God's shrinking role in salvation (2)

Conclusion: There is no such thing as a blind dance of atoms. Quantized energy-dependent changes link angstroms to ecosystems in all living genera via the physiology of reproduction. Serious scientists do not link “high-level cause and purposes” to anything that does not link what organisms eat from food energy to the physiology of reproduction. Only pseudoscientists claim that ideas about “emergence” are “…a remarkable synthesis across fields and levels.”
See: God’s shrinking role in salvation

These 6 Common Vegetables Are Actually All The Same Plant Species
The morphological traits are quantized energy-dependent, They link the de novo creation of plant microRNAs from the anti-entropic virucidal energy of sunlight to the physiology of reproduction in all living genera via the energy-dependent creation of microRNAs in animals.
See: 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 to provide a more ideal environment for these pathogens to thrive. Here, we explore those roles to obtain a better grasp of just how complicated disease truly is.

Disease is much more complicated when it cannot be linked from top-down causation via physics, chemistry, and molecular biology. See for comparison; ‘Liquid Light’ Can Bend Around Objects in a Frictionless Flow
Thanks to Fiona Myrglwitz for calling attention to this claim that they can:

…conceive and design future photonic superfluid-based devices where losses are completely suppressed.

That suggests they may link the metabolism of bacteria from the creation of uranium isotopes to the errors made in mathematical models of evolved traits. The errors in mathematical models fail to link quantized energy-dependent changes in the microRNA/messenger RNA balance to the biophysically constrained by the physiology of reproduction.The errors are magnified by the fact that they fail to link incompletely suppressed energy losses to all pathology via the virus-driven degradation of messenger RNA.

For comparison, the physiology of reproduction links the solar analemma to the biophysically constrained energy in uranium, which is the reason that radiation therapy is used to treat cancer. Everything known about the link from sunlight to radiation therapy can be placed into context via use of the Mobius strip.
It is an example of how nutrient energy-dependent pheromone-controlled choices made by all living genera must link feedback loops to the biophysically constrained virucidal energy of sunlight. Any loss of energy can potentially be linked to the proliferation of viruses via a slight drop in the potential of hydrogen (pH).

That fact makes it more be obvious that God’s shrinking role in salvation can be viewed in the context of medical practices that appear to make physicians and/or other medical professionals your savior(s). They will warn you to avoid too much sun exposure and treat your cancer with radiation because you did not get enough sun exposure to protect you via the increased production of Vitamin D.
They will tell you to use a chemical “sun-screen” and treat your cancer with chemotherapy that was caused by the chemical imbalance your body could no longer cope with.
See also: Electrolytes induce long-range orientational order and free energy changes in the H-bond network of bulk water
This was reported as: A single ion impacts a million water molecules
So far as I know there has been no discussion of the link from free energy changes in the H-bond network to the hydrophobicity of supercoiled DNA, which links quantum physics to the protection of all organized genomes from the virus-driven degradation of messenger RNA and genomic entropy.
Could the lack of discussion be attributed to the claim that no one understands quantum mechanics in an age where the speed of light on contact with water has been linked to all biodiversity via energy-dependent changes in angstroms to ecosystems in all living genera?
From last year: How Can Physics Underlie the Mind? Top-Down Causation in the Human Context

My review on Amazon (6/12/16)

Others linked the sun’s anti-entropic virucidal energy from energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.

Ellis comments on at least one of Schrodinger’s claims from “What is Life?” but he largely ignores the energy-dependent links from ecological variation to ecological adaptation that also were reported in two recent publications. See: “Structural diversity of supercoiled DNA” and “Epigenetics and Genetics of Viral Latency.”

Ellis cannot be held accountable for not knowing the most recent work (May 11, 2016) reported that “…viral latency is responsible for life-long pathogenesis and mortality risk…”

However, it seems inappropriate for anyone whose opinions are held in high regard to ignore everything else that is known about energy-dependent RNA methylation and the biophysically constrained morphological and behavioral diversity of all living genera. Experimental evidence has established facts that are being used to link the Precision Medicine Initiative to the National Microbiome Initiative via attempts to crack the olfactory code.

When researchers report the direct link from energy-dependent RNA methylation to differences in behavior, this book will be compared to Masatoshi Nei’s “Mutation-driven evolution.” The biggest difference between the two seems to be that Ellis tries to link emergence to evolution via Darwin’s “conditions of life.”

But he now bears the burden of the report in “Science” of nutrient energy-dependent pheromone-controlled weekend evolution of the bacterial flagellum: “Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system.”

The “resurrection” is obviously energy-dependent and it also links the innate immune system to biophysically constrained biologically-based cause and effect in species from microbes to humans via RNA-mediated amino acid substitutions. Resurrecting Darwin’s “conditions of life” after they were ignored by neo-Darwinists for many decades should not be attempted by physicists, cosmologists, or biologically uninformed theorists from any other discipline without first learning more about what is known about the RNA-mediated links from physics and chemistry to molecular epigenetics.

See for comparison, this review by

An admirable, systematic approach to the issue of emergence from physics to sociology, of great originality, broad scope, and deep understanding. George Ellis argues with admirable clarity of thought that much of the world we live in is governed not by the blind dance of atoms, but by high-level causes and purposes. This is a much needed book and a remarkable synthesis across fields and levels. I know of no other book where the evidence for emergence is presented so thoroughly and with as much insight.

There is no such thing as a blind dance of atoms. Quantized energy-dependent changes link angstroms to ecosystems in all living genera via the physiology of reproduction. Serious scientists do not link “high-level cause and purposes” to anything that does not link what organisms eat from food energy to the physiology of reproduction. Only pseudoscientists claim that ideas about “emergence” are “…a remarkable synthesis across fields and levels.”

See: God’s shrinking role in salvation (3)
Cytosis

From E. coli to monkeys and mankind: Theories vs models (5)

From E. coli to monkeys and mankind: Theories vs models (4)
CRISPR Is Taking Over Science, Breaks Out Of Labs And Invades Schools (5/29/17)

…used mathematical models to reveal that even in a uniform environment, metabolic competition generally leads to the steady coexistence of distinct microbes, collectively called a “consortium”. In a consortium, distinct microbes organize themselves to create a community-level metabolism that best exploits the nutrients present. The models showed that while growing, a consortium depletes the available pool of nutrients to such low levels that only members of the consortium can survive. The findings suggest that the benefit of metabolic diversity stems from the ability of a consortium to automatically deplete nutrients to levels at which no other microbes can invade.

