mediated the delivery of the food energy in microRNAs.
See also: Exosome Mediated Delivery of miR-124 Promotes Neurogenesis after Ischemia.

The intrinsic ability of neurogenesis after stroke has been proven weak, which results in insufficient repair of injury in the nerve system. Recent studies suggest multiple microRNAs (miRNAs) are involved in the neuroremodeling process. Targeted miRNAs delivery for amplification of neurogenesis is promising in promoting the prognosis after ischemia. Here, we showed that modified exosomes, with rabies virus glycoprotein (RVG) fused to exosomal protein lysosome-associated membrane glycoprotein 2b (Lamp2b), could efficiently deliver miR-124 to the infarct site. Systemic administration of RVG-exosomes loaded with miR-124 promoted cortical neural progenitors to obtain neuronal identity and protect against ischemic injury by robust cortical neurogenesis. Our study suggests that RVG-exosomes can be utilized therapeutically for the targeted delivery of gene drugs to the brain, thus having great potential for clinical applications.

The fact that “…multiple microRNAs (miRNAs) are involved in the neuroremodeling process…” makes the role of food energy-dependent RNA-mediated DNA repair perfectly clear to all serious scientists. For comparison, use of virus-assisted delivery has been linked to the predictable horror of gene editing technology.
See: Unexpected mutations after CRISPR-Cas9 editing in vivo
See for comparison: Cell proliferation in the subventricular zone by synthetic murine pheromones

The elucidation of the mechanisms by which specific compounds influence cell proliferation and neurogenesis, and eventually reproductive conditions in males and females should provide further insight as to how the odor environment controls and modulates the reproductive activities of animals.

See also: Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis
Clearly, researchers who use viruses to stimulate neurogenesis have not learned that all cell type differentiation is energy-dependent and controlled by feedback loops. Their use of viruses will continue ot link virus-driven energy theft from the degradation of messenger RNA to all pathology via the constraint breaking mutations the Masatoshi Nei, and many other biologically uninformed theorists have included in their stories about Mutation-Driven Evolution.

Exosome-delivered microRNAs modulate the inflammatory response to endotoxin 6/18/16

The functional relevance of exosomes in many different biological systems, including the immune system, is beginning to be demonstrated5,6,7,8,9,10,11.

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

…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution. The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, ; Duvarci, Nader, & LeDoux, ; Griggs et al., ; Monahan & Lomvardas, ) in adaptive evolution will certainly be discussed in published works that will follow.

See also: Humans Fit All Of The Government Criteria For ‘Endangered Species’ and Past 5,000 years prolific for changes to human genome
See for comparison: Independent and Stochastic Action of DNA Polymerases in the Replisome

It has been assumed that DNA synthesis by the leading- and lagging-strand polymerases in the replisome must be coordinated to avoid the formation of significant gaps in the nascent strands.

Reported as: Close-Up View of DNA Replication Yields Surprises

What looks like coordination is actually the outcome of a random process of starting, stopping and variable speeds. Over time, any one DNA polymerase will move at an average speed; look at a number of DNA polymerases synthesizing DNA strands over time, and they will have the same average speed.

See for comparison: The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity

…the metabolic enzyme, pyruvate kinase muscle (PKM), interacts with sub-pools of endoplasmic reticulum (ER)-associated ribosomes, exerting a non-canonical function as an RNA-binding protein in the translation of ER-destined mRNAs.

Metabolism is food energy-dependent. That fact should have eliminated all the pseudoscientific nonsense about the random process of starting, stopping and variable speeds. For example, autophagy is quantized energy-dependent and the energy from food protects all organized genomes from virus-driven energy theft and the degradation of messenger RNA that links mutations to all pathology.
See also: The evolution of ecosystem ascendency in a complex systems based model
Abstract conclusion:

Our findings support the validity of ecosystem ascendency as a meaningful measure of ecosystem organisation, which increases over evolutionary time scales and significantly drops during periods of disturbance. The results suggest a general trend towards both higher integrity and increased stability driven by functional and structural ecosystem coadaptation.

