Subatomic Archives - Scent of Eros

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

Kohl's Laws of Biology (codon-optimality revisited)

May 11, 2018

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

Summary: Kohl’s Laws help to explain what was missing from Darwin’s ‘conditions of life.’ Darwin knew nothing about genetics, which means he knew nothing about the epigenetic effects of food odors or pheromones.
Ancient hepatitis B viruses from the Bronze Age to the Medieval period 5/7/18

We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.

The complexity of biophysically constrained viral latency in all living genera refutes all pseudoscientific nonsense touted by neo-Darwinian theorists and Big Bang cosmologists.
See for example: Who were the Neanderthals? 5/5/18

Current evidence from both fossils and DNA suggests that Neanderthal and modern human lineages separated at least 500,000 years ago. Some genetic calibrations place their divergence at about 650,000 years ago.

No serious scientists believe in the nonsense that links genetic calibrations to “divergence” at about 650,000 years ago.
See for comparison: Efficient coding explains the universal law of generalization in human perception 5/11/18
Everything known to serious scientists about natural selection for energy-dependent codon optimality and RNA-mediated DNA repair is placed back into the context of evolution, which is subject to constraints (finding food and reproduction).
See also: Olfaction Warps Visual Time Perception (2017)
The creation of visual perception starts with the energy-dependent creation of enzymes.

High-resolution cryo-EM analysis of the yeast ATP synthase in a lipid membrane 5/11/18

…the enzyme transduces the energy of a proton gradient, generated by the electron transport chain, into the major energy currency of the cell, ATP.

The quantized energy-dependent creation of the enzyme was linked to the creation of ATP and RNA
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.

Natural selection interacts with recombination to shape the evolution of hybrid genomes 5/11/18

Hybridization is an important force in evolution.

That is a ridiculous assumption. Quantized energy is an important force in ecological adaptation. That is a fact.

Metabolic regulation of transcription through compartmentalized NAD⁺ biosynthesis 5/11/18

Competition between the NAD+ precursors—nuclear NMNAT-1 and cytosolic NMNAT-2…, regulates the balance between nuclear NAD+ synthesis for adipogenic gene regulation and cytosolic NAD+ synthesis used in metabolism.

Every aspect of what is currently know about life on Earth begins with the creation of quantized energy.
Energy efficiency drives the global seasonal distribution of birds 5/7/18
Reported as: A Thermodynamic Answer to Why Birds Migrate 5/7/18

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

In this 1996 review, we linked the sex differences in yeasts to sex differences in humans via alternative splicings of pre-mRNAs, which are now called microRNAs. From Fertilization to Adult Sexual Behavior

I linked quantized energy from subatomic particles to all biodiversity via the creation of microRNAs in:
2014 Preprint: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
2018 Publication: Nutrient-dependent Pheromone-Controlled Ecological Adaptations: From Angstroms to Ecosystems

Biological Laws

Biophysical constraints and biological laws appear to link ecological variation to ecological adaptations via conserved molecular mechanisms in all species. For example, nutrient-dependent ecological niche construction leads to pheromone-controlled social niche construction via the nutrient-dependent pheromone-controlled physiology of reproduction. The nutrient-dependent origin of amino acid substitutions in viruses [149-152], which also are manifested in plant and animal interactions, exemplifies a continuum of biological plausibility and ecological validity in the context of Laws of Biology. These Laws of Biology include Kohl’s Laws of Biology, which are so named because the surname of the first author or sole author on each of 7 peer-reviewed publications in the paragraph below is Kohl. The Kohls did not create the Laws of Biology; they merely independently incorporated what is known about them into what appears to be a cohesive series of published works.

Kohl’s Laws of Biology
Life is nutrient-dependent. That is a Biological Law. The ecological origin of all biological laws is apparent 1) in the context of systems biology [87]; 2) in the context of the metabolism of nutrients by microbes [153]; and 3) in the context of how the metabolism of nutrients results in species-specific pheromones that control the physiology of reproduction [154]. Taken together, the systems biology of nutrient metabolism to species-specific pheromones, which control the physiology of reproduction, can be expressed in a summary of Kohl’s Laws of Biology: 1) Life is nutrient-dependent.

