pheromone-controlled 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.

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

The eternal significance of microRNAs (5)

May 10, 2018

by James Kohl with No Comment Adaptations Autophagy Cytosis Diseases & Disorders Ecology RNA Directed RNA–Mediated Epigenetic Heredity

Excerpt: Researchers in South Korea, for example, have reminded the God-less Communist dictator of North Korea that one microRNA-mediated amino acid substitution in the influenza B virus could decimate the human populations that he thinks he rules.
Conclusion: Conserved energy biophysically constrains viral latency.

Ridiculously ignorant objections to my publication in what others claim is a predatory journal can be compared to my objection to publication of this article in PNAS.

Environmental selection during the last ice age on the mother-to-infant transmission of vitamin D and fatty acids through breast milk
1) They linked environmental selection to the frequency of the EDAR V370A variant in the mouse model via positive selection for modulation of thermoregulatory sweating.
2) They linked environmental selection to similarities in human populations in North Asia, East Asia, and the New World. But they virtually ignored the mouse model of food energy-dependent pheromone-controlled biophysically constrained ecological adaptation.
I linked the same food energy-dependent pheromone-controlled base pair change and microRNA-mediated fixation of the same amino acid substitution to all biodiversity in all living genera via feedback loops. See: Feedback loops link odor and pheromone signaling with reproduction

Others see what passes peer-review published in journals that support the expense of efforts made by pseudoscientists and other theorists, but they claim that the OMICS journals are predatory. I claim that pseudoscientists and other theorists do not know the difference between predation and sympatric speciation because they place predation into the context of evolved biodiversity.

For comparison see: Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

Reported as: Baleen Whale Genomes Point to Evolution With Gene Flow

Large baleen whales in the Balaenopteridae family (commonly known as rorqual whales) have undergone sympatric speciation — speciation without clear geographic barriers between them — despite ongoing hybridization, according to new research from investigators in Sweden and Germany.

System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes

Reported as:

“The patterns of synaptic connections perfectly mirror the fundamental differences in the feeding behaviours of P. pacificus and C. elegans”, Ralf Sommer concludes. A clear-cut result like that was not what he had necessarily expected.

Neo-Darwinian theorists and other biologically uniformed pseudoscientists have failed to use any common sense in attempts to link what organisms eat from the physiology of reproduction to biophysically constrained biodiversity. For comparison, serious scientists have forced the denuclearization of North Korea by reminding others to start with what is known about how food energy-dependent autophagy protects all life on Earth from the virus-driven degradation of messenger RNA.

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

…as a reviewer, it is tiresome to raise the same objections repeatedly, wondering why researchers have not fulfilled some of the basic requirements for establishing the occurrence of an autophagic process.

…appropriate assays depend in part on the question being asked and the system being used.

Researchers in South Korea, for example, have reminded the God-less Communist dictator of North Korea that one microRNA-mediated amino acid substitution in the influenza B virus could decimate the human populations that he thinks he rules.

See: A Single Amino Acid at the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses

Ecological adaptations vs the randomness of evolution (3)

May 8, 2018

by James Kohl with No Comment Adaptations base editing biophotonics Diseases & Disorders Ecology Human Pheromones Light Energy microRNA editing Model Organisms RNA Directed

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Environmental selection is natural selection (2)

April 26, 2018

by James Kohl with No Comment Adaptations base editing biophotonics Diseases & Disorders Ecology Human Pheromones 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

I believe that if you put enough biologically uniformed theorists in the same room, they will invent more theories to support the pseudoscientific nonsense they have touted in the past. See for example:

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

Acknowledgments

The synthesis presented here is a product of the American Association for the Advancement of Science’s 2017 annual meeting, as the ideas came together in the session entitled “Beringia and the Dispersal of Modern Humans to the Americas.”

Every aspect of every level of biophysically constrained food energy-dependent biologically-based cause and effect is placed back into the context of a ridiculous theory of human migration and evolution. The theory accurately attests to the link from one food energy-dependent base pair change to biodiversity in human populations via fixation of one amino acid substitution. But then, something goes horribly wrong.

The theory requires the fixation of the amino acid substitution to automagically occur in the context of the sun’s anti-entropic virucidal energy. The theory fails to mention the fact that the physiology of pheromone-controlled reproduction and the microRNA-mediated creation of all cell types in all living genera is required.

