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.

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.

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.

Conceptual critique: Innateness vs the death gene (1)

February 14, 2018

by James Kohl with No Comment Adaptations Alternative Splicings Diseases & Disorders Ecology Model Organisms RNA Directed RNA interference RNA-directed DNA methylation RNA-mediated gene silencing RNA–Mediated Epigenetic Heredity Variations

Summary: The term innate is used in psychological explanations. The so-called explanations ignore facts about the light energy-dependent activation of endogenous substrates. The anti-entropic virucidal energy of sunlight links the endogenous substrates to biophysically constrained viral latency and healthy longevity via the physiology of reproduction in all living genera.

“Proximate mechanisms” and “evolution” are terms used by biologically uninformed theorists. That fact becomes perfectly clear in the context of The conceptual critique of innateness (paywalled)

One proposal is that innateness can be defined in terms of the biological property of environmental canalization. On this view, a trait is innate to the extent that it is developmentally buffered against a range of different environments. Another proposal is that innateness serves as an explanatory primitive for cognitive science. This view holds that there exist a sharp boundary between psychological and biological explanations and that to identify a trait as innate means that it falls into the latter explanatory domain.

For comparison to the sharp boundary between psychological and biological explanations, we eliminated the concept of innateness and claims about evolution from our 1996 Hormones and Behavior review of experience-dependent epigenetically- effected RNA-mediated cell type differentiation: From Fertilization to Adult Sexual Behavior.

See how our section on molecular epigenetics was linked from effects on hormones to the affects of hormones on behavior via alternative splicings of pre-mRNAs.

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…

Also, in an award-winning 2001 review, other co-authors helped to link energy-dependent top-down causation to biophysically constrained cause and effect via the affects of hormones on behavior. Epigenetic effects on hormones and affects on behavior are studied and integrated in the context of human ethology. See: Human pheromones: integrating neuroendocrinology and ethology

If you ignore the history of all published works on energy-dependent microRNA-mediated (aka pre-mRNA-mediated) top-down causation during the past two decades, you can continue to tout “evolution” as if it had any explanatory power. But it does not have any explanatory power whatsoever in the context of human ethology.

Simply put, “evolution” does not link epigenetic effects on hormones to the affect of hormones on behavior. Evolution, innate, and proximate mechanisms are terms used by biologically uninformed theorists whose ridicuous theories have no explanatory power.
See for comparison: Hormonal: The Hidden Intelligence of Hormones — How They Drive Desire, Shape Relationships, Influence Our Choices, and Make Us Wiser (Feb 13, 2018)
See for examples of explanatory power: pre mrna + alternative splicing and microRNA
Item: 1 of 69876 in today’s search at 9:23 AM Eastern Time A Genetic Network for Systemic RNA Silencing in Plants

Non-cell autonomous RNA silencing can spread from cell to cell and over long-distance in animals and plants.

That fact is commonly known among serious scientists. For comparison, pseudoscientists and other theorists also use the term “proximate mechanisms” outside the context of the links from the food energy-dependent non-cell autonomous RNA silencing and pheromone-controlled physiology of reproduction, which were obviously included in Darwin’s “conditions of life.” (Darwin’s “conditions of life” were bastardized by those who invented neo-Darwinian nonsense, and linked the nonsense to explanations of behavior in the context of human ethology.)

See for example: Jay R. Feierman is the antagonistic passive-aggressive moderator of the Human Ethology Yahoo Group.
After brief discussion of my claims in Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013), Jay R. Feierman reported this to the group:

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.

and this:

Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.

See for comparison: Small RNA pathways responsible for non-cell-autonomous regulation of plant reproduction (reported in the context of my “Sokalian Hoax” series (1-10).
K.I. Nonomura and others have since published EAT1 transcription factor, a non-cell-autonomous regulator of pollen production, activates meiotic small RNA biogenesis in rice anther tapetum (February 12, 2018)

ETERNAL TAPETUM1 (EAT1) is a basic-helix-loop-helix (bHLH) transcription factor indispensable for induction of programmed cell death (PCD) in postmeiotic anther tapetum, the somatic nursery for pollen production.

It links what organisms “eat” (get it?)to the physiology of pheromone-controlled reproduction in species from microbes to humans via the honeybee model organism and everything known about biophysically constrained viral latency. Theorists and other pseudoscientists, like Jay R. Feierman, must continue to live in fear that their nonsense will be exposed in the context of what might otherwise have become a culture war.
Instead, this group of Japanese researchers appears to have an unparalleled, albeit somewhat biophysically constrained, sense of humor. Sarcasm, for example, is often a humorous way to force pseudoscientists to recognize the facts they have ignored. It is somewhat the same as a rabbinical debate that starts with “You Fool!”
For example, You fool! The link from ETERNAL TAPETUM1 (EAT1) and/or what you eat to a basic biophysically constrained helix-loop-helix (bHLH) transcription factor and/or cell death can be placed into the context of how the death gene is activated by stress in all living genera.
See: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene
The reduced expression is caused by the virus-driven theft of quantized energy, which links nutrient stress and/or social stress from mutations to all pathology via the degradation of messenger RNA in species from archaea to humans.
Virus-mediated archaeal hecatomb in the deep seafloor

See for comparison: The extent of codon usage bias in human RNA viruses and its evolutionary origin (2003)

Revealing the determinants of codon usage bias is central to the understanding of factors governing viral evolution.

