2018 March for Science vs microRNAs (2)

April 18, 2018

by James Kohl with No Comment Adaptations Autophagy biophotonics Cytosis Diseases & Disorders Ecology Light Energy microRNA editing Model Organisms Physics RNA Directed RNA interference RNA-directed DNA methylation RNA–Mediated Epigenetic Heredity

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

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

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

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

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

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

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

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

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

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

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

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

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

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

NSF's parrot and other parrots

April 3, 2018

by James Kohl with No Comment Adaptations biophotonics Diseases & Disorders Ecology Light Energy Physics Subatomic Variations

Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

“Isolated thymus nuclei transport amino acids into an intranuclear pool by a process which seems to depend on energy from nuclear ATP synthesis (20).”

The energy must be biophysically constrained: Long-range coherence and energy storage in biological systems (1968)
Human Pheromones: Linking Neuroendocrinology and Ethology (revisited) (2010)
Slide # 6 attests to the fact that the levels of biological organization have been known to all serious scientists for more than 50 years.
See for comparison: NSF’s Big Ideas: Understanding the Rules of Life and The Quantum Leap

Thursday, April 12, 2018 at 2-3 pm ET

Recently the National Science Foundation unveiled a set of “Big Ideas” that are bold, long-term research and process ideas that all scientists should be aware of if they seek funding opportunities for their research.

For instance, a half-century after the discovery of the double helix, new DNA sequencing methods began our feverish race towards more and more data on the linear sequences of genomes, from microorganisms to humans. In 2018 there is potential uncover deeper codes embedded in DNA—those involving non-Watson-Crick bases like the epigenome and non-Watson-Crick folding like G-quadruplexes—in order to fully translate the code into a cellular symphony.

In addition to the former research opportunity, many of today’s technologies like lasers, computers, GPS, and LEDs rely on the interaction of matter and energy at extremely small and discrete dimensions. That said how do we control the behavior of particles and energy at dimensions at least a million times smaller than the width of a human hair? There could be great impact with a new approach toward spectroscopic investigations with non classical light, where a new view of electronic states may be possible with the consideration of entangled states of light.

Join Angela Wilson of NSF, Cynthia Burrows of the University of Utah, Theodore Goodson of the University of Michigan, and Glenn Ruskin of ACS for an introduction of two of the most impactful “Big Ideas” as well as an overview of this innovative NSF program that will advance prosperity, security, health, and well-being in the United States.

What You Will Learn

What are the National Science Foundation’s “Big Ideas” and how to learn more about funding opportunities
How a combination of methylation and oxidation of DNA bases can ‘write’ markers onto the genome that are later ‘read’ and ‘erased’
Why oxidative stress, a normal process in cells responding to their environment, sets up a DNA response that can be considered not just as ‘DNA damage’ but also as a form of epigenetics
How guanine-rich sequences may be positioned in the genome to act as sensors of oxidative stress by impacting the folding of G-quadruplexes
What are entangled states of light and why they can be used to probe electronic processes in molecules
Why Quantum entangled processes may play a role in our understanding of biological processes
What are some of the new spectroscopic methods being developed to probe molecules with non classical states of light

A mental health problem at the highest level (3)

February 8, 2018

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

John Hewitt wrote:

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

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

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

For comparison, Roger M. Pearlman wrote:

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

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

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

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

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

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

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

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

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

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

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

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

See: What is Life? (1944)

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

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

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

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

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

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

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

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

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

The MicroRNAome Strikes Back: A Sokalian hoax (3)

January 24, 2018

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

One way to recognize a Sokalian hoax is to determine whether the claims can be linked from gravity or from the speed of light on contact with water to feedback loops that biophysically constrain viral latency and all biodiversity in all living genera.

See: Feedback loops link odor and pheromone signaling with reproduction

See for comparison: Chiromagnetic nanoparticles and gels

Reported as: Nanoparticle gel controls twisted light with magnetism

The trick, the researchers found, was to twist the nanoparticles themselves by coating them with amino acids.