See for comparison: Anything published since the time I learned about the importance of microRNAs during the 2012 Society for Neuroscience annual meeting in New Orleans, LA.

From 2000/10/15 to 2012/10/15 microRNA Items: 1 to 20 of 19910

From 2012/10/15 to 2018/04/26 microRNA Items: 1 to 20 of 53458

The number of biologically informed serious scientists who have linked the energy-dependent creation of microRNAs to biophysically constrained viral latency and all biodiversity via the pheromone-controlled physiology of reproduction in bacteria continues to rapidly increase.

This begs the question: When will biologically uninformed science idiots stop attending meetings that facilitate their attempts to invent more ridiculous theories?

2018 March for Science vs microRNAs

April 17, 2018

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

Summary: Only biologically uninformed theorists and other pseudoscientists do not seem to know that all carbon-based life is quantized energy-dependent and that biophotonic energy as information comes from the sun. It is obvious to all serious scientists that proton gradients link photons from quantized energy as information to the proton motive force, which is how the potential of hydrogen (pH) is linked to changes in the microRNA/messenger RNA balance that biophysically constrain viral latency in the context of hydrogen-atom transfer in DNA base pairs in solution that must be linked to supercoiled DNA.
The Second March for Science a Smaller Affair

…the events are not devoid of politics—either on signs or in rhetoric.

“It is a remarkable outpouring of scientists to talk about the marvelous accomplishments of science, the amazing relevance of science, and a call for defending the conditions under which science can thrive.” — Rush Holt, the CEO of the American Association for the Advancement of Science
Science is not thriving. See for comparison: All in the (bigger) family (2015)

…at a special symposium of the annual meeting of the Society for Integrative and Comparative Biology, researchers reported new parallels between these two very successful groups of animals and new insights about what it took for an ancient crustacean to give rise to insects.

Energy-dependent microRNA-mediated biophysically constrained viral latency was required. The scientific facts about food energy-dependent pheromone-controlled biophysically constrained viral latency and microRNA-mediated sympatric speciation probably contributed most to the reduced turnout at the ridiculous Marches for Science. All serious scientists know that science is not thriving, and pseudoscientists are finding out.
This is serious science: miRNA regulation of innate immunity

In this review, we discuss the contributory pathways and mechanisms by which several miRNAs influence the development of innate immunity and fine-tune immune response. Moreover, we discuss the consequence of deregulated miRNAs and their pathogenic implications.

Who needs more proof that neo-Darwinian theorists and Big Bang cosmologists are biologically uninformed science idiots?
When George Church reported in this interview that cyanobacteria fix light, he left no room for ridiculous claims about the emergence of energy or claims about mutation-driven evolution. Two months later, most theorists skipped the Marches.
I believe they probably stayed home and attempted to rewrite their grant proposals. But what I believe doesn’t matter. I can’t prove that they’ve been forced by serious scientists to eliminate “evolution” and/or their automagical “evolutionary processes” from the content/context.
But see at 15:10

“…the cyanobacteria turn out that they fix light ah as well or better than land plants…”

See for comparison, from the transcript:

The cyanobacteria fix [carbon via] light as well or better than land plants. Under ideal circumstances, they can be maybe seven to ten times more productive per photon.

Only biologically uninformed theorists and other pseudoscientists do not seem to know that all carbon-based life is quantized energy dependent and that biophotonic energy as information comes from the sun. It is obvious to all serious scientists that proton gradients link photons from quantized energy as information to the proton motive force, which is how the potential of hydrogen (pH) is linked to changes in the microRNA/messenger RNA balance that biophysically constrain viral latency in the context of hydrogen-atom transfer in DNA base pairs in solution that must be linked to supercoiled DNA.
Theorists have been left behind and anyone who participated in the 2018 March for Science has revealed their overwhelming ignorance. Why didn’t George Church warn them? Richard Feynman did:
See: Food energy for Feynman’s claim about human idiocy.
Alternatively, see: Energy as information and constrained endogenous RNA interference
See also: A 360 degrees view of circular RNAs: From biogenesis to functions

The pre-mRNA splicing machinery generates circRNAs via backsplicing reactions, which are often facilitated by intronic repeat sequences that base pair to one another and bring the intervening splice sites into close proximity.

