5th-6th Sept 2018 Dublin, Ireland

Ecological adaptations vs the randomness of evolution (3)

Summary: Fifty years later, only theorists and other pseudoscientists have failed to recognize the facts that link experimental evidence of differences in the energy of photons to the proton motive force, which links the potential of hydrogen (pH) to biophysically constrained viral latency and all biodiversity on Earth. In that context, Carl Zimmer serves as an important example of human idiocy each time he makes claims about evolution.
Serious scientists will meet during Schrödinger at 75 – The Future of Biology – September 2018 to discuss the overwhelming amount of human idiocy exemplified in the works of theorists who failed to learn that life is “All about that base.”
Without the quantized energy-dependent creation of the base pairs, viral latency could not be biophysically constrained and entropy would be used to explain the evolution of biodiversity manifested in sympatric speciation.
See for comparison: The costs of living at the edge: Seasonal stress in wild savanna-dwelling chimpanzees

Adaptations associated with shifting from a predominately forested habitat to a more open environment are considered a crucial step in hominin evolution.

The adaptations are food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans. For example, higher levels of dehydroepiandrosterone in humans are an adaptation.
See:  Dehydroepiandrosterone – is the fountain of youth drying out?

…humans are unique in having adrenals that secrete large amounts of the prohormone, dehydroepiandrosterone (DHEA) and its sulfate, DHEA-S, into the bloodstream of males and females. Even non-human primates produce only ~10% of the DHEA found in humans

Carl Zimmer places everything known about how ecological variation must be linked to energy-dependent ecological adaptations into the context of human evolution.
See: Hints of Human Evolution in Chimpanzees That Endure a Savanna’s Heat

Millions of years ago, our apelike ancestors gradually moved from woodlands to savannas and began walking upright at some point. The Fongoli chimpanzees demonstrate just how difficult that transition would have been — and how that challenge may have driven some major changes in our evolution, from evolving sweat glands to losing fur and walking upright.

Before she graduated from her medical technologist course (circa 2014), I mentioned to Misty ______ the importance of  β-lactamase testing to understanding how the energy-dependent creation of microRNAs would soon be linked to all biophysically constrained biodiversity on Earth via antibiotic susceptibility testing in the hospital medical laboratory.
Shared strategies for β-lactam catabolism in the soil microbiome

A hydrolase from the put operon was found to degrade in vitro benzylpenicilloic acid, the β-lactamase penicillin product.

This clearly exemplifies how the virus-driven degradation of messenger RNA in β-lactamase positive organisms is linked to antibiotic resistance via what all serious scientists know about the molecular mechanisms of energy-dependent cell type differentiation.
The findings were reported in the ridiculous context of claims about How Bacteria Eat Penicillin

…some of the bacteria could, in fact, eat the drugs… As it turned out, they were everywhere. He also found examples of the phenomenon in the scientific literature going back to the 1960s.

In 1964, McEwen et al, linked the creation of the sun’s anti-entropic virucidal energy from Schrödinger’s claims in What is Life? (1944) to the creation of ATP and the creation of RNA. Now, others like McEwen know that RNA interference biophysically constrains viral latency.
In 1968, Frohlich speculated that the highly ordered storage of quantized energy in species from microbes to humans linked hydrogen-atom transfer to the functional structure of cell membranes via the hydrogen bonds of molecules, or other dipolar constituents, which he linked to the shared energy supply that biophysically constrains life.
Fifty years later, only theorists and other pseudoscientists have failed to recognize the facts that link experimental evidence of differences in the energy of photons to the proton motive force, which links the potential of hydrogen (pH) to biophysically constrained viral latency and all biodiversity on Earth. In that context, Carl Zimmer serves as an important example of human idiocy each time he makes claims about evolution.
See also: UTX-mediated enhancer and chromatin remodeling suppresses myeloid leukemogenesis through noncatalytic inverse regulation of ETS and GATA programs

By integrating proteomic and genomic analyses, we link these changes to UTX regulation of ATP-dependent chromatin remodeling, coordination of the COMPASS complex and enhanced pioneering activity of ETS factors during evolution to AML.

They linked the anti-entropic virucidal energy of sunlight from the creation of ATP to chromatin remodeling during the evolution of pathology, which all serious scientists know is biophysically constrained by the physiology of food energy-dependent pheromone-controlled reproduction.
See: [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)] (1994)

A study of the influence of pheromone stressor(s) on proliferating germ and somatic cells was performed on laboratory lines of house mouse in the context of the physiological hypothesis of mutation process, proposed by M.E. Lobashev in 1947. Data from experiments are presented, and results obtained during last 10-15 years are discussed. The adaptive role of cytogenetic and other observed pheromonal effects is considered. The possible existence of interorganism systems of genetic regulation is discussed, the search for and study of which may help in more complete understanding of the regularities of functioning of genetic material.

