5th-6th Sept 2018 Dublin, Ireland

RNA-mediated nutritional psychiatry (2)

Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

Neo-Darwinian theorists dispense with Darwin’s food energy-dependent  “conditions of life.” They link mutations and disease to evolution via mathematical models. They exemplify human idiocy.
See for example: Neopterygian phylogeny: the merger assay
Reported as: Adaptive radiations in the Mesozoic

Bony fishes are the most diverse of all extant vertebrate groups. A comprehensive phylogenetic analysis of the group now provides new insights into its 250-million-year evolutionary history.

The claim about the 250-million-year evolutionary history can be compared to what happens when food energy-dependent fixation of a single RNA-mediated amino acid substitution occurs across a vertebrate lineage.
See: Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor

It is very surprising and fascinating that the coordinated evolutionary selection of amino acids participating in binding GnRH has resulted in such perfection, that no substitution with a natural amino acid in any position improves binding potency.

Evolution does not select amino acids. Natural selection for food energy-dependent pheromone-constrained viral latency links the substitution of achiral glycine in position 6 of the GnRH decapeptide to the biodiversity of all morphological and all behavioral phenotypes in all vertebrates.
See also: Handbook of Biologically Active Peptides (2013) Chapter 106 GnRH (LHRH)
Page 794 Figure 2 shows that food energy-dependent substitution of achiral glycine at position 6 stabilizes the folded conformation; increases binding affinity; and decreases metabolic clearance.

This feature is incorporated in all agonist and antagonist analogs.

Simply put, the substitution of achiral glycine in the GnRH decapeptide biophysically constrains viral latency in the context of ligand-receptor interactions and the physiology of pheromone-controlled reproduction.
See also: Role of olfaction in Octopus vulgaris reproduction
From the concluding paragraph:

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).

Kohl (2013) is Nutrient-dependent/pheromone-controlled adaptive evolution: a model
The facts that link vertebrates to invertebrates via olfaction and the 2013 model will almost undoubtedly be restated when Tuning Insect Odorant Receptors is published.
Until then, see:Evolution of Constrained Gonadotropin-releasing Hormone Ligand Conformation and Receptor Selectivity (2005)
Biophysical constraints link feedback loops from odors and pheromones to the functional structure of the GnRH decapepetide via achiral glycine in position 6. The link from food to the de novo creation of energy-dependent receptors is required in all organisms. They must select the right food, which helps to ensure their ability to reproduce.

5th-6th Sept 2018 Dublin, Ireland

RNA-mediated nutritional psychiatry

Summary: Young Genes are Highly Disordered as Predicted by the Preadaptation Hypothesis of De Novo Gene Birth
Stop this nonsense about de novo gene birth and you will help to stop the school shootings without more gun control.
See my presentation at the 2017 Precision Medicine Virtual Conference (2/15/17) Energy as information and constrained endogenous RNA interference
See also: Pat Sweeney et al (3/13/2017) Protein misfolding in neurodegenerative diseases: implications and strategies. 

A notable development is the creation of collaborative ecosystems that include patients, clinicians, basic and translational researchers, foundations and regulatory agencies to promote scientific rigor and clinical data to accelerate the development of therapies that prevent, reverse or delay the progression of neurodegenerative proteinopathies.

For consideration of protein folding in the context of my life’s works, see: From de novo to “de nono”: most novel protein coding genes identified with phylostratigraphy represent old genes or recent duplicates

Claudio Casola refers “… to the putative de novo genes that failed to pass the validation criteria as the ‘de nono’ genes.” Use of the term ‘de nono’ to refute Pat Sweeney’s neo-Darwinian pseudosceintific nonsense is brilliant! For instance, all serious scientists know that protein folding chemistry is energy-dependent.
 
 

The structural diversity biophysically constrains viral latency and the constraints are referred to in the context of RNA-mediated autophagy. Autophagy clearly makes “de novo” gene creation a no-no term. That is why serious scientists are not likely to use the term de novo. It is like claiming that something automagically occurs.

In the context of what is known about energy-dependent cell type differentiation, see also:

Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis (2011)

and

Formulation and evaluation of anti-suicidal nasal spray of Thyrotropin releasing hormone (2017)
The fact that food odors and pheromones biophysically constrain physical and mental pathology via alternative splicings of RNA has been addressed in published works since 1990.
See for a recent example: RNA splicing is a primary link between genetic variation and disease (2016)
See for examples of constraints:
Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults (E-pub 2014)
The catechol-o-methyltransferase Val158Met polymorphism modulates the intrinsic functional network centrality of the parahippocampal cortex in healthy subjects (2015)
Subsecond Regulation of Synaptically Released Dopamine by COMT in the Olfactory Bulb (2016)
The COMT Val158Met polymorphism exerts a common influence on avoidant attachment and inhibited personality, with a pattern of positive heterosis (2017)
In the context of energy-dependent constraints, the COMT VaL158Met amino acid substitution exemplifies the facts detailed in the context of: Hydrogen bonds directly detected for the first time (2017). The facts about hydrogen-atom transfer in DNA base pairs in solution have since been linked to all energy-dependent pheromone-controlled biodiversity in: Principles of Transgenerational Small RNA Inheritance in Caenorhabditis elegans (2017)
See also: Catechol O-methyltransferase (COMT) functional haplotype is associated with recurrence of affective symptoms: A prospective birth cohort study (1/15/2018)
Analysis of COMT Val158Met polymorphisms and methylation in Chinese male schizophrenia patients with homicidal behavior (2/20/2018)
Adjunctive nutrients in first‐episode psychosis: A systematic review of efficacy, tolerability and neurobiological mechanisms (3/21/18)
Reported as: Antioxidants and amino acids could play role in the treatment of psychosis 3/22/2018
See for comparison: March for Our Lives 3/24/18

Theme Gun violence awareness
Support of gun control

The focus on support of gun control ignores everything known to all serious scientists about biophysically constrained mental health and the virus-driven constraint-breaking mutations in the killers with guns. The future of school shootings depends on mental health treatment.

Why nutritional psychiatry is the future of mental health treatment

…29 clinical trials of antidepressant use in young people found no benefits at all. These trials revealed that instead of relieving symptoms of anxiety and depression, antidepressants caused children and young people to feel suicidal.

See for comparison: 7/25/13 Jay R. Feierman:

Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.

My understanding of biology is linked to my understanding of physics and chemistry via 40 years testing experience as a medical laboratory scientist (ASCP emeritus). Simply put, all organisms must eat and reproduce or species do not survive. The discovery of bacteria that eat electrons and create uranium ore was place into the context of this news:
Biologists discover electric bacteria that eat pure electrons rather than sugar, redefining the tenacity of life (2017)
The link from eating electrons to hydrogen-atom transfer in DNA base pairs in solution appears in the context of energy delivery to all cell types in organisms that have blood in their circulatory system. The claim that the human circulatory system evolved incorporates ‘de nono’ gene creation.
There is no such thing as de novo gene creation and ‘de nono gene creation’ can now be used in the context of post-publication ridicule of this model:
Basic Science Model of Blood as an Electron-Delivery Circuit Describes the Evolution of the Human Circulation (2017)
The anti-entropic virucidal energy of sunlight is the link from ecological variation to ecological adaptation in the context of the physiology of reproduction and biophysically constrained viral latency. Pseudoscientists will not stop trying to place that fact into the context of ridiculous neo-Darwinian theories.
Thankfully, ages 10+ can learn how energy-dependent life is biophysically constrained by playing the cell biology game “Cytosis” and the game that links energy-dependent changes from electrons to ecosystems in all living genera: “Subatomic“.
See my attempt to deliver that message in: There is no such thing as de novo control of electrons or the self-assembly of genes. (11/21/17)
But see: Young Genes are Highly Disordered as Predicted by the Preadaptation Hypothesis of De Novo Gene Birth
Stop this nonsense and you will help to stop the school shootings without more gun control.

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

Polymaths and paradigm shifts: from Asimov to Bear (3)

Polymaths and paradigm shifts: from Asimov to Bear (2)

Teilhardism And The New Religion: A Thorough Analysis of the Teachings of Pierre Teilhard de Chardin”, p.18, TAN Books

The evolutionist thesis has become more stringently unthinkable than ever before. — Dr. Wolfgang Smith (2015).

A Chat with Information Scientist Pedro Marijuán (2017)

I’ve based my informational scheme of the cell on this thinking of “distinction on the adjacent” — where molecular recognition is the essential phenomenon over which biological complexity has been developed.