Ecosystem ascendancy is food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction in all living genera.
Attempts to model general trends towards the increased stability of functional and structural ecosystems without linking the anti-entropic virucidal energy of sunlight to the physiology of reproduction are examples of what Richard Feynman referred to as human idiocy.

Richard Feynman was a Nobel prize winning Theoretical Physicist who popularized physics with his entertaining lecture style. This snippet is taken from one of his lectures in the series “The character of Physical Law” where he complains about all the different units that are used to measure the single concept of Energy.
See also: Structural diversity of supercoiled DNA

Six decades after the elucidation of its double helical structure, DNA continues to surprise us by revealing new information. Our cryo-ET, biochemical, and computational studies show the astounding versatility and dynamism of DNA depending on the degree of supercoiling. DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases. Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

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.
7/26/13
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.
See also:These groups are moderated by Robert Karl Stonjek, who is an example of human idiocy. He knows nothing about biophysically constrained energy-dependent cell type differentiation and consistently displays his ignorance by limiting ability to explain the role that the virus-driven degradation of messenger RNA plays in all pathology.
Psychiatry and Clinical Psychology
Neuroscience
Evolutionary Psychology News
Religion: Science and Psychology
Paleoanthropology Studies
Quantum Physics News
On his FB group for discussion of Sensescence on 6/16/17 I wrote:

All death is caused by trauma or the virus driven degradation of messenger RNA

On 6/17/17 Robert Karl Stonjek wrote (with my emphasis):

Or viruses, or bacteria, or degenerative disease, or genetic disease (there are many), or substance abuse (there are many), or obesity, or….the only one I can’t find in the regular literature is virus driven degradation of messenger RNA.

And then: Robert Karl Stonjek turned off commenting for this post. Can you die from old age?
The pervasive ignorance of those who moderate or censor the comments made by serious scientists via social media has overwhelmed all attempts to present what is known about the virus-driven degradation of messenger RNA, which causes the mutations that have been linked to all pathology.
See for comparison:

Theorists will cause the death of us all. Who will be the next of your loved ones to unnecessarily suffer and prematurely die from the ignorance of theorists?
America’s Dominance In The Scientific World Is shrinking

…while Chinese-born scientists who trained in the United States used to stay here to work, they are now going back to China after their education is over.
 

Denise Chen’s student, Wen Zhou did that. See: Olfaction Warps Visual Time Perception

Had she stayed in the United States, she would have been subjected to pseudoscientific nonsense like this:

Still, even in fruit flies, other sensory input besides pheromones — acoustic, tactile, and visual stimuli — play a role in sexual attraction, and sex specific responses to these stimuli appear to be innate rather than learned by association [36.]. We simply don’t know where the boundary between prespecified attraction and learned association lie in our own species, nor do we have compelling evidence for the primacy of one sense over another.” — Simon LeVay (2011) in his comments on my award-winning model – after it won a second award in 2007. See: The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences

See also:

… chemosignal enthusiasts point to a variety of studies in which sniffing body secretions or substances purified from secretions appears to have some psychological effect…” — Simon LeVay (2016)

He cited the review that won the first award (Kohl et al., 2001). Human pheromones: integrating neuroendocrinology and ethology

It does not surprise me that senior author Wen Zhou has since linked the sense of smell to the time-space continuum. She was the most promising student I ever met, and I was sad to see her return to China after developing her expertise in the context of what she learned from Denise Chen, who learned about olfaction and pheromones from Martha McClintock.
 
Earlier this year, Wen Zhou’s group showed that olfaction alters the perception of the space-time continuum, which also is warped by the distribution of mass and energy. She has helped to show how food energy and the pheromone-controlled physiology of reproduction are linked to energy-dependent subjective time. For comparison, theorectical physicists have failed to explain anything in the context of multisensory inputs. That is why I frequently refer to biologically uninformed theoretical physicists in the same context as the biologically uninformed neo-Darwinian theorists who have failed to link quantized energy to all healthy longevity and failed to link virus-driven energy theft from the degradation of messenger RNA to mutations and all pathology.
 
