5th-6th Sept 2018 Dublin, Ireland

The eternal significance of microRNAs (7)

Sales of human pheromone-enhanced fragrance products have been virtually eliminated by the pseudoscientific nonsense touted by neo-Darwinian theorists and Big Bang cosmologists. I may revisit their ridiculous claims at ScentofEros.com and Pheromones.com, but prefer to continue moving forward via my other domains: RNA-mediated.com and Autophagy.pro.

Summary: 2018 Update: Sympatric speciation has been linked to species diversity as an example of an ecologically validated proof-of-concept in all living genera.

Theorists, other psedoscientists and nearly all so-called science journalists have failed to use common sense in their ridiculous representations.
See for example: Beating the Odds for Lucky Mutations: If DNA repair makes useful mutations more likely, it could accelerate cells’ adaptations to harsh environments (8/16/17) by Jordana Cepelewicz
See: 4/18/18 Nutrient-dependent Pheromone-Controlled Ecological Adaptations: From Angstroms to Ecosystems by James V. Kohl
My model of ecological adaptations was placed into the context of this article in Quanta Magazine by Jordana Cepelewicz — less than one year after she published her article on “lucky mutations” in Aeon.
5/10/18 A Thermodynamic Answer to Why Birds Migrate

…research makes a forceful argument that energy supply and demand is a driving ecological principle shaping the global structure of biodiversity.

See for comparison: 10/12/16 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.

Evolutionary theorists and Big Bang cosmologists are forced to plagiarize the intellectual property of others like me and pretend that they are saying something new about the origin of all energy-dependent biophysically constrained biodiversity.
Jordana Cepelewicz is among the most serious offenders. I wonder why she thinks she can get away with directly contradicting the claims she made less than one year ago.
I have neglected some of the domains I established during the past 7 years because it became clear that pseudoscientists were not going to let people know that all aspects of sympatric speciation have been detailed in the context of food energy-dependent pheromone-controlled reproduction, which is required to biophysically constrain viral latency.
That fact was placed into the context of the cell biology game “Cytosis,” which was delivered to backers in October 2017.

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

See also: A transmissible RNA pathway in honey bees (2018)
The authors link my model of food energy-dependent pheromone-controlled biophysically constrained sympatric speciation from atoms to ecosystems in all living genera via my 2013 published review and my unpublished invited review of nutritional epigenetics.

Nutrient-dependent/pheromone-controlled adaptive evolution: a model (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.

For a historical perspective, see: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014 preprint)

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.

The facts about sympatric speciation for comparison to the neo-Darwinian pseudoscientific nonsense about mutation-driven evolution have been placed in to the context of 3 more recently published works.
A 360 degrees view of circular RNAs: From biogenesis to functions (2018)
Circular RNAs: Unexpected outputs of many protein-coding genes (2017)
The Output of Protein-Coding Genes Shifts to Circular RNAs When the Pre-mRNA Processing Machinery Is Limiting (2017)
It is no longer possible to successfully put the facts about sympatric speciation back into the context of ridiculous theories about the emergence of energy and evolution of all life on Earth. Anyone who returns to the links or to the published works I have posted here, will realize that pseudoscientists and most so-called science journalists know virtually nothing about food energy-dependent RNA-mediated cell type differentiation in any species.

Caption: Contemporary analyses of cell metabolism have called out three metabolites: ATP, NADH, and acetyl-CoA, as sentinel molecules whose accumulation represent much of the purpose of the catabolic arms of metabolism and then drive many anabolic pathways. Such analyses largely leave out how and why ATP, NADH, and acetyl-CoA (Figure 1) at the molecular level play such central roles. Yet, without those insights into why cells accumulate them and how the enabling properties of these key metabolites power much of cell metabolism, the underlying molecular logic remains mysterious. Four other metabolites, S-adenosylmethionine, carbamoyl phosphate, UDP-glucose, and Δ2-isopentenyl-PP play similar roles in using group transfer chemistry to drive otherwise unfavorable biosynthetic equilibria. This review provides the underlying chemical logic to remind how these seven key molecules function as mobile packets of cellular currencies for phosphoryl transfers (ATP), acyl transfers (acetyl-CoA, carbamoyl-P), methyl transfers (SAM), prenyl transfers (IPP), glucosyl transfers (UDP-glucose), and electron and ADP-ribosyl transfers (NAD(P)H/NAD(P)+) to drive metabolic transformations in and across most primary pathways. The eighth key metabolite is molecular oxygen (O2), thermodynamically activated for reduction by one electron path, leaving it kinetically stable to the vast majority of organic cellular metabolites

Odor activation of ATP (2)

Metabolic Regulation of Cytoplasmic DNA Synthesis (1974)

The curve that results when the rate of DNA synthesis is plotted as a function of ATP concentration is sigmoidal, suggesting that more than one site on the enzyme interacts with ATP and that these sites are acting cooperatively.

Odor activation of ATP is the obvious link to RNA-mediated feedback loops that control the food energy-dependent pheromone-controlled physiology of reproduction via the rate of DNA repair in species from microbes to humans.
See: “ATP activation
See for comparison: Feedback loops link odor and pheromone signaling with reproduction (2005)
See also: “ATP activation” microRNA
See also: Mapping malaria by combining parasite genomic and epidemiologic data

Here, we discuss the spatial epidemiology of malaria in the context of transmission-reduction interventions, and the challenges and promising directions for the development of integrated mapping, modeling, and genomic approaches that leverage disparate data sets to measure both connectivity and transmission.