Taillefumier et al. propose that consortia that arise naturally under conditions where there is a steady supply of nutrients produce the maximum mass of microbes. Future experiments that analyze the impact of fluctuating nutrient supply may help us to understand the benefit of metabolic diversity in real-world microbial communities.

Microbes do not organize themselves into consortia via the automatic depletion of nutrients. Natural selection for food energy-dependent codon optimality links quantum physics to the pheromone-controlled physiology of biophysically constrained viral latency. That is how metabolic networks must link ecological variation to ecological adaptation in all living genera.

Pseudoscientists who know nothing about energy-dependent quorum sensing and RNA-mediated cell type differentiation in microbial consoritia have wasted billions of dollars and nearly all the time that humans have existed on Earth. Now they tout automagically evolved consortia in attempts to subvert what is known about the nutrient energy-dependent protection from virus-driven energy theft, which is built into the molecular essence of all cell types. The pseudoscientists have led us to the brink of a viral apocalypse.

See: CRISPR gene editing can cause hundreds of unintended mutations (5/29/17)

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

Division of labor

Competition causes microbes to organize themselves into communities that make the most of the available nutrients.

Where do viruses come from? (2004)

…when virus-infected bacterial cells burst, their energy-rich cell contents spill into the water for other bacteria to scavenge. ‘Viruses tend to keep nutrients away from the big stuff and keep them going around in the little stuff,’ says Fuhrman. If so, viruses have shaped the entire structure of the ecosystem.”9

Virus-driven energy theft causes the degradation of messenger RNA that links mutations to all pathology.

Virus-mediated archaeal hecatomb in the deep seafloor (2016)

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.

People who believe in mutation-driven evolution are not likely to link virus-driven energy theft in archaea to the morphological and behavioral phenotype of bacteria or from the nutrient-dependent pheromone-controlled physiology of reproduction in bacteria to Alzheimer’s disease. People who believe in mutation-driven evolution may not be capable of understanding how the conserved molecular mechanisms detailed in the published works of serious scientists must be linked from viruses to the the degradation of messenger RNA that links the mutation-driven evolution of pathology to the increase in Alzheimer’s Deaths.

U.S. Alzheimer’s Deaths Jump 54 Percent

In the video that accompanies this report, the image from a brain scan is paired with the mention of biomarkers. microRNAs are the biomarkers. The changes in energy-dependent microRNA biosynthesis clearly predict the onset and severity of all pathology.

That’s why most people will not seek the most effective and least invasive treatment for Alzheimer’s. They won’t link the loss of olfactory acuity and specificity to the virus-driven degradation of messenger RNA and neurodegenerative diseases, because their physicians don’t understand enough about the creation of G protein-coupled receptors to link chemotaxis and phototaxis to all biodiversity via the physiology of reproduction.

See for comparison: microRNA Alzheimer

See also: Search Results for “alzheimer’s”

Reports about an article that I have not yet seen published in “Nature Methods” attest to facts about cell type differentiation that have been placed into this context:

Crack in CRISPR Façade after Unanticipated In Vivo Mutations Arise

“Researchers… may be missing potentially important mutations,” Dr. Tsang remarked. “Even a single nucleotide change can have a huge impact.”

That fact is not just a “Crack in the CRISPR Facade.” It dismisses all claims about mutation-driven evolution. Those ridiculous claims have been replaced by what is known to serious scientists about how viral latency must be biophysically constrained. It must be constrained by a light-activated endogenous substrate in all cell types of all living genera. The light comes from the sun. For example, the anti-entropic energy of ultraviolet light kills viruses.

SARCASM ALERT: Ask your doctor if sunlight could save your life.

Until the publication of “Unexpected mutations after CRISPR-Cas9 editing in vivo” is available to all serious scientists, watch how the prescient claims about food energy that have been made by people like Richard Feynman have forced theorists to do what they have always done. Expect that some of the censorship will end when the news about the unexpected mutations is linked to what all serious scientists have expected since the time that Thomas Hunt Morgan linked energy-dependent chromosomal inheritance to all biodiversity on Earth and virus-driven energy theft was linked to antibiotic resistance.

Kalevi Kull: Censorship & Royal Society Evo Event

Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge. —  Kalevi Kull

See: Nature Methods May 2017, Volume 14 No 5 pp457-540

For example:

Systems biology guided by XCMS Online metabolomics pp461 – 462

See also: Research Highlights

Defining developmental grammar p465

An iterative clustering approach finds the few genes that mark discrete cell states and their transitions during early mouse development.

It takes two to make an embryo pp466 – 467

In vitro culture of mouse embryonic and extra-embryonic stem cells recapitulates embryogenesis.

A light switch for kinases pp466 – 467

A photodissociable dimer of the Dronpa fluorescent protein can cage kinases, making these important signal transducers controllable by light.

A proteome-wide view of thermal stability p468

Proteome thermal stability is probed using limited proteolysis and mass spectrometry.

Dynamic measurement of membrane charges p471

A FRET sensor enables quantitative characterization of electrostatic potential of membranes in living cells.


See for comparison: 2012 Genome evolution: Unexpected relationship between mutation rate and genome complexity

Contrary to expectation, species that have experienced recently accelerated mutation rates have the largest genomes…

Biophysically constrained food energy-dependent pheromone-controlled viral latency protects the organized genomes of all living genera from the degradation of messenger RNA, which links virus-driven energy theft from mutations to all pathology regardless of the size of the organized genome. The measurement of membrane charges in the context of cryo-EM makes it possible to link virus-driven energy theft in bacteria to the degradation of messenger RNA in archaea and the degradation of messenger RNA in archaea to L-forms, which represent the virus-driven destruction of all created cell types. So far as is currently known, only the anti-entropic virucidal energy of sunlight can prevent the virus-driven death of all life on Earth.

L-form bacteria

Bacterial morphology is determined by the cell wall. Since the L-form has no cell wall, its morphology is different from that of the strain of bacteria from which it is derived.

The cell wall is important for cell division, which, in most bacteria, occurs by binary fission. This process usually requires a cell wall and components of the bacterial cytoskeleton such as FtsZ. The ability of L-form bacteria to grow and divide in the absence of both of these structures is highly unusual, and may represent a form of cell division that was important in early forms of life.[1]

The failure to recognize the fact that virus-driven degradation of the cell wall is an example of how cell type destruction occurs in all cells that contain a light-activated endogenous substrate, is also an example of pervasive ignorance among all theorists and other pseudoscientists.