Simply put, the multisensory inputs link quantized energy as information from the epigenetic landscape to the physical landscape of DNA at subsecond scales via neural energy and RNA-mediated amino acid substitutions.
 

The subsecond scales links femtosecond blasts of UV light to DNA repair, which is required to link quantum physics to quantum souls. That is the topic of my next interview with J.A. Parker, who sent me the questions in advance, so that I could try to keep the jargon to a minimum.

Until I am sucessful, see: Analysis sheds light on how metaphors like ‘sheds light’ evolved

Words that originally had only concrete or external meaning have grown to also have meaning in the realms of the abstract and internal.

Who else besides Schrodinger in “What is Life? (1944) and J.A. Parker of Quantum Souls knew that Dobzhansky’s “light of evolution” would be traced back to “Let there be Light” in Biblical Genesis via what is known about the anti-entropic virucidal energy of sunlight?

Amino acid modification FA_Epigenetics_Table1

Thinking about energy is not radical re-thinking

The brain: a radical rethink is needed to understand it

…Optogenetics, a technique that uses genetic modification of neurons so that their electrical activity can be controlled with light pulses – can help us to explore their specific contribution to brain function.

Optogenetics links the speed of light on contact with water to what is known about all energy-dependent cell type differentiation in all individuals of all living genera. Serious scientists, for example, have linked angstroms to ecosystems in all living genera because they know that brain function is experience-dependent and RNA-mediated.

Even in organisms that have no brain, cell type differentiation occurs in the context of biophysically constrained RNA-mediated protein folding chemistry. All chemistry is energy-dependent quantum chemistry and chemistry links quantum physics from the de novo creation of G protein-coupled receptors to the biological basis for all biodiversity on Earth.
For example, food odors link natural selection for energy-dependent codon optimality to the metabolism of food to pheromones. Biophysically constrained RNA-mediated feedback loops link the metabolism of food from the physiology of reproduction to supercoiled DNA, which protects all organized genomes from virus-driven entropy.
Simply put, quantum physics, quantum chemistry, and energy-dependent quantum biology prevent virus-driven entropy, which links everything known to serious scientists about niche construction to consciousness.
The Penrose Institute was established to link that fact to human consciousness in the context of everything known about cell type differentiation to everyone since the time that Lewis Thomas began making claims olfaction and smell.
A Fear of Pheromones (1971)
On Smell (1980)

The act of smelling is remarkably like the act of thinking itself.

See also:

I should think we might fairly gauge the future of biological science, centuries ahead by estimating the time it will take to reach a complete comprehensive understanding of odor. It may not seem a profound enough problem to dominate all the life sciences, but it contains, piece by piece, all the mysteries.  —  as cited in The Scent of Eros: Mysteries of Odor in Human Sexuality

In 1991, Roger Penrose, summarized what was known about all the mysteries in his forward to the reprint of Schrodinger’s “What is Life?”

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?

For comparison, see this comment by “Sonny” Williams to the International Society for Human Ethology’s yahoo group:

The empirical evidence is overwhelming that the brain is composed of highly specialized regions, whose neuronal members are unique in their cytoarchitecture (down to the molecular level).  Moreover, empirical evidence reveals that genes have directed these neural variations during corticogenesis; that is, most specialized neurons are differentiated early during development and directed to their place in the brain by intrinsic cues, and not activity-dependent cues.  This fact does not preclude later “rewiring,” or changes that are activity-dependent (plasticity), but this range of plasticity is constrained by the genetically derived regions.

Thus, the metaphor that the brain is “modular” is as accurate as any other metaphor.  HOWEVER, “modular” and functionally specialized regions has always included the fact that functional outcomes require a widely distributed network of specialized regions.  That is, modules do not exist in isolation, as islands of specialized function, but rather there existence as a specialized region is predicated upon their iterative communication with many other equally specialized regions.