The sun’s anti-entropic virucidal energy has been linked to protective food energy-dependent hemoglobin variants via 1700+ examples. The variants link interethnic similarities and differences to all extant human populations.
HbVar: A Database of Human Hemoglobin Variants and Thalassemias
SNPs or indels [insertions/deletions] link amino acid substitutions to hemoglobin variants. Molecular defects [mutations] in regulatory or coding regions of the human genes can minimally or drastically reduce their expression, leading to α-, β- or δ-thalassemia, respectively.
What can be said about so-called scientists and so-called science journalists who do not know the difference between how a food energy-dependent amino acid substitution is linked to ecological adaptations and how a mutation is linked to diseases?
Who was the first to say it?

Who will be the next to disagree:
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.

Darwin repeatedly asserted that “conditions of life” must be placed before natural selection. Without the sun’s anti-entropic energy, no species on Earth can adapt to ecological variation.

5th-6th Sept 2018 Dublin, Ireland

Diet-driven RNA interference and mental health (4)

See: Diet-driven RNA interference and mental health (3)

Social transmission and buffering of synaptic changes after stress

Transmission from the stressed subject to the naive partner required the activation of PVN CRH neurons in both subject and partner to drive and detect the release of a putative alarm pheromone from the stressed mouse.

Reported as: Researchers discover brain cells change following close contact with a stressed individual

“There has been other literature that shows stress can be transferred — and our study is actually showing the brain is changed by that transferred stress,” says Toni-Lee Sterley, an Eyes High postdoctoral fellow in Bains’s lab and the study’s lead author. “The neurons that control the brain’s response to stress showed changes in unstressed partners that were identical to those we measured in the stressed mice.”

The researchers discovered that the activation of the neurons causes the release of a chemical signal, an “alarm pheromone,” from the mouse that alerts the partner. The partner who detects the signal can, in turn, alert additional members of the group.

This links Bruce McEwen’s works on stress to my works. It completes details of how the mouse-to-human model links nutrient stress-linked and social stress-linked mutations from the virus-driven theft of quantized energy to all pathology. It predicts that fact that human pheromone-enhanced products will continue to be used to prevent or effectively treat Alzheimer’s disease and other neurodegenerative diseases, and to prevent suicide.
See: Formulation and evaluation of anti-suicidal nasal spray of Thyrotropin releasing hormone
See also: Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis
The unnecessary suffering and premature deaths of ~ 22 veterans per day and many others who commit suicide or who suffer through largely ineffective treatments for cancer can be place into the context of two reviews:
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013)
and Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
In my 2014 invited review of nutritional epigenetics, I linked one food energy-dependent base pair to fixation of one amino acid substitution and the stability of organized genomes in a modern human population. The stability was clearly linked from the creation of microRNAs via ingestion of sago palm-like leaves to an increase in endogenous vitamin C.
See also: Vitamins and Hormones Volume 106 Thyroid Hormone February 2018 (paywalled)
Vitamin C links a single base pair change to one amino acid substitution (V370A) in a modern human population. That fact can now be linked from my 2013 refutation of neo-Darwinian pseudoscientific nonsense to all biodiversity on Earth via the creation of sunlight and the Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

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

The model organism that best represent the facts about epigenetic regulation of biophysically constrained ATP-dependent RNA-mediated viral latency is featured here: Meet the creature that can regenerate its brain and resist cancer.

A good model with a good model organism predicts. The mouse to human model predicts that one base pair and one fixed RNA-mediated amino acid substitution link the pheromone-controlled physiology of reproduction to all vertebrate biodiversity via food odors.  Predictably, in the axolotyl (aka the “walking fish”), an iodine isotope and cryo-EM technology will soon be used to establish the facts about how the creation of sunlight must be linked from the creation of ATP and the creation of RNA to DNA repair and all biodiversity via the physiology of reproduction and healthy longevity in all living genera.

See also: Researchers ID New Mechanism for Keeping DNA Protein in Line

The actions of a protein used for DNA replication and repair are guided by electrostatic forces known as phosphate steering, a finding that not only reveals key details about a vital process in healthy cells, but provides new directions for cancer treatment research.
Electrostatic forces are not known as phosphate steering.
See: What is an Electrostatic Force?

Electrostatic force between electrons and protons is one of the strongest forces in the universe, even more powerful than gravity. A hydrogen atom, which contains only one electron and one proton, has the fundamental force of gravity keeping it together. However, each subatomic particle can develop electrostatic force as well, which becomes even stronger.

Pseudoscientists are prepared to attack serious scientists at every level of examination that includes aspects of how subatomic particles contribute to oxidative phosphorylation. Who doesn’t know about the role that subatomic particles play in biophysically constraining viral latency?
See: Subatomic: An Atom Building Game (2017)

Subatomic is a deck building game where players are competing to build a number of available Elements, which score them points. Each player starts with the same small deck of cards that consist of Proton, Neutron, and Electron Cards. They use these cards to build upon their current Atom (by playing these cards face-up as Subatomic Particles) in an attempt to construct one of the available Element Cards. Or players may use their hand of cards to purchase more powerful cards for later use (by playing them in combinations of face-down as energy and face-up as Subatomic Particles!) Subatomic introduces a unique variation on deck building with a highly accurate chemistry theme…