The interorganism systems of genetic regulation have since been placed into the context of sympatric speciation by all serious scientists.
See: Direct estimation of mutations in great apes reveals significant recent human slowdown in the yearly mutation rate
See also: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

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

EDAR V370A and sympatric speciation

Nick Lane and others like him refuse to reappraise their human mitochondrial DNA recombination dogma. All serious scientists know where the energy for recombination comes from. But, in his latest video clip, he touts the same unsubstantiated theoretical pseudoscientific nonsense.

See the: Aeon Video:

Life on earth – from mushrooms to humans and everything in between – seems enormously diverse. At the cellular level, however, almost all complex lifeforms are surprisingly similar. Why life is this way, though, remains mysterious. In this Aeon interview, the UK biochemist and author Nick Lane discusses his research on the connection between energy and genes, which, he hypothesises, made possible the radical transformation from single-celled organisms to complex life about 4 billion years ago.

See for comparison: Reappraising the human mitochondrial DNA recombination dogma

I’ve asked the authors: Are you prepared to address the comments that you might receive from people like Nick Lane in the context of “peer review?” How will you respond to those who do not accept the fact that the creation of ATP synthase and the creation of ATP must be linked to the creation of RNA and biophysically constrained viral latency in the context of SNPs and fixation of amino acid substitutions? What can be done when biologically uninformed theorists continue to link anything except biophysically constrained viral latency to all biodiversity?

I ask because there are still too many examples of human idiocy that are being considered outside the context of facts about energy-dependent RNA-mediated cell type differentiation.

See: Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant

See the claims about the selection of the EDAR variant placed back into the context of evolution.

Field-deployable viral diagnostics using CRISPR-Cas13

…we report the rapid (<1 week) design and testing of instrument-free assays to detect clinically relevant viral single-nucleotide polymorphisms.

The relevant energy-dependent single-nucleotide polymorphisms clearly protect all living genera from the clinically relevant viral single-nucleotide polymorphisms. The viral single-nucleotide polymorphisms link the virus-driven degradation of messenger RNA to all pathology via what is known to all serious scientists about the energy-dependent creation of the innate immune system in species from bacteria to humans.

Environmental selection during the last ice age on the mother-to-infant transmission of vitamin D and fatty acids through breast milk

The frequency of the human-specific EDAR V370A allele appears to be uniquely elevated in North and East Asian and New World populations due to a bout of positive selection likely to have occurred circa 20,000 y ago.

If any experimental evidence of biophysically constrained viral latency supported the claim about positive selection 20,000 y ago, it could be linked to Nick Lane’s claims about how chimeras and electricity allowed a sterile planet to give way to complex life 4 billion years ago. Since there is no experimental evidence to support his ridiculous theories, intelligent people may want to continue to link environmental selection from food selection to the physiology of reproduction and fixation of RNA-mediated amino acid substitutions such as V370A that stabilize the organized genomes of all species on Earth.

5th-6th Sept 2018 Dublin, Ireland

2018 March for Science vs microRNAs (2)

The anti-entropic virucidal energy of sunlight on contact with water has been linked from the creation of ATP synthase to the creation of ATP and to the creation of RNA. Energy-dependent RNA-mediated DNA repair has been linked to biophysically constrained viral latency via the creation of microRNAs and feedback loops linked to the food energy-dependent microRNA-mediated physiology of reproduction. The physiology of energy-dependent pheromone-controlled reproduction biophysically constrains viral latency in the context of the creation of the innate immune system and autophagy.
See: miRNA regulation of innate immunity (4/14/18)
None of the facts about the energy-dependent creation of the microRNAs or the microRNA-mediated regulation of innate immunity are included in: The Transcription Factor Runx3 Establishes Chromatin Accessibility of cis-Regulatory Landscapes that Drive Memory Cytotoxic T Lymphocyte Formation (4/17/18)
The regulatory landscape that drive memory cytotoxic T lymphocyte formation might just as well be framed in the context of magic or in the equally ridiculous context of gene-centric theories.
See this report: Your immune system holds the line against repeat invaders, thanks to this molecule

Runx3’s control of T cell differentiation is important because when our bodies fight off viruses and cancers—and our T cells burst into action—the vast majority tend to become effector cells. These effector cells are short-lived and do not persist once the infection resolves.

The control of all cell type differentiation is energy-dependent, RNA-mediated and biophysically constrained by the physiology of reproduction in all living genera. The cell biology game “Cytosis” for ages 10+ teaches the facts that link Schrödinger (1944) What is Life? to Schrödinger at 75 – The Future of Biology – September 2018
In 1944, Schrödinger wrote:

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.)

See for comparison (this gene-centric pseudoscientific nonsense):
– Part I: FINDING THE CODE (Run time: 12:10
The race to sequence the human genome was also billed as a race to end disease. What happened?