Biological complexity develops in the context of the olfactory code. Molecular recognition of food odors and pheromones biophysically constrains viral latency.

See: Fundamental principles of the olfactory code  Volume 164, February 2018, Pages 94-101 open access

Sensory coding represents a basic principle of all phyla in nature: species attempt to perceive their natural surroundings and to make sense of them. Ultimately, sensory coding is the only way to allow a species to make the kinds of crucial decisions that lead to a behavioral response.

Alternative splicing of microRNAs (aka pre-mRNAs) are required for a behavior response.

The splicing code  Volume 164, February 2018, Pages 39-48

…the splicing code depends on a myriad of different factors that in part are influenced by the background in which they are read such as different cells, tissues or developmental stages. Given the complexity of the splicing process, the construction of an algorithm that can define exons or their fate with certainty has not yet been achieved.

Algorithms define nothing. The availability of quantized energy as information must be linked to biophysically constrained viral latency and all biologically based cause and effect.

What is code biology?  Volume 164, February 2018, Pages 1-10

The great discontinuities of the history of life, in other words, can be explained as the result of the appearance of new codes.

New codes do not automagically occur. The new codes are energy-dependent and RNA-mediated in the context of the fixation of amino acid substitutions that differentiate the cell types of all living genera.

On universal coding events in protein biogenesis  Volume 164, February 2018, Pages 16-25

The complete ribosomal protein synthesis cycle and codon-amino acids associations are universally preserved in all life taxa on Earth. This process is accompanied by a set of hierarchically organized recognition and controlling events at different complexity levels. It starts with amino acid activation by aminoacyl tRNA synthetases…

The energy-dependent creation of the tRNA synthetases links hydrogen-atom transfer in DNA base pairs in solution to all energy-dependent biodiversity.

How prokaryotes ‘encode’ their environment: Systemic tools for organizing the information flow  Volume 164, February 2018, Pages 26-38

An important issue related to code biology concerns the cell’s informational relationships with the environment. As an open self-producing system, a great variety of inputs and outputs are necessary for the living cell, not only consisting of matter and energy but also involving information flows.

Quantized energy is the information that flows through every cell type in all prokaryotes.

Causation, constructors and codes  Volume 164, February 2018, Pages 121-127

A formal definition of codes in general, and organic codes in particular, allows the relational diagram to be extended so as to capture this translation of formal cause into process. The extended relational diagram is used to exemplify causal entailment in a diverse range of processes, such as enzyme action, construction of automata, communication through the Morse code, and ribosomal polypeptide synthesis through the genetic code.

The diverse range of processes starts with the creation of energy-dependent enzyme action. The anti-entropic virucidal energy of sunlight was first linked to the creation of all biodiversity on Earth in 1944: What is Life?

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)

If you think you can link anything except sunlight to all biodiversity on Earth, see: Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses
If you know that serious scientists do not link viruses to the evolution of anything except pathology, see:
Schrödinger at 75 – The Future of Biology – September 2018
The future of biology will not be left in the hands of biologically uninformed theorists.

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

Polymaths and paradigm shifts: from Asimov to Bear (2)

Polymaths and paradigm shifts: from Asimov to Bear (1)
See also: Search results for virus-driven energy theft
Summary: The creation of enzymes, such as ATP synthase is energy-dependent. The energy biophysically constrains viral latency via the creation of microRNAs and RNA-mediated amino acid substitutions that differentiate the cell types of all living genera.
Modifying Other’s Originality without Quote is an Act of Piracy

A writer who does not cite the sources in h/h feature article is committing piracy. Piracy is plagiarism… high level quality requires originality and creativity… these inattentions…should be strongly condemned… Accordingly, the originally contributing author may preserve the honor worthily and endeavor to further contribution in scientific study.

See for comparison: Here’s how viruses inactivate the immune system, causing cancer

It’s no new news that viruses cause cancer.

The full text of the article is free: DNA Tumor Virus Regulation of Host DNA Methylation and Its Implications for Immune Evasion and Oncogenesis

…virus-associated cancers show highly increased levels of DNMT expression [75,76,77,85,94,95,96,97,98,99]. In HBV-associated hepatocellular carcinoma (HCC), DNMT expression is inversely correlated with levels of tumor suppressor microRNAs (miRNAs), including miR-152 targeting DNMT1 [97] and miR-101 targeting DNMT3A [99]. Virus-induced DNA hypermethylation is commonly found on several tumor suppressor genes…

RNA-directed DNA methylation links the energy-dependent microRNA-mediated creation of tumor suppressor genes to biophysically constrained viral latency via the proton motive force. The proton motive force links differences in the energy of photons from hydrogen-atom transfer in DNA base pairs in solution to the light-activated endogenous substrates of RNA-mediated DNA repair.
See also: “There is no honor among thieves” is a pithy saying that captures Solomon’s observation concerning the wicked and those who choose their company.
A Twitter search returned several interesting comments related to what is known to serious scientists about the proton motive force and the claim that “There is no honor among thieves.” For instance, writers who modify the claims and questions about the proton motive force are plagiarists and/or thieves. See:

  1. 12 Sep 2010

What do proton motive force driven multidrug resistance transporters have in common?

2. 19 Jun 2010

The H+ gradient is called the proton-motive force. This force drives the H+ back across the membrane through H+ channels. ATP synthases aids

The creation of enzymes, such as ATP synthase is energy-dependent. The energy biophysically constrains viral latency via the creation of microRNAs and RNA-mediated amino acid substitutions that differentiate the cell types of all living genera.

 Philip Ball @philipcball Mar 2

This was filmed tonight, so you’ll soon get to see why Nick Lane thinks the key to the origin of life is not amino acids or RNA but proton gradients. (I think he may be right.)

See for comparison: snippet from our June 24, 2017 conversation about the claims of Philip C. Ball.

See also: The legacy of Frankenstein: A series of events celebrating 200 years of Frankenstein

The origin of life

Dr Frankenstein aimed to create new life from inanimate parts. But how did life first arise on Earth? Join Nick Lane in conversation with Phil Ball as they discuss the latest ideas, from warm ponds to space rocks and hydrothermal vents.

Ask when Nick Lane and/or Philip C. Ball first learned about proton gradients. See how much longer it takes them to link the creation of sunlight  from differences in the energy of photons to biophysically constrained viral latency and all biodiversity via the physiology of reproduction and this model: Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013)

Conclusion:

…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

See also: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

Abstract:

This angstroms to ecosystems model of ecological adaptation links nutrient energy-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements via the physiology of reproduction in species from microbes to humans. 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 ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity. Species-specific pheromones link quorum-sensing in microbes from chemical ecology to 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 for codon optimality links nutritional epigenetics to the behaviors that enable ecological adaptations. All biodiversity is an 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. Simply put, olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of supercoiled DNA in the organized genomes of species from microbes to man during their development.

See for comparison: On the Difference between Physics and Biology: Logical Branching and Biomolecules

In my model, microRNAs are the biomolecules that link the creation of sunlight to all energy-dependent biophysically constrained viral latency. Viral latency is required to link the physiology of reproduction to all biologically-based diversity in all species.

Claims about proton gradients that link physics to biology without starting with the creation of sunlight are made by biologically uninformed theorists.

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

Nature vs Science and Autophagy.pro

Conclusion: The anti-entropic virucidal energy of sunlight links food energy directly from the innate immune system to all morphological and behavioral diversity. It all about energy. It’s all about the creation of enzymes. It’s all about the base pairs.


Until the day that I launched Autophagy.pro, I had only one or two Facebook posts that were marked as spam. Since December 11, 2017, I have had ~5 posts marked as spam.

See for example: This comment was marked as spam at Ciência Biomédica, when I responded to  Synthetic protein packages its own genetic material and evolves

Packaging is energy-dependent and biophysically constrained. Nothing evolves. The concept is foolish. See: A universal trend of amino acid gain and loss in protein evolution 
Excerpt: Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.
 
Laboratory co-oximeters determine the %HbO2 (%SaO2 ) by measuring the amount a specific frequency of light is absorbed as it passes through a known volume of blood. In contrast, pulse oximetry (SpO2) measures the change in light absorbed at systole and diastole. This allows the pulse oximeter to distinguish between the constant amount of light absorbed by the tissue, bone, venous blood, etc. from the arterial blood (the blood in the volume change due to the pulse).
 