The fact that Discover’s “My Science Shop” does not yet include information on the game “Subatomic” can be explained because the game is not yet available. The fact that Discover’s “My Science Shop” does not mention the availabilty of “Cytosis” suggests they are not willing to admit that their past representations of neo-Darwinian pseudoscientific nonsense were removed from consideration in 1944 when Schrödinger published “What is Life?”
See: Schrödinger at 75 – The Future of Biology – September 2018
The most accurate of all chemistry themes has continued to link Schrödinger’s claims from  quantum physics and quantum chemistry to quantum biology via the conserved molecular mechanisms of biophysically constrained protein folding chemistry. The conserved molecular mechanisms link energy-dependent epigenetics to healthy longevity. The conserved molecular mechanisms also link the virus-driven theft of quantized energy to all pathology.
See also: A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution (2013)
Classical biophysics does not have a ready explanation for the role of docosahexanoic acid (DHA), which appears to be irreplaceable in the context of a light-activated endogenous substrate that functions as an electron tunnelling device. DHA provides precise quantized signals that are essential to visual accuity in the context of synaptic signaling. The link from quantum physics to classical physics helps to explain why the energy-dependent creation of photoreceptors has been linked to their counter intuitive orientation — away from the incoming light.
But, I digress. I am often forced to digress by theorists who invent new terms, such as phosphate steering, to obfuscate what is know about epigenetically-effected top-down causation, which starts with effects of sunlight linked to oxidative phosphorylation. Top-down causation does not start with phosphate steering. It starts with the creation of receptors. If any aspect of biophysically constrained life on Earth started with phosphate steering, there would be more than one citation to the claim. There is only one. See. “Phosphate steering.”
For comparison to what is known about the link from microRNAs to the brain and behavior, see:
microRNA brain and microRNA behavior
See also: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene (2011)
and Targeted expression of suicide gene by tissue-specific promoter and microRNA regulation for cancer gene therapy (2013)

See: Epigenetics study helps focus search for autism risk factors

Within the Shank3 promoter 6 region they identified a single nucleotide polymorphism (or SNP, a common type of genetic variation) known as rs6010065. Analyzing genomic data from a clinical study of 554 children with autism and 214 healthy controls, they found that rs6010065 is indeed associated with autism spectrum disorder.

I reiterate. The profiles are energy-dependent and the pheromone-controlled physiology of reproduction helps to ensure that viral latency is biophysically constrained by the dynamic processes. That fact can be compared to ridiculous claims about mutations and the “evolving profiles.”

See for example, this link from the food energy-dependent pheromone-controlled fixation of the BDNF val66met polymorphism amino acid substitution to behavior in human infants.

The BDNF val66met polymorphism and individual differences in temperament in 4-month-old infants: A pilot study

See for comparison: Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity

Reported as: Newly discovered windows of brain plasticity may help with treatment of stress-related disorders 

…they looked at mice genetically engineered to carry a genetic variant associated with development of depression and other stress-related disorders in humans [ the variant is (BDNF Val66Met)] and present in 33 percent of the population.

If you don’t know where to look, you might find where the information on the BDNF Val66Met is buried. But, if you look at the life’s works of Bruce S. McEwen, you will discover what is known to all serious scientists about stress linked RNA-mediated cell type differentiation.

Redefining neuroendocrinology: Epigenetics of brain-body communication over the life course (2017)

Heterozygous BDNF Val66Met mice are genetically susceptible to stress. The effects of stress on messenger RNA levels in wild-type mice was recapitulated but only via activation of immediate early genes when the heterozygous BDNF Val66Met mice were actually stressed. In the absence of stress, stress activated expression of immediate early genes is not worth studying. Similarly, it is not worth studying how nutrient stress is linked to social stress via c-fos activation in gonadotropin releasing hormone (GnRH) neuroscretory neurons.

However, if baseline studies had not already linked expression of the Fos protein to epigenetic effects of pheromones on luteinizing hormone in mice, the epigenetic effects of food odors and pheromones on humans might never have been linked to interethnic genetic differences in human morphology and behavior.

See: Influence of male rats on the luteinizing hormone-releasing hormone neuronal system in female rats: role of the vomeronasal organ (1993)

[Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)] (1994)

Human pheromones: integrating neuroendocrinology and ethology (2001)

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

The link from diet-driven RNA interference to mental health can now be considered in the context of gene gains and losses.

For example, see: APOBEC1

  1. Catalytic component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the postranscriptional editing of a CAA codon for Gln to a UAA codon for stop in the APOB mRNA.
  2. Also involved in CGA (Arg) to UGA (Stop) editing in the NF1 mRNA.
  3. May also play a role in the epigenetic regulation of gene expression by participating in DNA demethylation.

Loss of APOBEC1 RNA-editing function in microglia exacerbates age-related CNS pathophysiology

These data provide powerful evidence supporting the critical role of APOBEC1-mediated RNA editing in maintaining the balance between the homeostatic and activated immune functions of MG.

See also: Psychological Stress and Mitochondria: A Conceptual Framework (Part 1) and Psychological Stress and Mitochondria: A Systematic Review (Part 2)

Reported as: Cellular ‘powerhouses’ may explain health effects of stress

The findings are especially exciting for the field of psychosomatic medicine, with its traditional focus on re-integrating the mind (“psyche”) and body (“soma”). Emerging evidence on the role of mitochondria in translating the effects of stress on health “extend the reach of mind-body research into the cellular-molecular domain that is the core foundation of current biomedical training and practice,” Drs. Picard and McEwen write. They emphasize the need for further studies to test various elements of their model, especially in humans. “Future research should consider the dynamic bi-directional interactions between mitochondria and other important physiological systems,” the authors conclude.