I cannot recall any comment by Clarence “Sonny” Williams that might ever have made sense to a serious scientist. He is, in my opinion, a biologically uninformed science idiot. I once wondered who could have taught anyone to believe what biologically uninformed people believe in, or why they think what they were taught makes sense to serious scientists.
Then, I tried to discuss what I know about the energy-dependent links from angstroms to ecosystems in all living genera with the senior author of Complex Spike Patterns in Olfactory Bulb Neuronal Networks by Alister U Nicol, Anne Segonds-Pinchon, and Magnus S. Magnussen. It was also published as a book chapter in Discovering Hidden Temporal Patterns in Behavior and Interaction: T-Pattern Detection and Analysis with THEME™
Background:

T-pattern analysis is a procedure developed for detecting non-randomly recurring hierarchical and multiordinal real-time sequential patterns (T-patterns).

CONCLUSIONS:

We conclude that such sequences are an important physiological property of the neural system studied, and suggest that they may form a basis for encoding sensory information.

My summary: They link everything known to serious scientists about energy as information to non-randomly recurring patterns of biophysically constrained RNA-mediated protein folding chemistry and “…characterize these patterns in light of their putative role in processing sensory information.”
They ignore the fact that sunlight is the anti-entropic virucidal source of the energy that prevents genomic entropy via the pheromone-controlled physiology of reproduction in all living genera.
Apparently, like other biologically uninformed theorists, they did not realize what Dobzhansky (1973) did when he linked the light of evolution to all biophysically constrained biodiversity via the nutrient energy-dependent pheromone-controlled physiology of reproduction.
Dobzhansky was one of the first self-declared Creationists to level the playing field with his joke about evolution as if it occurred over billions of years.

I am a creationist and an evolutionist. Evolution is God’s, or Nature’s, method of Creation. Creation is not an event that happened in 4004 B.C.; it is a process that began some 10 billion years ago and is still under way.

Anyone who followed Dobzhansky’s works probably got the joke. He knew there was experimental evidence of God’s Creation. For example, he linked sensory input from what organisms eat and their physiology of reproduction to amino acid substitutions that differentiate all cell types in all living genera. He also knew that theorists had not found experimental evidence of biologically-based cause and effect that supported their claims about millions to billions of years of evolution.
All serious scientists were made aware of Dobzhansky’s rabbinical form of debate in 1964. He began by referring to theorists as bird-watchers and butterfly collectors.  A rather well known form of rabbinical begins with: “Thou fool….”
Dobzhansky was far less damning when he started his address with this:

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.

Dobzhansky probably was referring to himself in the third person when he made the claim about the unidentified Professor of Zoology. Still, to avoid ridicule by biologically uninformed theorists, he tempered the claim.

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.

Clearly, Dobzhansky knew that his claims about amino acid substitutions would be accepted by serious scientists and rejected by pseudoscientists, who have continued to reject the claims of all serious scientists. That’s what pseudoscientists have always done.
See for instance:

3/09/17 Jay Feierman: One can’t have Darwinian evolution by natural selection without either “random” mutations or directional selection. They are both necessary, proximate, contributing causes for genes and the proteins they code for changing in frequency over time in a population and by which the population becomes adaptively configured to the current environment.

3/17/17 Jay R. Feierman [NEW]: We are adaptively configured to the current environment because we are the most successful mammal on earth by any measure. There are 7 billion of us and we inhabit every continent on earth. We accomplished this by Darwinian natural selection adaptively influencing the structural design features we call genes and the proteins they make as well as the extra-genetic structural design features developed through our creativity and ingenuity where we pass the instructions on how to make them across generations by social learning. An iPhone is an example today and an obsidian arrow head was an example in the past.