Molecular Clocks and the Puzzle of RNA Virus Origins (2003)

…in the case of the primate lentiviruses, amino acid residues that are highly variable in HIV are sometimes conserved in chimpanzee SIV (19), and this may have a significant effect on dating estimates.

A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder (2007)

The observation that irradiated combs from affected colonies can be repopulated with naive bees suggests that infection may contribute to CCD.

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.

Theorists have been repeatedly told told that there is no such thing as the emergence of the sun’s anti-entropic virucidal energy. They have also been repeatedly told there is no such thing as mutation-driven evolution. They have been warned that serious scientists have linked top-down causation to energy-dependent biophysically constrained viral latency. But, biologically uninformed theorists continue to ignore the facts about virus-driven pathology, and their ignorance will probably continue to cause the unnecessary suffering that leads to premature death, which may lead to the death of nearly everyone and everything on Earth.
Sudden emergence of human infections with H7N9 avian influenza A virus in Hubei province, central China (2018)

There have been five waves of H7N9 avian influenza virus (AIV) infection in humans since its initial emergence in China in 2013, posing a significant threat to public health. Hubei province was free local transmission during the first four waves of H7N9 AIV. However, multiple cases of human H7N9 infection were reported in Hubei during January 2017.

The emergence of influenza viruses has typically been constrained by ultraviolet light. This group of researchers recently presented their findings in that context.
Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases

This approach may help limit seasonal influenza epidemics, transmission of tuberculosis, as well as major pandemics.

See also: Conceptual critique: Innateness vs the death gene (2)

Cryo-EM: Linking spatial and conformational constraints

February 13, 2018

by James Kohl with No Comment Adaptations biophotonics Cytosis Diseases & Disorders Ecology Light Energy Model Organisms Nutrigenomics Physics RNA Directed RNA interference RNA-directed DNA methylation

On Darwin Day (2018) Carl Zimmer suggested use of the twitter hashtag #Istudyevolution to report whatever aspect of biology people were studying. For example, Richard Lenski reported that he studied adaptation in E. coli. When I told others that ecological adaptation is nutrient-dependent and pheromone-controlled in species from microbes to humans, he blocked me from seeing his comments. Evidently he did not want people to know that he had been studying ecological adaptation for more than 2 decades but reporting the adaptations in the context of neo-Darwinian theories about mutations and evolution. For further clarification of that fact see:
Cryo-electron tomography reveals that dynactin recruits a team of dyneins for processive motility

…the mechanisms responsible for increased transport activity are not well understood, largely owing to limited structural information. We used cryo-electron tomography (cryo-ET) to visualize the 3D structure of the MT-bound dynein–dynactin complex from Mus musculus and show that the dynactin–cargo adaptor complex binds two dimeric dyneins. This configuration imposes spatial and conformational constraints on both dynein dimers.

This spatial and conformational constraints were reported as: Microscopic chariots deliver molecules within our cells

This discovery was totally unexpected, and will change how this motor complex is represented in cell biology and biochemistry text books,” says Saikat Chowdhury, PhD, a TSRI research associate and co-first author of the study.

“There had been years of biophysical experiments and biochemical experiments, and it was always assumed that there was just one dynein molecule,” Lander adds.

Assuming there was just one dynein molecule is something that only a biologically uninformed theorist would do. An energy-dependent difference in two molecules is required for movement and for biophysical constraints on movement. For comparison, all discoveries that link energy-dependent changes from electrons to ecosystems were anticipated by Richard P. Feynman in his claims about Plenty of Room at the Bottom.He linked his claims about the size of letters in a code from atoms to ecosystems in the context of Food Energy and denigrated the works of all theorists in The key to science (Cornell, 1964)
See also McEwen et al., (1964) Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”
Everything known to serious scientists links cryo-ET and cryo-EM technology from ecological niche construction to socio-cognitive niche construction via food energy-dependent amino acid substitutions in the microtubules, which link differences in animal behavior to human consciousness.
See: Untangling Neurodegenerative Diseases using Cryo-Electron Microscopy
Everything known about prevention of all pathology starts with the creation of sunlight.
See: Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases

In conclusion, we have shown for the first time that very low doses of far-UVC light efficiently inactivate airborne viruses carried by aerosols. For example, a very low dose of 2 mJ/cm² of 222-nm light inactivates >95% of airborne H1N1 virus. Our results indicate that far-UVC light is a powerful and inexpensive approach for prevention and reduction of airborne viral infections without the human health hazards inherent with conventional germicidal UVC lamps. If these results are confirmed in other scenarios, it follows that the use of overhead very low level far-UVC light in public locations may represent a safe and efficient methodology for limiting the transmission and spread of airborne-mediated microbial diseases. Public locations such as hospitals, doctors’ offices, schools, airports and airplanes might be considered here. This approach may help limit seasonal influenza epidemics, transmission of tuberculosis, as well as major pandemics.

