Polymaths and paradigm shifts: From Asimov to Bear (5)

March 14, 2018

by James Kohl with No Comment Adaptations Alternative Splicings base editing biophotonics Cytosis Diseases & Disorders Ecology microRNA editing Model Organisms Neuronal Plasticity Nutrigenomics Physics RNA editing RNA interference RNA-directed DNA methylation RNA-mediated gene silencing RNA–Mediated Epigenetic Heredity Subatomic What's in the News

Summary: Neil deGrasse Tyson and Lawrence Krauss are among those who have continued to substitute pseudoscientific nonsense for legitimate facts, which is what Hawking did in every book he ever wrote, and each time he made a spurious claim based on his abilities as a conniving theorist whose works still have not been confirmed-and-validated. Now that he is gone, others may proclaim the greatness of his intellect and lionize the magnitude of his influence because they also are biologically uninformed science idiots. Like Hawking, they refused to learn how Darwin’s “conditions of life” have been linked to the prevention of all virus-driven pathology.

Renowned Physicist Stephen Hawking Dies

The comments by Neil deGrasse Tyson and Lawrence Krauss can be linked to this discussion: 2013 Isaac Asimov Memorial Debate: The Existence of Nothing and to the 2017 representation of biomolecules in On the Difference between Physics and Biology: Logical Branching and Biomolecules.
The food energy-dependent pheromone-controlled creation of the biomolecules will be discussed during Schrödinger at 75 – The Future of Biology – September 2018 after the virus-driven degradation of messenger RNA and all pathology is discussed during Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses
For comparison, Stephen Hawking gained fame by collaborating with Roger Penrose and with George FR Ellis, who co-authored The Large Scale Structure of Space-Time.
In the forward to the reprint edition of What is Life?, Roger Penrose wrote

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

In the cell biology game Cytosis, anyone age 10+ can learn that the creation of energy as ATP protects all organized genomes from the virus-driven degradation of messenger RNA, which all serious scientists since Schrödinger have linked from mutations to all pathology.That’s all you need to know about Roger Penrose.
George FR Ellis is the co-author of On the Difference between Physics and Biology: Logical Branching and Biomolecules. He helped to link the food energy-dependent creation of microRNAs to biophysically constrained viral latency, but is determined to undermine the works of other serious scientists with his use of the ambiguous term biomolecules.
Taken together, Stephen Hawking, Roger Penrose, and George FR Ellis have done more than most to bastardize Darwin’s claims about the need to start with food energy-dependent “conditions of life.” Their unproven ideas from physics should never have been substituted for experimental evidence.
The evidence links the premise of the game “Subatomic” from what is known about particle physics to biophysically constrained viral latency and healthy longevity via this claim, which was made by Schrödinger.

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.)

Neil deGrasse Tyson and Lawrence Krauss are among those who have continued to substitute pseudoscientific nonsense for legitimate facts, which is what Hawking did in every book he ever wrote, and each time he made a spurious claim based on his abilities as a conniving theorist whose works still have not been confirmed-and-validated. Now that he is gone, others may proclaim the greatness of his intellect and lionize the magnitude of his influence because they also are biologically uninformed science idiots. Like Hawking, they refused to learn how Darwin’s “conditions of life” have been linked to the prevention of all virus-driven pathology.
See: DNA Tumor Virus Regulation of Host DNA Methylation and Its Implications for Immune Evasion and Oncogenesis
Reported as: Here’s How Viruses Inactivate the Immune System, Causing Cancer

“Ultimately viruses are causing these tumors to form and are further manipulating the immune system to allow tumors to keep growing,” Kuss-Duerkop says. “But these same mechanisms may be key in combating tumors with immune-based therapies or in keeping cancer from developing in the first place.”

If not for the bastardization of Darwin’s claims by theorists, Kuss-Duerkop and others like her probably would have learned that sunlight is the source of energy for the growth of food that links food energy to the pheromone-controlled physiology of reproduction in species from microbes to humans. The energy links changes in the microRNA/messenger RNA balance from virus-driven energy theft to all unnecessary suffering and premature death.The fact that Stephen Hawking suffered throughout his life with a neurodegenerative disease may be fitting in the context of his ignorance.
The 4 Scientific Lessons Stephen Hawking Never Learned

We have a tendency, when we turn people into heroes, to lionize their achievements and ignore their failings, but to do so cheats humanity out of recognizing all the facets of a complicated character.
May we memorialize him in the best way possible: by increasing our own knowledge and curiosity to live better lives.

Until then, see: Prominent Neuroscientist Fired by Columbia, HHMI
This is the first clear indicator of how the Trump administration will drain the academic swamp.
Jessell is the serior author of: Activity Regulates the Incidence of Heteronymous Sensory-Motor Connections

The positioning of newly born neurons is a tightly regulated process that is critical for the assembly of the nervous system. In the spinal cord, nuclear organization of motor neurons into pools is an elaborated morphogenetic feature at the basis of the wiring of spinal sensory motor circuits (Sürmeli et al., 2011, Hinckley et al., 2015, Bikoff et al., 2016). The events controlling motor neuron positioning during development have yet to be clearly defined.

The activity is food energy-dependent and RNA-mediated in the context of sensory input and the physiology of pheromone-controlled reproduction, which biophysically constrains viral latency in species from microbes to humans.
See for example: Meet the creature that can regenerate its brain and resist cancer.(video) The superimposed electron cloud over the yin yang symbol of Chinese philosophy and medicine is a clear representation of the complexity. If neuroscientists cannot link energy-dependent changes in electrons to ecosystems in all living genera, they will be dismissed and replaced with serious scientists.
For example, the facts about regenerating the brain and resisting cancer suggests Jessell’s termination occurred due to his ongoing failure to link the virus-driven degradation of messenger RNA to loss of motor control in all neurodegenerative diseases.
See for comparison: “Blood Music” (1985) by Greg Bear, who presciently linked energy-dependent changes in the microRNA/messenger RNA balance to the creation of an advanced human species via naturally occurring biophysically constrained viral latency.
See also: Actor Steven Kearney reads excerpts from Greg Bear’s 1985 novel Blood Music.

Bear was one of the first sci-fi authors to delve deep into the possibilities of synthetic biology. In this section, a biologist named Michael Bernard is infected with a killer virus that has wiped out most of North America. The virus is made up of tiny biological computers called “noocytes,” where were intended to improve the human body — giving it routine maintenance and maximizing human potential. Instead, it wiped out most of North America.