My comment:  After attempts to discuss energy-dependent biophysically constrained RNA-mediated cause and effect with Magnus S. Magnusson, I was not surprised to find support for some of Feierman’s claims about human adaptations in:

Complex spike patterns in olfactory bulb neuronal networks

Indeed, adaptations occur. But, in the same article, they failed to support Feierman’s claims that the adaptations randomly occur.

Abstract excerpt:

BACKGROUND:

T-pattern analysis is a procedure developed for detecting non-randomly recurring hierarchical and multiordinal real-time sequential patterns (T-patterns).

Conclusion: We conclude that such sequences are an important physiological property of the neural system studied, and suggest that they may form a basis for encoding sensory information.

My conclusion: People like Jay R. Feierman should try to support their assertions about adaptations with experimental evidence of biologically-based cause and effect like the evidence that was cited in the article linked above.

Any claims about how a population becomes adaptively configured to the current environment are not true outside the context of what is known about energy as information and biophysically constrained RNA-mediated protein folding chemistry. If those ridiculous claims were true, the experimental evidence of top-down causation that theorists think support the claims could be used to convince serious scientists that something besides natural selection for energy-dependent codon optimality and the physiology of pheromone-controlled reproduction could replace facts to support theories about mutation-driven evolution.

See also 3/18/17: [MODERATOR NOTE: I’m posting this submission even though it misquotes Feierman, who did not ever say or imply that “adaptations randomly occur.” jrf]
See alson 3/18/17: [MODERATOR NOTE: Adaptations and mutations are not synonyms. An adaptation is a mutation acted upon by natural selection to configure a population to the current environment. It would be an oxymoron to say that “adaptations randomly occur.” By definition, adaptations are mutations that have been acted upon by natural selection by which their frequency is increased in a population over time in a specific environment. jrf]

Amino acid modification FA_Epigenetics_Table1

Theistic evolutionists fight back and lose (3)

See also: Theistic evolutionists fight back and lose
See also: Theistic evolutionists fight back and lose (2)
For succinct representations of the claims made by people who are obviously biologically uninformed, see:

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:

How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy? — Roger Penrose (8 August 1991)

7/26/13
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.
See for comparison:

…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.) — Erwin Schrodinger (1944)

See also: Nutrient-dependent / Pheromone-controlled thermodynamics and thermoregulation (August 3, 2013)
Abstract excerpt:

Resurrected proteins reveal that ancestral uricases have steadily decreased in activity since the last common ancestor of mammals gave rise to descendent primate lineages. We were also able to determine the 3D distribution of amino acid replacements as they accumulated during evolutionary history…

The amino acid substitutions are not accumulated during evolutionary history. The substitutions link nutrient energy-dependent RNA-mediated top down causationk from ecological variation to ecological adaptation via the creation of heat shock proteins. The heat shock proteins “buffer” organized genomes to protect them from virus-driven energy theft and genomic entropy via the physiology of reproduction, which is controlled by pheromones in species from microbes to humans.
See also this discussion attempt: An epigenetics gold rush: new controls for gene expression
Sonny:

The other day, I read a new paper from a sociologist who wrote that epigenetics reveals that the environment is “more important than genes” in constructing the phenotype.  That is an egregiously misleading statement.

James Kohl

m6A is the link from energy-dependent changes in angstroms to ecosystems via learning and memory, which links ecological variation to ecological adaptation in the context of the physiology of pheromone-controlled reproduction.

Experience-Dependent Accumulation of N6-Methyladenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice

Excerpt: “The differential effects of m6A may depend on distinct cis-acting elements that are present on the RNA molecule which may interact with m6A, including micro-RNAs (Alarcón et al., 2015; Chen et al., 2015).” p. 6776

James Kohl: Ultimately, the biggest embarrassment to scientists who have linked energy-dependent changes from angstroms to ecosystems via chirality, autophagy, and supercoiled DNA is that other scientists start with the de novo creation of copy variants.

Sinclair et al., (January 25, 2017) Nucleic and amino acid sequences support structure-based viral classification

They conclude that no discussion of nutrient energy-dependent species-specific pheromone-controlled viral latency should allow others to challenge their claims about the energy-dependent RNA-mediated signals that link virus-driven energy theft to dysfunctional relationships among structure, amino acid sequence, and coding sequences.
 