The amount of light absorbed by the tissue, bone, venous blood etc., varies in the context of hydrogen-atom transfer in DNA base pairs in solution. Blood gas analysis in the medical laboratory links differences in hydrogen (H2) — as in H2O from quantized energy-dependent changes in the potential of hydrogen (pH) to all biophysically constrained biodiversity.
 

Measuring pH links what is known about nutritional epigenetics from the innate immune system to healthy longevity via everything known about autophagy. The measurements can be compared in the context of  what is known about virus-driven energy theft, which links stress from the replication of viruses to all pathology via critical care testing of other blood gas analytes such as pCO2, pO2, Sodium, Potassium, Chloride, Calcium, Glucose, Lactic Acid, and Hematocrit.

For example in a mammal, see: Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin (June 14, 2013)

See Fig. 2 Difference in the network of hydrogen bonds between high- and low-altitude Hb variants, HH-H and LL-L, respectively.

An external file that holds a picture, illustration, etc. Object name is nihms675257f2.jpg

My comment to the Science site (submitted 6/14/13 published 6/20/13):

In my model species-specific epistasis is nutrient-dependent and pheromone-controlled. An additional example of this showed up earlier this week in the context of the epigenetically-effected microRNA/messenger RNA balance: “miR-124 controls male reproductive success in Drosophila”

miR-14 acts in neurosecretory cells in the adult brain to control metabolism and miR-124 acts in the context of brain-directed neuroendocrine control of sexual differentiation and male pheromone production, which is controlled in mammals by gonadotropin-releasing hormone (GnRH) neurosecretory cells of the hypothalamus.

We can anticipate extension to mammals of the Drosophila model from the abstract of a forthcoming Science article: “MiR-200b and miR-429 Function in Mouse Ovulation and Are Essential for Female Fertility.” Given our earlier work in the context of molecular epigenetics and the concept of alternative splicings and sexual differentiation in Drosophila and C. elegans, I suspect we will see evidence for nutrient-dependent adaptive evolution of GnRH pulse frequency-controlled LH secretion and pheromone-controlled female fertility in mice.

If I’m correct, this evidence will link glucose and pheromones to feedback loops that control reproduction in invertebrates and vertebrates. (See Nutrient–dependent / pheromone–controlled adaptive evolution: a model). Model organisms exemplify these feedback loops in microbes, nematodes, insects, and other mammals. The mouse to human example that Kamberov et al., and Grossman et al., detailed is the most telling.

A single amino acid substitution appears to result in what seem to be nutrient-dependent changes in the thermodynamics of intracellular signaling, intranuclear interactions, stochastic gene expression, and selection for phenotype via organism-level thermoregulation in a human population that arose in what is now central China during the past ~30K years.

Using a model that integrates what is known about the common molecular mechanisms may help establish whether adaptive mutations lead to thermodynamic effects on organism-level thermoregulation and epistasis, or whether epigenetic effects of nutrients and their metabolism to species-specific pheromones that control reproduction via changes in the microRNA/messenger RNA balance are the driving force behind adaptive evolution in species from microbes to man.

See: Obligatory role of hypothalamic neuroestradiol during the estrogen-induced LH surge in female ovariectomized rhesus monkeys
Reported as:  Estrogen discovery could shed new light on fertility problems December 12, 2017

Estradiol builds in the bloodstream until it reaches a concentration that causes a surge of the hypothalamic and pituitary hormones, including one called luteinizing hormone, which in turn trigger an ovary to release an egg.

“It’s a feedback loop…

The feedback loop is food energy-dependent and pheromone-controlled.
See: Feedback loops link odor and pheromone signaling with reproduction
Energy-dependent autophagy is the link from feedback loops to ecological adaptation. Science Magazine now has the opportunity to challenge the pseudoscientific nonsense of published works from the Nature Publishing Group. There is no need to consider mutations and evolution outside the context of virus-driven energy theft, which links the degradation of messenger RNA from mutations to all pathology.
See also: Combating Evolution to Fight Disease

Darwin probably anticipated the insemination of population genetics that led to the bastardization of his detailed observations in the “Modern Synthesis.” He politely insisted that ‘conditions of life’ be considered before natural selection.

There are two ‘conditions of life.’ It is nutrient-dependent and pheromone-controlled. Rosenberg and Queitsch now note the work with Dobzhansky’s rarely acknowledged claim: “I am a creationist and an evolutionist.” They also declare the need for “Deep understanding of the mechanisms that generate variation at the molecular level…”

Deep understanding of the ‘conditions of life’ does not come from theory.

Problems with the “modern synthesis” now lead us back to the facts about biologically-based cause and effect that Darwin and Dobzhansky approached with humility, which are the same biological facts that evolutionists approached with ignorance about behavioral affects and the arrogance that accompanies that ignorance. Rosenberg and Queitsch echo the sentiments of those who have been subjected to academic suppression.

Clearly, however, “nothing in evolution makes sense except in the light of biology” is not an exaggeration. It is a common sense statement about the biologically plausible genesis of functional cell types. Population genetics and evolutionary theories abandoned the biophysical constraints of ecological variation and the physiology of reproduction, which enable epigenetically-effected nutrient-dependent pheromone-controlled receptor-mediated ecological adaptations and species diversity via the complexities of protein folding and niche construction.

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.

The retraction of Oligoarginine peptides slow strand annealing and assist non-enzymatic RNA replication attests to the amount of pseudoscientific nonsense published by the “Nature Publications Group” during the past few decades.
See: Retraction Watch

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

How many others who published via the Nature Publishing Group were blinded by their belief in pseudoscientific nonsense that failed to link the food energy-dependent creation of enzymes and the creation of RNA from blood gas analyses to patient outcomes?
See for comparison: 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.

Who did not know that? How did non-enzymatic RNA replication become a non-energy-dependent consideration for anyone associated with the Nature Publishing Group?
See for comparison: Mechanisms of mTORC1 activation by RHEB and inhibition by PRAS40

Here we present the 3.0 ångström cryo-electron microscopy structure of mTORC1 and the 3.4 ångström structure of activated RHEB–mTORC1. RHEB binds to mTOR distally from the kinase active site, yet causes a global conformational change that allosterically realigns active-site residues, accelerating catalysis.

The global conformational change that allosterically realigns active-site residues (i.e., amino acids), accelerating catalysis, is an energy-dependent change.
Reported as:  Scientists unlock structure of mTOR, a key cancer cell signaling protein

1) Like many proteins, mTOR is an enzyme, which binds to target molecules called substrates in a precise way to hasten chemical reactions. Specifically, it is a type of kinase, which removes phosphates (P) from ATP, the cell’s energy currency, and places them on other molecules.

The creation of the enzymatic activity of mTOR is quantized energy-dependent and it links the pheromone-controlled physiology of reproduction to biophysically constrained viral latency via autophagy. The retractions of Jack Szostak’s nonsense about the magical creation of enzymes after the energy of life emerged and organisms subsequently evolved in the context of differences in H2 to all biodiversity on Earth, can be placed into the context works by serious scientists.

2)  …mTOR is an enzyme, which binds to target molecules called substrates in a precise way to hasten chemical reactions. Specifically, it is a type of kinase, which removes phosphates (P) from ATP, the cell’s energy currency, and places them on other molecules. From that 2013 study, which took more than five years to complete, the team learned some key things about the protein, such as what the ATP-binding site looks like…

The study that took more than 5 years to complete was published as: mTOR kinase structure, mechanism and regulation

The structures also reveal active-site residues and conformational changes that underlie inhibitor potency and specificity.

They had experimental evidence of energy-dependent changes in active-site residues (i.e., amino acids). They subsequently failed to link anything known to serious scientists about the energy-dependent changes from angstroms to ecosystems in all living genera via the physiology of pheromone-controlled reproduction. They seemingly ignored all claims about RNA-mediated amino acid substitutions in the context of autophagy, which links base pair changes from changes in the microRNA/messenger RNA balance to RNA editing.
How could the Nature Publishing Group not know what all serious scientists know?
See for example: All Nobel Laureates in Physiology or Medicine

The Nobel Prize in Physiology or Medicine 2017

Jeffrey C. Hall, Michael Rosbash and Michael W. Young

“for their discoveries of molecular mechanisms controlling the circadian rhythm”

The molecular mechanisms are energy-dependent.
Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels  (1990) Hardin, Hall and Michael Rosbash
Who, besides Jack Szostak, does not know that the creation of energy must be linked to RNA-mediated cell type differentiation via messenger RNA levels?