See also: Dr. Gene Nelson wrote: “This year, I printed 500 copies of the handout that I wrote regarding CGNP’s battle with the CPUC and the plant’s owner. I returned with about 490 handouts.”
On April 19, 2018 “From Layout to Multi-Physics: Integrating Thermal and Photonics Simulation into the PIC Design Flow” will link the creation of the sun’s anti-entropic virucidal energy to thermal cycling.
The thermal cycles have been linked to cracks in the Vietnam Memorial Wall. This free Webinar will almost undoubtedly place the eternal significance of “The Wall” into the context of the eternal significance of microRNAs, which repair DNA damage in carbon-based life forms. Damage repair via the food energy-dependent creation of microRNAs is linked to the eternal significance of differences between organic and inorganic chemistry.
For instance, quantum physics can be linked to the biophysically constrained production of uranium isotopes by the physiology of reproduction in bacteria. And, the use of uranium isotopes in therapy attests to the fact that the unconstrained energy causes cracks in the human genome. The “cracks” are manifested in radiation-induced pathologies.
Treating glioblastoma with radiation may be ill-advised. For comparison, microRNA-mediated therapy has emerged as an effective treatment regimen based on naturally occurring prevention of all pathology.

Pseudoscientists are willing to let Vietnam Veterans and others with glioblastoma suffer unnecessarily and die prematurely. The pseudoscientists won’t admit that food energy-dependent changes in microRNAs have been linked to the stability of all organized genomes via sympatric speciation in all living genera.

See for example: Serious scientists published Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene (2011)

Pseudoscientists posted this preprint on April 16, 2018. Integrative analysis of DNA methylation suggests down-regulation of oncogenic pathways and reduced de-novo mutation in survival outliers of glioblastoma

There is no such thing as a de novo mutation. The virus-driven degradation of messenger RNA has been linked from mutations to all pathology via the death gene, which was discovered during the early 1990s by researchers who worked for Abcam.
See: Epigenetic modifications poster
See for comparison: A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution

Why is Jennifer Doudna still touting controlled evolution at a time when other serious scientists have linked every aspect of the quantized energy-dependent creation of microRNAs to the epigenetically modified physiology of reproduction and all ecological adaptations? What hasn’t she learned about biophysically constrained microRNA-mediated cell type differentiation in species from microbes to humans?
See: When the Most Potent Combination of Antibiotics Selects for the Greatest Bacterial Load: The Smile-Frown Transition (April 23, 2013)

Finding the most potent combinations of antibiotics in the lab can be a challenge if antibiotic interactions are not robust to evolutionary adaptation.

For nearly 5 years serious scientists have watched theorists try to escape from the traps that were set by their predecessors. All intelligent people now realize that there is no such thing as evolution of a new species. There is only ecological variation and quantized energy-dependent ecological adaptations to the virus-driven theft of quantized energy that comes from sunlight and sustains the physiology of pheromone-controlled reproduction in all living genera.
Reported as: The XV Collection: What Happens when the Antibiotic 1-2 Punch Backfires? (April 13, 2018)

Antibiotic-resistant mutants readily arise within almost any population of bacteria. If a population containing both susceptible and resistant mutants is treated with two antibiotics, the susceptible majority is, as expected, rapidly wiped out. But this also removes any competition for the resistant minority, enabling them to quickly grow and proliferate.

The food energy-dependent pheromone-controlled physiology of reproduction in bacteria biophysically constrains the virus-driven degradation of messenger RNA that links antibiotic resistance from mutations to all pathology.
Reported on June 14, 2013 as: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

That extension of the vertebrate/mammalian model to invertebrates occurred as researchers integrated what was known about human pheromones and their effects on neuroendocrine systems during the development of human behavior (Kohl et al., 2001). Invertebrate research rapidly progressed to include the epigenetic effects of nutrients and pheromones on gene expression and on hormone-organized and hormone-activated behavioral transitions throughout life (Elekonich & Roberts, 2005), which is consistent with their epigenetic effects throughout the life of vertebrates, including mammals.

The honeybee model organism exemplifies what has been learned from the study of invertebrates (De Loof, Lindemans, Liu, De Groef, & Schoofs, 2012). This includes what has been learned about the epigenetic effects of nutrients and pheromones on juvenile hormone (JH).