See also: Cytosis:

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

Biology to a Physicist

Energy as information and constrained endogenous RNA interference (4)

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

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

Precision Medicine virtual conference, Feburary 22-23, 2017

Title: Energy as information and constrained endogenous RNA interference

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

 

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

fruit-dove

The death of human ethology via ecology

Nutrient-dependent/pheromone-controlled adaptive evolution: a model Open access publication on June 14, 2013
Mutation-driven evolution also published on June 14, 2013
Variable habitat conditions drive species covariation in the human microbiota http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005435 Open access publication on April 27, 2017
Conclusion:

…we found that genetically related species respond to fluctuating habitat conditions in the same way, implying that they occupy similar ecological niches. Thus, current taxonomic groupings of bacteria are largely sufficient for explaining cross-sectional correlations in relative species abundances over the healthy human population. This result is not at odds with high rates of HGT; it simply implies ecologically derived constraints on evolution.

Reported on April 27, 2017 as: Resource availability drives person-to-person variations in microbes living in the body

Ecological model reveals relationships between resource availability and microbe species abundance

Historical perspective: “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.) (pp. 73 and 74)

From the forward to the reprint edition of “What is Life?” (1944)

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 August 8, 1991

All current extant literature attests only to the obvious role of ecological variation and food energy as information, which enables the ecological adaptations manifested in species diversity via the physiology of biophysically constrained pheromone-controlled reproduction. Nutrient energy-dependent changes in the microRNA/messenger RNA balance protect supercoiled DNA from virus-driven energy theft and the degradation of messenger RNA, which links mutations to all pathology. All serious scientists are now aware of these facts, but pseudoscientists are not convinced.
See for example:
7/24/13 James V. Kohl: “Evolution by natural selection cannot be the outcome if something is not first selected. Selection is always for nutrients. It is as simple as that.
Despite the facts expressed by Schrodinger and emphasized by Penrose as well as my claim (above), neo-Darwinian theorists still seem willing to accept the claims of biologically uninformed science idiots, such as this one:
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 for comparison:
Foote et al (2013)“Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4].
Chung et al (2014) “…ecological divergence and mate choice may produce reproductive isolation and speciation….
Plucain  et al (2014) “Ecological opportunities promote population divergence into coexisting lineages.
The pseudoscientific nonsense touted on this Yahoo group has not ended.

Human ethology is the study of the biology of human behavior, including the behavior’s phylogeny (evolutionary history), ontogeny (development), proximate causes, and adaptiveness (survival value). Postings relevant to these topics will be accepted.

Sonny Williams wrote:
Re: For the sake of all humanity, please ignore the shrill, uninformed cries of creationists and other types of supernaturalists.  Instead, talk to a regulatory geneticist.
I responded with a comment about the game: Cytosis: A Cell Biology Board Game

See: msg 86257

James Gray: Jay, I hope you can say that you missed the threat in this quote from Kohl. “What game will you be playing until your career as a researcher or philosopher or your life as as biologically uninformed atheist ends at the hands of those who are biologically informed young earth creationists?”

I know only two people who would take my comment about the game Cytosis, and perceive it as a threat that they would be killed by young earth creationists. James Gray is one; here is the other one:

Sonny Williams: Thanks for catching this, James…and warning me.  I consider Kohl a personal threat and think it is time he be banned from the group.

So far as I know, I am the only participant in the group that has published an award-winning review of human ethology.
See: Human pheromones: integrating neuroendocrinology and ethology (2001)
See also: msg 86274

Excerpt: “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.”

It will be interesting to see whether or not Sonny Williams and/or James Gray will claim that I threatened they would be killed by terrorists.
In any case, the regulatory geneticist Giacomo Cavalli and others have finally brought forth their claims about Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila
The claims were reported as: We are more than our DNA: Discovering a new mechanism of epigenetic inheritance

Cavalli and his team at the Institute of Human Genetics (University of Montpellier / CNRS) are the first to show that regulation of gene position can lead to transgenerational inheritance.

See for comparison: From Fertilization to Adult Sexual Behavior (1996)

Molecular distance. As measured in centimorgans, human and other species’ male and female chromosomes, including the autosomes, tend to have different lengths in various segments. To some extent, this suggests a correlation with physical distance but instead the differing lengths are based upon rates of recombination; although sections of most female chromosomes are longer than their homologous counterparts in male chromosomes, in some segments of various chromosomes opposite length-difference occurs, with males having larger centimorgan values than females in those regions (Lawrence, Collins, Keats, Hulten, and Morton, 1993; Murray, Buetow, Weber, Ludwigsen, Scherpbier-Heddema, Manion, Quillen, Sheffield, Sunden, and Duyk, 1994; Straub, Speer, Luo, Rojas, Overhauser, Ott, and Gilliam, 1993). While ramifications of these centimorgan sexual dimorphisms are not yet clearly established, in recent years cis- and trans-acting factors contributing to these recombination length differences have been reported for a specific part of the murine major histocompatibility complex (MHC) (Shiroishi, Sagai, Hanzawa, Gotoh, and Moriwaki, 1991).

See also:

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.

Anyone who claims they are the first to link the nutrient energy-dependent stability of polycombiic ecological adaptation via the transgenerational inheritance of chromatin states should be viewed with suspicion. Chromosomal inheritance was first linked to the transgenerational epigenetic inheritance of chromatin states by Thomas Hunt Morgan, who won the 1933 Nobel Prize in Physiology or Medicine for his works.
With all due respect Giacomo Cavalli may have come in third with publication in 2007 of  Combinatorial epigenetics, “junk DNA”, and the evolution of complex organisms.

The imposition at a distance of new chromatin structures with regulatory impact can occur in cis as well as in trans, and is examined as intrachromosomally spreading teleregulation and interchromosomal “gene kissing”. The chances for two or more particular epigenetically determined regulatory trends to occur together in a cell are increased thanks to the proposed low specificity requirements for most of the pertinent sequence changes in intergenic and intronic DNA or in the distribution of middle repetitive sequences that have teleregulatory impact. Inheritable epigenetic changes (“epimutations”) with effects at a distance would then perdure over the number of generations required for “assimilation” of the several regulatory novelties through the occurrence and selection, gene by gene, of specific classical mutations. These mutations would have effects similar to the epigenetic effects, yet would provide stability and penetrance. The described epigenetic/genetic partnership may well at times have opened the way toward certain complex new functions. Thus, the presence of “junk DNA”, through co-determining the (higher or lower) order and the variants of chromatin structure with regulatory effects at a distance, might make an important contribution to the evolution of complex organisms.