The Nobel Prize in Physiology or Medicine 2009

Elizabeth H. Blackburn, Carol W. Greider and Jack W. Szostak

“for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase”

Where did the enzyme telomerase come from?
Face the facts, Jack (Szostak) and others. Cell type differentiation is food energy-dependent and biophysically constrained at every level of examination. Biophysical constraints on viral latency are required for ecological adaptation. The anti-entropic virucidal energy of sunlight links food energy directly from the innate immune system to all morphological and behavioral diversity. It’s all about energy. It’s all about the creation of enzymes. It’s all about the base pairs.
See:  Structural diversity of supercoiled DNA

Difference in the network of hydrogen bonds between high- and low-altitude Hb variants, HH-H and LL-L, respectively

The α1 and β1 subunits of HH-H (light blue) and LL-L (light red) are superimposed, and van der Waals radii are shown for α-chain residues that are in atomic contact with β-chain residues of the opposing α2β2 dimer.

The overwhelming ignorance of sex researchers

Summary: J. Michael Bailey, and others like him, pretend to not know how non-coding variants are epigenetically linked from differences in hydrogen bonds to all energy-dependent biophysically constrained morphological and behavioral phenotypes.

Genome-Wide Association Study of Male Sexual Orientation [Energy-dependent changes in biophysically constrained viral latency]

We identified several [energy-dependent changes in] SNPs with p < 10−5, including regions of multiple supporting SNPs on chromosomes 13 (minimum p = 7.5 × 10−7) and 14 (p = 4.7 × 10−7). The genes nearest to these peaks have functions plausibly relevant to [biophysically constrained viral latency and] the development of  sexual orientation.

Reported as: Gene variants identified that may influence sexual orientation in men and boys

The findings by the team do not settle the argument of whether homosexuality in people is biology-based, but instead offers more evidence that suggests it is likely the case. Prior studies that looked at family histories have also offered some evidence of biology playing a role while other studies have found some differences in chromosomes. In this study, the number of samples tested was too small to offer conclusive evidence—larger studies will have to be undertaken to solidify the evidence.

I was not surprised to see J. Michael Bailey listed as a co-author. He is a biologically uninformed pseudoscientist and a passive/aggressive antagonist.

It’s been more than 4 years since food energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution were linked to biophysically constrained viral latency and all biodiversity via the pheromone-controlled physiology of reproduction in all living genera.

An external file that holds a picture, illustration, etc. Object name is nihms675257f2.jpg
Sex researchers like J. Michael Bailey, are still among the majority of those who have paid no attention to the extant literature since the time we published this 1996 review in Hormones and Behavior (with a section on molecular epigenetics.)

From Fertilization to Adult Sexual Behavior

Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus (Runge and Zakian, 1996; Wu and Haber, 1995).

All serious scientists know that everyone else must also start with differences in the quantized energy of hydrogen to get from epigenetic modifications to differences in morphological and behavioral phenotypes. Serious scientists also know that social science is pseudoscience and that pseudoscientific nonsense is the cause of all preventable unnecessary suffering and premature death.

See for instance:

1) Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin
2) Mutation-Driven Evolution
and my refutation of neo-Darwinian pseudoscientific nonsense. All three were published on June 14, 2013.
3) Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Please join the other serious scientists who have been quietly ridiculing people like J. Michael Bailey for more than 20 years.

QuEBS workshop has established itself as an outstanding stage to present the research in the intersection of physics, chemistry and biology. This field has been developed in Lithuania for more than 20 years already. The beginnings could be associated with a series of “Light-harvesting Physics” international conferences, which were held in Lithuania (in Preila, 1992 and 1994, and in Birštonas, 1996). During these conferences, discussion of notable scientists and pioneers of Quantum Biology, such as Graham R. Fleming, Shaul Mukamel, Rienk van Grondelle, Richard Cogdell, Alfred Holzwarth and others, established excitons in biology as the “must-talk-language” when describing the quantum effects in biological light-harvesting systems.

Light harvesting is the source of energy-dependent changes in hydrogen that link physics, chemistry, and molecular epigenetics to accurate representations of RNA-mediated cell type differentiation. All aspects of energy-dependent RNA-mediated cell type differentiation have been virtually ignored by J. Michael Bailey, who is the proud owner of the Sexnet listserver. It has been a consistent source of misinformation for all participants during the past two decades.
See for comparison my comments on: Evolution of a Vertebrate Social Decision-Making Network
1)

Re: Cause and effect. How could it not be the adaptive evolution from yeasts of the ligand-receptor binding exemplified across species by the conservaton of gonadotropin releasing hormone (GnRH) and diversification of its receptor? Model organisms like the threespine stickleback make clear the involvement of ecological niche construction. The honeybee invertebrate model organism makes clear the involvement of the nutrient dependent ecological niche in construction of the pheromone-dependent social niche. Invertebrate and vertebrate models collectively attest to the common molecular biology of adaptively evolved social decision-making networks. In mammals, the hypothalamic neurogenenic niche (probably located in the MPOA) responds to nutrients to enable fertility and responds to pheromones to enable sexual reproduction that has adaptively evolved from its origins in brewer’s yeast. Never before has there been such a clear reprentation of cause and effect across species from microbes to man, where nutrient chemicals calibrate the intracellular signaling and their metabolism to pheromones standardizes and controls the stochastic gene expression required for reproduction. Gene expression enables adaptive evolution of the brain and ensures that our ability to acquire nutrient chemicals is the first priority for reproduction via appropriate social behaviors, as it is in every species. For example, microbes eat the DNA of heterospecifics but not conspecifics, which indicate more social sense than what some people today are capable of recognizing in the design of biology (the evolved gene, cell, tissue, organ, organ system pathway that directly links sensory input to the mammalian neuroendocrine system and the hormones responsible for our behavior, which activates the same ‘organized’ pathway).

2)
Re: The Intersection of Neurotoxicology and Endocrine Disruption. NeuroToxicology, Bernard Weiss

Abstract excerpts: …hormones help steer the process of brain development.

…sex differences in behavior are primarily the outcomes of differences in how the brain is sexually differentiated during early development by gonadal hormones (the Organizational Hypothesis).

… environmental chemicals are capable of altering these underlying events and processes. Among those chemicals, the group labeled as endocrine disrupting chemicals (EDCs) offers the clearest evidence of such selectivity… —————– I have terminally argued to conclusion that the clearest evidence of chemicals that alter the underlying events and processes of brain development and its sexual differentiation are the nutrient chemicals and pheromones responsible for the adaptive evolution of species from microbes to man.

Focus on endocrine disruption establishes what happens when toxic chemicals alter the same events and processes of brain development and its sexual differentiation via epigenetic effects on gonadotropin releasing hormone (GnRH) pulsatility, luteinizing hormone, olfactory bulb neurogenesis, hippocampal neurogenesis, learning, and memory in vertebrates.

For contrast, I’ve modeled the epigenetic effects of food odors and pheromones on homeostasis and species diversification, and for many years, my friend Teresa Binstock and co-author (e.g., with Milton Diamond)stressed the importance of endocrine disruption (specifically due to bisphenol A and phthalates) on J. Michael Bailey’s “Sexnet”. Now that the basic principles of biology and levels of biological organization, which link sensory input from the environment directly to behavior via intracellular signaling and stochastic gene expression, have been clarified by work with model organisms, I look forward to learning if there are any reasons to avoid the incorporation of current information on endocrine disruption into existing studies of the homeostatic development of human sexual behavior.

Comparing typical and atypical epigenetic effects that appear to extend to those that are transgenerational seems even more important now than in 1996.

Kohl, J.V. (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Socioaffective Neuroscience & Psychology, 2: 17338

See also: Open Chromatin Profiling in hiPSC-Derived Neurons Prioritizes Functional Noncoding Psychiatric Risk Variants and Highlights Neurodevelopmental Loci

Our study shows that noncoding disease variants in OCRs can affect neurodevelopment, and that analysis of open chromatin regions can help prioritize functionally relevant noncoding variants identified by GWAS.

After Alan R. Sanders and others published this, the claims in Genome-Wide Association Study of Male Sexual Orientation can be viewed in the context of two decades of false claims and pleas for more funding.