– Part II: FIXING THE CODE (Run time: 13:07)
CRISPR — and the promise and pain of gene therapy that came before it. 

– Part III: SELLING THE CODE (Run time: 10:55)
Genetic testing has moved out of the labs into the masses. But even with your genome in hand, what can you believe?
The gene-centric pseudoscientific nonsense does not start with the creation of energy.  But every aspect of biophysically constrained life on Earth starts with the quantized energy-dependent creation of microRNAs. The epigenetically effected energy-dependent microRNA-mediated creation of the “Code” and the microRNA-mediated fixing of the “Code” is missing from the claims of biologically uninformed theorists who link beneficial mutations from natural selection to evolution. They have sold their gene-centric pseudoscientific nonsense to many people.
For example, some gene-centric biologically uninformed theorists share beliefs about abiogenesis for comparison to quantized energy-dependent microRNA biogenesis in articles like this: DNA Denaturing through UV-C Photon Dissipation: A Possible Route to Archean Non-enzymatic Replication
Conclusion:

Many of the fundamental molecules of life, those common to all three domains; bacteria, eukaryote, and archea, including RNA and DNA, amino acids, enzymes, vitamins, cofactors, and protoporphyrins, absorb photons in the UV-C 1. RNA or DNA in complexes with these molecules act as acceptor quenchers, providing the electronically excited pigment donor molecule with an extremely rapid (sub picosecond) non-radiative dexcitation channel, through internal conversion into vibrational energy of the nucleic acid and surrounding water molecules2.

See John Hewitt’s comment: You have just described the founding principle and thermodynamic function of life
In a classic example of human idiocy (See Feynman: food energy), biologically uninformed science idiots linked the dissipation of quantized energy to the origin of life via abiogenesis. The creation of biophysically constrained biophotonicaly based life in the context of the energy-dependent creation of microRNAs was reported in the context of photon dissipation and entropy as: Abiogenesis: A Theory on The Origins of Life

By now, we all know how evolution works. At least, most of us have a basic understanding of how it functions. At its most fundamental level, evolution is change over time. More specifically, it is changes within a biological population over successive generations.

Ultimately, biological complexity is one of the most important things to come out of evolution. Things started simple. Then genes mutated, cells interacted with their environment, mitochondria stopped being living organisms and started being part of a cell and—Tada—complex life.

A conflict arose between John Hewitt’s accurate representations of biophysically constrained life in The vibrational theory of olfaction for the win  and few months ago, Hewitt blocked me from seeing his tweets.

The same kinds of amino acid substitutions that control the separations and interactions of side chains in fluorescent proteins also play an essential role in tuning the proposed mechanism for vibration detection—inelastic electron tunneling. Life literally runs on electron tunneling through the respiratory chain complexes in mitochondria. These proteins employ complicated mechanisms including esoteric-soundings things like electron bifurcation and confurcation to pump protons across the mitochondrial inner membrane. When mitochondria go dark, cells can often continue to run for a short while, but it is only in the dim glow of the battery backup metabolism.

Here are some links to the reason for the conflict. Simply put, John Hewitt put everything known to serious scientists about energy-dependent microRNA biogenesis back into the context of abiogenesis.
2005 MicroRNA biogenesis: coordinated cropping and dicing
2015 Dysregulation of microRNA biogenesis and gene silencing in cancer
2015 RNA-mediated degradation of microRNAs: A widespread viral strategy?
Claims about abiogenesis exemplify what Richard Feynman referred to as human idiocy. So does John Hewitt and anyone else who believes in Michaelian’s pseudoscientific nonsense.
See other examples of Michaelian’s pseudoscientific nonsense and human idiocy by clicking here.
The energy-dependent creation of one domain of life links the physiology of reproduction in bacteria to biophysically constrained viral latency. The virus-driven degradation of messenger RNA is linked to the destruction of all life on Earth.
The degradation of messenger RNA links mutations to the creation of archaea and L-forms via entropy, which clearly links the weakening of the proton motive force to the elimination of the cell wall in L-forms (the last remnants of creation).
See also: Past 5,000 years prolific for changes to human genome
If you cannot link the miRNA regulation of innate immunity to all extant biodiversity via the physiology of pheromone-controlled reproduction and fixation of energy-dependent microRNA-mediated amino acid substitutions, thank a biologically uniformed science idiot.
 