I mayt never know if Giacomo Cavalli come in third with representations of intrachromosomally spreading teleregulation and interchromosomal “gene kissing” It is hard to evaluate his works, since he placed his finding into the context of epimutations and evolution via “junk DNA.”
For comparison, young earth creationists have been addressing the nonsense about “junk DNA” during the past two months.
See for instance: Major Evolutionary Blunders: Evolutionists Strike Out with Imaginary Junk DNA, Part 1

Scientists whose analysis is constrained to fit evolutionary theory will not see a brain, a digestive system, and other complicated biological phenomena as designed things but rather as conglomerations of parts cobbled together by nature. “We’re all here because of mutations,” claims molecular neuroscience professor Jernej Ule, who adds:

But most random mutations actually disrupt the functions of our genes and so are a common source of genetic diseases….How does nature resolve this conflict?…We’ve known for decades that evolution needs to tinker with genetic elements so they can accumulate mutations while minimising [sic] disruption to the fitness of a species.4

See also: Major Evolutionary Blunders: Evolutionists Strike Out with Imaginary Junk DNA, Part 2

I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century….The failure to recognize the full implications of this [important parallel information derived from non-coding DNA] may well go down as one of the biggest mistakes in the history of molecular biology

For more information on parallel information, which appears to be linked to non-coding DNA see: A universal trend of amino acid gain and loss in protein evolution

We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms.

See also: The death of human ethology via ecology (2)

rp_PO9583119-frontl.png

Epigenetically-effected nucleosome repositioning sheds Dobzhansky's light on evolution

Crystal structure of the overlapping dinucleosome composed of hexasome and octasome

My summary: Nucleosomes are dynamic entities that are repositioned by energy-dependent links from sunlight to ATP and RNA biosynthesis that act on DNA during the chromatin remodeling, which is biophysically constrained by the pheromone-controlled physiology of reproduction during the transgenerational epigenetic inheritance of all morphological and behavioral phentoypes. processes.

Reported as: Unveiling how nucleosome repositioning occurs to shed light on genetic diseases

…an incomplete formation of overlapping dinucleosome may trigger abnormalities in the genetic switch, turning normal cells into tumor cells. Accordingly, understanding the atomic structure of the overlapping dinucleosome may provide valuable information for understanding how the abnormal dynamics of chromatin are related to cancer…

The atomic structure of the dinucleosome is energy-dependent. The atomic structure links the sun’s anti-entropic virucidal energy to all healthy longevity via endogenous RNA interference (RNAi). RNAi is is the nutrient energy-dependent link from atoms to ecosystems via what is known to all serious scientists about supercoiled DNA. Virus-driven energy theft causes the incomplete formation of the overlapping dinucleosome and all pathology in all living genera.
See for comparison my invited review of nutritional epigenetics: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (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. 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.

See also: Structural diversity of supercoiled DNA and the parody from the Zechiedrich lab.

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.

Combating Evolution to Fight Disease

It’s time for biophysicists to tell theorists and pathologists how to differentiate between theories about the genesis of different cell types and the biological facts about the nutrient-dependent pheromone-controlled ecological adaptations that enable the genesis of different cell types in individuals of different species. Simply put, it’s time to stop trying to explain ecological adaptations in the context of mutations and evolution.

Feedback loops link odor and pheromone signaling with reproduction
Roles of differential expression of microRNA-21-3p and microRNA-433 in FSH regulation in rat anterior pituitary cells

Taken together, our results show that both miR-21-3p and miR-433 down-regulate FSHb expression and cause FSH secretion decreased. These findings provide insights into the effects of the regulatory mechanisms of miRNAs on the reproductive functions of the pituitary.

FSH secretion links the nutrient energy-dependent pheromone-controlled epigenetic effects on endogenous RNA interference to healthy longevity and biodiversity in all vertebrates via the substitution of achiral glycine in position 6 of the gonadotropin releasing hormone decapeptide.
See also: Gonadotropin releasing hormone and human sexual behavior (1991)

Targeting Gut Bacteria May Be The Key To Preventing Alzheimer’s   (2/21/17)

…mice with Alzheimer’s have a different gut bacterial profile than those that do not have the disease.


 

Cytosis: Biology Content

 

Help Me Write Some Biology Content

Project Update #5: Cytosis: A Cell Biology Board Game by John Coveyou (Genius Games)

Many of you have mentioned that you’d like to have an explanation of the biology behind Cytosis available… and I think that is an AWESOME plan. Every time I’ve taught the game to non-science players in the past, they say gameplay made even more sense (and was so much more enjoyable) when I explained the science as well. This way they knew WHY they were doing what they were doing!

If you’ve got a strong background in biology, love explaining complexities in a way that someone unfamiliar with biology could understand, and would be interested in volunteering to help me write a page or two of science explanatory content for the rulebook, please shoot me an email… with the subject line “Cytosis Biology Explanations – [Your Name]” and we can start discussing!

I wrote: Kohl’s Laws of Biology may help. See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

1) Life is nutrient-dependent. See for review [2, 31]. The physiology of reproduction is pheromone-controlled. See for review [30].

In the context of the game “Cytosis,” Kohl’s Laws link the epigenetic effects of food odors and pheromones to changes in the mitochondria of all cell types. The energy-dependent changes in the mitochondria are linked to healthy longevity.
If the epigenetic effects of food odors and pheromones did not clearly link cytosis to healthy longevity, we would be left with only the link from virus-driven energy theft to all pathology. The explanation for all pathology involves more complexity than most people are willing to examine even when it is placed into the context of a book for a general, albeit educated, target audience.
See: The Scent of Eros: Mysteries of Odor in Human Sexuality

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

Details for other serious scientists:

The synthesis of RNA is nutrient energy-dependent. From 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.

The anti-entropic virucidal energy of sunlight has since been linked to all biophysically constrained human cell type differentiation via representations in Feedback loops link odor and pheromone signaling with reproduction

The feedback loops link Dobzhansky’s claims about amino acid substitutions and RNA-mediated cell type differentiation from natural selection for energy-dependent codon optimality to the pheromone-controlled biodiversity of all living genera.

See: Combating Evolution to Fight Disease

…transient errors in mRNA synthesis can also cause heritable non-DNA-based phenotypic change. This is observed when low-abundance transcriptional regulators are affected by transcription errors. This disruption can cause a cell to alter its gene expression, resulting in a phenotype that may be heritable (2).