Remember, without the food energy-dependent pheromone-controlled RNA-mediated DNA repair that biophysically constrains viral latency:

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)

March 14, 2018

by James Kohl with One Comment Adaptations Alternative Splicings Autophagy base editing biophotonics Cytosis Diseases & Disorders Ecology Light Energy microRNA editing Model Organisms Nutrigenomics Physics RNA Directed RNA editing RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity Subatomic What's in the News

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:

Steven Bird‏ @stevenbird64 12 Sep 2010

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

2. Toya‏ @toyaj05 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.

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’.

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.

Subatomic: From thermophiles to humans (3)

February 13, 2018

by James Kohl with No Comment Adaptations Cytosis Diseases & Disorders Ecology microRNA editing Model Organisms Neuronal Plasticity Nutrigenomics RNA Directed RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated gene silencing RNA–Mediated Epigenetic Heredity Subatomic Variations

Summary: RNA-mediated cell type differentiation in species from insects to primates can be linked from claims about the lower percentage of food energy-dependent DNA methylation in Diet and cell size both affect queen-worker differentiation through DNA methylation in honey bees (Apis mellifera, Apidae) to the conclusion from “Cryo-electron tomography reveals that dynactin recruits a team of dyneins for processive motility.”
See also: Starfish reveal the origins of brain messenger molecules (February 9, 2016)

One of the neuropeptides found is similar to kisspeptin, a chemical that triggers the onset of puberty in humans.

The link from kisspeptin to GnRH helped to establish the link from food odors and pheromones to the RNA-mediated physiology of reproduction in all invertebrates and vertebrates.
Placing facts about neuropeptides into the context of human brain evolution thus seems to exemplify incredible ignorance of physics, chemistry, and molecular epigenetics.
See for comparison: The Importance of ncRNAs as Epigenetic Mechanisms in Phenotypic Variation and Organic Evolution
Conclusion:

The increasing number and diversity of these small and long ncRNAS in relation to the complexity and adaptability of living beings, explains that they have been paramount in complex biological processes and are not an evolutionary paradox.

The fact that miRNAs can be mobilized by the fluids of plants and animals, allows them to act at different distances to where they were transcribed, much like hormones or pheromones do. In addition, they can respond to environmental stimuli, favoring the adaptation of organisms through the modification of epigenetic marks and also a transgenerational inheredity and the evolution of species as part of a Neo-Lamarckian model.

There has never been a neo-Lamarkian model for the evolution of species. Lamarck put his observations into the context of Darwin’s “conditions of life.” If the conditions of life are met, ecological variation can be linked to food energy-dependent ecological adaptations. Only the bastardization of Darwin’s claims put natural selection for mutations first — when biologically uninformed theorist invented neo-Darwinian pseudoscientific nonsense.
SARCASM ALERT: Please do not tell anyone about this 2013 refutation of neo-Dawinism. Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Excerpt:

The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, 2012; Duvarci, Nader, & LeDoux, 2008; Griggs et al., 2013; Monahan & Lomvardas, 2012) in adaptive evolution will certainly be discussed in published works that will follow.

Conclusion:

See for comparison. Others are making the same claims:
Modulation of miRNAs by Vitamin C in Human Bone Marrow Stromal Cells

…identification of vitamin C-dependent microRNA regulation is important for understanding the basic mechanisms underlying BMSC differentiation and tissue engineering.

All cell type differentiation in all tissues of all species with tissues is energy-dependent and RNA-mediated. That fact is consistently thrown into the political ring of nonsense touted by theorists who attack the President of the United States.
See: Trump: Tell us about your flu shot

Why are so few Americans getting the flu vaccine? And why isn’t the CDC doing more to change that?

The CDC can do nothing. Intelligent people know that the flu virus adapts each season. The CDC will abandon their claims about mutations, which were linked to evolution. More people will be angry when they learn that only a single amino acid substitution can cause an adaption.
Trump-hating liberals may be forced to repurpose their anger and use it to rid the academic swamp of their idiot minions — the so-called science journalists who refused to join the serious scientists who are Combating Evolution to Fight Disease
Most of the anger will be directed toward biologically uninformed science journalists who have failed to present the facts about all virus-driven pathology. For example see: The Quest to End the Flu (2013)

New pandemics don’t come out of the blue. They evolve from viruses that infect animals—typically birds.

Pandemics “evolve” from viruses? What kind of so-called science journalist makes a claim like that?
Is Most of Our DNA Garbage? (March 5, 2015)

…junk DNA isn’t a sign of evolution’s failure. It is, instead, evidence of its slow and slovenly triumph.

The triumph is not slow and slovenly. One base pair change and fixation of one amino acid substitution is all that is required to start the process of ecological adaptation.
See for comparison: It’s time to put America’s health first

While the CDC neglected its mission here, Obama committed billions to build labs and train health personnel in Africa during the Ebola scare. Billions for a disease that killed only one person in the United States — and even he got infected elsewhere.

The so-called science journalists who also are Trump-haters have contributed to more unnecessary suffering and premature death than most people can begin to imagine. They spread their ignorance and hatred across the country and across the world. It is the pathology of their ignorance that must be removed if ever we are to put America’s health first. The first thing we must do, is rid ourselves of the unethical so-called science journalists.

From base editing to RNA editing (6)

December 27, 2017

by James Kohl with No Comment Adaptations Alternative Splicings base editing Cytosis Diseases & Disorders Ecology Human Brain Human Pheromones Light Energy microRNA editing Model Organisms Neuronal Plasticity Nutrigenomics Physics RNA Directed RNA editing RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity Variations

Summary: Now that others have linked food energy to biophysically constrained pheromone-controlled RNA-mediated cell type differentiation and to the prevention and treatment of PTSD, help for veterans and others who might be contemplating suicide is one step closer to the reality of implementation.
But wait, first the NIH must fund another 26.2 million dollars worth of worthless research on “social epigenomics.”
See for comparison: A distinct hematopoietic stem cell population for rapid multilineage engraftment in nonhuman primates
Reported as: Subset of stem cells identified as source for all cells in blood and immune systems
The link from quantum physics to biophysically constrained feedback loops and the transgenerational epigenetic inheritance of food energy-dependent pheromone-controlled viral latency was included in Daev et al (2014): Chemosignals from isolated females have antimutagenic effect in dividing the cells of bone marrow from male mice of the CBA strain

…specific, volatile, and zoosocial important chemosignals are a promising approach both to modeling posttraumatic stress disorders in humans [36] …

Daev et al (2014) cited our award-winning 2001 review:

Humans also have various pheromone-induced physiological effects, especially those associated with reproduction [46, 47]. This suggests that the human olfactory system is still an effective pathway for influencing environmental factors on the human nervous system.