Preprints are scientific manuscripts posted online prior to or concurrent with submission for peer review and publication in a scientific journal. They offer opportunities to share data and findings sooner and to get broader community feedback before publication. During outbreaks, decisions that can save lives must often be made quickly and with little information. The fast, open nature of preprint posting can help address these needs.

The posting of most preprints on the bioRxiv server obfuscates what is known to serious scientists about biophysically constrained energy-dependent microRNA-mediated sympatric speciation. The consistent focus of most preprints places the findings into the context of evolution because that is what biologically uninformed theorists have been taught to believe in.

Until everyone admits that the creation of microRNAs is food energy-dependent and biophysically constrained by the physiology of pheromone-controlled reproduction, the ability to respond to urgent and complex health challenges will be placed into the ridiculous context of evolutionary processes.

See for exception: A transmissible RNA pathway in honey bees

…RNA extracted from worker and royal jellies harbor differential naturally occurring RNA populations. Some of these RNAs corresponded to honey bee protein-coding genes, transposable elements, non-coding RNA and exogenous viruses. These results reveal an inherent property of honey bees to share RNA among individuals and generations. Thus, our findings suggest a transmissible RNA pathway, playing a role in social immunity and epigenetic dynamics among honey bees and potentially other closely interacting organisms.

See for comparison: SLC6A4 binding site and acute prosocial effects of (+/-)-3,4-methylendioxymethamphetamine (MDMA) are evolutionarily conserved in Octopus bimaculoides

Human and octopus lineages are separated by over 500 million years of evolution, and show divergent anatomical patterns of brain organization.

No experimental evidence of top-down causation or energy-dependent RNA interference suggests separation of the lineages by 500 million years of evolution.

See for comparison: Role of olfaction in Octopus vulgaris reproduction

From the concluding paragraph:

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).

See also: See Diamond et al., 1996: From Fertilization to Adult Sexual Behavior

Elekonich and Robinson (2000) linked our 1996 Hormones and Behavior review of RNA-mediated cell type differentiation to the honeybee model of food energy-dependent biophysically constrained biodiversity.

Effects of hormones on brain and behavior occur through three mechanisms: (1) behaviors both organized and activated by hormones, (2) behaviors only organized by hormones, and (3) behaviors only activated by hormones (reviewed in Arnold and Breedlove, 1985; Diamond et al., 1996).”

In this review we discuss the physiological and genetic mechanisms of this behavioral transition, which include large scale changes in hormonal activity, metabolism, flight ability, circadian rhythms, sensory perception and processing, neural architecture, learning ability, memory and gene expression.

Here we report on RNAi-silencing of IAPV infection by feeding bees with double-stranded RNA, as an efficient and feasible way of controlling this viral disease. The association of CCD with IAPV is discussed, as well as the potential of controlling CCD.

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

Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

Sympatric Speciation vs Pseudoscientific Nonsense (1)

April 7, 2018

by James Kohl with No Comment Adaptations Alternative Splicings Cytosis Diseases & Disorders Ecology microRNA editing Model Organisms 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

Summary: The “Science Behind the Game” from the cell biology game “Cytosis” supports all claims that clearly link energy-dependent alternative splicings of pre-mRNAs (aka microRNAs) to biophysically constrained viral latency. Game play by ages 10+ establishes the requirement for viral latency in the context of ecological variation and ecological adaptation outside the context of neo-Darwinian pseudoscientific nonsense. Simply put, Darwin presciently placed his “conditions of life” into the current perspective on ecological niche construction and sympatric speciation, which exemplifies ecological adaptation in all living genera.
For a historical perspective, see:
1996 From Fertilization to Adult Sexual Behavior

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

For obfuscation of our claims about cause and effect, which have since been linked to all biodiveristy, see: Altered microRNA expression and pre-mRNA splicing events reveal new mechanisms associated with early stage Mycobacterium avium subspecies paratuberculosis infection (2016)
Simply put, no new mechanisms were revealed. The well-known mechanisms of energy-dependent pheromone-controlled biophysically constrained RNA-mediated cell type differentiation were simply placed into the context of more unintelligible rhetoric.
See for comparison: 2013 Alternative splicings and amino acid substitutions (redux)
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].

For more information on the current perspective, which is the same as the historical perspective, see:
2018 Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

…speciation of rorqual evolution occurred under gene flow, which is best depicted by evolutionary networks. Especially in marine environments, sympatric speciation might be common; our results raise questions about how genetic divergence can be established.