See also: Carl Woese, Evolution’s Golden Revolutionary

…there is probably no other scientist but Carl Woese who could write about having “no use for natural selection” and have Nature magazine respond with a Nobel endorsement. It is Carl Woese who first identified the Archaea and introduced us to horizontal gene transfer.

Virus-driven energy theft causes the degradation of messenger RNA, which links negative supercoiling of DNA in bacteria to the creation of archaea and links the conserved molecular mechanisms from archaea to the evolution of all pathology. For comparison, horizontal gene transfer links the nutrient energy-dependent de novo creation of genes from the pheromone-controlled fixation of RNA-mediated amino acid substitutions to supercoiled DNA, which prevents virus-driven energy theft from causing more degradation of messenger RNA.

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

This invited review of nutritional epigenetics includes a model that links nutrient energy-dependent changes from atoms to ecosystems. Most theorists have been caught with their pants down because they are still making claims about mutations and evolution. How can serious scientists compete with pseudoscientists who make claims that link mutations to millions of year of evolution?  Most serious scientists know how to link quantized energy from chemistry to biologically-based cause and effect. Most biologically uninformed people accept the claims of pseudoscientists, atheists, and other theorists.

Some Harvard researchers are still trying to hide facts that link research on the synthesis of mRNA to all biophysically constrained biodiversity on Earth via hydrogen-atom transfer in DNA base pairs in solution and RNA-mediated amino acid substitutions in supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy. ATP-dependent cell type differentiation is placed into the context of conserved NAD+ and protein-protein interactions.

See:  A conserved NAD+ binding pocket that regulates protein-protein interactions during aging

See for contrast: Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention

It is now widely accepted that cancer is the result of the gradual accumulation of driver gene mutations that successively increase cell proliferation (1–3).

Johns Hopkins researchers framed everything known to serious scientists about cell type differentiation into the contest of cancer as ‘bad luck” as if cytosis was not energy-dependent and healthy longevity arose in the context of mutation-driven evolution — if species were lucky enough to evolve into other species.
No serious scientist has ever accepted that ridiculous claim.

See for comparison: Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity

…we characterize two distinct p120-associated complexes with antagonistic functions and we describe a microRNA (miRNA)-mediated mechanism through which the ZA suppresses transformed cell growth.

Backers and players of the game “Cytosis” will learn how the energy-dependent function of mitochondria must be linked to every aspect of healthy longevity or be linked from virus-driven energy theft to all pathology. They will be prepared to learn from the next game: “Photosynthesis,” which will link the sun’s anti-entropic virucidal energy to all biophysically constrained biodiversity via what is known to all serious scientists. They will not need to learn anything more than is required for them to reject the pseudoscientific nonsense of neo-Darwinian theories.

See what’s happened after 20 days of comments to this society. 

The information has been shared more than 450 times. The number of biologically informed students will force the biologically uninformed professors to stop playing the evolution game until they can begin supporting their ridiculous claims with facts. The facts must link ecological variation to ecological adaptations via what is known to serious scientists about hydrogen-atom transfer in DNA base pairs in solution.

Clearly, the facts tell us that all individuals of all species that live on Earth must eat and reproduce or they become extinct. None mutate and evolve into other species.

Thus, we regard as rather regrettable the conventional concatenation of Darwin’s name with evolution, because there are other modalities that must be entertained and which we regard as mandatory during the course of evolutionary time.

— Carl Woese and physicist Nigel Goldenfeld

I encourage others to support the development of games that teach what pseudoscientists do not want an interested target audience to learn. With enough support for an easy way to learn about energy-dependent cytosis compared to virus-driven pathology, the facts about RNA-mediated cell type differentiation will become clearer.

See also our section on molecular epigenetics in this review from 1996: From fertilization to adult sexual behavior

Every aspect of cytosis is food energy-dependent and RNA-mediated. Virus-driven energy theft cause all pathology. That fact makes sense in the context of all claims made by serious scientists. See for example:

 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.) (pp. 73 and 74)

— with forward by Roger Penrose who co-authored with George F.R. Ellis and Stephen Hawking

“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)

See also:

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

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

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


    17 Apr 2014 at 03:07am

George F R Ellis This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics.
This is explored here: http://rsfs.royalsocietypublishing.org/content/2/1.toc 

See also:

…every angstrom is dynamic from the 5 prime to the three…

See also: Genetic 3’UTR variation is associated with human pigmentation characteristics and sensitivity to sunlight

Sunlight exposure induces signalling pathways leading to the activation of melanin synthesis and tanning response. MicroRNAs (miRNAs) can regulate the expression of genes involved in pigmentation pathways by binding to the complementary sequence in their 3′-untrastaled regions (3’UTRs).

Top-down causation starts from the creation of the sun’s anti-entropic virucidal energy. Hydrogen atom transfer in DNA base pairs in solution links energy-dependent changes in the microRNA/messenger RNA balance from microRNA flanking sequences to RNA-mediated amino acid substitutions that alter the stability of supercoiled DNA in the context of the physiology of reproduction.

One base pair change and a single amino acid substitution makes the difference between healthy longevity and pathology during life history transitions. See for example: Epigenetic Regulation of BDNF Gene during Development and Diseases
See also: Δ133p53 Functions to Maintain Redox Homeostasis in Response to Low ROS Stresses
https://www.omicsgroup.org/articles-images/single-cell-signaling-response-oxidative-stresses-5-154-g001.png
See also: Keep science a priority. Stand with ASCB at the March for Science rally April 22.
Light-induced-conformer-intercoversion-of-hydrogen-bond

Light-activated feedback loops vs self-organization of ecosystems

John Lieff has been trying to update his ridiculous misrepresentations of biologically-based cause and effect to match the accurate representations we made in a section on molecular epigenetics in our 1996 Hormones and Behavior review.

From Fertilization to Adult Sexual Behavior

Nothing can stop him, but this will provide the next source for material that he must borrow as if he learned about it somewhere else.

Apoptosis analysis guide | Free ebook download

Virus-driven energy theft causes apoptosis, which releases cell contents for recycling in the context of autophagy, which helps to ensure food energy-dependent pheromone-controlled RNA-mediated DNA repair in species from microbes to humans.

Gene bivalency at Polycomb domains regulates cranial neural crest positional identity

Journal article abstract excerpt (figure: Epigenetic regulation of cranial NC cell identity.)