[46] is Kohl, J.V., Atzmueller, M., Fink, B., and Grammer, K., Human pheromones: integrating neuroendocrinology and ethology, Neuroendocrinol. Lett., 2001, vol. 22, pp. 309–321.
Now that others have linked food energy to biophysically constrained pheromone-controlled RNA-mediated cell type differentiation and to the prevention and treatment of PTSD, help for veterans and others who might be contemplating suicide is one step closer to the reality of implementation.
But wait, first the NIH must fund another 26.2 million dollars worth of worthless research to link “social epigenomics” (aka epigenetic effects of pheromones) from base editing to RNA editing and RNA-mediated cell type differentiation.

See: NIH Awards Grants Supporting Social Epigenomics Research

…funding to examine how socioeconomic/psychosocial conditions affect prenatal DNA methylation, miRNA expression, mRNA expression, and inflammation…

Altogether, this systematic analysis of ribosome-associated mRNAs and lncRNAs demonstrates that nutrient availability and translational regulation controls protein and small peptide-encoding mRNAs as well as a diverse cadre of regulatory RNAs.

Arabidopsis thaliana is a small flowering plant that is widely used as a model organism in plant biology. The nutrient energy-dependent physiology of reproduction was linked to the food energy-dependent pheromone-controlled physiology of reproduction via the ribosome-associated mRNAs in the context of the ATP-dependent creation of the RNA and fixation of amino acid substitutions that stabilize the organized genomes of all living genera.

More than 68,000 indexed publications on PubMed link food energy-dependent changes in microRNAs from RNA-directed DNA methylation to mRNA expression in the context of the physiology of pheromone-controlled reproduction and transgenerational epigenetic inheritance of all phenotypes in species from microbes to humans. A search for microRNA and virus links 4782 published works from the virus-driven degradation of messenger RNA to all pathology.

The waste of money on more research should be perfectly clear in the context of this invited review of nutritional epigenetics:

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

For example, I linked the availability of sago palm-like leaves to endogenous levels of vitamin C in humans. That allowed me to detail how the pheromone-controlled physiology of reproduction in mice was linked to humans via one base pair change and a single amino acid substitution. Natural selection for energy-dependent codon optimality is all that’s required to link RNA-mediated DNA repair from sunlight to the creation of microRNAs in plants and the vitamin C-enhance stability of the organized genomes in a modern human population in Central China.

1) …access to endogenous vitamin C in human populations, supports efficient metabolism and ecological niche construction [17].

2) ..vitamin C appears to stimulate histone demethylases, which appear to alter the de novo creation of functional olfactory receptor genes [19-23].

3) Researchers recently rediscovered a nutrient-dependent epigenetic variant that links vitamin C to what is probably a glucose and glucose dehydrogenase-dependent base pair change. The base pair change results in addition of a methyl group to a cytosine base, which takes on a hydroxyl group to form different 5-hydroxymethylcytosines (5hmCs). Different 5hmCs are associated with differences in cell types that have the same genetic backgrounds. Nutrient-dependent epigenetically-marked bases help to explain how hundreds of cell types in the human body and in the brain [24] are differentiated and how they maintain their glucose-dependent and other nutrient-dependent receptor-mediated identities [25].

Because vitamin C and other vitamins appear to epigenetically effect nutrient-dependent methylation at the level of single-base resolution in mammals, it has become more important to determine how base-pair changes alter intracellular interactions in embryonic stem cells or intercellular interactions in other cells that result in cascades of downstream intracellular and intercellular organizing interactions throughout life. Other vitamins, such as vitamin D, and metal ions such as calcium, iron, lead and manganese also appear to epigenetically alter these organizing interactions. Therefore, a biophysically constrained, nutrient-dependent, epigenetically-effected, receptor-mediated recognizable organized pattern of emergence can be viewed in the context of ecological variations and ecological adaptations.

4) Amino acid substitutions in humans are associated with loss of vitamin C synthesis and loss of uricase production at the advent of urate production as a substitute for vitamin C biosynthesis in primates.

Excerpt from the conclusion:

5) In mammals, for example, the explanatory power of a model of ecological variation and biophysically constrained nutrient-dependent pheromone-controlled ecological adaptations became clear with companion papers published in 2013. See for review [30].

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

Apparently, the effect of the epiallele was adaptive and it was manifested in the context of an effect on sweat, skin, hair, and teeth. In another mammal, such as the mouse, the effect on sweat, skin, hair, and teeth is probably due to a nutrient-dependent epigenetic effect on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. The pheromones appear to control the nutrient-dependent epigenetically-effected hormone-dependent organization and hormone-activation of reproductive sexual behavior in mammals such as mice and humans, but also in invertebrates and in microbes as previously indicated.

The ecological adaptations, which appear to be manifested in the human population are detailed in these two reports [162-163]. The ecological adaptations are likely to be nutrient-dependent and pheromone-controlled. If so, ecological variation probably leads to ecological, social, neurogenic, and socio-cognitive niche construction, which is manifested in increasing organismal complexity and species diversity. If not, there may be something as yet unknown about mutations and evolution that makes sense in the light of what is known about nutritional epigenetics and the molecular biology of species from microbes to man.

NIH funding for more research without first reviewing what is known to all serious scientists about energy-dependent RNA-mediated cell type differentiation is a horrid waste of money. If that fact is not perfectly clear, see any of these published works on microRNAs.

Two decades after Eugene Daev first linked pheromones to biophysically constrained viral latency, an article in Science asked the question: Do human pheromones actually exist?

…Wen Zhou, a behavioral psychologist at the Chinese Academy of Sciences in Beijing, contends that AND and EST may well be human pheromones. “My major concern with the experiments in this study is that they were not rigorously designed and conducted,” she wrote in an email to Science. Zhou, who in 2014 published a study finding that AND and EST do indeed influence whether participants judge walking dot figures with “genderless gaits” to be men or women, doubts the faces used were truly “gender neutral.”

See for comparison: Olfaction Warps Visual Time Perception
See also: The vibrational theory of olfaction for the win (John Hewitt)

…Turin also just published a much more sweeping treatise on molecular recognition in olfaction in the journal Advances in Physics: X. In it, he and his co-authors delve into more of the specifics of olfactory receptors, including particular amino acid motifs, metal binding capacities, and disulphide bridge redox status. It turns out that amino acid side chains alone frequently pull off some rather interesting electron transfer effects without the need for fancy co-enzymes or prosthetic groups.

The link from facts about amino acids in the context of vibrational theory to olfaction and receptor-mediated behaviors clearly extends from epigenetic effects on hormones to the unconscious affects of hormones on behavior.
Epigenetic effects on energy-dependent performance levels should also be reconsidered in the context of receptor-mediated biophysical constraints on amino acid substitutions that stabilize organized genomes, but in public/personal correspondence, John Hewitt professed his belief in evolution. On 11/27/17 he wrote:

I think mutation and natural selection is a woefully weak force in the evolution of multicellular organisms, but I surely believe things evolve.