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 (1)

Serious scientists start from the levels of biological organization required to link atoms to ecosystems in all living genera. They must link what is known about quantized energy to subatomic particles. See for example slide number 6 from: Human Pheromones: Linking Neuroendocrinology and Ethology (revisited)  (2010)
Subatomic particles must be the link to the creation of ATP synthase, which must link the creation of ATP to the creation of RNA.
See McEwen et al., (1964) Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

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

Odor activation of ATP completes the pathway that links the anti-entropic virucidal energy of sunlight to all quantized energy-dependent biophysically constrained RNA biosynthesis and viral latency. Viral latency links the physiology of pheromone-controlled reproduction to healthy longevity in species from microbes to other mammals and to humans.
See: ATP and Odor Mixture Activate TRPM5-Expressing Microvillous Cells and Potentially Induce Acetylcholine Release to Enhance Supporting Cell Endocytosis in Mouse Main Olfactory Epithelium

In sum, our results show that TRPM5-MCs dose-dependently respond to ATP and odor mixture and may release ACh to potentiate endocytosis in SCs, possibly promoting xenobiotic removal from the MOE. These results have unveiled cholinergic regulation in the MOE coordinating SC activity important for protecting the epithelium and airway. That TRPM5-MCs are sensitive to ATP and express multiple purinergic receptors also suggests an additional mechanism for the MOE to act in a concerted fashion with the rest of the respiratory mucosa to defend against xenobiotic insults. Taken together, these novel results of cholinergic paracrine signaling in the MOE increase our understanding of how the MOE maintains its function and prevents chemical-induced damage.

Simply put, the MOE links food odors and other sensory input to the pheromone-constrained viral latency presciently reported in:
Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.) (1994)

A study of the influence of pheromone stressor(s) on proliferating germ and somatic cells was performed on laboratory lines of house mouse in the context of the physiological hypothesis of mutation process, proposed by M.E. Lobashev in 1947. Data from experiments are presented, and results obtained during last 10-15 years are discussed. The adaptive role of cytogenetic and other observed pheromonal effects is considered. The possible existence of interorganism systems of genetic regulation is discussed, the search for and study of which may help in more complete understanding of the regularities of functioning of genetic material.

See for earlier and later publications in the English Language:
Gonadotropin releasing hormone and human sexual behavior (1991) in Neuropeptides and Psychiatric Disorders
Induction of FOS immunoreactivity in central accessory olfactory structures of the female rat following exposure to conspecific males (1992)

The findings indicate that exposure of female rats to reproductively relevant stimuli resulted in induction of fos-like immunoreactivity within the AOS and that both olfactory and nonolfactory cues probably contributed to this effect.

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

Olfactory information processed by the vomeronasal system is reported to influence reproductive functions in a variety of mammals. The present studies were designed to determine if male-associated cues affect the luteinizing hormone-releasing hormone (LHRH) neuronal system…

Vomeronasal organ-mediated induction of fos in the central accessory olfactory pathways in repetitively mated female rats (1994)

Removal of the VNO significantly reduced the enhancement of lordosis and the induction of fos immunoreactivity in luteinizing hormone-releasing hormone (LHRH) neurons in ovariectomized estrogen-primed rats.

Pheromones (2010) in Stress Science: Neuroendocrinology
See for comparison: The Expanding Landscape of Alternative Splicing Variation in Human Populations

Alternative splicing variation has been linked from the food energy-dependent pheromone-controlled physiology of reproduction to all extant biodiversity in species from microbes to humans.

Biologically uninformed theorists still think in terms of evolution.
See: The human microbiome in evolution
Most of them have no idea how to link subatomic particles to biophysically constrained viral latency.

Subatomic: An Atom Building Board Game

A deck-building game where particle physics & chemistry collide! Use quarks to build subatomic particles & particles to build Atoms!

See instead: Cytosis: A Cell Biology Board Game

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

See for comparison: Genetic variation in a human odorant receptor alters odour perception
Gene-centric theories about altered odor perception have failed to link energy-dependent top-down causation to biophysically constrained viral latency and healthy longevity. The ridiculous theories will continue to cause unnecessary suffering and premature death until pseudoscientists admit that they learned virtually nothing about RNA-mediated cell type differentiation during the past 20 years of scientific progress.
See for example, anything published by Leslie B. Vosshall
Specifically, Laying a controversial smell theory to rest (2015)

Some have pointed out that it is a waste of time to expend effort to refute a controversial theory that has few advocates, and that attention should be turned instead toward how smell works (, ).

This is how smell works: ATP and Odor Mixture Activate TRPM5-Expressing Microvillous Cells and Potentially Induce Acetylcholine Release to Enhance Supporting Cell Endocytosis in Mouse Main Olfactory Epithelium

5th-6th Sept 2018 Dublin, Ireland

Anti-entropic sunlight: Schrödinger’s Creationist Secret? (5)

Anti-entropic sunlight: Schrödinger’s Creationist Secret? (3)


The list of those scheduled to present has changed. Michael Rosbash has been added. John E. Walker is not scheduled, which suggests that everyone else already knows that the creation of the sun’s anti-entropic virucidal energy is the link from the creation of ATP to the creation of RNA and all biophysically constrained viral latency via feedback loops and the physiology of reproduction.
Rosbash, as all serious scientists know,  started with energy-dependent changes in cycles of RNA biosynthesis. Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels (1990). Pseudoscientists failed to link the energy from feedback to biophysically constrained viral latency.
But see: Permeability transition in human mitochondria persists in the absence of peripheral stalk subunits of ATP synthase

Production of ATP depends on the oxidation of energy-rich compounds to produce a chemical potential difference for hydrogen ions, the proton motive force (pmf), across the inner mitochondrial membrane (IMM).