What kind of carefully-designed “trick” is that? Could it be linked by serious scientists to the prevention of all pathology?

See:

Energy-dependent light-modulated reversible chemical changes in the chirality of the nanoparticles produces is linked to a heightened sensitivity to magnetism that strengthens the interactions with circularly polarized light. That suggests the next thing that theorists will learn about is achiral glycine in position 6 of the gonadotropin releasing hormone decapeptide. Achiral glycine is the food energy-dependent pheromone-controlled RNA-mediated amino acid substitution that stabilizes all organized genomes in vertebrates that supposedly evolved during the past 600 million years.

See: Evolution of Constrained Gonadotropin-releasing Hormone Ligand Conformation and Receptor Selectivity

These findings indicate that the substitution of glycine for a chiral amino acid in GnRH during evolution allows a more constrained conformation for receptor binding and that this subtle single amino acid substitution in a site remote from the ligand functional domains has marked effects on its structure and activity.

In the context of food and pheromones the “nanoparticles” are microRNAs that link what organisms eat from the pheromone-controlled physiology of reproduction to all biophysically constrained biodiversity via the anti-entropic virucidal effects of sunlight.

There is a model for that:

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.

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.

If serious scientists are right about the protection of organized genomes that has repeatedly been place into the context of feedback loops and autophagy, which protects all orgnanized genomes from virus-driven degradation of their messenger RNA, the recent series of Abcam buyouts can readily be explained.

See: Abcam acquires rights to over 700 Roche products in new licensing deal

The deal marks the latest in a series of moves by Abcam to expand its portfolio, which now includes more than 120,000 products. Since 2011, the biotech has made a number of acquisitions to this end, including AxioMx, Ascent Scientific, Epitomics, Firefly Bioworks and MitoSciences.

This is a fitting end to my efforts to inform others about the amount of pseudoscientific nonsense they have been subjected to during the past few decades. The discovery of the death gene was made by serious scientists working for Abcam in the early 1990s. It was linked from the discovery of pre-mRNAs (now called microRNAs and many other things) and prevention of cancer cell type proliferation in glioblastoma.

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

It is time for anyone still touting the pseudoscientific nonsense about mutation-driven evolution to prepare for this conference. Mechanisms of Recombination conference

The first preparatory step should be to admit that your commercial interests or your interest in pursuing an academic career in the academic swamp prevented you from examining truth or telling it to help stop the unnecessary suffering and premature death of millions. The next step should be to find a place to hide until all other pseudoscientists proclaim that evolution is ecological adaptation and that they have always known that.

See for comparison: Study finds convergent evolution of gene regulation in humans and mice January 18, 2018

Organisms that aren’t closely related may evolve similar traits as they adapt to similar challenges. It’s called convergent evolution…

No, ecological adaptation is not called convergent evolution.

Legionella pneumophila RpoS (LpRpoS), an alternative sigma factor of RNA polymerase (RNAP), is essential for virulence and stress resistance. To investigate the mechanism of RpoS in the intracellular pathogen L. pneumophila, we determined the high-resolution crystal structure of the LpRpoS 95–195 containing a partial region 1.2 and region 2. The structure of LpRpoS 95–195 reveals that the conserved residues are critical for promoter melting, DNA and core RNAP binding. The differences in regulatory factor binding site between Escherichia coli RpoS and LpRpoS suggest that LpRpoS may employ a distinct mechanism to recruit alternative regulatory factors controlling transcription initiation.

Compare the claims about the “alternative sigma factor of RNA polymerase” and virulence or stress resistance in the context of what is known about food energy-dependent microRNA-mediated biophysically constrained viral latency and healthy longevity.

microRNA Items: 1 to 20 of 69027

See also: The Postmodernism Generator web page (generates a random postmodernist article each time loaded)

Via the use of terms for microRNA that have bastardized the concept of energy-dependent biophysically constrained viral latency, you might be able to create a Postmodernism Generator for pseudoscientists who do not want anyone to know that Abcam applications of current technology will help to prevent or effectively treat activation of your death gene.