Reported as: Special UV light safely kills airborne flu virus, finds study

In the study, aerosolized H1N1 virus—a common strain of flu virus—was released into a test chamber and exposed to very low doses of 222 nm far-UVC light. A control group of aerosolized virus was not exposed to the UVC light. The far-UVC light efficiently inactivated the flu viruses, with about the same efficiency as conventional germicidal UV light.

They confirmed the fact that UV light biophysically constrains the degradation of messenger RNA that links mutations to all pathology.
See also: Photon-Mediated Quantum Gate between Two Neutral Atoms in an Optical Cavity

Quantum logic gates are fundamental building blocks of quantum computers. Their integration into quantum networks requires strong qubit coupling to network channels, as can be realized with neutral atoms and optical photons in cavity quantum electrodynamics. Here we demonstrate that the long-range interaction mediated by a flying photon performs a gate between two stationary atoms inside an optical cavity from which the photon is reflected. This single step executes the gate in $2 μ s$ . We show an entangling operation between the two atoms by generating a Bell state with 76(2)% fidelity. The gate also operates as a cnot. We demonstrate 74.1(1.6)% overlap between the observed and the ideal gate output, limited by the state preparation fidelity of 80.2(0.8)%. As the atoms are efficiently connected to a photonic channel, our gate paves the way towards quantum networking with multiqubit nodes and the distribution of entanglement in repeater-based long-distance quantum networks.

Reported as: Light controls two-atom quantum computation

This interaction is the basis for performing characteristic gate operations between the atoms, for example the operation as a CNOT gate or the generation of entanglement. The new method offers a variety of advantages: for example, the gate operations take place within microseconds which is an asset for quantum information processing.

Quantized energy is the information that must be biophysically constrained and transferred from hydrogen-atoms in DNA base pairs in solution. That fact seems to have escaped the attention of biologically uninformed pseudoscientists and most so-called science journalists. The pseudoscientists and other theorists linked the emergence of the energy to the evolution of all biodiversity outside the context of the physiology of reproduction and autophagy, which biophysically constrains viral latency.
See for comparison to what serious scientist have done:Experimental Evidence of Radiation Reaction in the Collision of a High-Intensity Laser Pulse with a Laser-Wakefield Accelerated Electron Beam

The dynamics of energetic particles in strong electromagnetic fields can be heavily influenced by the energy loss arising from the emission of radiation during acceleration, known as radiation reaction. When interacting with a high-energy electron beam, today’s lasers are sufficiently intense to explore the transition between the classical and quantum radiation reaction regimes. We present evidence of radiation reaction in the collision of an ultrarelativistic electron beam generated by laser-wakefield acceleration ( $ϵ > 500 MeV$ ) with an intense laser pulse ( $a_{0} > 10$ ). We measure an energy loss in the postcollision electron spectrum that is correlated with the detected signal of hard photons ( $γ$ rays), consistent with a quantum description of radiation reaction. The generated $γ$ rays have the highest energies yet reported from an all-optical inverse Compton scattering scheme, with critical energy $ϵ_{crit} > 30 MeV$ .

Reported as: Intense laser experiments provide first evidence that light can stop electrons

“One thing I always find so fascinating about this is that the electrons are stopped as effectively by this sheet of light, a fraction of a hair’s breadth thick, as by something like a millimetre of lead. That is extraordinary.”

The data from the experiment also agrees better with a theoretical model based on the principles of quantum electrodynamics, rather than Maxwell’s equations, potentially providing some of the first evidence of previously untested quantum models.

Effects of quantized energy as information cannot be defined in the context of equations, which is why physicists have traditionally been ridiculed for any attempt to explain energy-dependent top-down causation in the context of biophysically constrained healthy longevity.

All species on Earth exhibit an undefined, incalculable, innate ability to biophysically constrain energy-dependent viral latency. That ability is food energy-dependent and controlled by the physiology of reproduction. Food energy comes from sunlight, either directly or indirectly via plant grown and the creation of microRNAs in plants. Serious scientists know how to light the sun’s anti-entropic virucidal energy to DNA repair.
See: Watson–Crick Base Pairing Controls Excited-State Decay in Natural DNA (2014)
Reported as: Base-pairing protects DNA from UV damage

…the Watson-Crick base-pairing mechanism itself controls the dissipation of the absorbed UV energy. This contradicts the conventional wisdom, which holds that the base sequence within the same strand is responsible for the deactivation of excited states,” says Wolfgang Zinth.

Ultrafast deactivation pathways bestow photostability on nucleobases and hence preserve the structural integrity of DNA following absorption of ultraviolet (UV) radiation. One controversial recovery mechanism proposed to account for this photostability involves electron-driven proton transfer (EDPT) in Watson–Crick base pairs. The first direct observation is reported of the EDPT process after UV excitation of individual guanine–cytosine (G⋅C) Watson–Crick base pairs by ultrafast time-resolved UV/visible and mid-infrared spectroscopy. The formation of an intermediate biradical species (G[−H]⋅C[+H]) with a lifetime of 2.9 ps was tracked. The majority of these biradicals return to the original G⋅C Watson–Crick pairs, but up to 10 % of the initially excited molecules instead form a stable photoproduct G*⋅C* that has undergone double hydrogen-atom transfer. The observation of these sequential EDPT mechanisms across intermolecular hydrogen bonds confirms an important and long debated pathway for the deactivation of photoexcited base pairs, with possible implications for the UV photochemistry of DNA.

