ecological adaptations Archives

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.

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.

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.

Environmental selection is natural selection

April 26, 2018

by James Kohl with No Comment Adaptations base editing biophotonics Diseases & Disorders Ecology Human Pheromones Model Organisms Nutrigenomics RNA Directed RNA-directed DNA methylation RNA–Mediated Epigenetic Heredity Variations

Environmental selection during the last ice age on the mother-to-infant transmission of vitamin D and fatty acids through breast milk was published on April 23, 2018

The ectodysplasin A receptor (EDAR) gene has a range of pleiotropic effects, including sweat gland density, incisor shoveling, and mammary gland ductal branching. 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.

The authors placed my claims about the mouse-to-human model of the EDAR V370A variant back into the context of an evolutionary adaptation. They seem unwilling to accept the fact that the EDAR V370A variant is a nutrient-dependent pheromone-controlled ecological adaptation in mice and in humans. It links energy-dependent changes from angstroms to ecosystems in all living genera via natural selection for energy-dependent codon optimality.
The EDAR V370A allele is also known as rs3827760, 1540T/C, 370A, or Val370Ala. It is a SNP in the ectodysplasin A receptor EDAR gene on chromosome 2.
See the author’s copy of my invited review of nutritional epigenetics, which was returned without review :
Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

In the context of climate change and changes in diet, the story began with what probably was a nutrient-dependent base pair change and a variant epiallele that arose in a human population in what is now central China. Apparently, the effect of the epiallele was adaptive and it was manifested in the context of an effect on sweat, skin, hair, and teeth. In another mammal, such as the mouse, the effect on sweat, skin, hair, and teeth is probably due to a nutrient-dependent epigenetic effect on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. The pheromones appear to control the nutrient-dependent epigenetically-effected hormone-dependent organization and hormone-activation of reproductive sexual behavior in mammals such as mice and humans, but also in invertebrates and in microbes as previously indicated.

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

More than four years later, biologically uninformed theorists have again tried to make natural selection something different than environmental selection. Nina G. Jablonski is one of the co-authors. I’m tempted to think that all the others also are biologically uninformed science idiots who cannot link physical and chemistry from subatomic particles to ecosystems via what organisms eat and the physiology of pheromone-controlled reproduction, which biophysically constrains viral latency in all living genera.
See also: microRNA and ADAR1 microRNA
For example:
Combinatory RNA-Sequencing Analyses Reveal a Dual Mode of Gene Regulation by ADAR1 in Gastric Cancer (April 25, 2018)
Virus-encoded miRNAs in Ebola virus disease (April 24, 2018)

MicroRNA-mediated denuclearization (6)

April 25, 2018

by James Kohl with No Comment Adaptations biophotonics Diseases & Disorders Ecology

Summary: The EDAR V370A isoform links one quantized energy-dependent base pair change from changes in ultraviolet light (UV) exposure to fixation of one amino acid substitution. The substitution differentiates the cell types of mice and humans in the context of a mouse-to-human model of nutritional epigenetics and microRNA-mediated denuclearization in North Korea.

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

…a genetically isolated population living in this environment during the LGM ∼20,000 y ago experienced selection for polymorphisms in the FADS gene cluster and for EDAR V370A because of the advantage these genetic variants likely confer in transmitting nutrients from mother to infant through breast milk under conditions of extremely low UV.

Nina G. Jablonski (a co-author), is known for her research into the evolution of skin color in humans. Her neo-Darwinian pseudoscientific nonsense is refuted in this representation of natural selection for food energy-dependent codon optimality.
Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

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

The food energy-dependent pheromone-controlled amino acid optimality code has been linked to biophysically constrained viral latency in all living genera via the physiology of pheromone-controlled reproduction.
The EDAR V370A isoform links one quantized energy-dependent base pair change from changes in ultraviolet light (UV) exposure to fixation of one amino acid substitution. The substitution differentiates the cell types of mice and humans in the context of a mouse-to-human model of nutritional epigenetics and microRNA-mediated denuclearization in North Korea.

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

The scientific creationists in South Korea know how to protect organized genomes from the virus-driven degradation of messenger RNA. Atheistic communists believed vaccines would protect their supercoiled DNA in their organized genomes.
The communists and other atheists lost their battle to promote atheism and vaccines because serious scientists in South Korea liked the accurate representations of the creationists. The serious scientists proceeded to support scientific creationism and Americanism with experimental evidence of top-down causation and biophysical constraints.
Pseudoscientists still tout their nonsense about constraint-breaking mutations. See: Mutation-Driven Evolution
Kalevi Kull: Censorship & Royal Society Evo Event

Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge. — Kalevi Kull

The links from particle physics to biophysically constrained viral latency will be placed into the context of the game “Subatomic,” which should be available by the end of this year.