A Polycomb-dependent poised chromatin organization underlies the positional plasticity of cranial premigratory NC cell progenitors. This chromatin prepattern is maintained through migration. In response to local cues encountered by the NC cells during or after their migration, the regulatory elements (E) and promoters (P) of differentially expressed genes switch from a poised to an active chromatin state, establishing transcriptional identities specific to subpopulations of NC cells.

The use of the term “chromatin prepattern” must be linked from endogenous RNA interference to all all biodiversity via transgenerational epigenetic inheritance. Watch closely as all pseudoscientists, atheists and other biologically uninformed theorists finally realize there is no such thing as mutation-driven evolution except in the context of virus-driven energy theft, apoptosis, and the evolution of pathology. Virus-driven energy theft causes degradation of messenger RNA in the absence of nutrient energy-dependent pheromone-controlled RNA-mediated amino acid substitutions and DNA repair.

MicroRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos

Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We discovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability.

Reported as: The role of tiny RNA in genetic diversity March 28, 2017

All species, from zebrafish to humans, possess a genetically diverse collection of traits that allow them to adapt to changing environments. Yet scientists do not fully understand how organisms reach a state of optimal diversity—just enough variability to respond to environmental risks but not too much to function properly.

Natural selection for energy-dependent codon optimality is the link to optimal diversity. Conserved molecular mechanisms of nutrient-dependent pheromone-controlled biodiversity have been linked from quorum sensing in bacteria to all cell type differentiation in all individuals of all species.
See: Feedback loops link odor and pheromone signaling with reproduction

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

Escherichia coli and the peppered moth typically are typically used by biologically uninformed theorists as examples of mutation-driven evolution.
See: The Man Who Bottled Evolution
See the refutation: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

…this system enables us to understand the adaptive process in detail at the genetic and phenotypic level [over the weekend]. We identified a tractable model for gene network evolution and observed, in real time, the rewiring of gene networks to enable the incorporation of a modified component (NtrC′) creating a novel regulatory function by a highly repeatable two-step evolutionary pathway with the same point mutations often recurring in independent lineages.

They failed to differentiate between the term mutation and what occurs in the context of energy-dependent pheromone-controlled changes in the microRNA/messenger RNA balance via fixation of RNA-mediated amino acid substitutions in supercoiled DNA.
See: 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: Helicoverpa armigera images

Identification and Evaluation of Suitable Reference Genes for Normalization of MicroRNA Expression in Helicoverpa armigera (Lepidoptera: Noctuidae) Using Quantitative Real-Time PCR

…10 candidate genes of H. armigera were selected and analyzed for their expression stability under different biotic and abiotic conditions….  miR-9 and U6 snRNA for developmental stages, miR-100 and U6 snRNA for larval tissues, miR-100 and miR-305 for adult tissues, miR-9 and miR-279 for parasitic treatment, miR-998 and U6 snRNA for nuclear polyhedrosis virus infection, miR-9 and U6 snRNA for insecticide treatment, miR-92a, miR-100, and miR-279 for temperature treatment, miR-92a, miR-305, and miR-998 for starvation treatment, miR-9 and miR-279 for light treatment, miR-305 and miR-998 for hormone treatment, and there was not one reference gene suitable for all samples.

Nutrient-dependent pheromone-controlled reproduction in this moth species links the works of Karlson and Luscher (1959) Pheromones: a new term for a class of biologically active substances to the Bruce McEwen’s works on stress via Effects of Carnitine on Fatty-Acid Oxidation by Muscle (1959) and Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

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

Taken together, these works are linked to energy-dependent Normalization of MicroRNA Expression. The anti-entropic virucidal energy of sunlight is the obvious link from the de novo creation of microRNAs to the ATP-dependent biosynthesis of messenger RNA and healthy longevity.  Virus-driven energy theft clearly links the degradation of messenger RNA, which would otherwise link the creation of microRNAs from sunlight to the nutrient energy-dependent pheromone-controlled biosynthesis of ATP and all cell type differentiation in all living genera.

For example see: Genetic 3’UTR variation is associated with human pigmentation characteristics and sensitivity to sunlight

To our knowledge, this is the first time that these two 3’UTR SNPs have been associated with sun-sensitivity traits. We state the potential implication of these SNPs in human pigmentation and sensitivity to sunlight, possibly as a result of changes in the level of gene expression through the disruption of putative miRNA-binding sites.

See also:: Race-dependent association of sulfidogenic bacteria with colorectal cancer

reported as: Study links sulfide-producing bacteria and colon cancer in African-Americans

“These bacteria are using nutrients associated with an animal-based diet,” Gaskins said.

For information on the biophysically constrained energy-dependent origins of race-dependent associations see:

Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism

…precursors of amino acids glycine, serine, alanine and threonine, are inevitable by-products of this RNA assembly chemistry…

Like all chemistry, this can be placed into the context of how quantum physics must be linked from quantum chemistry to quantum biology via food as energy.

The link from food enery to the nutrient-dependent pheromone-controlled physiology of reproduction and racial differences in colon cancer was predicted based on difference in diet and links from the National Microbiome Initiative to the Precision Medicine Initiative.

See for comparison: Sonny Williams

Re: … much ado about nothing — Jay R. Feierman.

SONNY [NEW]: As we’ve discussed many times, I reject your criteria for judging the merits of a scientific observation.  Arguing that something is “much ado about nothing,” if “the results can’t be predicted by common sense or by simple observation and deductive reasoning,” is exceptionally poor reasoning.  Frankly, I’m bewildered that someone like you would cling to it.  I’ll repeat:  any judgment that includes an evaluation based on “common sense” is DOA.  It’s useless.  Whose “common sense” do you intend to use?

More importantly, the authors DID establish a pre-observation “prediction.”

They predicted that young children will show the same variation in temperament as adults, and which is associated with the various BDNFval/66met polymorphisms.  They wrote, “To the best of our knowledge, there are no studies investigating the role of BDNFval66met with regard to individual differences in temperament during infancy, a period in which genetically-based behavioral traits are hypothesized to be more easily observed (Posner & Rothbart, 2009; Rothbart et al., 2000). Hence, the purpose of the current study was to explore the association between the BDNFval66met polymorphism and individual differences in temperament in a sample of healthy 4-month-old full-term infants.”

Moreover, the authors did a far better job than you did in discussing limitations.