There is clear evidence that femtosecond blasts of UV light repair DNA in the context of energy-dependent changes in the microRNA/messenger RNA balance and autophagy, which protects all organized genomes from virus-driven energy theft and the degradation of messenger RNA.

The failure to integrate the Nobel Prize winning works of Ben Feringa (Chemisty 2016) and Yoshinori Ohsumi (Physiology or Medicine 2016) prevents theorists from linking what organisms eat to their pheromone-controlled physiology of reproduction in the context of Schrodinger’s claims in “What is Life?”(1944) and this claim by Roger Penrose in the reprint edition:

“How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?” (Roger Penrose 8 August 1991)

See also: From Fertilization to Adult Sexual Behavior In our section on molecular epigenetics, we wrote:

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…

The food energy that is linked from alternative splicing techniques of pre-mRNA to the chemistry of protein folding and the pheromone-controlled physiology of reproduction in all living genera seems to be largely ignored by those who are not Nobel Laureates.

It links the virus-driven theft of quantized energy from the degradation of messenger RNA to mutations and all pathology, and physicists cannot explain that fact with math and definitions. They tried with de Vries 1902 definition of mutations, and they have failed miserably ever since.

See: Amino acid–base interactions: a three-dimensional analysis of protein–DNA interactions at an atomic level (2001)

To assess whether there are universal rules that govern amino acid–base recognition, we investigate hydrogen bonds, van der Waals contacts and water-mediated bonds in 129 protein–DNA complex structures. DNA–backbone interactions are the most numerous, providing stability rather than specificity. For base interactions, there are significant base–amino acid type correlations, which can be rationalised by considering the stereochemistry of protein side chains and the base edges exposed in the DNA structure.

See also: Systematic prediction of DNA shape changes due to CpG methylation explains [quantized energy-dependent] epigenetic effects… (2018)
The effects of sunlight and quantum chemistry link energy-dependent fixation of RNA-mediated amino acid substitutions to the differentiation of all cell types in all living genera via the physiology of reproduction, which is controlled by pheromones in species from microbes to humans. Pheromones biophysically constrain viral latency in all animals that need to eat for their species to survive.

Cryo-EM technology predicts RNA-mediated DNA shape, which means the technology can be used to link the virus-driven degradation of messenger RNA from mutations to all pathology in the context of the games “Cytosis” and “Subatomic.”
When “Subatomic” is available, players will link what is known to all serious scientists who present during “Schrodinger at 75” to the overwhemling amount of pseudoscientific nonsense touted by theorists during the past 75 years.

Schrodinger linked the anti-entropic virucidal energy of sunlight to all biophysically constrained biodiversity via the physiology of reproduction in all plants and animals. Pseudoscientists decided to use mutations and natural selection instead of Darwin’s “conditions of life.” That is why pseudoscientists can — and soon may be — blamed for all extant pathology.

Subatomic: An Atom Building Board Game (Update #2)

Theorists failed to link subatomic particles to biophysically constrained viral latency via the “Virus Expansion” from “Cytosis.” That fact led to this admission of ignorance:

Microscopic chariots deliver molecules within our cells https://phys.org/news/2018-02-microscopic-chariots-molecules-cells.html

Excerpt: This discovery was totally unexpected, and will change how this motor complex is represented in cell biology and biochemistry text books,” says Saikat Chowdhury, PhD, a TSRI research associate and co-first author of the study.

“There had been years of biophysical experiments and biochemical experiments, and it was always assumed that there was just one dynein molecule,” Lander adds.

My comment: All the discoveries that have since linked energy-dependent changes from electrons to ecosystems were anticipated by Richard P. Feynman in his claims about “Plenty of Room at the Bottom.” Everything known to serious scientists links cryo-EM technology from ecological niche construction to socio-cognitive niche construction via food energy-dependent amino acid substitutions in the microtubules that link differences in animal behavior to human consciousness.

It will good to see “Subatomic” placed into the context of the admission that there are two dynein molecules. Others may begin to see the levels of complexity that must be represented in game play to prevent further assumptions based on ignorance of particle physics and energy transfer that biophysically constrains viral latency.

The fact that many people can readily learn more than most theoretical physicists have learned about subatomic particles and cell biology by playing games for fun is an exciting development for scientists and laypersons.

Magnus S. Magnusson wrote: James Kohl it [the Neil deGrasse Tyson meme] was not aimed at you, of course, understand that it is about the genera educational situation. BTW Einstein mostly missed biology and Hawking says the 21. century will be that of biology, which I also believe.”
The Icelandic atheist and hate monger, blocked me before I could comment further on Neil deGrasse Tyson’s overwhelming display of ignorance.
George FR Ellis, who co-authored with Stephen Hawking in the 60’s has already validated my model. See: Understanding and accounting for relational context is critical for social neuroscience

George F R Ellis This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics.