Conclusion:

In this study, the number of samples tested was too small to offer conclusive evidence—larger studies will have to be undertaken to solidify the evidence.

For God and Country

Faith in evolution: Paleontology as a molecular science

Keeping the faith

For the last 20 years, Mary Schweitzer, a paleontologist at North Carolina State University in Raleigh, has amassed a wealth of evidence that she’s isolated protein fragments from dinosaurs as much as 80 million years old. That bucks the conventional wisdom among paleontologists who argue that proteins, which are made of chains of amino acids, can’t survive more than 1 million years or so. So far, no group other than Schweitzer and her collaborators has managed to replicate the findings. She contends that’s because others don’t follow her methods. If Schweitzer is right and outside researchers eventually do confirm her findings, it could transform dinosaur paleontology into a molecular science. That, in turn, could help researchers answer long-standing questions, such as whether dinosaurs were warm- or cold-blooded, and work out the dinosaur family tree.

The evidence does not show that the protein fragments are from dinosaurs as much as 80 million years old. No experimental evidence of biophysically constrained biologically-based cause and effect suggests that is possible. But she is keeping her faith in evolution despite the fact the nothing but mathematical models support that pseudoscientific nonsense.
See for comparison: Paths of the Trinity: Being-in-Relationship as Theology, an Answer to Zen Buddhism
In the comments, Jay Kimooyoung wrote:

As people get more informed of the range of interpretive tools that have been avalialbe across different times and different cultures, with their commonality and distinctions, both apparent and real, hopefully they will interact with the world more freely, and then collectively enter into a more ‘enlightend’ stage in the next chapter of our history.

The 2017 Nobel Laureates in Chemistry shared their prize for linking energy-dependent changes from electrons to ecosystems in all living genera via the cryo-EM technology that enables observation at the level of changes in atoms and hydrogen-atom transfer in DNA base pairs in solution. Virus-driven theft of quantized energy occurs at that level of examination, which is how the degradation of messenger RNA is linked to all pathology. If you are not willing to “inform yourself” or to believe serious scientists, do not wait for anyone to “…enter into a more ‘enlightend’ stage in the next chapter of our history.”
Energy is information. The virus driven energy theft that links the degradation of messenger RNA to all pathology is proof that the number of biologically uninformed science idiots who claim to be scientists is greater than the number of serious scientists. The number of self-serving theologians is of secondary concern.
Jay Kimooyoung

New discoveries are made through numerous attempted experiements. Such attempts require huge investment of energy and accumulated information. In the development of science, they are as much the integral part as pigeonhalling confirmed data. Attempted memes are the background soil for the progress in science.

And more so is with the situation of theology. What ultimately validates is not correspondence according to objectified criteria. It is the extent of sincere dedication that serves to carry the weight of life. In that sense, every theology contains element of self-service. Concern could be a matter of degree rather.

To my horror, “Answers in Genesis” just published Celebrate Your Inner Virus — a reversal of their long-standing theological perspective that links the “Curse” from the virus-driven degradation of messenger RNA to all pathology.

It is important that we understand the design present in viruses because God made them

See for comparison: Did God Make Pathogenic Viruses?

Pathogenesis is evidence of something gone wrong, a mutation or the accidental movement of genes, and not evidence of a system deliberately designed to cause human disease and suffering.

My life’s works have served to refute all the pseudoscientific nonsense touted by neo-Darwinists and “Big Bang” cosmologists. “Answers in Genesis” now appears to be supporting them.
See for comparison: https://www.youtube.com/watch?v=HaKf2VuOyl0&feature=youtu.be Video interview about the death of Robin Williams Quantum Souls Published on 10 May 2017
https://www.youtube.com/watch?v=OIkbH9dcAkw&feature=youtu.be Superbugs, Bacteriophages and Phage Therapy: An Interview with James Kohl Published on 17 May 2017
https://www.youtube.com/watch?v=iTvT0p9Q5TY Food Energy-Dependent Cell Type Differentiation Refutes Theory of Evolution
https://www.youtube.com/watch?v=wfPy5QDJp7w&feature=youtu.be How to Treat Cancer as a Disorder of Energy Transfer
https://www.youtube.com/watch?v=s7_fQ2fS5UY&feature=youtu.be Charles Darwin Taught Conditions of Life, Not Mutations
https://www.youtube.com/watch?v=HCQI7fMi8ts Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 1
https://www.youtube.com/watch?v=ObHVOdi99Rw Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 2
See also: Base-pair opening dynamics of the microRNA precursor pri-miR156a affect temperature-responsive flowering in Arabidopsis

Based on these results, we propose that fine-tuning of the base-pair stability at the cleavage site is essential for efficient processing of pri-miR156a at a low temperature and for reduced flowering sensitivity to ambient temperature changes.

All the co-authors are from South Korea and so is Jay Kimooyoung.
I ride for God and country with the American Legion Riders. See for comparison: Energy as information and constrained endogenous RNA interference

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy. The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection.

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

Re: The viral hecatomb
In his 2010 publication “The Great Pheromone Myth“, Richard L. Doty challenged all accurate representations of the top-down energy-dependent creation of RNA and biophysically constrained pheromone-controlled biodiversity.
On 5/16/17, he published: Olfactory dysfunction in neurodegenerative diseases: is there a common pathological substrate?

…antibodies or other evidence of viral infection have been found to be higher in the autopsied brains of people with neurodegenerative diseases with the most smell loss (figure 2), relative to the brains of healthy controls. Whether a close relationship exists between smell dysfunction and antibodies or other indicators of viral involvement is unknown.

The close relationship that exists between smell dysfunction indicators of viral involvement has been exquisitely detailed in my life’s history of published works and presentations. All of them link what is now known about the virus-driven degradation of messenger RNA from mutations to all pathology in species from microbes to humans.
See: Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

Currently, only a limited number of miRNA and miRNA-like RNAs have been found in bacteria and viruses, a number that is sure to increase rapidly in the future. 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.

See also: Deep-Sea Viruses Destroy Archaea
See also: High potential for temperate viruses to drive carbon cycling in chemoautotrophy-dominated shallow-water hydrothermal vents

…inducible provirus-host interactions occurring in these systems can profoundly influence the functioning of the microbial food web and the efficiency in the energy transfer to the higher trophic levels.

Summary: The virus-driven theft of quantized energy prevents the efficient transfer of energy that is required to link the physiology of pheromone-controlled reproduction to all biodiversity on Earth. Instead, the virus-driven degradation of messenger RNA has been linked to all pathology.
Remember, anytime a pseudoscientist like Richard L. Doty claims that mammalian pheromones and/or human pheromones do not exist, that pseudoscientist is trying to cover up a history of ignorance. The history of ignorance has caused the unnecessary suffering and premature death of millions of people during the past two decades. Pseudoscientists have placed their faith in evolution and in the nonsense touted by people like Doty, who never learned to link the metabolism of food energy to pheromones or linked species-specific pheromones from the physiology of reproduction to biophysically constrained viral latency and all biodiversity.
See for comparison: “Cytosis

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

See also: Subatomic

Subatomic introduces a unique variation on deck building with a highly accurate chemistry theme, with the ultimate goal of building Elements to score points, but allowing many varying types of strategies.

Lethal virus kills 5 billion people?

Until death: Virus-driven failure of multisensory integration (2)

Summary: The virus-driven degradation of messenger RNA is clearly linked to frontotemporal dementia (FTD) by altered language, personality, behavior, cognition and motor function. What causes FTD? If the virus-driven degradation of messenger RNA causes all pathology, I would expect to find a link from microRNAs to the pathology and to the effective treatment.

The social and economic burden of frontotemporal degeneration

Reported as: Study reveals staggering economic burden of dementia in younger people

Frontotemporal degeneration (FTD) accounts for 20 to 50 percent of dementia cases in people under the age of 65. FTD ravages an individual’s quality of life by dramatically altering their language, personality, behavior, cognition and motor function.

FTD alters language, personality, behavior, cognition and motor function. What causes FTD? If the virus-driven degradation of messenger RNA causes all pathology, I would expect to find a link from microRNAs to the pathology and to the effective treatment.
See for instance: Tumour necrosis factor-α (TNF-α) and miRNA expression in frontal and temporal neocortex in Alzheimer’s disease and the effect of TNF-α on miRNA expression in vitro
See also: miR-106b inhibits tau phosphorylation at Tyr18 by targeting Fyn in a model of Alzheimer’s disease
The facts that link the virus-driven degradation of messenger RNA to all pathology have also been placed into the context of this report: Global Sensory Impairment Predicts Morbidity and Mortality in Older U.S. Adults
I mentioned before that this was reported in the news as: Problems with senses may predict older adults’ overall health, ability to function

Researchers have mainly focused on what happens after people lose one or two of their senses. However, we know that losing more than two senses occurs frequently for older adults. Until now, no studies have examined how losing multiple senses affects older adults.