See for review [27,155]. The physiology of reproduction is pheromone-controlled. See for review [26]. In the context of nutrient-dependent epigenetically-effected human reproduction, it is clearer that the epigenetic effects of human pheromones integrate neuroendocrinology and behavior [100], which includes the neuroendocrinology of mammalian behavior associated with the development of sexual preferences [156].

Kohl’s Laws help to explain what was missing from Darwin’s ‘conditions of life.’ Darwin knew nothing about genetics, which means he knew nothing about the epigenetic effects of food odors or pheromones.

The eternal significance of microRNAs (7)

May 11, 2018

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

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.

ATP and RNA-mediated chromosomal stability

May 9, 2018

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

Cytosis, a cell biology game for ages 10+ links ATP to viral latency and the protection of all organized genomes from the virus-driven degradation of messenger RNA that serious scientists have linked to all pathology.
It is time for a new measure of cell function: Quantifying Cellular ATP Production Rate…(2018)

Adenosine triphosphate (ATP) is the most common high energy intermediate of living organisms. Cells utilize the energy derived from the breakdown of cellular fuels to synthesize ATP from ADP and inorganic phosphate. The free energy released from ATP hydrolysis is then used to sustain various cellular functions such as growth, movement, and response to the environment. Mammalian cells tightly regulate production and consumption of ATP – i.e. supply and demand are balanced to maintain intracellular ATP levels quite constant. Therefore, measuring the rate of ATP production enables a view into cellular function that is not provided by simply measuring the amount of ATP in the cell. The Agilent Seahorse XF Real-Time ATP Production Rate Assay quantifies ATP Production Rates from mitochondrial respiration and glycolysis in real time with live cells providing a unique insight into cellular phenotype and function.

See also: Ferrick DA Remember that ATP does not create itself. The creation of ATP and the creation of RNA are energy-dependent and biophysically constrained by the anti-entropic virucidal energy of sunlight.
For example: Assessment of drug-induced mitochondrial dysfunction via altered cellular respiration and acidification measured in a 96-well platform

…respiration and acidification changes upon addition of the thiazoldinediones were cell-type specific, with the rank order of mitochondrial impairment in whole cells being in accord with the known adverse effects of these drugs.

Cell-type specific drugs alter the mitochodrial production of ATP, which alters the production of RNA via changes in the potential of hydrogen (pH).
See also: Analysis and interpretation of microplate-based oxygen consumption and pH data

…this chapter also provides a detailed accounting of proton production during glucose oxidation in the context of plate-based assays.

Difference in proton production link differences in the energy of photons from the proton motive force and proton gradients to energy-dependent RNA-mediated cell type differentiation.
Pseudoscientists and other theorists complain about so-called predatory publishing and use their complaints to attack anyone who does not “toe the line” of dogmatic consensus. See for example: OMICS Publishing Group
See also: Prominent Cell Biologist Fired After Data Manipulation Investigation

The University of Tokyo confirmed last August that Yoshinori Watanabe tampered with research-related images, and dismissed him in late April.

In 2015, his group stomped on the toes of biologically uninformed theorists. The group published:
The inner centromere–shugoshin network prevents chromosomal instability

Artificial restoration of the ICS network suppresses chromosome segregation errors in a wide range of CIN+ cells, including RB- and BRCA1-deficient cells. Thus, dysfunction of the ICS network might be a key mechanism underlying CIN in human tumorigenesis.

Food energy-dependent RNA-interference has since emerged as an effective treatment for all chromosomal instability, which appears to be caused by the virus-driven theft of quantized energy.
Additional details about energy-dependent healthy longevity will be found in the Science Behind the Game Subatomic which will link biophysically constrained viral latency from Cytosis to all biophysically constrained biodiversity via what organisms eat and the physiology of their pheromone-controlled reproduction.
See also: New EU-wide tests to tackle ‘food apartheid’

…recent comparisons of food samples showed that big Western brands use cheaper ingredients in products sold in former communist countries.