At a time when all food energy-dependent pheromone-controlled biodiversity has clearly been linked from the speed of light on contact with water to biophysically constrained viral latency in all genera, what excuse is left for the ignorance of theorists who have never examined the facts in published works like these:

Virus-mediated archaeal hecatomb in the deep seafloor

Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

New Testament Book Cover Refutes Theistic Evolution

July 31, 2017

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

Goats, bookworms, a monk’s kiss: Biologists reveal the hidden history of ancient gospels

Collins already had developed a method to identify ancient species by differences in the amino acid sequences of collagen and other proteins preserved in fossils.

See: Protein power by Robert F. Service

…methods to sequence amino acids lag behind DNA sequencing.

The report of 300 million year old proteins is based on ridiculous theories that failed to include what was known about food energy-dependent RNA-mediated fixation of amino acid substitutions.
Natural selection for energy-dependent codon optimality links the pheromone-controlled fixation of the substitutions to cell type differentiation in all individuals of all living genera.
Collins has since used the method he developed to recover amino acid sequences that reveal which animal skin was used for the leather cover for the Gospel of Luke.

Collins so-called revelation about the species-specificity of amino acid sequences was reported in Dobzhansky (1964) and again in 1973.

Pseudoscientists have ignored this fact:

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).” — Dobzhansky (1973)

The sequences of amino acids link what animals eat to the food energy-dependent pheromone-controlled morphological and behavioral biodiversity manifested in every species on Earth. See: Feedback loops link odor and pheromone signaling with reproduction

See also: Cytosis: A Cell Biology Board Game A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

The energy-dependent de novo creation of the sense of smell links food odors and natural selection for codon optimality to the physiology of reproduction. Feedback loops link the sense of smell in bacteria to all biodiversity via the pheromone-controlled physiology of reproduction.

Metaphorically, the sense of smell is like a time machine that links our experiences from the past to our behaviors throughout life. Experimental evidence of biologically-based cause and effect links the creation of the sense of smell to representations of food energy-dependent pheromone-controlled biodiversity in invertebrates to vertebrates. The fact that bookworms are invertebrates has aroused interest in the context of the Gospel of Luke.

Goats, bookworms, a monk’s kiss: Biologists reveal the hidden history of ancient gospels (revisited)

Others were more interested in the bookworms. Hedges announced that the wormholes he measured in the Gospel of Luke were 1.3 millimeters in diameter, suggesting that they were made by Anobium punctatum, a northern European beetle. That would confirm that the book was made in the United Kingdom or northern Europe, rather than in southern Europe. The DNA of bookworms “can provide clues as to when and where objects such as books originated and were transported,” Hedges says.

The energy-dependent creation of RNA-mediated amino acid substitutions in different species links experimental evidence of creation to the Dawn of Creation.

The New Testament Book Cover provides experimental evidence of how our visual perception of mass and energy is linked to the space-time continuum via olfaction and representations in Biblical Genesis that link energy as information at the “Dawn of Creation” for comparison to claims and theories about the emergence of energy and the evolution of all biodiversity.

See also: Researchers may have solved origin-of-life conundrum by Robert F. Service

… a pair of simple compounds, which would have been abundant on early Earth, can give rise to a network of simple reactions that produce the three major classes of biomolecules—nucleic acids, amino acids, and lipids—needed for the earliest form of life to get its start.

The origin of life is energy-dependent and RNA-mediated. Robert F. Service seems to be perfectly poised to prevent the dissemination of accurate information about how the virus-driven degradation of messenger RNA is linked from mutations to all pathology.
He has failed to link the energy-dependent creation of nucleic acids, amino acids, and lipids to the creation of the innate immune system and the pheromone-controlled physiology of reproduction in all living genera, which protects all organized genomes from the virus-driven energy theft that links mutations to all pathology.
Simply put, in the context of the Gospel of Luke, Robert F. Service has failed to link any aspect of biologically-based cause and effect from amino acid substitutions to biodiversity via supercoiled DNA.