See for comparison from December 2007:
Sex and Smell: Molecular Biology of Pheromone Perception (Catherine Dulac)
Talk Overview

Pheromones have evolved to signal the sex and the dominance status of animals and to promote social and mating rituals.

No experimental evidence of biologically-based cause and effect supports that claim that pheromones evolved to do anything. All experimental evidence provided by serious scientists who use it to support their claims attests to this fact from December 2012:
The activity-dependent histone variant H2BE modulates the life span of olfactory neurons (co-authored by Catherine Dulac)
An experience-dependent epigenetic trap stabilizes the organized genomes of all living genera. See: An Epigenetic Trap Stabilizes Singular Olfactory Receptor Expression.
The “epigenetic trap” links the speed of light on contact with water to all food energy-dependent biodiversity via olfaction and the pheromone-controlled physiology of reproduction.
Dynamic control of chirality and self-assembly of double-stranded helicates with light
Senior author Ben L. Feringa won the 2016 Nobel Prize in Chemistry for works that link the anti-entopic virucidal energy of sunlight on contact with water from the creation of microRNAs to experience-dependent changes in electrons to ecosystems via changes in the microRNA/messenger RNA balance.
Something has gone horribly wrong. In the iBiology alert I received this morning, ‘Tis the Season to be Sensing, this claim was made:

While you take off time for a holiday vacation, not everyone will be taking a break. Your body’s cells will be clocking overtime to ensure you can enjoy all of the festivities. They are responsible for everything from hearing the chatter of loved ones and the tasting of delicious food to seeing all of the bright and colorful decor. Consider taking some time this holiday to learn about all the hard work your cells are doing to help you enjoy the holiday cheer!

Hearing, seeing and tasting occur only in the context of experience-dependent epigenetic effects that link feedback loops to all biodiversity via the sense of smell. See: Feedback loops link odor and pheromone signaling with reproduction
See also: Evolution Flipped Course

Fundamentals such as Darwinian evolution, genetic variation and natural selection are covered. In addition, leading scientists present their research in areas as diverse as the evolution of multicellularity, the discovery a fossil intermediate between fish and tetrapods, the co-evolution of plants and predators, and how viruses constantly evolve to “outsmart” their hosts.

Session 10: Viral Evolution

In this session, Drs. Turner and Malik focus on the ability of viruses to rapidly evolve and adapt to changing environments. Turner explains how some viruses have evolved to infect many hosts while others infect a single cell type. He also uses experimental evolution to study the ability of a virus to survive under different environmental conditions versus its ability to effectively reproduce.

They obfuscate the difference between mutations and amino acid substitutions because the food energy-dependent RNA-mediated fixation of amino acid substitutions prevents all virus-driven pathology. Only theorists continue to tout their pseudoscientific nonsense.
Serious scientists make claims like this (although some must be forced to do it):
The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.
See also: Mitochondrial pyruvate metabolism controls neuronal function and excitotoxic death

…we show that glutamate is readily used as a metabolic substrate in cortical neurons in response to mitochondrial pyruvate carrier (MPC) inhibition. Reductions in mitochondrial pyruvate uptake do not compromise viability or energy metabolism, but rather rewire mitochondria to increase reliance on glutamate to fuel anaplerosis and ATP production.

The ATP-dependent rewiring is energy-dependent and RNA-mediated. Food energy is required for error-free DNA repair and that fact was first accurately represented in 1964:
Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

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

Antagonist Jay R. Feierman has done more than anyone to prevent people from learning the facts about how food energy and pheromones protect all organized genomes from the virus-driven degradation of messenger RNA.
For a historical record of his ignorance, see: 90689 Re: [evol-psych] Re: [human-ethology] Phenotype, Form, and Function
Conclusion:

…it is doubtful if such constructive criticism will change anyone’s views on this subject, as the views regarding psychological paradigms are held together in many people with the same emotional glue that hold political and religious views together. The next generation will think differently.

See also his constructive criticisms of my model: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
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.
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.

Who created your virus-driven death gene? (2)

December 12, 2017

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy base editing biophotonics Cytosis Diseases & Disorders Ecology Human Brain Human Pheromones Light Energy microRNA editing Model Organisms Neuronal Plasticity Nutrigenomics Physics RNA Directed RNA editing RNA interference RNA methylation RNA-directed DNA methylation Variations

Evolution of Constrained Gonadotropin-releasing Hormone Ligand Conformation and Receptor Selectivity

These findings indicate that the substitution of glycine for a chiral amino acid in GnRH during evolution allows a more constrained conformation for receptor binding and that this subtle single amino acid substitution in a site remote from the ligand functional domains has marked effects on its structure and activity.

The difference between an energy-dependent RNA-mediated amino acid substitution and a mutation has been largely ignored as pseudoscientists linked accidents to evolution.
See for example: Can watery asteroids explain why life is ‘left-handed’? (2009)

Sandwalk readers will know that I [Larry Moran] prefer an evolutionary explanation.

My summary of his evolutionary explanation:
The simplest amino acid is glycine where the R group is just a hydrogen atom. Glycine is not a chiral compound and there’s no such thing as L-glycine or D-glycine. All other natural amino acids are chiral. Larry Moran claims that glycine might have formed spontaneously. If so, the exclusive presence of L-amino acids instead of D-amino acids is just an accident. But it is an accident that somehow started with the spontaneous formation of glycine. The spontaneous formation of anything would be considered to be a miracle by those who do not believe in evolutionary explanations.
Anyone who does not recognize the fact that people like Larry Moran think in terms of the accidental creation of the only achiral amino acid, which stabilizes the organized genomes of all vertebrates, should not read further.
It is a waste of time to examine facts after you decide to believe in more pseudoscientific nonsense than any serious scientist has ever considered. If you have not learned the difference between a mutation and an energy-dependent amino acid substitution, are you a well-trained medical practitioner?
See: Updates of the HbVar database of human hemoglobin variants and thalassemia mutations

Hemoglobinopathies are the commonest single-gene genetic disorders in humans, resulting from pathogenic genome variants in the human α-like and β-like globin gene clusters (reviewed in 1). Single nucleotide substitutions or indels [INsertions/DELetionS] can lead to several hemoglobin variants owing to amino acid replacements, while molecular defects in either regulatory or coding regions of the human HBA2, HBA1, HBB or HBD genes can minimally or drastically reduce their expression, leading to α-, β- or δ-thalassemia, respectively.