The Genius Games series from John Coveyou is the way forward. The games successfully link the creation of the sun’s anti-entropic virucidal energy from top-down causation to all biophysically constrained biodiversity via a model that links electrons to ecosystems.

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

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.

The tipping point (revisited): 68,000 publications

December 21, 2017

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy base editing biophotonics Cytosis Diseases & Disorders Ecology Human Pheromones Light Energy microRNA editing Model Organisms Neuronal Plasticity Nutrigenomics Pharmacogenomics 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 What's in the News

MicroRNA Items: 1 to 20 of 68011 (earlier today, on 12/21/17)

See for example: In Vitro Validation of miRNA-Mediated Gene Expression Linked to Drug Metabolism 12/20/17

The approaches described can be employed broadly for the validation of miRNA-mediated negative regulation of any gene. Determining miRNA-mediated regulation of enzymes and transporters affecting drug metabolism is a critical step in designing personalized therapy and for understanding the mechanisms responsible for variations in the responses to therapeutic agents.

The “…miRNA-mediated regulation of enzymes and transporters affecting drug metabolism…” links the National Microbiome Initiative to the Precision Medicine Initiative and to all healthy longevity or to all virus-driven pathology in all living genera via differences in energy as information.
For review, see: Energy as information and constrained endogenous RNA interference

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

For a historical perspective on what is known about energy-dependent RNA-mediated (aka microRNA-mediated) cell type differentiation, see:
The quantum / classical RNA-mediated ‘tipping point’ 3/26/15
The tipping point? 50, 000 publications 5/16/16
The tipping point? 50, 000 publications (2) 5/16/16
The tipping point? 50,000 publications (3) 5/17/16
The tipping point? 50,000 publications (4) 5/26/16
The tipping point? 50,000 publications (5) 7/27/16
The tipping point (revisited): 60,000 4/20/17
By May 16, 2016, the innate antiphage defense strategy was linked from quantum physics to classical physics by 50,000 publications that mentioned microRNAs. Nineteen months later, every aspect of the microRNA-mediated gene expression that had already been linked to drug metabolism attests to the fact that not all scientists have followed the extant literature.
Many scientists are still among the pseudoscientists who who failed to notice the most obvious links from the antiphage defense strategy to healthy longevity. Perhaps they were also too busy to notice the most obvious links from the virus-driven degradation of messenger RNA to the need for drug therapies.
If so, that may explain why the drug therapies have been largely ineffective. The drug therapies may be like vaccinations. They appear to link the virus-driven degradation of messenger RNA to more mutations, which clearly link the virus-driven theft of quantized energy to all pathology.
With more than 18,000 published works in the past 19 months, (8,000 in the past 8 months) it is time to again address the tipping point between quantum physics and classical physics in the context of food energy-dependent pheromone-controlled microRNA-mediated cell type differentiation via what is known about autophagy.
In the context of drug metabolism, the energy-dependent microRNA-mediated creation of enzymes was linked from the metabolism of food to all biodiversity on Earth via pheromone-controlled physiology of reproduction.
See for example page 19 of the sample report from Alpha Genomix that you can download as a pdf here. The food energy-dependent creation of the CYP enzymes protects our organized genome by biophysically constraining viral latency.

See for comparison: Our Top 17 in ’17: The Year in Science at PLOSBLOGS

…the far-reaching war on science being conducted by the Trump administration, an assault on facts which, as several of our bloggers have noted, constitutes a removal of scientific evidence from the formation and discussion of public policy and an evisceration of funding and communication of vital research in medical research and regulation, public health, climate, energy, agriculture and education.

The only war on science that I know about, is the one in which serious scientists are Combating Evolution to Fight Disease. To place that claim into the context of what has happened during 2017, see the retraction of this article.
Biomechanical Characteristics of Hand Coordination in Grasping Activities of Daily Living [retracted]
It was retracted because the authors mentioned the creator of the hand. The creation of the hand occurs only in the context of biophysically constrained viral latency.

See for comparison: Retraction Watch

In retrospect, we were totally blinded by our belief [in our findings]…we were not as careful or rigorous as we should have been (and as Tivoli was) in interpreting these experiments.

Where else besides PLOS have you seen a retraction for the mention of a creator? Where did PLOS report on the retraction for misrepresentations in “Nature Chemistry?” Who still believes that microRNA and messenger RNAs created each other so that they could automagically constrain viral latency?
Who else besides PLOS is waging a far-reaching war on science?
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems 4/10/14

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

Obama Advisers Urge Action Against CRISPR Bioterror Threat 11/17/16

Scientific advisers to President Obama warn that the U.S. urgently needs a new biodefense strategy and should regularly brief President-elect Donald Trump on the dangers posed by new technologies like CRISPR, gene therapy, and synthetic DNA, which they say could be coöpted by terrorists.

See for comparison: 2017 Global Infectious Diseases Threats to the United States 12/22/16

Flu. Influenza remains one of the greatest threats to the US population killing on average 3,000-49,000 Americans annually. People at the greatest risk of severe flu and death are pregnant women, residents of long-term care facilities, the very old (adults over the age of 65), the very young (children less than 2), Native American populations, and those with underlying chronic conditions such as asthma, COPD, heart disease, obesity, and other conditions. Timely vaccination remains the most proven and effective way to avoid serious injury from influenza.