Other serious scientists have consistently linked photophosphorylation from oxidative phosphorylation to all biodiversity via the physiology of pheromone-controlled reproduction in species from soil bacteria to humans
Speakers (new copy-protected list)
Speakers (old list)
See also: Viral Resistance Project
The differences in innate immunity and ecological adaptation are obviously nutrient energy-dependent and transgenerationally inherited in the context of the epigenetically-effected physiology of pheromone-controlled reproduction and the affects of hormones on behavior. For instance, pheromones biophysically constrain viral latency via the fixation of amino acid substitutions.
See for comparison: Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses
There are several neo-Darwinian theorists who are scheduled to present, which means they may be ready to accept the ridicule from serious scientists.
See for example: A universal trend of amino acid gain and loss in protein evolution

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

See also: Why I got rid of my friends
Some of my former friends kept dumping their garbage about evolution on others in the same way that I. King Jordan and Eugene Koonin did it with their comment about the evolution of the amino acid composition of proteins. See for comparison: All About that Base (Meghan Trainor Parody) 12/10/14 and Energy as information and constrained endogenous RNA interference 2/15/17
Help others who are Combating Evolution to Fight Disease

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.

George Church refutes theistic evolution (4)

See: George Church refutes theistic evolution (February 9, 2017)
See also: Energy as information and constrained endogenous RNA interference (February 15, 2017)

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 for comparison: Church Speaks  George Church (February 14, 2018)

[Arctic grass and] cyanobacteria, on the other hand, they fix [carbon]. Cyanobacteria turn carbon dioxide, a global warming gas, into carbohydrates and other carbon-containing polymers, which sequester the carbon so that they’re no longer global warming gases. They turn it into their own bodies. They do this on such a big scale that about 15 percent of the carbon dioxide in the atmosphere is fixed every year by these cyanobacteria, which is roughly the amount that we’re off from the pre-industrial era. If all of the material that they fix didn’t turn back into carbon dioxide, we’d have solved the global warming problem in a year or two. The reality, however, is that almost as soon as they divide and make baby bacteria, phages break them open, spilling their guts, and they start turning into carbon dioxide. Then all the other things around them start chomping on the bits left over from the phages.

The anti-entropic virucidal quantized energy of sunlight links the creation of ATP to the creation of microRNAs and changes in the energy-dependent microRNA/messenger RNA balance, which link what organisms eat to RNA-mediated fixation of amino acid substitutions that differentiate all cell types in all individuals of all living genera. Simply put, sunlight, food energy, and pheromones biophysically constrain the DNA damage that is done by phages.
Release of the cell biology game “Cytosis” and the forthcoming conference Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses (4 – 8 July 2018 Salzburg – Austria) have forced George Church and others like him to begin telling the scientific truth about how the virus-driven theft of quantized energy is either biophysically constrained, or linked from the virus-driven degradation of messenger RNA to mutations and all pathology.

Preliminary List of Confirmed Speakers (41)
Chantal Abergel >
Aix-Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Marseille, France
Gustavo Caetano Anolles >
Department of Crop Sciences, Evolutionary Bioinformatics Laboratory, University of Illinois at Urbana-Champaign Urbana, USA.
Marlene Belfort >

Department of Biological Sciences and RNA Institute, University at Albany, New York, USA
Felix Broecker >
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
Department of Chemistry & Biochemistry, University of California, Santa Barbara, USA
Julian Chen >
Department of Chemistry and Biochemistry, Arizona State University, Tempe, USA
Jean-Michel Claverie >
Centre National de la Recherche Scientifique & Aix-Marseille University, Marseille, France
Bryan Cullen >
Department of Molecular Genetics and Microbiology and Center for Virology, Duke University Medical Center, Durham, USA
Valerian Dolja >

Department of Botany and Plant Pathology, Oregon State University, Corvallis, USA
Cedric Feschotte >
Department of Human Genetics, University of Utah, School of Medicine, Salt Lake City, USA
Matthias Fischer >
Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, Heidelberg, Germany
David Gilmer >
Institut de biologie moléculaire des plantes, Integrative virology, Strasbourg, France
Reynald Gillet >
Université de Rennes 1, Translation and Folding Team, Rennes cedex, France Institut Universitaire de France
Jordi Gomez >
Instituto de Parasitología y Biomedicina ‘López-Neyra’ (CSIC), Granada, Spain
Matti Jalasvuori >

Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, Finland
I.King Jordan >
School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
Eugene Koonin >
National Center for Biotechnology Information, National Library of Medicine, Bethesda, USA.
Dusan Kordis >
Department of Molecular and Biomedical Sciences, Josef Stefan Institute, Ljubljana, Slovenia
Mart Krupovic >

Unit BMGE, Department of Microbiology, Institut Pasteur, Paris, France
Erez Levanon >
Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
German Martinez >
Dept. of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
John Mattick >
Garvan Institute of Medical Research, Darlinghurst, Australia
Jeff Miller >
California NanoSystems Institute, University of California, Los Angeles, USA
Karin Moelling >
Max Planck Institute for molecular Genetics, Berlin, Germany
Sabine Müller >
Universität Greifswald, Institut für Biochemie , Greifswald , Germany
Ulrich Müller >
Department of Chemistry & Biochemistry, University of California, San Diego, USA
Mariusz Nowacki >
Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
David Prangishvili >
Department of Microbiology, BMGE, Institut Pasteur, Paris, France
Lennart Randau >
Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
Forest Rohwer >
Department of Biology, San Diego State University, San Diego, CA, USA
Corrado Spadafora >
Institute of Translational Pharmacology, CNR, Rome, Italy
James Shapiro >
Department of Biochemistry and Molecular Biology , University of Chicago , IL , USA
Jason Shepherd >
Biochemistry and Ophthalmology & Visual SciencesUniversity of Utah, School of Medicine Salt Lake City, USA
Ravindra Singh >
Department of Biomedical Sciences, Iowa State University, Ames, USA
Keizo Tomonaga >
Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Japan
Peter Unrau >
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
Luis P. Villarreal >
Center for Virus Research, University of California, Irvine, Irvine, CA, USA
Andreas Werner >
RNA biology group, Institute for Cell and Molecular Biosciences, Newcastle University, UK
Eric Westhof >
Architecture and Reactivity of RNA, Institute of Molecular and Cellular Biology of the CNRS, University of Strasbourg, France
Bojan Zagrovic >
Department of Structural and Computational Biology, Max F. Perutz Laboratories, Vienna, Austria
Steven Zimmerly >
Department of Biological Sciences, University of Calgary, Calgary, Canada

 

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.

 

An evolutionary theory killer

A reversible TCA cycle in a thermophile (2)

Summary: The energy-dependent creation of ATP has been linked from the energy-dependent creation of RNA to feedback loops that link the pheromone-controlled physiology of reproduction to biodiversity in species from microbes to humans via olfaction and pheromones. Anyone who continues to try to place the facts into the context of brain stimulation by visual input and ignore the facts about how the creation of microRNAs must be linked from creation of the sense of smell to all biophysically constrained viral latency and all biodiversity is playing a fool’s game.
See first: A reversible TCA cycle in a thermophile
See also: Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels (1990)
Thermodynamic cycles of ATP-dependent protein biosynthesis and/or the virus-driven degradation of messenger RNA have since been linked to healthy longevity or from circadian disruption to diseases of the brain and body, such as depression, Crohn’s disease, IBD, heart disease or cancer.
See: Timing is everything, to our genes

 This will have huge impact on understanding the mechanisms or optimizing cures for at least 150 diseases.”

If that was true, the work in the 1990’s that led to Rosbash sharing the 2017 Nobel Prize for Physiology or Medicine would already have been placed into the context of this published work.Olfactory Receptor Patterning in a Higher Primate (2014).
See also, Feedback loops link odor and pheromone signaling with reproduction another work by LInda Buck, who shared the 2004 Nobel Prize for Physiology or Medicine and who coauthored both articles.
Instead of linking the energy-dependent pheromone-controlled feedback loops from the physiology of reproduction in thermophiles to the physiology of food energy-dependent pheromone-controlled feedback loops in humans, we have been left the examples of human idiocy in the context of Richard Feynman’s claims and the claims of all other serious scientists.
See:

See also: Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex Published online: 11 December 2017

Activity-dependent transcriptional responses shape cortical function.

Reported as: Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex  on December 13, 2017

…these results reveal the dynamic landscape of the stimulus-dependent transcriptional changes occurring across cell types in the visual cortex; these changes are probably critical for cortical function and may be sites of deregulation in developmental brain disorders.

Reported on and on February 8, 2018 Single-cell analysis reveals diverse landscape of genetic changes in the brain after a sensory experience

Experience and environmental stimuli appear to almost constantly affect gene expression and function throughout the brain. This may help us to understand how processes such as learning and memory formation, which require long-term changes in the brain, arise from the short bursts of electrical activity through which neurons signal to each other,” Greenberg said.

One especially interesting area of inquiry, according to Greenberg, includes the regulatory elements that control the expression of genes in response to sensory experience. In a paper published earlier this year in Molecular Cell, he and his team explored the activity of the FOS/JUN protein complex, which is expressed across many different in the brain but appears to regulate unique programs in each different cell type.