Difference in mass resulting from the change of a single amino acid

The mass of normal alpha chain is 15126.3 Da and that of the normal beta chain 15867.5, the changes induced by single point mutations are given above (only those allowed by the genetic code are given). As an example the change from Asp to His will increase the normal mass by 22 units and the reverse change will decrease the mass by the same amount.

The example links an increase in the stability and/or a decrease in the stability of the organized genome to a mutation and also to an amino acid substitution. The stability of all organized genomes is food energy-dependent and biophysically constrained via differences in hydrogen atom transfer in DNA base pairs in solution. The differences are measured in the context of blood gas analyses, and you should already know that the potential of hydrogen (pH) will determine the patient outcome — before you order the test.

If you do not understand this, find someone from the medical laboratory me to discuss it with. You may feel like a fool, but you will be less likely to kill someone via your ignorance.

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

The differences in the network of hydrogen bonds between high- and low-altitude Hb variants should be placed into the context of why medical laboratory scientists must be trained to calibrate blood gas analyzers based on the barometric pressure at the location of the lab. For comparison to a somewhat less technical approach to the link from the circulatory system to nutrient energy-dependent microRNAs and pheromone-controlled biodiversity, see: Primo Vascular/Meridian System 2016

Thornton Streeter claimed that this a small contribution to understanding energy medicine. It links everything known about the creation of energy-dependent hemoglobin variants to all food energy-dependent biodiversity via the pheromone-controlled physiology of reproduction and the vascular/meridian system of humans.

See also: Ugur Murat Ozdemiroglu Admin of WORLD CONGRESS OF OBSTETRICS & GYNECOLOGY FORUM reported Yesterday at 3:36am on 12/11/17

By far the most important disease resulting from a mutation to an abnormally functioning hemoglobin is sickle cell disease, in which a single base change in the DNA results in a substitution of valine for glutamic acid at the sixth position in the beta globin chain.

Like all other quantized energy-as-information/food energy-dependent ecological adaptations, this hemoglobin variant is frequently reported to be a mutation. The link from one base pair change to the pheromone controlled physiology of reproduction and fixation of an amino acid substitution in the organized genomes of human populations protects them from extinction. The extinctions are caused by the virus-driven degradation of messenger RNA that most people indirectly link from malarial parasites to hemoglobin variants such as Hemoglobin S. Most people do not link viruses to all pathology, despite the historical record.

See: Biology, molecular and organismic (1964)

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

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

Link opens pdf: Participation of glycolysis, and the citric acid cycle, in nuclear adenosine triphosphate synthesis (1963)

…thymus nuclei appear to have an endogenous substrate, and some experiments are presented which suggest that this substrate is probably not glycogen or glucose.

Ten years after McEwen et al., (1963) linked the creation of ATP to the creation of RNA via an endogenous substrate in all cell types of all living genera, Dobzhansky placed everything known about the creation of all biodiversity on Earth into the context of: Nothing in Biology Makes Any Sense Except in the Light of Evolution (1973)

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.

A single base pair change and one amino acid substitution differentiates the cell types of gorillas compared to chimpanzees and modern humans. That fact has finally forced pseudoscientists to begin to examine the role that viruses play in all pathology.

See: Virus-mediated archaeal hecatomb in the deep seafloor

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

The virus-driven degradation of messenger RNA in bacteria is linked to the creation of archaea and the virus-driven degradation of messenger RNA in humans is linked to the creation of non-human primates by the conserved molecular mechanisms that were reported in MicroRNAs: Milk’s epigenetic regulators

Our perception of milk has changed from a “simple food” to a highly sophisticated maternal-neonatal nutrient and communication system orchestrating early programming of the infant. Milk miRNAs delivered by exosomes and milk fat globules derived from mammary gland epithelial cells play a key role in this process. Exosomes resist the harsh intestinal environment, are taken up by intestinal cells via endocytosis, and reach the systemic circulation of the milk recipient. The most abundant miRNA found in exosomes and milk fat globules of human and cow’s milk, miRNA-148a, attenuates the expression of DNA methyltransferase 1, which is critically involved in epigenetic regulation. Another important miRNA of milk, miRNA-125b, targets p53, the guardian of the genome, and its diverse transcriptional network. The deficiency of exosomal miRNAs in infant formula and the persistent uptake of milk miRNAs after the nursing period via consumption of cow’s milk are two epigenetic aberrations that may induce adverse long-term effects on human health.

Only the best medical practitioners and researchers have grasped the fact that Carl Woese was wrong when he reported there were three domains of life. There is only one domain of life and the virus-driven degradation of messenger RNA is linked to all pathology in all living genera.

November 22, 2017 Sci-Hub, often referred to as the “Pirate Bay of Science,” lost three of its domain names this week.

Sci-hub.io, sci-hub.cc, and sci-hub.ac now have the infamous “serverhold” status which suggests that the responsible registries intervened. The status, which has been used previously when domain names are flagged for copyright issues, strips domains of their DNS entries.

November 23, 2017 RNA quality Items: 1 to 20 of 604

Unless you can find access to Sci-Hub, you might find it difficult to access information on RNA quality.

See: The determinants of alternative RNA splicing in human cells

Alternative splicing represents an important level of the regulation of gene function in eukaryotic organisms. It plays a critical role in virtually every biological process within an organism, including regulation of cell division and cell death, differentiation of tissues in the embryo and the adult organism, as well as in cellular response to diverse environmental factors. In turn, studies of the last decade have shown that alternative splicing itself is controlled by different mechanisms. Unfortunately, there is no clear understanding of how these diverse mechanisms, or determinants, regulate and constrain the set of alternative RNA species produced from any particular gene in every cell of the human body. Here, we provide a consolidated overview of alternative splicing determinants including RNA-protein interactions, epigenetic regulation via chromatin remodeling, coupling of transcription-to-alternative splicing, effect of secondary structures in pre-RNA, and function of the RNA quality control systems. We also extensively and critically discuss some mechanistic insights on coordinated inclusion/exclusion of exons during the formation of mature RNA molecules. We conclude that the final structure of RNA is pre-determined by a complex interplay between cis- and trans-acting factors. Altogether, currently available empirical data significantly expand our understanding of the functioning of the alternative splicing machinery of cells in normal and pathological conditions. On the other hand, there are still many blind spots that require further deep investigations.

…we compared gene measures of RNA quality (RIN) and of dementia status (before and after accounting for RIN).

See also: “Study finds infection and schizophrenia symptom link“ November 22, 2017

…activation of the maternal immune system in rats was sufficient to produce impaired timing, which is likely critical to other schizophrenia symptoms and impairments.Impaired ability to judge time accurately is a primary symptom in patients and this is also thought to be related to other symptoms, such as hallucinations, and cognitive impairment.