The cheaper ingredients could alter the innate immunity of human populations in former Communist countries, where God-less Communism was supported by ridiculous theories.
See: Darwinian Theory Proved by Video Game? Robert J. Marks Begs to Differ (2017)

We’ve begun developing support materials for teachers and students to help them use ‘Darwin’s Demons’ to demonstrate and teach evolutionary concepts.

A National Science Foundation grant for evolution studies helped pay for the project.

Conclusion:

Adaptation, if anything, demonstrates intelligent design, not Darwinism. Of course they won’t tell you that at the University of Idaho, or most anywhere else. Instead they’ll stick you in front of a video game and tell you the stale, old fable.

Ecological models of food energy-dependent pheromone-controlled biophysically constrained adaptations have replaced evolutionary concepts except within the school system of the US and other backward countries.
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.

All serious scientist know the difference between evolution and adaptation.
See: Are Evolution and Adaptation the Same? (2018)
The energy-dependent de novo creation of the cell links ATP to RNA biosynthesis and the physiology of reproduction via food odors and pheromones in the context of this board game.

Cytosis is a worker placement game that takes place inside a Human Cell! Players utilize the organelles within a cell to collect cellular resources such as mRNA from the Nucleus, Lipids from the Smooth E.R., ATP from the Mitochondria, etc. and score points when they use these resources to complete Hormones, Receptors or Enzymes!

It refutes neo-Darwinian pseudoscientific nonsense by starting with Darwin’s energy-dependent “conditions of life.”

Conditions of life are mediated by RNA interference. See also: RNA-Guided Human Genome Engineering

A single base change refutes theistic evolution (2)

May 9, 2018

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

Announcing publication of a model that links the creation of quantized energy from changes in subatomic particles to biophysically constrained viral latency and sympatric speciation in all living genera.

Nutrient-dependent Pheromone-Controlled Ecological Adaptations: From Angstroms to Ecosystems

This angstroms to ecosystems model of ecological adaptation links nutrient energy-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA/messenger RNA balance and chromosomal rearrangements via the physiology of reproduction in species from microbes to humans.

The invited review of nutritional epigenetics was returned without review and the preprint was posted 4 years ago as:

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

The only significant change to the manuscript was a change in the title. Atoms to ecosystems became Angstroms to Ecosystems when quantized energy-dependent changes in angstroms were linked to ecological adaptation by what is known to all serious scientists in this 2014 parody.
All About that Base (Meghan Trainor Parody) 12/10/14
Repeat after them (and me): “… every angstrom is dynamic from the 5 prime to the three…”
See also the 2015 publication: Structural diversity of supercoiled DNA

DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases.

George Church and others may have been the first to place the naturally occurring biophysically constrained energy-dependent processes of ecological adaptations into the context of a patent. (It is extremely unusual for anyone to attempt to patent a naturally occurring process.) That explains why there is no patent litigation, which still plagues those who claimed to discover the CRISPR-Cas 9 innate immune system of bacteria, which biophysically constrains viral latency and prevents the degradation of messenger RNA that links the energy-dependent creation of bacteria to the virus-driven creation of archaea and L-forms. All biophysically constrained virus-driven pathology has since been placed back into the context of embryogenesis and the dynamics of energy-dependent gene expression at the level of single-cell resolution as if bacteria somehow evolved into humans.

See:

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis
Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo
The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution
Chronicling embryos, cell by cell, gene by gene
Reported as: How one cell gives rise to an entire body
See for comparison our section on molecular epigenetics in: From Fertilization to Adult Sexual Behavior (1996)
Watch pseudoscientists continue to make ridiculous claims that fail to link the creation of biophysically constrained thermonuclear energy to autophagy and all biodiversity in the context of the cell biology game Cytosis and most of the forthcoming presentations during Schrödinger at 75 – The Future of Biology – September 2018.
Remember to note that at the end of the parody All About that Base, the research group politely refers to Neil deGrasse Tyson as a big ass (er, a bass). Try not to use the acronym ROTFLMAO in attempts to discuss what is known to all serious scientists with theorists.