The new Trump Administration will face a formidable array of global and indigenous infectious disease threats in 2017. A Global Health Security Agenda will help provide a framework for tackling some of these tough issues, but enhanced efforts will be needed to prevent new epidemics, especially from vector-borne and zoonotic neglected tropical diseases, measles, and the ever-constant threats from AMR and flu.

The biggest threat that the Trump administration has faced in the first year is the fake news. The most recent example accused him of censorship at the CDC for his director’s efforts to biophysically constrain energy-dependent viral latency. The CDC director’s efforts to help others with budget concerns were linked to censorship, and the President of the United States was compared to Hitler. Wake up and “Remember the Alamo.”
SARCASM ALERT: No, that was a different war. Wake up and remember the Manhattan Project, which also linked censorship about energy to the winning of a war.

From base editing to RNA editing (4)

November 1, 2017

by James Kohl with No Comment Adaptations Alternative Splicings base editing Cytosis Diseases & Disorders Ecology Human Pheromones Light Energy Model Organisms Neuronal Plasticity Nutrigenomics Pharmacogenomics 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Predicting who wins the 2017 Nobel Prizes (2)

October 2, 2017

by James Kohl with No Comment Adaptations Diseases & Disorders Ecology Model Organisms RNA Directed RNA interference RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA–Mediated Epigenetic Heredity Variations What's in the News

Summary: Endogenous RNA interference is the energy-dependent epigenetic link from the physiology of pheromone-controlled reproduction to biophysically constrained viral latency. The stress-linked virus-driven degradation of messenger RNA has been linked to all pathology.
Three Americans win Nobel medicine prize for body rhythm work [But they failed to link Americanism to Creationism]

I predicted that Wen Zhou would win for linking the energy-dependent creation of G protein-coupled receptors to all biodiversity via olfaction and the space-time continuum in the context of RNA-mediated cell type differentiation via the physiology of pheromone-controlled reproduction. See: Olfaction Warps Visual Time Perception.
She returned to China after training in the United States of America, but is a good example of someone who appears to practice Americanism, which is an ideology that appears to be integrated into her research. I do not know what people in China refer to in the context of this ideology.

In the words of Theodore Roosevelt, “Americanism is a question of spirit, conviction, and purpose, not of creed or birthplace.”^[3]

After Ben Feringa (Chemistry/chirality) and Yoshinora Ohsumi (Physiology or Medicine/autophagy) won last year, I thought that all gene-centric nonsense would be eliminated. It became perfectly clear that energy-dependent changes in chirality must be linked to autophagy, which protects all organized genomes from the virus-driven degradation of messenger RNA.
Instead, see:

Excerpt 1) The awardees’ work stems back to 1984, when Rosbash and Hall, who was then also at Brandeis, along with Young isolated the “period gene” in fruit flies. Hall and Rosbash found that a protein encoded by the gene accumulated during the night and degraded during daytime. A decade later, Young discovered another “clock gene.”

Excerpt 2) “The paradigm-shifting discoveries by the laureates established key mechanisms for the biological clock,” the Nobel Assembly said in its prize statement.

See for comparison: The Nobel Prize in Physiology or Medicine 1973 Karl von Frisch, Konrad Lorenz and Nikolaas Tinbergen

for their discoveries concerning organization and elicitation of individual and social behaviour patterns.

The organization and elicitation of individual social patterns of behavior is energy-dependent and it links what organisms eat to the metabolism that links the energy to the physiology of pheromone-controlled reproduction in species from microbes to humans.
Since 1973, and especially during the past 13 years, there has not been a gene-centric theory that has successful been linked to a paradigm shift. For example, all paradigm-shifting Nobel Prizes in Physiology or Medicine during the past 13 years have linked the energy-dependent creation of ATP and the creation of messenger RNA to protection from the virus-driven energy theft that serious scientists have linked from the degradation of messenger RNA to all pathology.
See for examples:
2016: Yoshinori Ohsumi of Japan for his work on autophagy—a process whereby cells “eat themselves”—which when disrupted can cause Parkinson’s and diabetes.
2015: William Campbell (US citizen born in Ireland) and Satoshi Omura (Japan), Tu Youyou (China) for unlocking treatments for malaria and roundworm.
2014: John O’Keefe (Britain, US), Edvard I. Moser and May-Britt Moser (Norway) for discovering how the brain navigates with an “inner GPS”.
2013: Thomas C. Suedhof (US citizen born in Germany), James E. Rothman and Randy W. Schekman (US) for work on how the cell organises its transport system.
2012: Shinya Yamanaka (Japan) and John B. Gurdon (Britain) for discoveries showing how adult cells can be transformed back into stem cells.
2011: Bruce Beutler (US), Jules Hoffmann (French citizen born in Luxembourg) and Ralph Steinman (Canada) for work on the body’s immune system.
2010: Robert G. Edwards (Britain) for the development of in-vitro fertilisation.
2009: Elizabeth Blackburn (Australia-US), Carol Greider and Jack Szostak (US) for discovering how chromosomes are protected by telomeres, a key factor in the ageing process.
2008: Harald zur Hausen (Germany), Francoise Barre-Sinoussi and Luc Montagnier (France) for work on the viruses causing cervical cancer and AIDS.
2007 Mario R. Capecchi, Sir Martin J. Evans and Oliver Smithies for their discoveries of principles for introducing specific gene modifications in mice by the use of embryonic stem cells.
2006 Andrew Z. Fire and Craig C. Mello for their discovery of RNA interference – gene silencing by double-stranded RNA.
2005 Barry J. Marshall and J. Robin Warren for their discovery of the bacterium Helicobacter pylori and its role in gastritis and peptic ulcer disease.
2004 Richard Axel (US) and Linda Buck (US) for their discoveries of “odorant receptors and the organization of the olfactory system.
Endogenous RNA interference is the energy-dependent epigenetic link from the physiology of pheromone-controlled reproduction to biophysically constrained viral latency. The stress-linked virus-driven degradation of messenger RNA has been linked to all pathology.
Addendum 1)
This morning I spoke with a 10-year veteran who had served in Iraq. He was not happy with the treatment for PTSD that he was receiving from the VA because he and his wife know he is getting worse (e.g., hyper-vigilance and more nightmares).