All Brain Perception is Rhythmic and Cyclical Says Newest Neuroscience

“We have suspected for some time that the senses are not constant but are processed via cyclical, or rhythmic functions; these findings lend new weight to that theory.”

It’s not a theory. Experimental evidence of biophysically constrained top-down causation links the energy-dependent RNA-mediated constraints on viral latency to healthy longevity via everything known to serious scientists since the time that the energy-dependent creation of ATP was linked to the energy-dependent creation of RNA.
See: Olfaction Warps Visual Time Perception
For comparison: This is a ridiculous theory.
Evolution of Epigenetic Mechanisms in Animals and Their Role in Speciation

DNA methylation is involved in gene regulation, silencing of transposons, imprinting, polyphenism, and consolidation of speciation. It may even act as a driver of evolution via stochastic developmental and environmentally induced epigenotype diversification, transgenerational inheritance of epigenetic patterns with phenotypic effects, and differential selection and genetic fixation of these phenotypes.

All ridiculous theories can be compared in the context of: To forget or to remember? Memory depends on subtle brain signals, scientists find

“The idea is, constantly as we learn information, there is a slow process that whittles away memories, and it continues whittling them away unless another part of the brain signals the memory is important and overrides it,” Davis said.

It may be that the process of acquiring and forgetting memories ebbs and flows in a state of balance, he said. Important memories like the taste of mom’s pumpkin pie might be forever retained, but trivialities like what you wore 10 years ago can fade into oblivion without consequence.

“If you have too much memory that is old and unnecessary, why keep them around? Why shouldn’t you have a system for removing those for optimal function of the brain?” Davis asked. “We’re getting all this information, all this learning during the day, and the brain may be saying, ‘No, no, bring me back to my basal, my happy state.'”

Many questions remain to be solved, Davis noted. “We need to figure out what is downstream—walk down the pathway to find the complete signaling system for forgetting,” he said. “We are very early in this research.”

Researchers who think “WE” are very early in this research are biologically uninformed science idiots. The COMT Val158Met amino acid substitution links food odor and pheromones to the biophysically constrained creation of one enzyme, which has been linked to differences in the dopaminergic reward system during the transition from adolescence to adulthood.
See:Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
I’m not sure why anyone would not already know how to link food odors and pheromones to enzymes and metabolism in humans in the context of the Human Microbiome Initiative and Precision Medicine Initiative. But I understand why losers tend to claim that winners are still very early in this research.
Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge. — Kalevi Kull
See for comparison: Book Review by Mark Sergeant

The Scent of Eros is certainly an engaging text that informs the reader about the majority of key studies performed on human olfaction. Where it is let down is a lack of supporting evidence for some of the ideas considered, and a lack of critical consideration for some of the evidence that is presented. A reader unfamiliar with olfaction research could come away from this text unaware of several key debates within the field…

The Scent of Eros: Mysteries of Odor in Human Sexuality
By James Vaughn Kohl and Robert T. Francoeur
On page 298, we linked levels of DHEA to schizophrenia and to the odor of schizophrenics via the metabolism of DHEA to androsterone and etiocholanolone, which are indicators of nutrient stress and/or social stress. All stress-linked illnesses have since been linked from the virus-driven degradation of messenger RNA to pathology in species from microbes to humans.

See also: Epigenetic modifications poster
See also: Epigenetics round-up of 2014

Changes in histone acetylation may aid memory reconsolidation in post-traumatic stress disorder

See also: Formulation and evaluation of anti-suicidal nasal spray of Thyrotropin releasing hormone
The fact that the virus-driven degradation of messenger RNA has been linked to all pathology in all living genera has been established by serious scientists.
See also: Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis
Clearly, another question must be asked:
The first question: Who created your virus-driven death gene?

The next question: Who wants the virus-driven death gene to continue to be activated?

For example: The antagonism of the biologically uninformed science idiot who is the moderator of the Human Ethology Yahoo group increases each time scientific progress is made towards prevention of neurodegenerative diseases or suicide prevention. Instead of linking the virus-driven degradation of messenger RNA to suicide and Alzheimer’s, he posts information like this.

Choice of a suicide method: Trends and characteristics

Efforts towards suicide prevention in our veterans and others are replaced with information on their choice of a suicide method.

Epigenetic facts vs variable recombination theories

November 7, 2017

by James Kohl with No Comment Adaptations Alternative Splicings base editing Diseases & Disorders Ecology Human Pheromones Model Organisms Neuronal Plasticity Nutrigenomics Physics RNA Directed RNA editing RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity Variations

6/14/13 Nutrient-dependent/pheromone-controlled adaptive evolution: a model

….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’.

7/25/13
Jay R. Feierman: Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.
7/26/13
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.

Facts:

Epigenetic modifications poster
DNA repair pathways poster
Epigenetic Dynamics in Stem Cells and Differentiation webinar
Epigenetic Editing: Permanently Modulate Gene Expression webinar
Histone modifications: a guide
Epigenetic Mechanisms in Early Mammalian Development webinar
DNA Methylation Changes During Cell Differentiation webinar
Chromatin: from nucleosomes to chromosomes
Epigenetics round-up of 2014

Changes in histone acetylation may aid memory reconsolidation in post-traumatic stress disorder

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

Theme issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’ (2017)
Recombination rate variation in sexual organisms is energy-dependent and RNA-mediated. Variation is biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans. See: From Fertilization to Adult Sexual Behavior (1996)

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.
A potential ramification of epigenetic imprinting and alternative splicing may be occurring in Xq28, a chromosomal region implicated in homosexual orientation (Brook, 1993; Hu, Pattatucci, Patterson, Li, Fulker, Cherny, Kruglyak, and Hamer, 1995; Turner, 1995). Xq28 contains one of the X chromosome’s two pseudoautosomal regions (PARs), adjoins the telomere, and has various means of gene expression control (D’Esposito, Ciccodicola, Gianfrancesco, Esposito, Flagiello, Mazzarella, Schiessinger, and D’Urso (1996). Xq28, therefore, is a chromosomal region that has many of the heterochromatic and telomeric characteristics that participate in sexual determination and behavior in other species.