Nutrient-dependent pheromone-controlled feedback loops

May 3, 2018

Summary: The link from positive selection to one food energy-dependent base pair change and fixation of the mouse-model-to-human-specific EDAR V370A allele in populations on different continents attests to sympatric speciation at every level of examination that refutes the pseudoscientific nonsense of neo-Darwinian mutation-driven evolution.

Reported on 5/3/18 as: SWAT team of immune cells found in mother’s milk

“There is a feedback loop,” says Yu. It’s known that some immune cells like leucocytes, another white blood cell that fights infection, increase in the milk in response to an infection in the baby.

…the largest immune cell population in breast milk is macrophages, which ILCs are known to direct. Macrophages, which literally means ‘big eaters,” are the largest of the white blood cells and much-better studied than ILCs. They are known for their ability to envelop unwanted items like bacteria, viruses…

Environmental selection during the last ice age on the mother-to-infant transmission of vitamin D and fatty acids through breast milk 4/23/18

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. The dental pleiotropic effects of this allele suggest an even higher occurrence among indigenous people in the Western Hemisphere before European colonization. We hypothesize that selection on EDAR V370A occurred in the Beringian refugium because it increases mammary ductal branching, and thereby may amplify the transfer of critical nutrients in vitamin D-deficient conditions to infants via mothers’ milk. This hypothesized selective context for EDAR V370A was likely intertwined with selection on the fatty acid desaturase (FADS) gene cluster because it is known to modulate lipid profiles transmitted to milk from a vitamin D-rich diet high in omega-3 fatty acids.

Reported as: Gene linked to breastfeeding may have boosted survival of earliest Americans (4/23/18)

…they carried a genetic mutation—revealed in ancient teeth—that boosted the development of milk ducts in women’s breasts, which may have helped nursing mothers pass more nutrients to their infants.

The obvious link from infant nutrition to healthy longevity was reported in the context of a ridiculous gene-centric theory of species survival. Gene-centric theories are all that pseudoscientists have left. They use them to hold back the scientific progress made by serious scientists like those who reported this:
Feedback loops link odor and pheromone signaling with reproduction (2005)

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.

Ecological Adaptations vs the Randomness of Evolution (2)

May 1, 2018

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

Summary: See for comparison: Make ‘Em Resistant to Viruses

In the new proposal — which Science says was released in advance of a meeting today — GP-write leaders say “ultrasafe” cells could be developed by making some 400,000 changes to the human genome.

A Fast One–Step Digestion of DNA or RNA for Global Detection and Characterization of Nucleotide Modifications (link opens pdf)
Product information:

The Nucleoside Digestion Mix is an optimized mixture of enzymes that provides a convenient one-step method to generate single nucleosides from DNA or RNA for quantitative analysis by liquid chromatography-mass spectrometry (LC-MS), eliminating the need for sequential multi-step, time-consuming digestion protocols.

Digests both DNA and RNA to single nucleosides

A source of anti-entropic energy is required to create nucleosides and nucleotides. The quantized energy as information was available to modify nucleotides after the creation of sunlight.
See also: Nucleoside vs. Nucleotide

A nucleoside consists of a nitrogenous base covalently attached to a sugar (ribose or deoxyribose) but without the phosphate group. A nucleotide consists of a nitrogenous base, a sugar (ribose or deoxyribose) and one to three phosphate groups.

Nucleoside = Sugar + Base
Nucleotide = Sugar + Base + Phosphate

The link from the”optimized mixture of enzymes” to Digestion of DNA or RNA links the quantification of epigenetic modifications and the activity of nucleic acid modifying enzymes from energy-dependent microRNA biogenesis to the functional structure of cellular RNA, which has been linked to viral latency and ecological adaptations in all living genera.
The facts about the energy-dependent creation of microRNAs and ecological adaptations have been placed into the context of High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development.

These data are provided in easily accessible formats for both craniofacial researchers and clinicians to aid future experimental design and interpretation of noncoding variation in those affected by craniofacial abnormalities.