Reported as: Baleen Whale Genomes Point to Evolution With Gene Flow

The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…

Viruses are the dynamo of change that we see in the modern genome. . . .

Cytosis_Booklet_Science.pdf (63 KB) (Log in or Register [for free] to download.) The “Science Behind the Game” from the cell biology game “Cytosis” supports all claims that clearly link energy-dependent alternative splicings of pre-mRNAs (aka microRNAs) to biophysically constrained viral latency. Game play by ages 10+ establishes the requirement for viral latency in the context of ecological variation and ecological adaptation outside the context of neo-Darwinian pseudoscientific nonsense. Simply put, Darwin presciently placed his “conditions of life” into the current perspective on ecological niche construction and sympatric speciation, which exemplifies ecological adaptation in all living genera.
Cytosis is described as: A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!
The collaborative efforts of 20 serious scientists who validated the details in the game include the mention of Stephen J. Bush. See: Bush, SJ et al., (2017) Alternative splicing and the evolution of phenotypic novelty

Alternative splicing, a mechanism of post-transcriptional RNA processing whereby a single gene can encode multiple distinct transcripts, has been proposed to underlie morphological innovations in multicellular organisms. Genes with developmental functions are enriched for alternative splicing events, suggestive of a contribution of alternative splicing to developmental programmes. The role of alternative splicing as a source of transcript diversification has previously been compared to that of gene duplication, with the relationship between the two extensively explored. Alternative splicing is reduced following gene duplication with the retention of duplicate copies higher for genes which were alternatively spliced prior to duplication. Furthermore, and unlike the case for overall gene number, the proportion of alternatively spliced genes has also increased in line with the evolutionary diversification of cell types, suggesting alternative splicing may contribute to the complexity of developmental programmes. Together these observations suggest a prominent role for alternative splicing as a source of functional innovation. However, it is unknown whether the proliferation of alternative splicing events indeed reflects a functional expansion of the transcriptome or instead results from weaker selection acting on larger species, which tend to have a higher number of cell types and lower population sizes.

This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.
See for comparison: Retraction: Oligoarginine peptides slow strand annealing and assist non-enzymatic RNA replication
Reported as: RNA Replication Paper Retracted
Szostak and others got busted for their pseudoscientific nonsense about non-enzymatic emergence by someone who understands quantized energy as information-dependent RNA-mediated top-down causation. People over age 10+ who play the cell biology game “Cytosis” may now force all biologically uninformed theorists to retract their claims, which typically have been placed into the context of mutation-driven evolution.

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.

Laws of Biology / Rules of Life

April 3, 2018

by James Kohl with No Comment Adaptations Cytosis Diseases & Disorders Ecology Light Energy Model Organisms Physics RNA Directed Subatomic What's in the News

Summary: Slide number 6 clearly states the “Levels of Biological Organization” that the “NSF’s 10 Big Ideas” finally places into the context of what has been known to all serious scientists for more than a century. Simply put, Hugo de Vries definition of mutation (sudden energy jumps) should never have been accepted as anything besides the claim of a biologically uninformed science idiot. Instead, the definition bastardized every aspect of what is now known about biophysically constrained viral latency and all epigenetically-effected biodiversity on Earth.
The epigenetic effects start with the creation of quantized energy as information carried in sunlight.
Understanding the Rules of Life: Predicting Phenotype

Rules of Life projects… may have these characteristics:

Addresses a fundamental question in the life sciences

Crosses different scales (spatial, temporal, levels of biological organization and complexity)

Generates results that will be broadly generalizable beyond the system under investigation, so that a rule can be formulated

Enables the forecasting or prediction of change in a biological system

The characteristics of the so-called “Rules of Life” were predicted in the context of Darwin’s “conditions of life,” and in What is Life? (1944)
Biologically uninformed science idiots took this claim from 1944 and placed it into the ridiculous context of mutation-driven evolution:

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

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

Kohl’s Laws of Biology

…summary of Kohl’s Laws of Biology: 1) Life is nutrient-dependent. See for review (J. V. Kohl, 2012; M. Lynch, 2007). The physiology of reproduction is pheromone-controlled. See for review (J. V. Kohl, 2013). In the context of nutrient-dependent epigenetically-effected human reproduction, it is clearer that the epigenetic effects of human pheromones integrate neuroendocrinology and behavior (J. V. Kohl, et al., 2001), which includes the neuroendocrinology of mammalian behavior associated with the development of sexual preferences (J.V. Kohl, 2007).