He has a 20% disability and my antagonists are causing it to get worse with their claims that my life’s works are “bullspit” and/or that “nobody cares.”

How can anyone convince a veteran that people care at a time when most will not take the time to watch a short video like this one? Superbugs, Bacteriophages and Phage Therapy: An Interview with James Kohl Published on 17 May 2017

See for comparison:3/09/17 Jay Feierman: One can’t have Darwinian evolution by natural selection without either “random” mutations or directional selection. They are both necessary, proximate, contributing causes for genes and the proteins they code for changing in frequency over time in a population and by which the population becomes adaptively configured to the current environment.

Adaptations are food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans.The claim that populations are adaptively configured are nothing more than pseudoscientific nonsense.

If you let our veterans, as individuals, continue to think they are less than human because a mutation or something else causes their failure to adapt to the challenges of life after returning from military service overseas, how will you convince yourself that you are not contributing to the death rate by suicide?

Addendum 2) Las Vegas Shooting: Live Updates (with video)

Other lawmakers woke up to the news and offered thoughts and prayers. Governor Brian Sandoval of Nevada called the shooting a “heinous act of violence.”

All heinous acts of violence are caused by the virus-driven degradation of messenger RNA, not by the natural selection for mutations as claimed in Mutation-Driven Evolution

(2) Natural selection is for saving advantageous mutations and eliminating harmful mutations. Selective advantage of the mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation.

See for comparison: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

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

Energy-dependent physical and biophysical constraints (8)

July 27, 2017

by James Kohl with One Comment Adaptations Alternative Splicings biophotonics Cytosis Diseases & Disorders Ecology Human Brain Human Pheromones Model Organisms Neuronal Plasticity Nutrigenomics Physics RNA Directed RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA–Mediated Epigenetic Heredity Variations

Summary: The role of vitamin C in the treatment of pain: new insights links what is known about the “superfood” Spirulina (blue-green algae), which is grown in marine and freshwater environments, to the stability of all organized genomes via its biological activities, such as antioxidant, anti-diabetic, cholesterol-controlling and insulin resistance effects. The biological activities are energy-dependent and they link the anti-entropic virucidal energy of sunlight to all biodiversity via the pheromone-controlled physiology of reproduction and microRNAs in plants and animals.
For example, see: Hypothalamic stem cells control ageing speed partly through exosomal miRNAs

Energy-dependent physical and biophysical constraints (7)

7/26/17 Brain’s stem cells slow ageing in mice

…these cells may have a role in regulating the neurons that release a hormone called GnRH, which is secreted by the hypothalamus and is associated with ageing. Imai would also like to know whether the microRNAs from the cells can pass into the bloodstream, which would carry them throughout the body.

I would like to know why Shin-ichiro Imai, who studies ageing at Washington University in St Louis, Missouri, claims to know nothing about food energy-dependent pheromone-controlled RNA-mediated biophysically constrained viral latency, which prevents the degradation of messenger RNA. I expect that anyone who studies aging to learn that the virus-driven degradation of messenger RNA links mutations to all pathology via effects on all cell types in all individuals of all living genera. Perhaps Shin-ichiro Imai, and others who have not learned anything about energy-dependent cell type differentiation can play the game “Cytosis” when it is released in September, 2017. Or, perhaps they all are neo-Darwinian theorists who prefer not to examine any of the experimental evidence that links energy-dependent microRNAs to healthy longevity and virus-driven energy theft to all pathology.

See for 63,127 examples: MicroRNA
See for comparison: The NAD World 2.0: the importance of the inter-tissue communication mediated by NAMPT/NAD+/SIRT1 in mammalian aging and longevity control by Shin-ichiro Imai

See also: 7/27/11 via my Pheromones Research FB page and Pheromones.com
This is very technical, but begins to address the role of pheromones in anti-aging medicine, particularly with regard to neurodegenerative diseases. Pheromones are used to increase neurogenesis in the area of the brain that is responsible for learning and memory.