The facts were reported in Blueprint for the skull: A search for cleft palate’s cause reveals a map of the facial genome

He studies the human genome, but not the genes that tell the body what proteins to make. Instead, he focuses on regulators, parts of the DNA that tell genes when and where to act. These regulators, also known as enhancers, tend to be linked to specific parts of the body.

microRNA cleft palate
1 of 33: A functional polymorphism in the pre-miR-146a gene is associated with the risk of nonsyndromic orofacial cleft.
enhancer cleft palate
1 of 35 Genome-Wide DNA Methylation Analysis During Palatal Fusion Reveals the Potential Mechanism of Enhancer Methylation Regulating Epithelial Mesenchyme Transformation.
The link from the energy-dependent creation of microRNAs to food energy-dependent genome-wide RNA-directed DNA methylation is perfectly clear until the term enhancer is used in the context of a potential mechanism regulating epithelial mesenchyme transformation.
The conserved molecular mechanisms of energy-dependent epigenetically-effected cell type differentiation are missing and the substitution of a potential mechanism of methylation can be used to support neo-Darwinian nonsense about mutation-driven evolution.
Even after pseudoscientists admit that their theories of craniofacial development are ridiculous, since development is energy-dependent and epigenetically effected, they try to place their findings back into the context of gene-centric theories.
Alternatively, they must know that the virus-driven theft of quantized energy links Zika virus-damaged DNA to craniofacial development with the most severe effects on the size of the brain and skull.
See also: Incomplete host immunity favors the evolution of virulence in an emergent pathogen

Partially protective vaccination can sometimes select for increasingly virulent pathogens.

Reported as: In nature, an imperfect immune system drives the evolution of deadly pathogens

As annual flu shot patrons know, immune systems are not perfect and must be constantly reinforced to protect against rapidly evolving pathogens.

Also:

…birds that eat at feeders are more likely to be infected with the disease, which causes red, swollen eyes and often blindness that results in death.

The link from what the birds and the bees eat to healthy longevity was detailed in my 2013 refutation of neo-Darwinian pseudoscientific nonsense.

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

Scientific creationists in the US have started to tout my model without attribution.
See: Are Evolution and Adaptation the Same?

Mechanisms of adaptation are made up of complex integrated components, including environmental sensors, signaling pathways, feedback and feed-forward loops, and information control systems in the creature’s DNA.

The sentinel discovery that prokaryotes (bacteria and archaea) have heritable adaptive immunity mediated through CRISPR and CRISPR-associated (Cas) proteins has led to transformative advances in molecular biology, most notably in gene editing (2).

The discovery of heritable adaptive immunity ended the pseudoscientific nonsense about mutation-driven evolution. It linked vaccinations and gene editing to unpredictable outcomes in species from microbes to humans by altering the perfection of our innate immune system. The alterations link the virus-driven degradation of our messenger RNA to all pathology.
But see: Cytosis for ages 10+

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: Make ‘Em Resistant to Viruses

In the new proposal — which Science says was released in advance of a meeting today — GP-write leaders say “ultrasafe” cells could be developed by making some 400,000 changes to the human genome.

Environmental selection is natural selection (6)

April 30, 2018

by James Kohl with No Comment Adaptations Autophagy base editing biophotonics Diseases & Disorders Ecology Subatomic

Massive Science Reports

You Don’t Know GMOs

We’re working with a team of geneticists, biologists, and environmental scientists to bring you the most up-to-date report on the science, history, and safety of genetically-modified organisms.

Coming May 2018

I know how GMOs are linked to the forthcoming viral apocalypse. Do you? Atheistic communists in North Korea have learned. When will you?

Environmental selection is natural selection (5)

April 30, 2018

by James Kohl with No Comment Adaptations biophotonics Cytosis Diseases & Disorders Ecology Light Energy microRNA editing Model Organisms Nutrigenomics Physics RNA Directed RNA editing RNA interference RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA–Mediated Epigenetic Heredity Subatomic

Summary: Atheistic Chinese Communists realize that vaccinations cannot protect them. Their attempts to develop a universal vaccine have failed. Bill Gates promotes vaccinations, which led us to the brink of the next pandemic.