See also: Mitochondrial alterations and neuropsychiatric disorders

Mitochondria are membrane-enclosed organelle found in most eukaryotic cells, where they generate the majority of the cell’s supply of adenosine triphosphate (ATP), used as a source of chemical energy. In addition, they are involved in a range of other processes, such as signalling, cellular differentiation, cell death, as well as the control of the cell cycle and cell growth. Mitochondria have been implicated in several neuropsychiatric disorders, in particular, depression, anxiety, schizophrenia, autism, and Alzheimer’s dementia. Furthermore, the presence of mutations at the level of mitochondrial or nuclear DNA (mtDNA and nDNA, respectively) has been linked to personality disorders, behavioral disturbances, thought alterations, impulsivity, learning impairment, cognitive failures until dementia. The aim of this paper is to review the literature on the relationship between psychiatric symptoms or syndromes and mtDNA mutations or mitochondrial alterations, while highlighting novel therapeutic targets for a broad range of disorders.

 

5th-6th Sept 2018 Dublin, Ireland

Diet-driven RNA interference and mental health (3)

Discover’s “My Science Shop” now advertises the games that led to development of the cell biology game: “Cystosis,” which is a neo-Darwinian evolutionary theory-killer. Cytosis links the creation of anti-entropic viruidal light to all biodiversity on Earth via the physiology of reproduction and biophysically constrained viral latency.

See the dumbed-down version of that fact: Missing Mutations Suggest a Reason for Sex

Summary: A good model with a good model organism predicts. The mouse-to-human model of biophysically constrained viral latency predicts that one base pair and one fixed RNA-mediated amino acid substitution link the pheromone-controlled physiology of reproduction to all vertebrate biodiversity via food odors.  Predictably, in the axolotyl (aka the “walking fish”), an iodine isotope and cryo-EM technology will soon be used to establish the facts about how the creation of sunlight must be linked from the creation of ATP and the creation of RNA to DNA repair and all biodiversity via the physiology of reproduction and healthy longevity in all living genera.

See for example: A Conserved MicroRNA Regulatory Circuit Is Differentially Controlled during Limb/Appendage Regeneration

…we employ next-generation sequencing to identify shared, differentially regulated mRNAs and noncoding RNAs in three different, highly regenerative animal systems: zebrafish caudal fins, bichir pectoral fins and axolotl forelimbs.

See for comparison: Mutation, Not Natural Selection, Drives Evolution also reported as: We are all mutants (March 2014)

In 1972, he devised a now widely used formula, Nei’s standard genetic distance, which compares key genes of different populations to estimate how long ago the groups diverged. In the early ’90s, Nei was a co-developer of free software that creates evolutionary trees based on genetic data. Two decades later, Molecular Evolutionary Genetics Analysis, or MEGA, remains one of the most widely used and cited computer programs in biology.

But it’s his natural selection-busting theory, which Nei developed in the ’80s and expanded on in the 2013 book Mutation-Driven Evolution, that the researcher wants to see embraced, cited and taught in schools.

That’s not going to happen except in the context of teaching students the difference between a ridiculous theory and facts about ecology!
See: Israeli Middle Schools School to Include Theory of Evolution

…learning about evolution is not the primary function of the decision, but rather to use it as a building block for students to learn more about their ecology.

See also: Asymmetric Auxin Distribution is Not Required to Establish Root Phototropism in Arabidopsis

…we conclude from our current data that the phototropic response in Arabidopsis roots is induced by an unknown mechanism…

No intelligent person on Earth is going to teach students that any phototropic response is induced by an unknown mechanism.
See for comparison: Overexpression of microRNA408 enhances photosynthesis, growth, and seed yield in diverse plants and Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis
Instead, students who are 10 years old or older will learn cell biology in the context of accurate representations of how what organisms eat biophysically constrains viral latency in the context of the physiology of reproduction. Students who learn to play the games that led to the development of the game “Cytosis” can start with the creation of microRNAs in plants and link the creation of sunlight to all biodiversity via the physiology of reproduction in plants and animals.
They will learn that embracing a ridiculous theory of mutation-driven evolution led to acceptance of  evolutionary trees based on mathematical models of genetic data. They will learn how biophysically constrained top-down causation links RNA-mediated fixation of amino acid substitutions to all cell type differentiation in all living genera via what is known to serious scientists about sensing and signaling in the context of quantitative proteomics.
Ras/ERK-signalling promotes tRNA synthesis and growth via the RNA polymerase III repressor Maf1 in Drosophila

These findings suggest that stimulation of tRNA synthesis may be one way that Ras promotes mRNA translation to drive cell and tissue growth.

The light induced stimulation of tRNA synthesis links sensing and signaling from energy-dependent protein biosynthesis and degradation in the context of microRNA-mediated switches that are “flipped” by the availabilty of nutrients, water, and oxygen. Oxidative phosphorylation is required to link the switches to the energy-dependent stability of supercoiled DNA, which protects all organized genomes from the virus-driven degradation of messenger RNA.

See: Quantitative proteomics identifies redox switches for global translation modulation by mitochondrially produced reactive oxygen species (open access)

Reported as: Nano-switches in the cell: A team with researchers has discovered a new mechanism for the regulation of protein synthesis.