The energy-dependent creation of ATP has been linked from the energy-dependent creation of RNA to feedback loops that link the pheromone-controlled physiology of reproduction to biodiversity in species from microbes to humans via olfaction and pheromones. Anyone who continues to try to place the facts into the context of brain stimulation by visual input and ignore the facts about how the creation of microRNAs must be linked from creation of the sense of smell to all biophysically constrained viral latency and all biodiversity is playing a fool’s game. They should stop doing that long enough to play the cell biology game “Cytosis” and wait to link particle physics to from quantum chemistry to all biodiversity by what is known to serious scientists about energy-dependent top-down causation is biophysically constrained by the physiology of reproduction.

5th-6th Sept 2018 Dublin, Ireland

A mental health problem at the highest level (3)

Summary: It has been 75 years since Erwin Schrödinger exposed the pseudoscientific nonsense of mutation-driven evolution in the lecture series that was published as What is Life? (1944)
The mental health of so-called science journalists must be addressed. Many of them seem to be pathological liars or, at best biologically uninformed science idiots who cannot link physics and chemistry from molecular epigenetics to all energy-dependent biodiversity on Earth.
The Biggest Myth In Quantum Physics by Ethan Siegel
Conclusion:

Take ourselves out of it, and all we have are the equations, the results, and the answers that the physical Universe gives. Physics cannot answer questions about “why” the Universe works the way it does; it can only explain how it works at all. If you’re interested in the fundamental nature of reality, ask the Universe questions about itself, and when it tells you its secrets, listen. Anything else that you layer atop it was put there by you, not by the Universe. Avoid that temptation, and you’ll never fall for the greatest myth about quantum physics: that it needs an interpretation at all.

The claim that quantum physics does not require a meaningful approach to explaining how energy is linked to all biodiversity in the context of interpretation of facts is ridiculous. Astrophysicist and author Ethan Siegel is the founder and primary writer of the blog “Starts With A Bang!” His books include Treknology and Beyond The Galaxy, Simply put, he is a biologically uniformed science idiot, like others who have failed to link their ridiculous theories to all biodiversity on Earth.
See for comparison: Refined control of cell stemness allowed animal evolution in the oxic realm
Reported as: Why animals diversified on Earth: Cancer research provides clues 

Just the presence of free oxygen is the result of some microbes finding a way of using sunlight to get energy. This was also a biological event.

The difference between how animals diversified and why they diversified is perfectly clear to all serious scientists. Energy is required!
McEwen et al (1964) linked the biological event from the creation of ATP to the creation of RNA and the creation of all biophysically constrained biodiversity. All other serious scientists have since followed his lead. Dobzhansky (1964) suggested that would happen.

The notion has gained some currency that the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists! I have heard a man whose official title happens to be Professor of Zoology declare to an assembly of his colleagues that “a good man cannot teach zoology. A good man can teach, of course, only molecular biology.

Such pronunciamentos can be dismissed as merely ridiculous. They are, however, caricatures of opinions entertained by some intelligent and reasonable people, whose views deserve an honest and careful consideration and analysis. Science must cope with new problems that arise and devise new approaches to old problems. Some lines of research become less profitable and less exciting and others more so.

The claims made in the fake news about Donald Trump’s mental state can now be linked to the mental heath of his antagonists who have never seen Dozhansky’s “light of evolution.”
Nothing in Biology Makes Any Sense Except in the Light of Evolution

For example, the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).”

The anti-entropic virucidal effect of sunlight was linked from ecological variation to ecological adaption in all living genera via the pheromone-controlled physiology of reproduction in soil bacteria in: What is Life? (1944)

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.)

Seventy-four years later we have this example of human idiocy: Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis
Reported as: Counting chromosomes: Plant scientists solve a century-old mystery about reproduction (2018)

Today, a team of geneticists reveals a remarkable mechanism that enables plants to count their chromosomes, solving a century-old mystery.

Molecular mechanisms are energy-dependent. That’s no mystery. See: How an RNA gene silences a whole chromosome (2015)
Most science journalists have refused to inform themselves. They have not linked sunlight on contact with water to all energy-dependent biodiversity via the physiology of reproduction. For example, John Hewitt wrote:

If anything we know the Sky Fathers totally forgot about selenium during most of the design phase and then had to write him in at the end as a walk-on.

I was surprised by his sarcastic attack on religion and wrote:

Let’s not do this. See instead: A third of Americans don’t believe in evolution 

Those who do not believe in evolution understand that energy-dependent RNA-mediated amino acid substitutions must be linked from the physiology of reproduction to chromosomal rearrangements that biophysically constrain viral latency. If you can place your claim about selenium into the context of protection of all life on Earth from the virus-driven degradation of messenger RNA, we could discuss your claim. What is it?