Vaccines prevent ecological adaptations in some cell types. Does Bill Gates, a non-scientist, think that people from God-fearing non-communist countries can do better than the atheistic Communists?

Bill Gates calls on U.S. to lead fight against a pandemic that could kill 33 million

Gates and his wife, Melinda, have repeatedly warned that a pandemic is the greatest immediate threat to humanity. Experts say the risk is high, because new pathogens are constantly emerging and the world is so interconnected.

New pathogens do not emerge. Read Quantico. The viruses that cause all pathology ecologically adapt by stealing the quantized energy that all differentiated cell types need to survive.

Bill Gates thinks a coming disease could kill 30 million people within 6 months — and says we should prepare for it as we do for war

If you were to tell the world’s governments that weapons that could kill 30 million people were under construction right now, there’d be a sense of urgency about preparing for the threat, Gates said.

The one time the military tried a sort of simulated war game against a smallpox pandemic, the final score was “smallpox one, humanity zero,” Gates said.

…a strategy was developed in 2009, but it’s carried out by several government agencies in an uncoördinated approach…

Bill Gates has been promoting vaccinations as a strategy. The vaccinations led us to the brink of the pandemic. Vaccines prevent ecological adaptations in some cell types. The atheistic Chinese Communists now realize that vaccinations cannot protect them. Their attempts to develop a universal vaccine have failed, miserably. Does Bill Gates, a non-scientist, think that people from non-communist countries can do better than the atheistic Communists?
Perhaps he doesn’t know how South Korea forced the denuclearization of North Korea, which will probably lead to proclamations of world peace.
See: Engineered virus has artificial amino acid allowing it to serve as a vaccine (2016)

A team of researchers at Peking University has developed a new type of vaccine that they claim may allow for a new approach to generating live virus vaccines which could conceivably be adapted to any type of virus.

Their “new approach” failed. The uncoordinated strategy against the CRISPR bioterror threat has failed to address the established scientific facts. All ecological adaptations are quantized energy-dependent and biophysically constrained by the physiology of pheromone-controlled reproduction in species from microbes to humans. That fact is presented in the context of the Holy Bible, which explains why scientific creationists from South Korea were able to force denuclearization on atheistic communists.
Now Gates accuses the US Government (the Trump Administration?) of failing to protect US citizens.
On April 26, 2018, I discussed factual representations of biologically-based cause and effect that probably led to the death of Timothy J. Cunningham. I told a friend that Cunningham’s publication record clearly reveals his ability to link viruses to the failed differentiation of all cell types in all living genera.
See his publications on

1)”Racial Disparities in Age-Specific Mortality”
2) “Sex-specific relationships between adverse childhood experiences”
3) “Associations between antioxidants and all-cause mortality”
and
4) “Health and Safety Issues for Travelers”