..increased levels of reactive oxygen species inhibit protein synthesis. Using biochemical and cell biological methods, she showed that damaged mitochondria can signal their metabolic state to the protein synthesis machinery via reactive oxygen species and, thereby, slow down cellular protein synthesis. It is assumed that the temporary reduction of the protein synthesis rate under oxidative stress has a positive effect on the survival of the cells as it is believed to help to restore cellular homeostasis. This also prevents the cell from synthesizing proteins that cannot be taken up by damaged mitochondria, which, as a consequence, accumulate in the cytoplasm and thus need to be degraded.

Anyone who knows anything about energy-dependent microRNA-mediated autophagy will recognize the ridiculous representation and claim about the discovery of a new mechanism for the regulation of protein synthesis. The creation of the sun’s anti-entropic virucidal energy links the creation of ATP to the creation of enzymes and microRNAs. The microRNAs regulate protein biosynthesis and degradation. There is nothing new about that. Yoshinora Ohsumi won the 2016 Nobel Prize in Physiology and Medicine for details about autophagy in the context of a published work from 1998.
He was the senior author of A protein conjugation system essential for autophagy

This conjugation can be reconstituted in vitro and depends on ATP. To our knowledge, this is the first report of a protein unrelated to ubiquitin that uses a ubiquitination-like conjugation system. Furthermore, Apg5 and Apg12 have mammalian homologues, suggesting that this new modification system is conserved from yeast to mammalian cells.

The modification system is ATP-dependent and microRNA-mediated.
See: The tipping point (revisited): 68,000 publications
See also: The tipping point (revisited): 69,000 publications
For updates, see: MicroRNA at PubMed
Moving forward, it is time to link the creation of microRNAs from fixation of RNA-mediated amino acid substitutions to mental health.
See: Diet-driven RNA interference and mental health (4)

5th-6th Sept 2018 Dublin, Ireland

Anti-entropic sunlight: Schrödinger’s Creationist Secret? (2)

 

Arabidopsis mRNA decay landscape arises from specialized RNA decay substrates, decapping-mediated feedback, and redundancy

The decay of mRNA plays a vital role in modulating mRNA abundance, which, in turn, influences cellular and organismal processes. In plants and metazoans, three distinct pathways carry out the decay of most cytoplasmic mRNAs: The mRNA decapping complex, which requires the scaffold protein VARICOSE (VCS), removes a protective 5′ cap, allowing for 5′ to 3′ decay via EXORIBONUCLEASE4 (XRN4, XRN1 in metazoans and yeast), and both the exosome and SUPPRESSOR OF VCS (SOV)/DIS3L2 degrade RNAs in the 3′ to 5′ direction. However, the unique biological contributions of these three pathways, and whether they degrade specialized sets of transcripts, are unknown.

 
A claim like this could be used as cannon-fodder for any serious scientist who wanted to target a neo-Darwinian theorist. I will do what Daniel Dennet suggested and re-express my target’s position.
You should attempt to re-express your target’s position so clearly, vividly, and fairly that your target says, “Thanks, I wish I’d thought of putting it that way. — Daniel Dennett

Ready… Aim… Fire

Simply put, the target claims that the molecular mechanisms of energy-dependent microRNA-mediated cell type differentiation remove a protective 5′ cap, allowing for 5′ to 3′ decay. But, they place their claim into something that supposedly is unknown about how the biological contributions of three pathways prevent mRNA decay.
The problem with the target’s position: A one-sided attack on Schroedinger’s claims fails to link the epigenetic landscape to the physical landscape of supercoiled DNA in the context of energy-dependent feedback loops. The feedback loops link the physiology of reproduction from the creation of RNA to prevention of the decapping.
The energy-dependent creation of RNA is required to prevent the virus-driven theft of quantized energy that causes the decapping of the mRNA complex and link mutations to all pathology. For contrast, the food energy-dependent creation of microRNAs has repeatedly been linked from RNA-mediated DNA repair and the fixation of  amino acid substitutions to the stability of supercoiled DNA in the organized genomes of all living genera.
See: Evidence for Amino Acid Sequence Differences among Proteins Resembling the L-chain Subunits of Immunoglobulins (1965)

…we believe that this remarkable type of amino acid sequence variation reflects in part the mechanism by which specificity is conferred.

Note: The co-author, Lee E. Hood is scheduled to present at Schrödinger at 75 – The Future of Biology – September 2018 
Supercoiled DNA protects organized genomes from the virus-driven degradation of messenger RNA that the authors of the article on mRNA link to  specialized RNA decay substrates, decapping-mediated feedback, and redundancy without linking the energy-dependent feedback to healthy longevity via the fixation of RNA-mediated amino acid substitutions and DNA repair.
The article is paywalled, so you may need to take my word for the fact that they seem to be deliberately deceptive. The level of their obfuscation became clear to me in the context of their Figure 6.  They placed the role of energy-dependent RNA-mediated amino acid substitutions into the proper perspective of everything known to serious scientists about biophysically constrained viral latency.
Also, in the article text, they conclude that studies of oxidative phosphorylation attest to facts about prevention of mRNA decay components in response to nutrient stress or social stress, which they refer to as “osmotic stress.” They link the stress from changes in the mRNA half-life and suggest that energy-dependent regulation of the half-life could arise in the context of the direct modulation of mRNA decapping machinery.
The direct modulation is obviously energy-dependent but they place the modulation into some other context that seemingly involves upstream pathways and the creation of proteins. Simply put, they are swimming upstream at a time when all serious scientists are starting with energy-dependent top-down creation of microRNAs.
They conclude with a plea for funding of more pseudoscientific nonsense that fails to link the creation of the sun’s anti-entropic virucidal energy to healthy longevity via the creation of microRNAs that prevent the virus-driven degradation of messenger RNA, which serious scientist have linked from mutations to all pathology.  They claim that an important area of future research includes research that might lead to a better understanding of how stress is linked to pathology via conserved molecular mechanisms. I claim they are using correlations from the bottom-up to replace top-down causation and biophysically contrained cause and effect.
See for comparison: ORACLE: Options to Read in the Archive: Churchland Lab’s Experience
They highlight 7 comp/systems neuro papers to help others keep up with the amount of information that is being published in bioRxiv Neuroscience preprints.
For example: Human POMC processing in vitro and in vivo revealed by quantitative peptidomics

Human obesity can result from the aberrant production or processing of proopiomelanocortin (POMC) in hypothalamic neurons, but it is unclear which human POMC-derived peptides are most relevant to body weight regulation.