Theories:

Review article: Variation in recombination frequency and distribution across eukaryotes: patterns and processes
Jessica Stapley, Philine G. D. Feulner, Susan E. Johnston, Anna W. Santure and Carole M. Smadja
Phil. Trans. R. Soc. B December 19, 2017 372 20160455; doi:10.1098/rstb.2016.0455
http://rstb.royalsocietypublishing.org/content/372/1736/20160455
Review article: The impact of recombination on human mutation load and disease
Isabel Alves, Armande Ang Houle, Julie G. Hussin and Philip Awadalla
Phil. Trans. R. Soc. B December 19, 2017 372 20160465; doi:10.1098/rstb.2016.0465
http://rstb.royalsocietypublishing.org/content/372/1736/20160465
Opinion piece: Connecting theory and data to understand recombination rate evolution
Amy L. Dapper and Bret A. Payseur
Phil. Trans. R. Soc. B December 19, 2017 372 20160469; doi:10.1098/rstb.2016.0469
http://rstb.royalsocietypublishing.org/content/372/1736/20160469
Review article: Coevolution between transposable elements and recombination
Tyler V. Kent, Jasmina Uzunović and Stephen I. Wright
Phil. Trans. R. Soc. B December 19, 2017 372 20160458; doi:10.1098/rstb.2016.0458
http://rstb.royalsocietypublishing.org/content/372/1736/20160458
Review article: Evolution of recombination rates between sex chromosomes
Deborah Charlesworth
Phil. Trans. R. Soc. B December 19, 2017 372 20160456; doi:10.1098/rstb.2016.0456
http://rstb.royalsocietypublishing.org/content/372/1736/20160456
Research article: Low recombination rates in sexual species and sex–asex transitions
Christoph R. Haag, Loukas Theodosiou, Roula Zahab and Thomas Lenormand
Phil. Trans. R. Soc. B December 19, 2017 372 20160461; doi:10.1098/rstb.2016.0461
http://rstb.royalsocietypublishing.org/content/372/1736/20160461
(openaccess) Review article: The consequences of sequence erosion in the evolution of recombination hotspots
Irene Tiemann-Boege, Theresa Schwarz, Yasmin Striedner and Angelika Heissl
Phil. Trans. R. Soc. B December 19, 2017 372 20160462; doi:10.1098/rstb.2016.0462
http://rstb.royalsocietypublishing.org/content/372/1736/20160462
(openaccess) Research article: The Red Queen model of recombination hot-spot evolution: a theoretical investigation
Thibault Latrille, Laurent Duret and Nicolas Lartillot
Phil. Trans. R. Soc. B December 19, 2017 372 20160463; doi:10.1098/rstb.2016.0463
http://rstb.royalsocietypublishing.org/content/372/1736/20160463
(openaccess) Research article: Background selection as null hypothesis in population genomics: insights and challenges from Drosophila studies
Josep M. Comeron
Phil. Trans. R. Soc. B December 19, 2017 372 20160471; doi:10.1098/rstb.2016.0471
http://rstb.royalsocietypublishing.org/content/372/1736/20160471
(openaccess) Review article: Recombination rate plasticity: revealing mechanisms by design
Laurie S. Stevison, Stephen Sefick, Chase Rushton and Rita M. Graze
Phil. Trans. R. Soc. B December 19, 2017 372 20160459; doi:10.1098/rstb.2016.0459
http://rstb.royalsocietypublishing.org/content/372/1736/20160459
(openaccess) Review article: Are the effects of elevated temperature on meiotic recombination and thermotolerance linked via the axis and synaptonemal complex?
Christopher H. Morgan, Huakun Zhang and Kirsten Bomblies
Phil. Trans. R. Soc. B December 19, 2017 372 20160470; doi:10.1098/rstb.2016.0470
http://rstb.royalsocietypublishing.org/content/372/1736/20160470
Research article: What drives the evolution of condition-dependent recombination in diploids? Some insights from simulation modelling
Sviatoslav R. Rybnikov, Zeev M. Frenkel and Abraham B. Korol
Phil. Trans. R. Soc. B December 19, 2017 372 20160460; doi:10.1098/rstb.2016.0460
http://rstb.royalsocietypublishing.org/content/372/1736/20160460

Evolutionary theories of epigenetic drift

September 15, 2017

by James Kohl with No Comment Adaptations Diseases & Disorders Ecology Model Organisms RNA Directed RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing Variations

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

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

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

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

Energy as information is epigenetically linked from the food that organisms eat to the physiology of pheromone-controlled reproduction in all living genera by RNA-directed DNA methylation and amino acid substitutions that differentiate all cell types in all individuals.
All serious scientists have linked RNA-mediated amino acid substitutions from the differentiation of cell types in yeasts to the differentiation of cell types in primates.
Nothing in Biology Makes Any Sense Except in the Light of Evolution

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.

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

In the mouse model, the diet of the mice determines their nutrient-dependent pheromone production and social interactions with other mice. The mouse model also reveals something that was not revealed in the context of dogs and wolves (Axelsson et al., 2013; Lord, 2013). The aversive human body odor associated with fish odor syndrome can be epigenetically controlled by reducing dietary choline intake. It can also be controlled through antibiotic use (citations in Li et al., 2013). This may be important in the context of chemical ecology and epigenetic effects of genetically predisposed nutrient-dependent pheromone-controlled human interactions (Martin et al., 2010; Preti & Leyden, 2010).

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

Nematodes

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

Insects

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

Mammals

Species-specific health and reproductive fitness is associated with nutrient-dependent amino acid substitutions and with pheromone-controlled reproduction. Disease is associated with mutations exemplified in cancer where perturbations of the glucose-dependent thermodynamic/thermoregulatory equilibrium are equally clear (Locasale, 2012).

Humans

Two additional recent reports link substitution of the amino acid alanine for the amino acid valine (Grossman et al., 2013) to nutrient-dependent pheromone-controlled adaptive evolution. The alanine substitution for valine does not appear to be under any selection pressure in mice. The cause-and-effect relationship was established in mice by comparing the effects of the alanine, which is under selection pressure in humans, via its substitution for valine in mice (Kamberov et al., 2013).

See for comparison: Feynman on social science
See also:

Inventing "Transcriptome Trajectory Turning Points"

September 12, 2017

by James Kohl with No Comment Adaptations Diseases & Disorders Ecology Model Organisms Nutrigenomics RNA Directed RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing Variations

Summary: They invented the term “Transcriptome Trajectory Turning Points” to prevent others from learning that virus-driven energy theft is the cause of all pathology.
Scientists discover genetic timetable of brain’s aging process

The biggest reorganisation of genes occurs during young adulthood, peaking around age 26, the team found. These changes affected the same genes that are associated with schizophrenia.

The team says this could explain why people with schizophrenia do not show symptoms until young adulthood, even though the genetic changes responsible for the condition are present from birth.

See for comparison: microrna schizophrenia

There is no such thing as a genetic timetable of aging outside the context of epigenetic effects on hormones that affect behavior.

Food energy-dependent pheromone-controlled changes in the microRNA/messenger RNA balance link fixation of experience-dependent RNA-mediated amino acid substitutions to supercoiled DNA, which protects us from the virus-driven degradation of messenger RNA.