That may explain why on 2/17/16, I received a message from Bob Grant who claimed to moderate reader comments on posts at www.the-scientist.com.

He claimed that many of my posts were off-topic and excessively long, and asked me to limit both the length and the focus of my comments in the future. He warned “If you continue to post long, rambling, or incoherent comments, I’ll be forced to bar you from our discussion board, something I do not want to do.”

I’ve been banned from many discussions, and consistently see why I am banned. Discussions of pseudoscientific nonsense prevails. For example, see:

First Support for a Physics Theory of Life Thanks to Oleksander Savsunenko for bringing this to my attention.

Take chemistry, add energy, get life. The first tests of Jeremy England’s provocative origin-of-life hypothesis are in, and they appear to show how order can arise from nothing.

My comment to Quanta Magazine

See for comparison: Olfaction Warps Visual Time Perception https://www.ncbi.nlm.nih.gov/pubmed/28334302

They link the energy-dependent creation of the sense of smell in bacteria to our visual perception of mass and energy in the context of the space-time continuum and everything known to serious scientists about RNA-mediated cell type differentiation via the physiology of reproduction.

Compared to the claims of Jeremy England, they start with Darwin’s food energy-dependent “conditions of life.”

Richard Feynman commented on the “conditions of life” and linked Jeremy England’s claims to examples of “human idiocy.” No one will complain that Jeremy England is an idiot (i.e., someone with no professional expertise), but everyone should remember that he has no professional expertise that can be linked to biologically-based top-down causation.

See: Food energy https://www.youtube.com/watch?v=roX2NXDUTsM
Richard Feynman, complains about all the different units that are used to measure the single concept of Energy.

Re: “Take chemistry, add energy, get life.” But do not tell a serious scientist about your theory.
And, do not expect those who moderate discussions to understand anything a serious scientist claims.
My follow-up to Bob Grant, who did not reply:

I am left with this impression.

I could respond to Roy Niles’ comment by linking virus-perturbed protein folding chemistry from loss of olfactory receptor genes to pathology in species from nematodes to humans. But, you might ban me.

See: Neuroscience of Early-Life Learning in C. elegans

The information comes from Cori Bargmann’s group, and she married Richard Axel, who shared the 2004 Nobel prize in Medicine with Linda Buck. Linda Buck extended our 1996 Hormones and Behavior review of RNA-mediated cell type differentiation across species from microbes to man when she co-authored: Feedback loops link odor and pheromone signaling with reproduction



				Feedback loops link odor and pheromone signaling with re… Cell. 2005 Nov 18;123(4):683-95. Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov’t

				View on www.ncbi.nlm.nih.gov	Preview by Yahoo

I know a few others who have since linked viruses to perturbed thermodynamic cycles of RNA-mediated protein folding chemistry via amino acid substitutions but you’re not likely to be hearing from them, either. Eugene Daev and Anna Di Cosmo are among those who people like Roy Niles are indirectly responsible for censoring. Simply put anyone who understood our claims in the section on molecular epigenetics from our 1996 review, has made progress akin to the progress of my mentor, Bruce McEwen, whose group just linked a single nutrient-dependent RNA-mediated amino acid substitution from stress to life history transitions in human behavior via the mouse model and BDNF Val66Met. Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity

From Fertilization to Adult Sexual Behavior



				Pacific Center for Sex and Society: From Fertilization t… REFERENCES Adler, B. K., and Hajduk, S.L. (1994). Mechanisms and origins of RNA editing. Curr. Opin. Genet. Dev. 4, 316-322. Anderson, D. K., Fleming, D. E., Rh…

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Most polymaths live in a world of their own because others don’t want to learn enough to catch up, and the polymaths are too far ahead to explain what they have known for several decades.