They prefer that others, like Masatoshi Nei in “Mutation-driven evolution” (2013) place their claims into the context of how discussions about signaling between viruses and the supercoiled DNA of all organized genomes can be placed into the context of possible evolutionary relationships.
 
The evolutionary relationships do not link energy-dependent changes in chirality from autophagy via the innate immune system to endogenous RNA interference and all biodiversity on Earth.
 

Without the energy-dependent changes, the virucidal effects of femtosecond blasts of UV light on energy-dependent codon optimality and DNA repair cannot link the de novo creation of the energy in hydrogen atoms to the biophysically constrained coding sequence in all living genera via the physiology of reproduction.

See for comparison: Nutrient-dependent/pheromone-controlled adaptive evolution: a model and this presentation. Energy as information and constrained endogenous RNA interference

Keeping up-to-date with the primary literature just got a little easier

Today, Springer Nature is pleased to announce the launch of an innovative service which we believe will significantly improve the workflows of researchers by saving time and enabling access to the most relevant content, allowing users to access a new way to keep up to date without visiting any new websites.

Recommended is a service which we believe will help all primary researchers in the natural sciences keep up to date with the literature that really matters to them.  It is a personalised service that suggests relevant papers for users, regardless of publisher, based on what they have previously read across all Springer Nature services.

The “Nature Publications Group” banned me from commenting on their publications several months ago.
Comments on this news are disabled for everyone, which means the Nature Publications Group knows how to hide from any accountability for the lies they have told in the context of gene-centric theories.
See: The RNA code comes into focus Published online
See also:

The presence of an N1 methyl group on adenine bases in DNA and RNA was thought to be a form of damage. Results now show that it also occurs at specific sites in messenger RNAs, where it affects protein expression.

This nutrient energy-dependent methyl mark link RNA methylation from learning and memory to biophysically constrained RNA-directed DNA methylation, which is now represented in the context of endogenous RNA interference (RNAi). The link from the epigenetic landscape to RNAi and to the physical landscape of supercoiled DNA has repeatedly been placed into the context of via RNA-mediated protein folding chemistry and amino acid substitutions that differentiate all cell types in all living genera via the physiology of reproduction.
Typically, the physiology of reproduction prevents the transgenerational epigenetic inheritance of virus-driven pathology in all living genera — until the landscape changes to one in which energy-dependent RNA-mediated DNA repair can no longer keep up with the virus-driven energy theft.

Alternative splicing of pre-mRNA

Energy-dependent de novo creation and neurogenesis (2)

See also: Energy-dependent de novo creation and neurogenesis
12/7/16 Atlas of the RNA universe takes shape
Excerpt:

MicroRNA are very mysterious. They are really relics of the RNA world—pieces of RNA that are highly reactive, very small and which pair and bind other RNA and facilitate catalytic reactions,” Mangone says. “We don’t know much about them—where they come from or how they regulate gene expression, but they are very misregulated in many diseases.

See also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model Published 14 Jun 2013
Excerpt:

…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution. The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, 2012; Duvarci, Nader, & LeDoux, 2008; Griggs et al., 2013; Monahan & Lomvardas, 2012) in adaptive evolution will certainly be discussed in published works that will follow.

My comment: Only if you lived among wolves or among theorists for the past 10 years would you not know that more than 55,000 indexed publications link energy-dependent changes in the microRNA/messenger RNA balance to healthy longevity. For comparison, all serious scientists also know that virus-driven energy theft links viral microRNAs from mutations to all pathology.
You need only search for “RNA mediated” to find information on how cellular and viral microRNAs are linked from energy-dependent changes to RNA-mediated amino acid substitutions and biophysically constrained protein folding chemistry. For example, this is all it takes to recognize the amount of pseudoscience that is packaged in claims that we don’t know much about microRNAs.
See also: Published to Figshare 10 April 2014

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches.