John Hewitt wrote:

Sky Daddy likes cranberries so much he gave them sequence-level machinery for producing selenocysteine in their mitochondrial genome

I could not get  him to make sense. I wrote:

This is the type of cryptic sarcastic claim that kills people. Thousands  of them. Quit playing your silly games. Who are you calling “Sky  Daddy?”  Sequence-level molecular machinery does not exist outside the context of the creation of the sun’s anti-entropic virucidal energy. 

For comparison, Roger M. Pearlman wrote:

name one person you know that can explain Neo-Darwinian Theory (NDT) so it adds up, and how you know it adds up otherwise don’t knock the NDT adherents here as they are equally inept at making NDT add up as are the leading NDT scientists

How can anyone who wants to discuss NDT not know about this published work from 1973? Nothing in Biology Makes Any Sense Except in the Light of Evolution

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

The differences in the amino acid sequences are Koonin’s proof of evolution. See: A universal trend of amino acid gain and loss in protein evolution

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

If the differences in the amino acid sequences are energy-dependent and RNA-mediated, NDT is the most ridiculous example of pseudoscientific nonsense that has every been touted by people who claim to be more intelligent than their primate ancestors.

Proof of that fact was published as: Modern diversification of the amino acid repertoire driven by oxygen

..we demonstrate an immediate survival benefit conferred by the enhanced redox reactivity of the modern amino acids tyrosine and tryptophan in oxidatively stressed cells. Our data indicate that in demanding building blocks with more versatile redox chemistry, biospheric molecular oxygen triggered the selective fixation of the last amino acids in the genetic code. Thus, functional rather than structural amino acid properties were decisive during the finalization of the universal genetic code.

Selective fixation of amino acid substitutions in organized genomes is energy-dependent and controlled by the physiology of reproduction.

That fact was reported as: Quantum Chemistry Solves The Question of Why Life Needs So Many Amino Acids 

If you were representing the amino acids as circles, they could be drawn as multiple concentric circles representing differing energy levels, rather than one single circle of the same chemical hardness and energy level – kind of like in the photo below.

Few people would make the connection from the amino acids as circles representing different energy levels to the claim that de Vries (1902) made when he invented the term mutation.

See:  What is Life? (1944)

But about forty years ago the Dutchman de Vries discovered that in the offspring even of thoroughly pure-bred stocks, a very small number of individuals, say two or three in tens of thousands, turn up with small but ‘jump-like’ changes, the expression ‘jump-like’ not meaning that the change is so very considerable, but that there is a discontinuity inasmuch as there are no intermediate forms between the unchanged and the few changed. De Vries called that a mutation. The significant fact is the discontinuity. It reminds a physicist of quantum theory -no intermediate energies occurring between two neighbouring energy levels. He would be inclined to call de Vries’s mutation theory, figuratively, the quantum theory of biology. We shall see later that this is much more than figurative. The mutations are actually due to quantum jumps in the gene molecule. But quantum theory was but two years old when de Vries first published his discovery, in 1902. Small wonder that it took another generation to discover the intimate connection!

It has been 75 years since Erwin Schrödinger exposed the pseudoscientific nonsense of mutation-driven evolution in the lecture series that was published as What is Life? (1944)

In the 1991 reprint edition, a forward by Roger Penrose who has co-authored with George F.R. Ellis, Stephen Hawking, Stuart Hameroff and others wrote:

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

It is worth repeating the claim the food energy is required to link quantum physics from quantum chemistry to quantum biology and quantum souls until all pseudoscientists lean the difference between a mutation and an amino acid substitution. Until then, the mental health problem at the highest level will be maintained at the highest level by the highest level of human idiocy every known to have eliminated common sense from consideration in the context of biologically based cause and effect.

For example, Darwin’s claims were based on “conditions of life” that required all organisms to find food and reproduce. Nothing was known about mutations, and even then Darwin could not possibly have been foolish enough to put them first in the context of natural selection for mutation-driven pathology.

See also: Analysis of experience-regulated transcriptome and imprintome during critical periods of mouse visual system development reveals spatiotemporal dynamics

Visual system development is light-experience dependent, which strongly implicates epigenetic mechanisms in light-regulated maturation. Among many epigenetic processes, genomic imprinting is an epigenetic mechanism….

…through which monoallelic gene expression occurs in a parent-of-origin-specific manner.

See: An Epigenetic Signature for Monoallelic Olfactory Receptor Expression
This explains why John Hewitt claims I’m providing BS. He is a biologically uninformed science journalist who does not understand the facts about light energy-dependent changes in organized genomes.
Any journalist who publishes anything like The vibrational theory of olfaction for the win should prepare to defend his claims in the context of serious scientists who know how energy must be linked to the vibrations and how the vibrations link quantum physics from quantum chemistry to quantum souls via the physiology of pheromone-controlled reproduction and fixation of RNA-mediated amino acid substitutions.

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)