The eternal significance of microRNAs (1)

April 10, 2018

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

Common Allele Linked to Sugar Consumption Leads to Lower Body Fat, Higher Blood Pressure
One energy-dependent change in a base pair is linked from the FGF21 rs838133 variant to microRNA-mediated changes in morphology and behavior. The quantized energy as information link from microRNAs to morphology and behavior is common to my mouse-to-human model of sympatric speciation.

By linking the common allele to sugar consumption, the authors attest to the fact that sympatric speciation is quantized energy-dependent. Energy as information biophysically constrains viral latency in the context of the game Cytosis for ages 10+.
See also: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
Theorists have been reluctant to comment on this invited review of nutritional epigenetics, which I posted to Figshare.com on 4/10/14. As of today, the model of food energy-dependent pheromone-controlled ecological adaptations / sympatric speciation has been available for 4 years.
In my mouse-to-human model, the variant is rs3827760, aka 1540T/C, 370A or Val370Ala. It is a SNP in the ectodysplasin A receptor EDAR gene on chromosome 2.
Summary: The energy-dependent creation of ATP synthase, ATP, microRNAs, messenger RNA, and supercoiled DNA biophysically constrains viral latency in the context of the “Levels of Biological Organization” I included in this presentation from 2010: Human Pheromones: Linking Neuroendocrinology and Ethology (revisited) See slide # 6.
See also, our award-winning 2001 review: Human pheromones: integrating neuroendocrinology and ethology

Complexity: Routes and Patterns (4)

April 5, 2018

by James Kohl with No Comment Adaptations Diseases & Disorders Ecology RNA Directed

Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors (2015)

…the current models are both consistent with available and new experimental data and offer a number of predictions – notably, through revelation of highly constrained residues (Supplementary Data 9–10) – to guide and visualise structure-function analyses of these unusual sensory receptors.

No experimental evidence of top-down causation links anything except the quantized energy-dependent creation of enzymes, hormones, and receptors to biophysically constrained viral latency and ecological adaptations.

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

See for comparison: Tuning Insect Odorant Receptors (2018)

Analyzing the variation of insect OR protein amino acids during evolution revealed a model for transmembrane domain arrangement that is unrelated to GPCRs (Hopf et al., 2015).

Try to refute my model with the latest pseudoscientific nonsense about coevolved amino acids.

SARCASM ALERT:Alternatively, evolve and fly away.

Psychophysical Laws of Biology: RNA-mediated nutritional psychiatry (3)

March 27, 2018

by James Kohl with No Comment Adaptations Alternative Splicings biophotonics Cytosis Diseases & Disorders Ecology Human Brain Human Pheromones Light Energy microRNA editing Model Organisms Neuronal Plasticity Nutrigenomics Physics RNA Directed 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

Psychophysical Laws and the Superorganism (open access)

…superorganisms may also exhibit such behaviour, suggesting that these laws arise from fundamental mechanisms of information processing and decision-making.

Reported on Jun 14, 2013 as Nutrient-dependent/pheromone-controlled adaptive evolution: a model

and again on: Mar 27, 2018 as Honeybees may unlock the secrets of how the human brain works

The study… found that superorganisms may obey the same laws as the human brain.

Kohl’s “Laws of Biology” and Darwin’s “conditions of life” can now be compared in the context of how quantized energy as information was linked to biodiversity in this invited review of nutritional epigenetics: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)
See also for review:

Functional and evolutionary aspects of chemoreceptors (2012)
Sensory receptors—design principles revisited (2013)
Moving forward: See: Tuning Insect Odorant Receptors (in press)

Among the insect olfactory receptors the odorant receptors (ORs) evolved in parallel to the onset of insect flight. A special property of this receptor type is the capability to adjust sensitivity of odor detection according to previous odor contacts. This article presents a current view on regulatory processes affecting the performance of ORs and proposes a model of mechanisms contributing to OR sensitization.