What Bill Gates Fears Most may be the revelations of facts about vaccines. Gates seems to be still promoting the live (or dead) virus-containing vaccines that have failed to protect anyone since the time they were supposed to start protecting us all.
Is he aware that An error made in 1925 led to a crisis in modern science?
The error replaced the creation of energy with models of statistical significance as if the answer to the question “What is Life?” was akin to computers that automagically emerged with the energy to run themselves.
See also: Arrowsmith (1925). If Bill Gates had studied US history, he might have learned that the 1925 Scopes Trial in Dayton, Tennessee predicted that teaching neo-Darwinian evolution would cause the next pandemic.
Instead see: Gates Foundation launches $12M Grand Challenge for universal flu vaccine, as Bill Gates urges world to prepare for war on pandemics
When Europeans “invaded” the Americas, indigenous human populations were decimated by the virus-driven degradation of their messenger RNA. Few American Indians had the amino acid substitution that protected them from the virus-driven pathology manifested in the deep sea. The virus-driven pathology has been linked to all physical and mental diseases/disorders on Earth via the 1918 Spanish influenza pandemic.
For comparison, everything known to all serious scientists about quantized energy-dependent RNA-mediated cell type differentiation has been linked to biophysically constrained viral latency.
See: Virus-mediated archaeal hecatomb in the deep seafloor and Cytosis.
See for comparison: Environmental selection during the last ice age on the mother-to-infant transmission of vitamin D and fatty acids through breast milk
The V370A adaptation came from populations in what is now Central China, but dietary changes eliminated the need for the adaptation in the Americas, where indigenous populations had adapted to other viruses. When Europeans introduced the viruses to indigenous populations on other continents, the 6,000 year history of ecological adaptations in species from mice to humans became clear.
See: Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant
The EDAR variant is V370A, which is also known as The ectodysplasin receptor variant (EDARV370A) and as rs3827760, which is also known as 1540T/C, 370A or Val370Ala. It is a SNP in the ectodysplasin A receptor EDAR gene on chromosome 2. The fact that one food energy-dependent variant in one SNP was linked from the creation of a receptor to biophysically constrained RNA-mediated cell type differentiation in species from mice to humans proved that environmental selection links quantized energy-dependent changes in the microRNA/messenger RNA balance from the creation of sunlight to viral latency in all living genera.
See for comparison: Here Are Michelle Wolf’s Boldest Moments At The White House Correspondents’ Dinner
See also the bold moves made by scientific creationists in South Korea, who forced the denuclearization of North Korea (in the same week as the “dinner”) with prior publication of two articles that link viruses to the decimation of populations of atheistic Communists.
Whether or not the US, and/or if South Korea invades, they could decimate the populations of atheists without firing more than one shot to deliver a payload of virus-modified yeasts. The lives of well-nourished troops could be saved for the take-over/occupation.
See:
1) A Single Amino Acid at the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses 4/13/18

Several amino acid mutations were identified in PB2, PB1, PA, BM2, and/or NS1 protein coding regions, and one concurrent lysine (K)-to-arginine (R) mutation in PA residue 338 (PA K338R) was found in both maVc_BR60 and maYm_WI01 viruses.

2) Emergence of Human G2P[4] Rotaviruses in the Post-vaccination Era in South Korea: Footprints of Multiple Interspecies Re-assortment Events 4/18/18

…17-24 amino acid changes, specifically A87T, D96N, S213D, and S242N substitutions in G2 epitopes, were observed.

If the only thing atheistic Communists want is to not be invaded, they probably know that vaccines and nuclear weapons cannot protect them from the decimation that could be caused by a single amino acid substitution in a virus.

Why tempt our Creator to show them the error of their ways, when atheistic Communists do not believe in Him? Ask also, “Who killed Timothy J. Cunningham?” — and/or anyone else who is killed or goes missing during the transition to Global Peace.
See also: [evol-psych] Sorry but Yahoo! groups have blocked all my news items — Robert Karl Stonjek 4/30/18
Wait for this to happen with the Human Ethology Yahoo group, where you can still find the atheistic pseudoscientific nonsense touted by the moderator, Jay R. Feierman.
See for example:
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 also: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.
See for comparison: Tracking niche variation over millennial timescales in sympatric killer whale lineages

Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4].
The differences in amino acid composition among different tissues can lead to large differences in trophic discrimination [38].

Many evolutionary theorists and Big Bang cosmologists are among the hate-mongers who would rather combat Christianity than make any efforts towards Combating Evolution to Fight Disease.

Environmental selection is natural selection (4)

April 30, 2018

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy base editing biophotonics Cytosis Diseases & Disorders Ecology Model Organisms Physics Subatomic

Conclusion: Only biologically uninformed science idiots still believe in the pseudoscientific nonsense of neo-Darwinian evolution.
VISUALIZING APOPTOSIS AS IT HAPPENS

Apoptosis is a highly regulated and critical homeostatic process in multicellular organisms.