See also: Association of a lincRNA postmortem with suicide by violent means and in vivo with aggressive phenotypes

In a living cohort, carriers of the minor allele of a SNP associated with increased LINC01268 expression in brain scored higher on a lifetime aggression questionnaire and show diminished engagement of prefrontal cortex (BA10) when viewing angry faces during fMRI. WGCNA highlighted the immune response. Conclusions: These results suggest that LINC01268 influences emotional regulation, aggressive behavior and suicide by violent means; the underlying biological dynamics may include modulation of genes potentially engaged in the immune response.

See also: The behavioral and neurobiological effects of reduced Brd1 expression in mice are sex-biased and implicate gender dependent dysregulation of nuclear receptor mediated signaling in mental disorders

…we provide in vitro evidence that BRD1 modulates the transcriptional drive of a subset of nuclear receptors (e.g. the vitamin D and glucocorticoid receptors). Moreover, we demonstrate enrichment of psychiatric disorder risk in the target genes of nuclear receptors, sex-biased expression of several nuclear receptor genes in the adult brain of Brd1+/- mice, and that sex-biased genes in general are enriched with nuclear receptor genes particularly at the earliest developmental stage of the human brain. Overall, our data suggests that the spatio-temporal interaction between BRD1 and subsets of nuclear receptors in the brain is sex-biased and that hampered BRD1 mediated regulation of target genes governed by certain nuclear receptors may significantly contribute to sex differences in psychopathology.

For comparison, this was published on the same day: Evolutionary conserved neural signature of early life stress affects animal social competence
What do claims about evolutionary conserved neural signatures represent to serious scientists who understand the facts about energy-dependent top-down causation and biophysically constrained viral latency?

Alternative splicing of pre-mRNA

Epigenetic facts vs variable recombination theories

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

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

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

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

Alternative splicing of pre-mRNA

From base editing to RNA editing (4)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

From base editing to RNA editing

Base Editing Now Able to Convert Adenine-Thymine to Guanine-Cytosine

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

The creation of quantized energy in sunlight links energy as information from electrons to ecosystems via the physiology of reproduction in all living genera. The claim that “Nature” provides us with cytosine deaminase enzymes makes it seem that the enzymes emerged and automagically evolved to become purposeful and meaningful in the context of ridiculous theories about mutation-driven evolution.
See for comparison: All about that base (video parody)
See also: RNA Editing Possible with CRISPR-Cas13

Introducing specific sequence changes into RNA molecules could allow researchers to answer questions about alternative splicing mechanisms, translation, and even editing, he says. “There’s a lot of scope.”

The entirety of that scope was addressed in the context of energy-dependent RNA-mediated cell type differentiation in our section on molecular epigenetics from this 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior
Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (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.
All biophysically constrained RNA-mediated energy-dependent cell type differentiation has since been linked from the pheromone-controlled physiology of reproduction to supercoiled DNA via the fixation of amino acid substitutions and chromosomal rearrangements.
The facts about the amino acid substitutions in the context of transgenerational epigenetic inheritance link electrons to ecosystems via the cryo-EM technology that won the 2017 Nobel Prize in Chemistry.
See: Chemists know (video parody)
See also:

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy. The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection. This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes. For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes

Cytosis

Host-derived creation of all pathology (2 of 2)

Summary: All serious scientists know that all epigenetic diversity is food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction.

See for comparison: 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.”

A Bacterial Messenger Molecule Extends Healthspan

…indole, a molecule produced by commensal bacteria, extends “healthspan” not only in mice but in the nematode worm Caenorhabditis elegans and in fruit flies as well. Taking away the bacterial production of the molecule ablated these anti-aging gains.

Does anyone need to repeatedly be reminded that food energy is required for the production of any molecule associated with nutrient-dependent pheromone-controlled anti-aging gains? The epigenetically effected gains are consistently manifested in the survival of species via the physiology of reproduction.
The food energy-dependent production of indole is the obvious link from nutrient-dependent pheromone-controlled feedback loops to biophysically constrained viral latency and ecological adaptation in all living genera. Testing for indole is used to determine the ability of an organism to split (deaminate) the amino acid tryptophan.  Indole contributes to fecal odor and it is a chemical messenger that has been indirectly or directly included in detailed representations of biologically-based pheromone-controlled energy-dependent cause and effect like these.
See: Feedback loops link odor and pheromone signaling with reproduction (2005)
There is a model for that! See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013)
The food energy-dependent pheromone-controlled physiology of reproduction in species from microbes to humans biophysically constrains the virus-driven degradation of messenger RNA. That fact links constraint-breaking mutations to all pathology in all living genera. A test protocol established that fact in the context of this book chapter, which links the test for indole to differences in the microRNA/messenger RNA balance in humans.