See also: MicroRNAs: the future of genomic science?
Excerpt:

The ubiquity of miRNA occurrence is reflected in the current literature, which reports a wide range of potential biomarker applications for this highly conserved molecule.

My comment: MicroRNAs are biomarkers that clearly link energy-dependent biophysically constrained changes in base pairs from RNA-mediated amino acid substitutions to cell type differentiation in all living genera. The energy-dependent links from the innate immune system to the physiology of reproduction also link all metabolic networks to all genetic networks in species from microbes to humans.
See for comparison: A single splice site mutation in human-specific ARHGAP11B causes basal progenitor amplification

…we hypothesize that the novel, human-specific C-terminal sequence of modern ARHGAP11B has a key role in the mechanism by which this protein promotes BP amplification. In this regard, the present data show that this sequence is due to a single C→G base substitution, which creates a novel splice donor site that results in the replacement of the ancestral C-terminal sequence of the ARHGAP11B GAP domain. The present data also demonstrate that this single C→G base substitution underlies the ARHGAP11B-mediated BP amplification implicated in neocortex expansion.

Reported as: Small Mutation Contributed to Evolution of Bigger Human Brains
Excerpt:

A single base change in a human gene likely played an important role in evolutionary expansion of the human brain, researchers say.

My comment: They claim that a single cytosine to guanine substitution created a novel splice site. They failed to mention that base pair (BP) amplification is nutrient energy-dependent. They also failed to mention that the de novo creation of a novel splice donor site must be linked from the energy-dependent fixation of an RNA-mediated amino acid substitution to the physical landscape of supercoiled DNA via the physiology of reproduction.

Svante Paabo is one of the co-authors who reported this:

Hence, it is not the ARHGAP11 partial gene duplication event ~5 million years ago, as such, that impacted human neocortex evolution. Presumably, ARHGAP11A and ancestral ARHGAP11B coexisted as functionally similar proteins for some time after the gene duplication event. The ability of ARHGAP11B to amplify BPs likely arose more recently from a change that is tiny on a genomic scale but substantial in its functional and evolutionary consequences.

My comment: No experimental evidence of biologically-based cause and effect suggests that any partial gene duplication event ~5 million years ago could have linked a mutation and the altered de novo creation of genes that Svante Paabo (and co-authors) placed into the context  of biophysically constrained biodiversity in:

Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees

My comment: Natural selection for energy-dependent codon optimality is the only way to link the de novo creation of genes from autophagy to RNA-mediated amino acid substitutions and nutrient-dependent polycombic ecological adaptation.
See: From Fertilization to Adult Sexual Behavior

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). 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 also: PTBP1 and PTBP2 Serve Both Specific and Redundant Functions in Neuronal Pre-mRNA Splicing
Excerpt:

…the two paralogs displayed similar RNA binding across the transcriptome, indicating that their differential targeting does not derive from their RNA interactions, but from possible different cofactor interactions.

My comment: The cofactors are nutrient energy-dependent microRNAs, which are linked to healthy longevity and all biodiversity and viral microRNAs, which are linked from mutations to all pathology.
See also: Viral and cellular messenger RNA targets of viral microRNAs

…viral miRNAs may be particularly important for regulating the transition from latent to lytic replication and for attenuating potentially inhibitory host antiviral immune responses.

See also: Nothing in Biology Makes Any Sense Except in the Light of Evolution
Excerpt:

…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).”

See also: Light- and Carbon-Signaling Pathways. Modeling Circuits of Interactions

…carbon either attenuated or potentiated light repression of ASN1 in light-grown plants. These studies indicate the interaction of carbon with blue, red, and far-red-light signaling and set the stage for further investigation into modeling this complex web of interacting pathways using systems biology approaches.

My comment: When did theorists decide to take the light as information and energy out of systems biology and ecological adaptations? Who decided to replace the anti-entropic virucidal energy of light with mutations and evolution?