I also mentioned that the virus-driven loss of G protein-coupled receptors has been linked to the loss of multiple senses in all organisms at all ages.
See: Olfaction Warps Visual Time Perception
For comparison, pseudoscientists reported Brain wiring affects how people perform specific tasks

“Individuals organize themselves into densely interconnected communities, like the dormitories and sports teams, though individuals within these groups also have connections with people outside of those groups. Brains are the same way: Brain regions are organized into communities with lots of connections between regions in the community and fewer connections to regions outside of the community. But people’s brains are different. Some people have brains that are better described as having rigid community structure—or higher modularity—while other people have brains without such rigid community structure—or lower modularity.”

The individuals of all species must find food to reproduce. That’s how the individuals become part of a species. Their pheromone-controlled physiology of reproduction has been linked to all biodiversity in all genera. The claim “Individuals organize themselves…” is foolish. Claims about higher or lower modularity could be linked to the pseudoscientific nonsense touted in reports like this: The fusiform face area and occipital face area show sensitivity to spatial relations in faces
See also: The Blur of Pleasure: Appetitively Appealing Stimuli Decrease Subjective Temporal Perceptual Acuity
Reported as:  Appetizing imagery puts visual perception on fast forward

“Our research shows that emotionally-charged stimuli, specifically positive and negative images, may influence the speed, or the temporal resolution, of visual perception…”

See for comparison: Supercool Protein Imaging Gets the Nobel Prize

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

See for comparison: How childhood trauma affects the brain

The researchers’ conclusion is that experiencing abuse in early life “may lastingly disrupt” the connectivity between the areas of the brain that are key in cognitive and emotional processes.

Receptor mediated epigenetic effects on hormones are the link to affects on behavior via energy-dependent RNA-mediated cell type differentiation in the context of the creation of enzymes and the physiology of pheromone-controlled reproduction. See anything ever published by Bruce McEwen for examples of how a single amino acid substitution predicts differences in behavioral development.
 
Keep in mind that “Bump stock” is not a person. It’s an invention that can be examined in the context of cryo-EM to explain why someone would use reports on the “bump stock” technology to obfuscate the facts about the cryo-EM technology. The facts about cryo-EM and supercoiled DNA can be used to eradicate all virus-driven pathology.
 
For example, the ability to examine virus-driven changes in the transfer of energy in DNA base pairs can be linked to what is known about food energy-dependent RNA-mediated amino acid substitutions in organized genomes. The substitutions typically stabilize the organized genomes of people like Stephen Paddock.
 

See also: Irreversibility and the Arrow of Time in a Quenched Quantum System

Reported as: Physicists confirm thermodynamic irreversibility in a quantum system

“Our experiment shows the irreversible nature of quantum dynamics, but does not pinpoint, experimentally, what causes it at the microscopic level, what determines the onset of the arrow of time,” coauthor Mauro Paternostro at Queen’s University in Belfast, UK, told Phys.org. “Addressing it would clarify the ultimate reason for its emergence.”

For comparison, see: Charles Darwin’s 150-year-old theory of how life on earth emerged gets thumbs-up from scientists

Their ridiculous theories can be placed into the context of Lewis Carrol’s attribution of this thought process to “Humpty Dumpty.”

 

“Emergence” and “evolution” are meaningless terms outside the context of ridiculous theories and pseudoscientific nonsense touted by researchers who are biologically uninformed science idiots. They seem to think that they can put the pieces of biophysically constrained life on Earth back into their theories as if “Humpty Dumpty” exemplified a creature with an evolved shell.

Cryo-EM has helped to pinpoint why the nature of quantum dynamics is irreversible. At the microscopic level of hydrogen-atom transfer in DNA base pairs in solution, the creation of energy as information has been linked to healthy longevity in all living genera. Virus-driven energy theft has been linked from the degradation of messenger RNA to all pathology.

See also: Neuropathology of suicide: recent findings and future directions

“…the unravelling of the unique epigenetic processes that occur in the brain has opened promising avenues in suicide research.”

Reported without citation in the context of: How childhood trauma affects the brain

What led my former FB friends to claim that my life’s works and efforts toward suicide prevention were “bullspit” or that “nobody cared?” The Nobel Prize in Chemistry just validated my model in the context of what is known about cryo-EM.
 

What led researchers who are biologically uninformed science idiots to criticize my model? Criticisms of the nutrient-dependent pheromone-controlled evolutionary model

Who will be the first to apologize for the role they played in the suicide death of Stephen Paddock and the unnecessary suffering and death of his victims?

Moving forward, what role will “apologetics” play in consoling the victims of virus-driven energy theft and all pathology?

See: Celebrate Your Inner Virus 

…we seek to highlight the strengths of what makes a virus on this Virus Appreciation Day.

Answers in Genesis is an apologetics ministry, dedicated to helping Christians defend their faith and proclaim the gospel of Jesus Christ.

Virus appreciation is interesting in the context of claims this group made since 1999.

See: Did God Make Pathogenic Viruses? (1999)

Without viruses, the genetic revolution we are now experiencing would be impossible. They also serve numerous beneficial functions that we are just beginning to research and understand.

Viral Genome Junk Is Bunk (2015)

…mammalian viruses may not have existed at all before the Curse, but after mankind’s sin may have been allowed to develop from DNA sequence already present in the now-fallen people and animals of the earth. Again, cutting-edge genome research confirms the Genesis account of origins.

I agree, but the Genesis account of origins puts the Curse before the creation of viruses, which have been linked from the virus-driven degradation of messenger RNA to mutations and all pathology during the past 5-10,000 years.

See: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

Reported as: Past 5,000 years prolific for changes to human genome

Of 1.15 million single-nucleotide variants found among more than 15,000 protein-encoding genes, 73% in arose the past 5,000 years, the researchers report. 164,688 of the variants — roughly 14% — were potentially harmful, and of those, 86% arose in the past 5,000 years. More broadly, the results suggest that humans are carrying around larger numbers of deleterious mutations than they did a few thousand years ago. But this doesn’t mean that humans now are more susceptible to disease, says Akey. Rather, it suggests that most diseases are caused by more than one variant, and that diseases could operate through different genetic pathways and mechanisms in different people.

Stress has different effects on different people.

See for comparison: Epigenetic Regulation of the Kappa Opioid Receptor by Child Abuse

…this receptor may be epigenetically regulated by stressful experiences, in particular as a function of early social life.

See also: Cell stress response sheds light on treating inflammation-related cancer, aging

A Traumatic Experience Can Reshape Your Microbiome

The stress-linked reshaping of  your microbiome has repeatedly been linked from the virus-driven failure of multisensory integration to suicide.

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

Predicting who wins the 2017 Nobel Prizes (4)

As you wait to learn who won the 2017 Nobel Prize in Physics and in Chemistry, please consider how these recent reports will be linked from electrons to ecosystems. Every aspect must start with the creation of energy, which must link chemistry to biophysically constrained biologically based life on Earth in the context of the physiology of pheromone-controlled reproduction and Schrodinger’s claims in “What is Life? (1944). Without mention of the anti-entropic virucidal energy of sunlight, the theories of physicists and chemists have no explanatory power. Experimental evidence of top-down causation is expected to be part of the criteria for awarding these two Nobel Prizes. Will the experimental evidence include anything known to serious scientists about the anti-entropic virucidal energy of sunlight?
High-order multiphoton Thomson scattering

…the experiment’s potential to generate attosecond-duration hard X-ray pulses can enable the study of ultrafast nuclear dynamics.

Reported as: One billion suns: World’s brightest laser sparks new behavior in light

That phenomenon stemmed partly from a change in the electron, which abandoned its usual up-and-down motion in favor of a figure-8 flight pattern. As it would under normal conditions, the electron also ejected its own photon, which was jarred loose by the energy of the incoming photons. But the researchers found that the ejected photon absorbed the collective energy of all the scattered photons, granting it the energy and wavelength of an X-ray.