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.

M. Lynch (2007) is The frailty of adaptive hypotheses for the origins of organismal complexity

…emergent biological features such as complexity, modularity, and evolvability, all of which are current targets of considerable speculation, may be nothing more than indirect by-products of processes operating at lower levels of organization.

See for comparison: Evolutionary determinants of genome-wide nucleotide composition (2018) with senior author Michael Lynch
Reported as: Scientists explore mysteries behind diversity of DNA composition among species

…mutation drives the overall pattern, but selection for G’s and C’s over A’s and T’s boosts the genome content above the neutral mutational expectation.

Natural selection for energy-dependent codon optimality is the driving force that links the sun’s anti-entropic virucidal energy to biophysically constrained viral latency and all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans.
I reiterate:

“…selection for G’s and C’s over A’s and T’s boosts the genome content above the neutral mutational expectation.”

Selection is quantized energy-dependent and RNA-mediated. The energy comes from sunlight!
See also: Cytosis and Subatomic
See also: Human Pheromones: Linking Neuroendocrinology and Ethology (revisited) (2010)
Slide number 6 clearly states the “Levels of Biological Organization” that the “NSF’s 10 Big Ideas” finally places into the context of what has been known to all serious scientists for more than a century. Simply put, Hugo de Vries definition of mutation (sudden energy jumps) should never have been accepted as anything besides the claim of a biologically uninformed science idiot. Instead, the definition bastardized every aspect of what is now known about biophysically constrained viral latency and all epigenetically-effected biodiversity on Earth.
The epigenetic effects start with the creation of quantized energy as information carried in sunlight.

Part 3: Light-controlled cell biology (revisited)

March 23, 2018

by James Kohl with No Comment Adaptations Autophagy biophotonics Diseases & Disorders Ecology Light Energy Physics RNA Directed RNA interference RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA–Mediated Epigenetic Heredity Variations

Your cells are constantly being shed and replaced—so is your body ever completely refreshed? Does anything remain of the body that existed on Jan. 1, 2017? 2007? The day you were born? (video)

Out of Order: Undaunted

…as I prepared for this issue’s Special Report on Microbiomics (starting on page 19), I am stunned by what I am only starting to understand. That our individual existence as humans may only be 10 percent of what we see in the mirror—and that perhaps only 1 percent of our personal ecological genome is a human genome…

When you understand the concept of biophysically constrained energy-dependent ecology (Frohlich, 1968), you may begin to understand the difference between ecological adaptation and evolution. Each cell type represents biophysically constrained viral latency, not mutation-driven evolution.

Outside the context of energy-dependent RNA-mediated DNA repair (aka autophagy), no cell types exist. Bacteria become archaea and archaea become L-forms and the L-forms become non-cells. The energy for cell type differentiation comes from sunlight or from food. It is biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans.

Theorists used the term “de novo” in the context of de novo transcription and other aspects of energy-dependent cell type differentiation that they cannot explain with their ridiculous theories. For instance, David Sinclair has touted pseudoscientific nonsense until now.

He knows that the cell biology game, “Cytosis” for ages 10+ has exposed him to ridicule, and obviously won’t go away without a fight to maintain some scientific credibility.

State of art:
TDP-43 and FUS, two RNA-binding proteins (RBPs), have been recently the subject of increased attention due to their role in Amyotrophic Lateral Sclerosis (ALS) and FrontoTemporal Lobar Degeneration (FTLD). In non-pathological conditions, these proteins are mostly found in the nucleus where they participate to mRNA biogenesis and regulation of alternative splicing. However, TDP-43 and FUS are also present in the cytoplasm and they are able to shuttle from one compartment to another. TDP-43 and FUS notably participate in cytoplasmic functions such as mRNA transport and localized translation, which are of critical importance for neuron physiology. In neurons of ALS and FTLD patients, TDP-43 and FUS form insoluble cytoplasmic aggregates with fibrillar structure that can further spread the disease to other areas of the brain.

If this is the state of the art, was the information used to treat the late Stephen Hawking, or was he left to suffer unnecessarily until he died?

Scent of Eros

Posts tagged: pheromone-controlled