For example, the test protocol links the creation of energy as information to all biodiversity via the physiology of reproduction and links the virus-driven degradation of messenger RNA to all pathology. The complexity of the testing can be reduced via the focus on the energy-dependent creation of microRNAs.

See the abstract:

Disease research and treatment development have turned to the impact and utility of microRNA. The dynamic and highly specific expression of these molecular regulators can be used to predict and monitor disease progression as well as therapeutic treatment efficacy and safety…

MicroRNAs are identified and monitored through the use of locked nucleic acid (LNA)™-based detection probes. The LNA™ technology enhances the sensitivity and specificity of target binding for short, highly similar, microRNA sequences, which help to differentiate cell types in the context of everything known to serious scientists about how to link physics and chemistry from molecular epigenetics to all biodiversity via fixation of RNA-mediated amino acid substitutions.

The availability of this testing was predicted in: Energy as information and constrained endogenous RNA interference (7-min video)

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

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

This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes.

For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

See also: The phylogenetic utility and functional constraint of microRNA flanking sequences
See also: From Fertilization to Adult Sexual Behavior (1996)
See for comparison: Metabolic, Epigenetic, and Transgenerational Effects of Gut Bacterial Choline Consumption (2017)

There is no such thing as transgenerational epigenetic inheritance of morphological or behavioral phenotypes outside the context of feedback loops that link food odors from the metabolism to pheromones and biophysically constrained viral latency. The consumption of choline by bacteria links food energy to protection from viral latency via the test for indole. The virus-driven theft of quantized energy can be linked from reduced amount of choline that link viruses in the bacteria to their ability to overwhelm the immune system. The effects of virus-driven energy theft link the CRISPR-Cas9 technology of gene-editing to DNA repair via exogenous RNA-interference because energy-dependent endogenous RNA-interference protects all organized genomes from virus-driven entropy.
Corporate America is not willing to tell the truth about that. You will probably suffer unnecessarily and die prematurely because the goal of every corporation is to make more money.

See also: Americans Are Dying Younger, Saving Corporations Billions

Absent a war or an epidemic, it’s unusual and alarming for life expectancies in developed countries to stop improving, let alone to worsen. “Mortality is sort of the tip of the iceberg,” says Laudan Aron, a demographer and senior fellow at the Urban Institute. “It really is a reflection of a lot of underlying conditions of life.”

Darwin’s “conditions of life” were food energy-dependent. Serious scientists have since learned that all “conditions of life” also are fixed in the organized genomes of all living genera via the physiology of reproduction. Without the link from ecological variation to ecological adaptation via fixation of amino acid substitutions in supercoiled DNA, natural selection for energy-dependent codon optimality would link mutations to evolution instead of linking mutations to all pathology.

Instead, the reality of cell type differentiation was reported as: Microbes compete for nutrients, affect metabolism, development in mice

 …new research that shows mice that harbor high levels of microbes that eat choline are deprived of this essential nutrient.
 

I placed that fact into the context of this excerpt from my 2013 review: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

Sex-dependent production of a mouse ‘chemosignal’ with incentive salience appears to have arisen de novo via coincident adaptive evolution that involves an obvious two-step synergy between commensal bacteria and a sex-dependent liver enzyme that metabolizes the nutrient chemical choline.

The result of this synergy is (1) a liver enzyme that oxidizes trimethylamine to (2) an odor that causes (3) species-specific behaviors. Thus, the complex systems that biology required to get from nutrient acquisition and nutrient metabolism to species-specific odor-controlled behavior is exemplified by adaptive evolution of an attractive odor to mice that repels rats (see for review Li et al., 2013).

Addendum: Fish odor syndrome is the link from the virus-driven theft of quantized energy. The odor links ecological variation to failed ecological adaptation and all pathology when there is insufficient food energy. Any scientist who does not already know that based on the facts known to every medical laboratory scientist is an example of “human idiocy” (Feynman) or a biologically uninformed science idiot (Kohl).

Serious scientists have begun to effectively use energy-dependent microRNAs to the prevention of all virus-driven pathology. That fact is being reported in the context of gene therapy using ‘junk DNA’  at a time when all serious scientists realize there is no such thing as ‘junk DNA.’

Gene therapy using ‘junk DNA’ could lower risk for heart disease

The LeXis gene belongs to a unique group of genes that until recently were considered “junk DNA” because scientists believed they served little purpose. However, evidence from the human genome project led to the discovery that genes like LeXis are actually active. The study of these genes, now referred to as long noncoding ribonucleic acids, or lncRNAs, is a rapidly evolving area in biology.

Long Noncoding RNA Facilitated Gene Therapy Reduces Atherosclerosis in a Murine Model of Familial Hypercholesterolemia

Long noncoding (lnc) RNAs form the vast majority of transcriptionally active regions and are arbitrary defined as transcripts >200 bps that biochemically resemble mRNA and yet do not template protein.2

Diet and drug-induced changes in LeXis link energy as information to liver X receptor activation of genes via the “promoter binding of RNA-binding proteins.” That fact supports the claim that a transcriptional coactivator for genetically predisposed cholesterol biosynthesis in the mouse liver links promoters, enhancers, quantitative trait loci, et al., to the transciptional coactivator referred to as “Rally” without mention of energy-dependent changes in the microRNA/messenger RNA balance.
If you believe that the long noncoding ribonucleic acids (RNAs) are genes, you may be convinced that mutations in RNA are the same as mutations in genes. But mutations are the cause of all pathology. Linking mutations in RNA to pathology outside the  context of energy-dependent healthy longevity allows others with no expertise in laboratory testing to continue to believe that mutation-driven evolution is the link from natural selection to the origin of new species. That belief is probably common among others who believe that the Universe itself may be conscious.