Biologically uninformed theorists have claimed the conserved molecular mechanisms of energy-dependent apoptosis in multicelluar organisms arose after energy emerged. Aberrations in this form of energy-dependent programmed cell death have been linked from the virus-driven theft of quantized energy to all pathology. That helps to explain why biologically uninformed science idiots continue to link emergence to the evolution of all biodiversity but serious scientists present experimental evidence of highly regulated apoptosis.
Every level of biological organization has now linked the anti-entropic virucidal energy of sunlight to the proton motive force from apoptosis to all biodiversity via what is known about biophysically constrained viral latency.
For more evidence of obfuscation that theorists have used in their attempts to support their pseudoscientific nonsense “Download this eBook from The Scientist and Biotium to find out more about”

– The intrinsic and extrinsic apoptosis pathways
– The biochemical and morphological stages of apoptosis
– Apoptosis signs and signals
– Nuclear events during apoptosis

Quantized energy-dependent changes link the extrinsic pathway to the instrinsic pathway via changes in the microRNA/messenger RNA balance, which links the physiology of pheromone-controlled reproduction to biophysically constrained RNA-mediated fixation of amino acid substitutions and ecological adaptations in the context of viral latency.
For links to what is known about the role of anti-entropic virucidal energy links the proton motive force from protection of the mitochondrial membrane to all biophysically constrained biodiversity, see:
Reappraising the human mitochondrial DNA recombination dogma
Substitute energy-dependent ecological adaptation each time you see others suggest that human mitochondrial DNA recombination evolved.
See also: If you can’t explain something in simple terms, you don’t understand it

Sizing up his audience perfectly, Feynman said, “I’ll prepare a freshman lecture on it.” But he came back a few days later to say, “I couldn’t do it. I couldn’t reduce it to the freshman level. That means we don’t really understand it.”

He died in 1988. Anyone who continues to claim that we still do not understand the links from quantum physics to quantum souls exemplifies human idiocy. See: Food energy
Only biologically uninformed science idiots still believe in the pseudoscientific nonsense of neo-Darwinian evolution.

MicroRNA-mediated denuclearization

April 21, 2018

by James Kohl with No Comment Adaptations biophotonics Diseases & Disorders Ecology microRNA editing Model Organisms RNA Directed RNA–Mediated Epigenetic Heredity Subatomic Variations What's in the News

Kim Says North Korea Is Stopping Nuclear and Missile Tests

Early today, he said the country was stopping nuclear and missile tests and shuttering its atomic test site, which has “done its job.” Those concessions were long demanded by the U.S., lifting hopes that next Friday’s planned summit between Kim and South Korean President Moon Jae-in will be conducted in good faith.

Added Perspective
Emergence of Human G2P[4] Rotaviruses in the Post-vaccination Era in South Korea: Footprints of Multiple Interspecies Re-assortment Events
Viruses do not emerge. They adapt in the context of proton gradients and microRNA-mediated changesin energy-dependent protein folding chemistry. The food energy-dependent fixation of RNA-mediated amino acid substitutions links interspecies re-assortment events to healthy longevity.
See for comparison: A Single Amino Acid at the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses
The ability of researchers in South Korea to create genetically modified viruses with increased pathogenicity links quantum physics from virus-driven energy theft to the degradation of messenger RNA and extinctions in many different populations of extinct organisms during the past 6,000 years.
See: Virus-mediated archaeal hecatomb in the deep seafloor

The population of North Korea could have been the next to be decimated by a genetically engineered virus if Kim Jong Un had not agreed to denuclearization.
See also: Reappraising the human mitochondrial DNA [mtDNA] recombination dogma

…studies dealing with human variation and evolution have assumed that human mtDNA does not recombine and should be considered as pathological or very infrequent. Using both direct and indirect approaches, we provide consistent evidence of mtDNA recombination in humans.

Food energy-dependent mtDNA recombination in humans appears to protect all organized genomes in all extant human populations. mtDNA recombination may be the best protection from extinction that any species already has. Given what is known to serious scientists about cell type differentiation, the link from light-activated endogenous substrates and the physiology of reproduction in all living genera causes many people to ridicule the assumptions still touted in the context of theories invented by neo-Darwinian theorists.
See also: Mechanisms of Recombination conference