Jo Rockafellor Is this the stuff you created James?

James Kohl I have nothing to do with the patent, but am responsible for the concept and first linking pheromones, luteinizing hormone, and neurodegenerative disease associated with aging.

Coleen Powell Keep searching for a cure!

7/27/17 James Kohl The cure is treatment with food energy-dependent microRNAs. See:Hypothalamic stem cells control ageing speed partly through exosomal miRNAs. Liberals hate that fact because it refutes their ridiculous theories about the emergence of energy and the evolution of all biodiversity via mutations and natural selection. They would rather watch people like Dick suffer and die prematurely from cancer than admit that they are biologically uninformed science idiots. (idiot: someone with no professional expertise)
Without labeling them, Feynman claimed that liberals were examples of human idiocy. He failed to differentiate between the beliefs of conservatives and liberals, but those differences have become perfectly clear.
Even those who have learned nothing about “The character of Physical Law” understand that all organisms must eat. That is why Feynman complained about the different units that are used to measure the single concept of energy. The energy that sustains life and all biodiversity via the physiology of reproduction comes from food.
Reported by James Kohl on 7/27/14 Study shows epigenetic changes can drive cancer
“Potential applications of this novel mouse model include the testing of targeted epigenetic therapies for prevention and treatment of human cancer.” http://www.jci.org/articles/view/76507
“Our straightforward approach to epigenetic engineering should be useful in testing the causal role of other epigenetic alterations implicated in carcinogenesis, and broadly applicable toward elucidating epigenetic etiology in a wide range of diseases.”
Their straightforward approach confirms that cell type differentiation is nutrient-dependent and pheromone-controlled in species from microbes to man, which refutes any aspect of mutation-initiated natural selection in the context of the evolution of biodiversity.

Ecological variation in the nutrient supply leads to ecological adaptations via the pheromone-controlled physiology of reproduction. Evolutionary theory should have been replaced by biological facts more than 18 years ago. We could have avoided the past 18 years of pseudoscientific nonsense about mutations and cancer and learned more about its origins, prevention, and effective treatments.
7/27/15 Reported by James Kohl
New Technology Lets Scientists Easily Rewrite Living Organisms’ Genetic Code
[For scientists to rewrite the genetic code, they must know how it was created.] 7/22/15 Sexuality is fluid – it’s time to get past ‘born this way’ reported 7/27/15 by James Kohl
[For people to get past the ‘born this way’ pseudoscientific nonsense, they must learn how energy-dependent RNA-mediated cell type differentiation occurs in the context of the nutrient-dependent pheromone-controlled physiology of reproduction in species from microbes to humans.] Bacterial Hunger Games reported 7/27/15 by James Kohl
[Survivors find enough food to reproduce in the context of quorum sensing and the weekend resurrection of the bacterial flagellum, which was reported in P. fluorescens.] Go ahead, be sarcastic: Research uncovers creative benefits in using sarcasm when people trust each other reported 7/27/15 by James Kohl
[I’ve tried presenting facts; using examples of top-down causation, and discussing the facts and examples with biologically uninformed science idiots after sarcasm did not work.
Study identifies ‘major player’ in skin cancer genes reported 7/27/15 by James Kohl
[The virus-driven degradation of messenger RNA causes all pathology] Honeybees Show Evidence of Insecticides reported 7/27/15 by James Kohl
[I used the honeybee model organism as an example of nutrient-dependent pheromone-controlled RNA-mediated cell type differentiation in Nutrient-dependent/pheromone-controlled adaptive evolution: a model
CONCLUSION:
An environmental drive evolved from that of nutrient ingestion in unicellular organisms to that of pheromone-controlled socialization in insects. In mammals, food odors and pheromones cause changes in hormones such as LH, which has developmental affects on pheromone-controlled sexual behavior in nutrient-dependent reproductively fit individuals across species of vertebrates.]

Addendum: Environmental drives are food energy-dependent and pheromone-controlled in the context of feedback loops linked from supercoiled DNA to chromosomal rearrangements and all biodiversity. I used the term evolved to get past the ignorance of any potential reviewers who would most likely be theorists. In “The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002) we used the term mutation for the same reason. The editor at Continuum rightfully insisted.

The CRISPR craze: genome editing technologies poised to revolutionize medicine and industry reported 7/27/15 by James Kohl
[The CRISPR craze of using viruses to edit organized genomes is the example of more ignorance in medicine and industry than most people can comprehend.] See also: CRISPR–Cas systems exploit viral DNA injection to establish and maintain adaptive immunity

The acquisition of new spacer sequences from foreign DNA elements, also known as adaptation, is a hallmark of the CRISPR–Cas immune response1.

Any intelligent scientist would ask where the spacer sequences came from and learn that the spacers are food energy-dependent microRNAs that prevent the virus-driven degradation of messenger RNA and all pathology in all genera.
See Energy-dependent physical and biophysical constraints (9) (in prep) for examples of those who might otherwise seem to be intelligent scientists.