Hard Two-Photon Contribution to Elastic Lepton-Proton Scattering Determined by the OLYMPUS Experiment

The OLYMPUS Collaboration reports on a precision measurement of the positron-proton to electron-proton elastic cross section ratio, R2γ, a direct measure of the contribution of hard two-photon exchange to the elastic cross section.

Reported as: OLYMPUS experiment sheds light on structure of protons

…most of the time, only one of the photons has high energy, while the other must carry very little energy indeed, according to Richard Milner, a professor of physics and member of the Laboratory for Nuclear Science’s Hadronic Physics Group, who led the experiment.

The difference between the theoretical and experimental results means further experiments may need to be carried out in the future, at even higher energies where the two-photon exchange effect is expected to be larger, Hasell says.

Probing electronic binding potentials with attosecond photoelectron wavepackets

The central goal of attosecond science is to visualize, understand and ultimately control electron dynamics in matter over the fastest relevant timescales.

Reported as: First look at electrons escaping atoms

Electrons behave differently when they can feel the tug of sub-atomic forces from a nucleus and neighbor electrons, and the farther away they get from an atom, those forces diminish. Though breaking free takes less than a femtosecond (one quadrillionth of a second), this study shows how an electron’s momentum changes many times along the way as it loses contact with individual parts of the atom. Those changes take place on the scale of attoseconds (thousandths of a femtosecond, or quintillionths of a second).

Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution

The observation of these sequential EDPT mechanisms across intermolecular hydrogen bonds confirms an important and long debated pathway for the deactivation of photoexcited base pairs, with possible implications for the UV photochemistry of DNA.

UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair

…excitation of a guanine (G) adenine (A) sequence leads to reformation of the intact thymine (T) bases. The involvement of two bases for the repair points to a long-living charge transfer state between G and A to be responsible for the repair.

Polarization-entangled photons from an InGaAs-based quantum dot emitting in the telecom C-band

The ability to generate entangled photons is a key prerequisite for several quantum applications like quantum information processing,

All energy-dependent information processing is quantum information processing because the quantized energy comes from sunlight.
Reported as: Researchers change wavelengths of entangled photons to those used in telecommunications

The researchers used quantum dots created from an indium arsenide and gallium arsenide platform, producing pure single photons and entangled photons. Unlike parametric down-conversion techniques, quantum dots allow for photons to be emitted only one at a time and on demand, crucial properties for quantum computing.

See also:  A sea of spinning electrons: Discovery could spawn a wave of new electronic devices

Collective chiral spin modes are propagating waves of electron spins that do not carry a charge current but modify the “spinning” directions of electrons. “Chiral” refers to entities, like your right and left hands, that are matching but asymmetrical and can’t be superimposed on their mirror image.

Chiral spin modes must be linked from energy-dependent changes in subatomic particles and chirality to biophysically constrained autophagy in the context of the physiology of reproduction in all living genera.
See for example: Soilborne fungi have host affinity and host-specific effects on seed germination and survival in a lowland tropical forest
Reported as: Tropical diversity takes root in relationships between fungi and seeds

…the fungi affected seed mortality and germination in a species-specific manner.

“One fascinating result was that if a fungus had a pathogenic effect on one plant species, it was likely to have the opposite effect on another,” said coauthor Paul-Camilo Zalamea, a Smithsonian postdoctoral fellow.

All biodiversity is energy-dependent and biophysically constrained by the physiology of reproduction. The anti-entropic virucidal energy comes from sunlight. Nothing takes root without it.

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)

See also: Prairie strips improve biodiversity and the delivery of multiple ecosystem services from corn–soybean croplands

Loss of biodiversity and degradation of ecosystem services from agricultural lands remain important challenges in the United States…

Reported as:  Strips of prairie plants slow loss of soil, nutrients and water from ag fields, double biodiversity

Researchers report that replacing 10-20 percent of cropland with prairie strips increased biodiversity and ecosystem services with minimal impacts on crop production.

m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs

The different propensities to form Hoogsteen base pairs in B-DNA and A-RNA may help cells meet the opposing requirements of maintaining genome stability, on the one hand, and of dynamically modulating the structure of the epitranscriptome, on the other.

Alternative splicing of pre-mRNA

Sexual communication signals: New Insights!

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

New insights in the evolution of sexual communication signals

Abstract excerpt:

Our research focuses on identifying a) the genes underlying sexual signals and responses in both sexes2-4, and b) ecological factors that may cause divergence in sexual communication. Factors that we found to affect sexual communication are closely related species with similar mating signals5, low nutritional quality, (toxic) secondary plant metabolites and pathogens6.

Elizabeth Pennisi reported on this 2017 conference presentation and claimed:

The results “demonstrate the importance of the social environment,” Halfwerk says. “One form does not attract males on its own, only in close proximity of the other form.” That result also parallels what’s been found in humans: that an attractive woman in a crowd of less attractive women also seems to attract more attention. But pinning down exactly why this happens should be much easier in moths than people, she notes. “That’s the nice thing about insects.”

See: Sexy females help ‘Plain Jane’ moths snag their mates

No experimental evidence of biologically-based sexual communication suggests that sex signals evolved. The fine-tuned systems of communication among individuals and species pose an evolutionary dilemma because they are food energy-dependent. Ecological variation must be linked from food energy to biophysically constrained ecological adaptations by the pheromone-controlled physiology of reproduction in all living genera. Also, everything known to serious scientists about energy-dependent top-down creation links the anti-entropic virucidal energy of sunlight from the creation of ATP to the creation of messenger RNA. That fact does not appear to be coincidental.

See: 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.

Detailed experimental evidence also links the virus-driven degradation of messenger RNA from mutations to all pathology. That fact leaves neo-Darwinian theorists and “Big Bang” cosmologists without any acceptable theory of anything or any theory of everything.

See for comparison: A New Physics Theory of Life and Jeremy England’s idea that “You start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant.” 

Theorists and philosophers cannot link energy as information or “big bang” cosmology to biodiversity without the creation of energy. Most of them ignore the fact that they do not know where the energy in a hydrogen atom came from.

Without the de novo creation of energy, they cannot link hydrogen-atom transfer in DNA base pairs in solution from microRNA flanking sequences to SNPs, and they cannot link food energy as information to fixation of RNA-mediated amino acid substitutions in organized genomes. For comparison, all serious scientists have linked what is known about the food energy-dependent fixation of amino acid substitutions to the structure and function of supercoiled DNA, and all serious scientists have linked energy-dependent RNA-mediated cause and effect to all biodiversity via the physiology of pheromone-controlled reproduction.

That fact helps to explain why Richard Feynman referred to some theoretical physicists as examples of human idiocy.

See: Food energy

That suggests Elizabeth Pennisi is a biologically uninformed. She reported: “That’s the nice thing about insects.” If she was not a biologically uninformed science idiot, she would have linked food energy to the physiology of reproduction in all invertebrates and vertebrates. That is how the pheromone-controlled physiology of reproduction is linked from ecological variation to all biodiversity via what is known to all serious scientists about ecological adaptation.
See: Feedback loops link odor and pheromone signaling with reproduction and Olfaction Warps Visual Time Perception

For comparison to the science reporting by Elizabeth Pennisi,  J.A. Parker is the only person besides me, who has reported on this 2017 conference presentation:

See also: All in the (bigger) family by Elizabeth Pennisi with my comment:

The 2015 Society for Integrative and Comparative Biology (SICB) presenters may not recognize how much progress has been made since the 2013 ecological epigenetics symposium. For example, since then authors claimed “…ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.” http://dx.doi.org/10.1038/nature13400

Six months later, other authors traced signaling factors found in vertebrates to the origin of nerve cell centralization via the diffuse nerve net of animals like the sea anemone. http://dx.doi.org/10.1038/ncomms6536 That fact suggests ecological variation is linked to ecological adaptations in morphological and behavioral phenotypes via signaling protein concentrations that differentiate various cell types in body axes and the central nervous system.

Links across species from the epigenetic landscape to the physical landscape of DNA in organized genomes appear to have their origins in the conserved molecular mechanisms of RNA-directed DNA methylation and RNA-mediated protein folding. Two weeks after the publication that refuted ideas about independently evolved neural systems or muscle specification — and perhaps refuted the independent evolution of anything else, SICB presenters linked crustaceans to insects.

Apparently, they’ve learned that the same set of microRNAs controls expression of the genes for rate-limiting enzymes that control the hormone production of different hormones in insects and crustaceans.