Future attempts to place psychophysical laws of biology back into the context of neo-Darwinian pseudoscientific nonsense will continue to pit ridiculous theories about experience-dependent tuning of odor receptors against everything known to serious scientists about RNA-mediated biophysically constrained viral latency and supercoiled DNA.
See for comparison:
Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment (2003)
Seeking the foundations of cognition in bacteria: From Schrödinger’s negative entropy to latent information (2006)
Learning from Bacteria about Natural Information Processing (2009)
Stability of the hybrid epithelial/mesenchymal phenotype (2016)

Epithelial-to-Mesenchymal Transition (EMT) and its reverse – Mesenchymal to Epithelial Transition (MET) – are hallmarks of cellular plasticity during embryonic development and cancer metastasis.

Cellular plasticity was linked from the energy-dependent pheromone-controlled physiology of reproduction in bacteria to our visual perception of energy and mass in the context of the space-time continuum.
See: Olfaction Warps Visual Time Perception (2017)

The behavioral gain produced by a congruent relative to an incongruent odor is accompanied by elevated neural oscillatory power around the object’s flicker frequency in the right temporal region ~150-300 ms after object onset, and is not mediated by visual awareness. In parallel, odors bias the subjective duration of visual objects without affecting one’s temporal sensitivity.

See also: Schrödinger at 75 – The Future of Biology – September 2018
The scheduled speakers will undoubtedly link the Science Behind the Game “Cytosis” to the Science Behind the Game “Subatomic” via everything known to all serious scientists based on Schrodinger’s prescient claims in What is Life? (1944).
See also: What is life when it is not protected from virus driven entropy

The anti-entropic force of virucidal ultraviolet light links guanine–cytosine (G⋅C) Watson–Crick base pairing from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. For example, protection of DNA from permanent UV damage occurs in the context of photosynthesis and nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to DNA repair. In the context of thermodynamic cycles of protein biosynthesis and degradation, DNA repair enables the de novo creation of G protein coupled receptors (GPCRs). Olfactory receptor genes are GPCRs. The de novo creation of olfactory receptor genes links chemotaxis and phototaxis from foraging behavior to social behavior in species from microbes to humans. Foraging behavior links ecological variation to ecological adaptation in the context of this atoms to ecosystems model of biophysically constrained energy-dependent RNA-mediated protein folding chemistry. Protein folding chemistry links nutrient-dependent microRNAs from microRNA flanking sequences to energy transfer and cell type differentiation in the context of adhesion proteins, and supercoiled DNA that protects all organized genomes from virus-driven entropy.

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

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

See also “Outer Membrane Vesicles” microRNA (4 of 4 from a 3/27/18 search)

How Our Other Genome Controls Our Epi-Genome (2016)

Secretable Small RNAs via Outer Membrane Vesicles in Periodontal Pathogens (2017)

Tiny RNAs and their voyage via extracellular vesicles: Secretion of bacterial small RNA and eukaryotic microRNA (2017)

Molecular Paths Linking Metabolic Diseases, Gut Microbiota Dysbiosis and Enterobacteria Infections (2018)

See also: March 28, 2018 sponsored by System Biosciences

Webinar: Deciphering how bacteria utilize outer membrane vesicles (OMVs) to communicate and infect

Outer Membrane Vesicles (OMVs) are membrane vesicles secreted by bacteria that contain DNA, RNA, proteins and endotoxins. Bacteria respond to many environmental factors by secreting specifically-enriched OMVs, which makes these bacteria more fit for their environment. For example, OMVs may be enriched with invasion proteins at the host-pathogen interface. OMVs have recently gained attention as a novel mechanism for transmission of molecular information within bacteria as well as between bacteria and mammalian cells. Owing to their similarities to well-studied extracellular vesicles (EVs), OMVs are being utilized by researchers to study host-bacterial interactions in pathogenesis, cancer therapy, host immune response modulation, as well as bacterial OMV engineering for use as vaccines. This webinar will give an overview of recent studies on the role of OMVs in host-pathogen interactions and discuss their bioengineering potential as vehicles for cargo delivery. We will also introduce our new & revolutionary ExoBacteria™ OMV Isolation Kit, which will enable you to achieve faster, simpler & better OMV isolation.

Learn how OMVs are being utilized by researchers to study host-bacterial interactions in pathogenesis, cancer therapy, host immune response modulation, as well as bacterial OMV engineering for use as vaccines.

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

Odor activation of ATP (2)

March 26, 2018

by James Kohl with No Comment Adaptations Diseases & Disorders Ecology Model Organisms Physics RNA Directed Subatomic

Metabolic Regulation of Cytoplasmic DNA Synthesis (1974)

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

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

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

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

Who will be the next to disagree:
7/25/13
Jay R. Feierman:

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

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

Scent of Eros

Posts tagged: ecological adaptations