See for comparison: Scientists Now Believe the Universe Itself May Be Conscious

For the behavior of subatomic particles and the systems they constitute promises to be fully explained by physics and the other physical sciences.

 See for comparison: Subatomic

Subatomic is a deck building game where players are competing to build a number of available atoms. Each player starts with the same small deck of cards that consist of Proton Cards, Neutron Cards, Electron Cards and Energy Cards and a beginning hand limit of 5 cards. They use these cards to build upon their current Atom, in an attempt to construct one of the available Atom Cards, and/or use their hand of cards to purchase more powerful atom building cards for later use, or increase their hand limit. The deck building cards are simple and clean, but offer a number of interesting combinations. Players also have an energy track that allows them to store energy, which introduces a “push-their-luck” type of mechanic enabling players to pay energy to shuffle through their deck quicker, or to offset the cost of more powerful deck building cards.

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

The question arises: “Who needs this kind of nonsense?” Does anyone at any level of examination believe that “the Universe is always looking” is the best representation of what we can expect from a “Conscious Universe?”

See for comparison: Cytosis: A Cell Biology Board Game

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

 Chromogenic In Situ Hybridization Methods for microRNA Biomarker Monitoring of Drug Safety and Efficacy was reported on the Exiqon FB page. Exiqon is a biotechnology company that specializes in RNA products and services. I recommend that they purchase this domain (RNA-mediated.com) in an attempt to promote their products, which obviously link energy-dependent healthy longevity to all biodiversity and also link virus-driven energy theft to all pathology via changes in the microRNA/messenger RNA balance.

See also: ‘Chromatin modifiers and remodellers in DNA repair and signalling’ The fact that food energy as information must be linked from ecological variation to ecological adaptation via the pheromone-controlled physiology of reproduction in all living genera appears to be the focus of this Theme issue.

But wait: Here is one of the articles from  the Theme issue:

Nucleosome remodelling, DNA repair and transcriptional regulation build negative feedback loops in cancer and cellular ageing

Nucleosome remodelling (NR) regulates transcription in an ATP-dependent manner, and influences gene expression required for development and cellular functions, including those involved in anti-cancer and anti-ageing processes. ATP-utilizing chromatin assembly and remodelling factor (ACF) and Brahma-associated factor (BAF) complexes, belonging to the ISWI and SWI/SNF families, respectively, are involved in various types of DNA repair.

See for comparison, from 1964: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

McEwen et al., knew that “The synthesis of RNA in isolated thymus nuclei is ATP dependent.” That statement of fact was the beginning of the abstract from 1964. When he told me my model could not be validated unless I started with energy-dependent gene activation in gonadotropin releasing hormone (GnRH) neurons, I had no reason to doubt him. When I learned that Robert L. Moss had already linked pheromones to energy-dependent gene activation in GnRH neurons, I continued to pursue top-down causation as if it was energy-dependent — because it obviously is energy-dependent.

I never considered that my model of food energy-dependent pheromone-controlled biophysically constrained gene activation would not be accepted by theorists. See for comparison:

Induction of FOS immunoreactivity in central accessory olfactory structures of the female rat following exposure to conspecific males (1992)

See also: Gonadotropin releasing hormone and human sexual behavior (1991) in Neuropeptides and Psychiatric Disorders (1991)

Is anyone else interested in linking the facts from our 1996 Hormones and Behavior review From Fertilization to Adult Sexual Behavior or from any other works I have published before Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013) to what is known about all biophysically constrained biologically- based cause and effect?
If so, see: Worldwide patterns of human epigenetic variation

We found that population-specific DNA methylation mirrors genetic variation, and has greater local genetic control than mRNA levels. We estimated the rate of epigenetic divergence between populations, which indicates far greater evolutionary stability of DNA methylation in humans than has been observed in plants. This study provides a deeper understanding of worldwide patterns of human epigenetic diversity…

All serious scientists know that all epigenetic diversity is food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction.
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.
See for comparison: Quantum Biology: An Introduction (video) by Philip Ball and Quantum common sense

To turn quantum to classical, we don’t need a conscious mind to measure or look; we just need an environment full of stuff. With or without us, the Universe is always looking.

See also these restricted and unrestricted articles: ARTICLES 

Light-induced-conformer-intercoversion-of-hydrogen-bond

Light-activated feedback loops vs self-organization of ecosystems

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

From Fertilization to Adult Sexual Behavior

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

Apoptosis analysis guide | Free ebook download

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

Gene bivalency at Polycomb domains regulates cranial neural crest positional identity

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

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

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

MicroRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos

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

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

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

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

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

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

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

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

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

See for comparison: Helicoverpa armigera images

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See for comparison: Sonny Williams

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

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

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

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

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

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

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

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

From Fertilization to Adult Sexual Behavior

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

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

At least 10,000 neurons in 26 different brain areas appear to transmit signals directly to GnRH neurons.  GnRH neurons appear to transmit signals to as many as 30,000 or more neurons in 34 brain areas, consistent with previous studies showing GnRH+ fibers and GnRH receptors in multiple brain regions. These results may reflect a strategy wherein GnRH neurons can modify diverse functions in order to coordinate the internal state of the animal and its behavior with reproduction in order to optimize reproductive success.