They wrote as follows: “The current study had some limitations. First of all, due to sample size findings cannot be generalized and future studies with larger samples are needed in order to differentiate the impact of met-homozygous and heterozygous profiles of BDNFval66met genotype. Second, infants’ temperament was measured through a parent-reported measure. A more direct account of the effects of BDNF met allele on observed temperament and regulatory behavior is warranted to be investigated in future research. Finally, single polymorphism studies are at risk of underrepresenting the role of environmental conditions, including maternal caregiving behavior. As the quality of early caregiving has been found to regulate BDNF transcriptional functioning (Unternaehrer et al., 2015), we suggest that upcoming studies should target gene x environment interactions using genetic and epigenetic approaches.

To the best of our knowledge, this study is unique in providing evidence of an association between the BDNFval66met polymorphism and infants’ temperament at 4 months of life. The present study adds to previous genetic association research on temperament in infants looking at other polymorphisms (Auerbach et al., 2001; Ivorra et al., 2011), preliminarily suggesting a further genetic factor involved in temperament. Future research is warranted to investigate the BDNF-temperament association in greater populations of infants at low- and high-risk (e.g., preterm infants) and assuming a gene-x-gene and gene-x-environment approach (Papageorgiou & Ronald, 2013).”

Sonny Williams and Jay R. Feierman are antagonists who ignore the facts that link our predictions to all energy-dependent biophysically constrained biodiversity from our 1996 Hormones and Behavior. Our predictions were based on Bruce McEwen’s advice to start with the activation of genes. That is why we included a section on molecular epigenetics.

From Fertilization to Adult Sexual Behavior

All predictions have since been linked from the anti-entropic virucidal energy of sunlight to biophysically constrained RNA-mediated biodiversity by changes in base pairs linked from amino acid substitutions to differences in morphological and behavioral phenotypes during the development of moths and humans. The epigenetic effects of sunlight were predicted in the context of the nutrient energy-dependent de novo creation of microRNAs.
Anything ever linked to the gene-centric theories of neo-Darwinists has been replaced by what is known about energy-dependent endogenous RNA interference and all biophysically constrained biologically-based biodiversity on Earth. For example, pheromones biophysically constrain the physiology of reproduction in all living genera. They protect against virus-driven entropy by linking what organisms eat to the species-specific pheromone-controlled transgenerational epigenetic inheritance of species from microbes to humans.
See also: Epigenetic regulation of face formation
See also: Explaining the accelerating expansion of the universe without dark energy

See also: A distinct role for Lgr5+ stem cells in primary and metastatic colon cancer
Reported by Genentech as: Cancer stem cells have long been thought to influence tumor growth, but a clear link has been difficult to show. Now, in a new study in Nature, our scientists show for the first time that removing cancer stem cells in a model of colorectal cancer can indeed reduce tumor growth. See how these findings could help guide new therapies aimed at targeting cancer stem cells.
What took them so long to link virus-driven energy theft from messenger RNA degradation to the negative supercoiling of DNA via G protein-coupled receptors?
Feedback loops link odor and pheromone signaling with reproduction

At least 10,000 neurons in 26 different brain areas appear to transmit signals directly to GnRH neurons.  GnRH neurons 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. 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.

 

rp_levels-of-organization.jpg

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!

3/27/17 My comment:

On March 24, 2017 this article was published in ‘Science.’ A conserved NAD+ binding pocket that regulates protein-protein interactions during aging

The article linked virus-driven energy theft from hydrogen-atom transfer in DNA base pairs in solution to all pathology.

On March 24, 2017 this article also was published in ‘Science.’ Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention

The authors failed to link the anti-entropic virucidal energy of sunlight to all biophysically constrained biodiversity via protection of organized genomes manifested in supercoiled DNA.

It seems likely that without “Cytosis,” another generation of biologically uninformed researchers would fail to link top-down causation from quantum physics to all energy-dependent healthy longevity via endogenous RNA interference.

Without “Cytosis” the unnecessary suffering and premature deaths caused by the virus-driven degradation of messenger RNA might never be stopped by serious scientists who known how cell type differentiation occurs.

Are you planning to develop a game about “Photosynthesis” to show others how to link physics and chemistry from molecular epigenetics to all biophysically constrained cell type differentiation via the physiology of reproduction? If so, I could help with some of the more technical aspects.

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]

rp_tumblr_ngykp0yfND1r5gzz6o1_500.jpg

Allen Institute confirms food energy is information

See also: Theistic evolutionists fight back and lose
Excerpt: Predictably, Paul Allen will be the next to start funding works that might help to prevent the viral apocalypse, now that Bill Gates is mentally prepared to do so.

Allen Institute FB page

3/3/17 Fascinating new research on stem cell division
Scientists discover an unexpected influence [of food] on dividing stem cells’ fate

One particular protein, Pex11b, caught her attention. It is associated with the membrane that surrounds the peroxisome, an organelle that helps to free energy from food.

“While some evidence already suggested the distribution of organelles, including energy-producing mitochondria, can influence the outcome of cell division, we have shown for the first time that this phenomenon is essential to the proper behavior of and formation of the tissue,” says Fuchs, who is also a Howard Hughes Medical Institute Investigator.

This unexpected influence of food energy on endogenous RNA interference and cell type differentiation in skin cells from mice was first reported one month ago. However, the influence of food on the survival of all species is known to all serious scientists.

For example, see Schrodinger (1944). He linked the anti-entropic energy of sunlight from all energy-dependent biophysically constrained viral latency to healthy longevity before Roger Penrose (1991) mentioned this in his forward to the reprint edition:

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?

In 1991, Penrose reduced the systems complexity of biophysically constrained top-down energy-dependent viral latency to the question of where the energy in a hydrogen atom comes from.comes from. Schrodinger suggested it came from sunlight in an attempt to stop the pseudoscientific nonsense about mutations that was touted after de Vries defined “mutation” in 1902. So far, no experimental evidence of biologically-based cause and effect has limited the claims about mutations and evolution that are made by biologically uninformed theorists.

See for comparison:

OLYMPUS experiment sheds light on structure of protons

A mystery concerning the structure of protons is a step closer to being solved, thanks to a seven-year experiment led by researchers at MIT. Credit: Christine Daniloff/MIT

Hard Two-Photon Contribution to Elastic Lepton-Proton Scattering Determined by the OLYMPUS Experiment (March 3, 2017)

The resulting values of R2γ, presented here for a wide range of virtual photon polarization 0.456<ε<0.978, are smaller than some hadronic two-photon exchange calculations predict, but are in reasonable agreement with a subtracted dispersion model and a phenomenological fit to the form factor data.