They invented the term “Transcriptome Trajectory Turning Points.” That is typical of what pseudoscientists must do to prevent others from learning that virus-driven energy theft is the cause of all pathology.

See for comparison: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

One amino acid substitution in supercoiled DNA can make the difference between healthy longevity and virus-driven pathology at any point in life. That is true for all individuals of all species and all serious scientists are using that fact as they continue Combating Evolution to Fight Disease.

The structure and mechanism of heterotrimeric G proteins has been studied at atomic resolution (Oldham and Hamm, 2008).

The energy-dependent de novo creation of G protein coupled receptors links the sense of smell in bacteria to our visual perception of mass and energy in the context of the physiology of pheromone-controlled reproduction and the time-space continuum. See: Olfaction Warps Visual Time Perception

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

Sexual communication signals: New Insights!

August 31, 2017

by James Kohl with No Comment Adaptations Alternative Splicings Cytosis Diseases & Disorders Ecology Human Pheromones Light Energy Model Organisms Nutrigenomics Physics RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing Subatomic

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 sexes^2-4, 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

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.

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, 2012; Duvarci, Nader, & LeDoux, 2008; Griggs et al., 2013; Monahan & Lomvardas, 2012) in adaptive evolution will certainly be discussed in published works that will follow.

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.

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.

Energy-dependent de novo creation and neurogenesis

December 8, 2016

by James Kohl with One Comment Adaptations Alternative Splicings Diseases & Disorders Ecology RNA Directed RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity Variations

Developmentally defined forebrain circuits regulate appetitive and aversive olfactory learning

reported as: When neurons are ‘born’ impacts olfactory behavior in mice

My summary:

The de novo creation of different cell types is placed into the context of their energy-dependent birth and the transgenerational epigenetic inheritance of molecular mechanisms that link virus-driven energy theft to all pathology via olfaction, food odors, and human pheromones.

See for comparison: Metabolism and neurogenesis

…it seems quite obvious that cellular metabolism determining for example the cell’s energy status will be linked to NSPC activity and neuronal differentiation processes, as cell division and differentiation are associated with an increase in cell volume and biomass production and require substantial amounts of energy for DNA replication and organelle synthesis [7].

…the underlying amino acid sequence can vary slightly for each of the 400 receptor proteins, resulting in one or more variants for each of the receptors.

See my comments:

1) The truth revealed in the context of amino acid substitutions is that the theory of mutation-driven evolution does not make sense and it never did.

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

“…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution.”

One reason you may not know this yet is that you were taught to believe in a theory that was never supported by experimental evidence from any species.
See for review: An experimental test on the probability of extinction of new genetic variants.

2) For contrast, note the insistence by the moderator of the International Society for Human Ethology’s yahoo group. He thinks that random mutations are the substrates on which directional natural selection acts. This is what happened when I told him that natural selection is for food:

https://groups.yahoo.com/neo/groups/human-ethology/conversations/topics/48182

Jay R. Feierman, best known to me for his ridiculous question: “What about birds?” wrote:

“It is very sad for me to see that when several different people on this group, all with doctorate degrees, tell you that you are not correct, you don’t consider that they might be telling you something helpful. Instead, you respond with arrogance and ignorance. I’ll add my voice to the other people on this group who have told you that you are not correct in terms of your understanding of what “variation” means in Darwinian biological evolution and what is doing the selecting. Variation is not nutrient availability…”

All experimental evidence of biologically-based energy-dependent cause and effect has proved that Jay R. Feierman and others like him are biologically uninformed and that they choose to remain that way. This evidence from December 2012 shows that nutrient availability is the only variant that can be directly linked from the energy-dependent physiology of reproduction in bacteria to neurogenesis in the human brain!

Addressing sex as a biological variable

Each new misrepresentation of biophysically constrained cell type differentiation outside the context of energy-dependent differences or sex as a biological variable must be viewed in the context of how theorists must continue to try to deceive those who might otherwise become serious scientists.
In this case, the journal article about the TET proteins, Tet proteins influence the balance between neuroectodermal and mesodermal fate choice by inhibiting Wnt signaling, claims: “…Wnt3 was shown to activate Nodal expression directly through its proximal epiblast enhancer at the gastrulation stage (58, 59).”
58. Blaschke, K., Ebata, K. T., Karimi, M. M., Zepeda-Martinez, J. A., Goyal, P., Mahapatra, S., et al. (2013). Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells. Nature, 500(7461), 222-226.
59. Hashimoto, H., Pais, J. E., Zhang, X., Saleh, L., Fu, Z.-Q., Dai, N., et al. (2013). Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA. [Letter]. Nature.
If you are not told that the epiblast enhancers must first link nutrient energy-dependent changes in base pairs to cell type differentiation via RNA-mediated amino acid substitutions before the structure of functional proteins can be linked to anything else, you are less likely to learn that fixation of the substitutions in organized genomes only occurs via the physiology of reproduction. The pheromone-controlled physiology of reproduction links the metabolism of nutrients to all morphological and behavioral diversity in species from microbes to humans via the conserved molecular mechanisms of transgenerational epigenetic inheritance.
There is no question that transgenerational epigenetic inheritance is nutrient-dependent and pheromone-controlled is species from microbes to humans. That fact is now appearing in articles co-authored by the guest editors of a special issue of “Nutrients” who invited me to submit this review of nutritional epigenetics.

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

My invited review was returned without review. Since then, one of the guest editors incorporated my claims into this: Insights from Space: Potential Role of Diet in the Spatial Organization of Chromosomes Published: 10 December 2014

The other guest editor incorporated my claims into this: The Interaction between Epigenetics, Nutrition and the Development of Cancer Published: 30 January 2015

Many academics clearly cannot be trusted with accurate representations of biophysically constrained biologically-based cause and effect. Unless they have a record of accurate representations they are forced to try to establish a record after-the-fact. For example, see: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. This is the 2013 published review that led Justin O’Sullivan and Lynnette Ferguson to request the invited review of nutritional epigenetics, which they returned without review.

My model was cited in Role of olfaction in Octopus vulgaris reproduction

It was also cited in Two fatty acyl reductases involved in moth pheromone biosynthesis (see #10)

Studies over the last two decades have pinpointed that the epigenetic effect of pheromone-driven adaptive evolution is one of the major factors driving the successful diversification of Lepidopteran insects10. In moths, a few substitutions in critical amino acids in the key pheromone biosynthetic enzymes are sufficient to create a novel pheromone component11,12.

If others had not cited my model, which is a refutation of neo-Darwinian pseudoscientific nonsense, there would be no record of experimentally established facts that link energy-dependent changes in the microRNA/messenger RNA balance to all cell type differentiation via RNA-mediated amino acid substitutions in all invertebrates and vertebrates.