Why were they left with any questions about how crustaceans and insects could all be part of one big family? They linked RNA-mediated cell type differentiation to what we described in our section on molecular epigenetics in our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior http://www.hawaii.edu/PCSS/biblio/articles/1961to1999/1996-from-fertilization.html

See also: Sex differences in microRNA-mRNA networks: examination of novel epigenetic programming mechanisms in the sexually dimorphic neonatal hypothalamus

Integrating miRNAs and their broad actions on gene function into our conceptualization of the factors directing sexual differentiation of the brain could be a highly informative next step in efforts to understand the complexities behind these processes.

They linked sex differences in microRNAs to the sexual differentiation of all cell types in all living genera that sexually reproduce via microRNA-mRNA networks.
See also: The phylogenetic utility and functional constraint of microRNA flanking sequences

…miRNAs can be employed as both qualitative [9] and quantitative markers, with the latter demonstrated clearly here. Our investigation demonstrates the utility of miRNA sequences as classical phylogenetic markers, and shows this usage is robust to different algorithms of phylogenetic analysis and the analysis of fast-evolving lineages. Such a method provides novel characters for assessing phylogenetic relationships that will be of use in a range of contexts for resolving branches across the tree of life.

See also: Role of olfaction in Octopus vulgaris reproduction

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).

Kohl (2013) is: Nutrient-dependent/pheromone-controlled adaptive evolution: a model (June 14, 2013)

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

Elekonich and Robinson (2000) cited:  From Fertilization to Adult Sexual Behavior (1996)
At the time of our 1996 Hormones and Behavior review, microRNAs were called pre-mRNAs. See our section on molecular epigenetics:

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.

Social odors are still called pheromones and we linked the food energy-dependent pheromone-controlled physiology of reproduction to all biophysically constrained biodiversity on Earth via sex differences in microRNAs (pre-mRNAs).
The sex differences in microRNAs will soon be linked to sex differences in healthy longevity and to sex differences in diseases in the context of the cell biology game: “Cytosis.” Next, the game “Subatomic” will teach others how to build an atom.
The fact that this invited review linked energy-dependent changes in atoms to ecosystems may still go unnoticed, since the invited review was returned without review.
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
But, for God’s sake, see for comparison: 7/25/13
Jay R. Feierman:

“Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.”

Do not ignore the fact that Jay R. Feierman has no understanding of how ecological variation must be linked to energy-dependent ecological adaptation via the pheromone-controlled physiology of reproduction.
See also: December 5, 2016

[MODERATOR NOTE: I’m not going to post more from Kohl until he answers the very direct and simple question posed to him by anon, which is whether he (Kohl) believes that RNA splicing can change DNA.]

What I believe about RNA splicing is irrelevant unless someone else links the creation of energy to ATP and the creation of RNA outside the context of energy-dependent alternative splicings of pre-mRNA and the link from energy to the creation of the pre-mRNAs and to energy-dependent biophysical constraints on supercoiled DNA in all living genera.

As Heyn points out, “we still do not fully understand the mechanisms that drive epigenetic variation in populations.”

Natural selection for energy-dependent codon optimality links RNA-directed DNA methylation to all biophysically constrained biodiversity via the pheromone-controlled physiology of reproduction. That fact seems to be missing from this representation of a failed paradigm (neo-Darwinian evolution).
Claims that facts about natural selection and epigenetic variation in populations are not fully understood can be viewed in the context of reports by those who understand the facts about Darwin’s “conditions of life.” They are energy-dependent and RNA-mediated
See for example: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition and Olfaction Warps Visual Time Perception
It has become obvious to all serious scientists that the sense of smell in bacteria must be linked from mRNA stability to our visual perception of mass and energy in the context of natural selection across the time-space continuum via the pheromone-controlled physiology of reproduction. The complexity of that fact may not be understood by biologically uninformed theorists, but no theorist should claim that the mechanisms of food energy-dependent pheromone-controlled biophysically constrained cell type differentiation are not understood by all serious scientists.
Re: …a strong link between population-specific DNA methylation, mRNA levels, and genotypes.
See also: Methylation Variation Documented Between Human Populations

“Our analysis of five worldwide populations revealed a strong correspondence between population-specific DNA methylation, [messenger RNA] levels, and genotypes,” the authors wrote. “The correlation with genetic divergence was stronger for DNA methylation, and, consistent with this, our results suggest stronger local genetic control of population-specific DNA methylation levels than of mRNA expression levels.”

The strong link and/or strong correspondence between food energy-dependent DNA methylation, messenger RNA levels and genotypes is biophysically constained by the pheromone-controlled physiology of reproduction in all livng genera. See for example: 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.

Glycolysis and the citric acid cycle appear to provide the free energy for nuclear ATP synthesis and the food-energy-depenent biosynthesis of messenger RNA. If so, all pathology is caused by the virus-driven degradation of messenger RNA, which links mutations but not from ecological variation to ecological adaptations.
See also: Back to Basics: Next-generation sequencing methods and applications (with my emphasis)

…another common NGS application (although one currently more of a research application than a front-line clinical tool) is to examine the transcriptome of a sample—that is, the identity and relative abundance of mRNA transcripts present. Sometimes referred to as “exome sequencing,” this approach is efficient in that it applies resources only to that small portion of the genome which is functionally expressed. Of course, not all significant genetic aberrations occur within coding regions; but by observing levels (or even presence/absence) of transcripts in comparison to reference “normal” conditions, important mutations in non-coding regions such as gene promoters or splice site regulators can be inferred. When such findings are plausibly related to a disease condition, more directed studies to confirm the root cause can then be undertaken as or if needed.

See also: microRNA “exome sequencing Items: 1 to 20 of 55 There is no need to infer that splice site regulators are not food energy-dependent and yet that is what biologically uninformed neo-Darwinian theorists have consistently done with their claims about Mutation-driven evolution. For comparison, all serious scientists are Combating Evolution to Fight Disease.
See also: Global Epigenomic Reconfiguration During Mammalian Brain Development July 4, 2013

DNA methylation is implicated in mammalian brain development and plasticity underlying learning and memory. We report the genome-wide composition, patterning, cell specificity, and dynamics of DNA methylation at single-base resolution in human and mouse frontal cortex throughout their lifespan. Widespread methylome reconfiguration occurs during fetal to young adult development, coincident with synaptogenesis. During this period, highly conserved non-CG methylation (mCH) accumulates in neurons, but not glia, to become the dominant form of methylation in the human neuronal genome. Moreover, we found an mCH signature that identifies genes escaping X-chromosome inactivation. Finally, whole-genome single-base resolution 5-hydroxymethylcytosine (hmC) maps revealed that hmC marks fetal brain cell genomes at putative regulatory regions that are CG-demethylated and activated in the adult brain, and that CG demethylation at these hmC-poised loci depends on Tet2 activity.

See also: Inherited chromosomally integrated human herpesvirus 6 genomes are ancient, intact and potentially able to reactivate from telomeres, which was reported as: “Study of inherited herpes virus finds links to ancient humans” August 30, 2017

We used molecular dating methods to compare, for example, the inherited HHV-6B genomes in five individuals from Sardinia, Orkney and England, and estimated that the most recent common ancestor with the inherited HHV-6B existed 24,500 ±10,600 years ago.

The molecular dating methods are evaluated outside the context of what is known about energy-dependent pheromone-controlled feedback loops, which have been linked from the sense of smell in bacteria to our visual perception of mass and energy in the context of the space-time continuum. But, rather than repeat myself, I will simple support my claims with a link to: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants, which was reported in January, 2013, as: Past 5,000 years prolific for changes to human genome. The changes can be place into the context of exome sequencing, but not mutation-driven evolution.
The recent origin of most human protein-coding variants can be linked from food energy-dependent changes in exomes that are biophysically constrained by the pheromone-controlled physiology of reproduction in all living genera. The recent origin of the variant can also be linked from the virus-driven degradation of messenger RNA to all pathology.

Of 1.15 million single-nucleotide variants found among more than 15,000 protein-encoding genes, 73% in arose the past 5,000 years, the researchers report. 164,688 of the variants — roughly 14% — were potentially harmful, and of those, 86% arose in the past 5,000 years.

See also: Whole-Exome Sequencing Reveals a Rapid Change in the Frequency of Rare Functional Variants in a Founding Population of Humans (2013)
I repeat:

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