The phenomenological fit links the claims of Schrodinger and concerns of Penrose to this report on the Lepton-Proton Scattering. The title includes the joke about the link from sunlight to evolution that Dobzansky (1973) reported as: Nothing in Biology Makes Any Sense Except in the Light of Evolution. Dobzhansky’s clever creationist attack on neo-Darwinian theorists, who failed to link the creation of the sun to all biologically-based cause and effect went virtually unnoticed despite his claim:

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

No experimental evidence of biologically-based cause and effect links Dobzhansky’s claims about amino acid substitutions to evolution. For contrast, all claims made by other serious scientists link sunlight to energy-dependent changes in angstroms to ecosystems in all living genera.

The two-photon contribution to the structure of protons and the biophysically constrained functional structure of supercoiled DNA was reported as:

OLYMPUS experiment sheds light on structure of protons

…experiments had previously led researchers to assume that the electric and magnetic charge distributions are the same, and that one photon—an elementary particle of light—is exchanged when the protons interact with the bombarding electrons.

…two photons are indeed exchanged during electron-proton interactions.

However, unlike the theoretical predictions, analysis of the OLYMPUS measurements suggests that, most of the time, only one of the photons has high energy, while the other must carry very little energy indeed…

Natural selection for the higher energy photon is the most likely link from the anti-entropic effects of sunlight to energy-dependent codon optimality and cell type differentiation in all living genera via the physiology of pheromone-controlled reproduction and endogenous RNA interference.
The links from higher energy photons to energy-dependent changes in chirality and autophagy extend what is known about RNA-mediated DNA repair. The molecular mechanisms of DNA repair helped to establish sunlight as the energy source for hydrogen-atom transfer in DNA base pairs in solution. The most recent report on one carbon metabolism also extends what is known about subatomic particles to the creation of the energy in hydrogen atoms and differences in the structure of teeth.
See: Evidence for dietary change but not landscape use in South African early hominins (2012)
Reported as: Millions of years of evolutionary history recorded in teeth (March 3, 2017)
The nonsense about the evolutionary history was refuted in 2013. See: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes
A change in diet was linked to differences in C. elegans and a predatory nematode with teeth. They claimed that the differences emerged during 200 million years, but no experimental evidence of biologically-based cause and effect has ever supported such ridiculous claims.
See also:
Subatomic Particles, Part 1: Leptons 
Subatomic Particles, Part 2: Baryons, the Substance of the Cosmos
Subatomic Particles, Part 3: Mesons
See also: Feedback loops link odor and pheromone signaling with reproduction

Please place the feedback loops into the context of how PCR applications are linked to what is known about cell type differentiation via virus-driven degradation of messenger RNA (mRNA), or linked by nutrient energy-dependent endogenous RNA interference to healthy longevity.

A snapshot of the most common PCR application

1) “Another possible application: looking for an RNA target, either viral or an endogenous mRNA.”
2) “…the IC [internal control] should be RNA to reflect the desired sample type.”
3) Conclusion: An understanding of the overall method workflow and some of the possible causes of false positive or negative results is thus beneficial in appropriately interpreting test results in the full clinical context.The light energy as information-induced de novo creation of RNA, protein, and lipid precursors links the common origin of amino acids to cell type differentiation in all living genera via endogenous RNA interference and the physiology of reproduction, which links supercoiled DNA to chromosomal inheritance.
See: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
John Brunstein indirectly suggests that supercoiled DNA prevents mutation-driven evolution. Unless the mutations can be linked from amino acid substitutions to pathology, he also seems to also be suggesting that neo-Darwinian theories are sources of errors.  Researchers are virtually guaranteed to fail, if they start with theories and try to link the possible causes of energy-dependent  false positive or negative results from the National Microbiome Initiative cell type differentiation in the context of the Precision Medicine Initiative.
I hope that someone like John Brunstein will comment on facts about the degradation of messenger RNA (mRNA). For example, virus-driven energy theft appears to link mRNA degradation to all pathology.  If he does not agree, I hope he knows of an alternative model that links energy-dependent RNA-mediated amino acid substitutions to all healthy longevity and something else to all pathology.
In any case,  I believe it is past time to eliminate neo-Darwinian theories, which link beneficial mutations to the stability of organized genomes in all living genera, but link amino acid substitutions to the stability of viruses.
See: Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

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

See for comparison: Perhaps no single tool in the human arsenal explains our existence more than fire.

Watch Jason Silva tell you about the importance of fire in an attempt to link the pseudoscientific nonsense touted by theorists to survival of all species except those that do not need to eat. Those species must have emerged and automagically evolved to become people like Jason Silva who can tell others how that happened, but won’t.

He can tell others about the importance of fire. Watch as everyone else in the world starts to link energy-dependent endogenous RNA interference to biophysically constrained gene activation and link virus-driven energy theft to all pathology during the cell type differentiation of all species from microbes to humans.

See for example: Services – QuantSeq 3’ mRNA-Seq Libraries

Lexogen provides a fully integrated service-workflow for generation of QuantSeq 3’ mRNA-Seq libraries, multiplexed sequencing, and data analysis. QuantSeq libraries are produced from total RNA to yield Illumina-compatible sequences close to the 3’ end of polyadenylated RNA.

Then wait for someone to tell you more about the importance of fire.

See also this video representation of the link from sunlight to biodiversity in marine life.
Alternatively, place everything known about energy-dependent RNA-mediated cell type differentiation back into the context of “Nature.”
See: Nature Fights Back Against Gene Editing
Then, stop calling it “Nature” and learn what serious scientists already know about the energy-dependent links from angstroms to ecosystems in all living genera. If not, now that the Allen Institute has linked food energy as information to brain development, you will be asked to tell others how “Nature” created everything from subatomic particles to the hydrogen-atom energy. Then, the next question will be about how the energy is transferred in DNA base pairs in solution to allow natural selection for energy-dependent codon optimality and the physiology of reproduction in all living genera.
See also: The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular Function
See also: A Revised Tree of Life
See also: A Chat with Leeuwenhoek Medalist Jeffery Errington

Suzan Mazur: Do viruses play a role in regulating L-form bacteria?

Jeffery Errington: That’s a good question. Of course, much of the research on bacteriophages has shown that they tend to bind to components of the cell wall, so certainly you’d anticipate that L-forms would be resistant to many forms of virus. But I don’t know if much work has been done on this.

Anyone who does not know how much experimental evidence links food energy to all biodiversity via the pheromone-controlled physiology of reproduction is not likely to know enough about anything that could be linked from bacteriophages to all pathology via the degradation of messenger RNA.