A 6-hour long conversation with Bruce McEwen in 1991 led to my breakfast conversation in 1995 with Gene Garfield, which is when he learned enough about cell type differentiation from me and his octogenarian friend “Bill” Turner, to comment on my book in the year it was published. Greg Bear linked the information from my works to his stories about the evolution of a new human sub-species. Evolution rising from the grave; Living with the Neanderthals

I’m not sure if “The Scientist” will help others continue to move forward if you think my comments are off topic — and ban me when I try to elaborate on the link to the topic of RNA-mediated cell type differentiation for comparison to the thoughts of others about mutation-driven evolution. I lost any linear thinking skills I might have had before writing the book, and without the help of my co-author — it wouldn’t have made sense even to Gene.

Thanks for the opportunity to vent my frustrations,

James V. Kohl

Medical laboratory scientist (ASCP)
Independent researcher

http://rna-mediated.com/

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 (5)

July 26, 2017

by James Kohl with One Comment Adaptations Cytosis Diseases & Disorders Ecology Human Pheromones Model Organisms Neuronal Plasticity Nutrigenomics Physics RNA Directed RNA interference RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression Variations

Summary: Emmy Noethe’s theorems were developed in the early 1900’s. Richard Feynman inadvertently or purposefully alluded to them as examples of human idiocy.
Discover Magazine resurrected the examples of human idiocy in a 2017 article. For comparison, Choi et al., (2017) support the claims that intercellular and interkingdom communication is energy-dependent and controlled by the metabolism of food energy to pheromones.
It is obvious that pheromones biophysically constrain the virus-driven degradation of messenger RNA. That fact links everything currently known about RNA-mediated cell type differentiation to human love in the context of established links from quantum physics to quantum souls. It may surprise some people to know that the virus-driven evolution of love is the antithetical to the food energy-dependent physiology of pheromone-controlled reproduction in all living genera. Indeed, some people may realize that the virus-driven evolution of anything is based upon ridiculous theories that were invented by Emmy Noethe.
See: Energy-dependent physical and biophysical constraints (4)
Natural selection links odors and the food energy from what organisms eat to the de novo creation of microRNAs. The creation of microRNAs is linked to biophysically constrained energy-dependent codon optimality.
Odor and food energy-dependent changes in microRNAs link hydrogen-atom transfer in DNA base pairs in solution from the creation of amino acids to the ability to sense energy and mass in the context of the space-time continuum. The sense of smell in bacteria has been linked to our food energy-dependent visual perception of the space-time continuum.
Publication of Olfaction Warps Visual Time Perception precedes the September 2017 release of the cell biology game Cytosis. The cell biology game links virus-driven energy theft to all pathology.

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

Taken together, the facts about olfaction link the sense of smell in bacteria from quorum sensing to our visual perception of mass and energy in the context of the space-time continuum. It is no trouble for a serious scientist to consistently link quantum physics from food energy to the creation of quantum souls via changes in the microRNA/messenger RNA balance and the pheromone-controlled physiology of reproduction.
Richard Feynman inadvertently did that when he claimed that the different measures for units of energy used by other theoretical physicists were examples of human idiocy.

See for comparison: The Universe According to Emmy Noethe (Discover Magazine, 2017)

…energy may not be conserved “locally” — that is, in an arbitrarily small patch of space — but everything works out when the space is sufficiently large. That was one of two theorems she proved that year in Göttingen, Germany. The other theorem, which would ultimately have a far greater impact, uncovered an intimate link between conservation laws (such as the conservation of energy) and the symmetries of nature, a connection that physicists have exploited ever since. Today, our current grasp of the physical world, from subatomic particles to black holes, draws heavily upon this theorem, now known simply as Noether’s theorem.

Emmy Noethe’s so-called theorems, which she developed in the early 1900’s, attempted to explain how the concept of entropy might not appear to defy everything known to serious scientists about the biophysically constrained energy-dependent physiology of pheromone-controlled reproduction, which links feedback loops from odors and pheromones to the creation of all energy-dependent biodiversity on Earth.
Simply put, more than 100 years ago Emmy Noethe’s theorems suggested that all representations of energy-dependent biologically-based cause and effect are wrong. For a current representation of what is known, see: Feedback loops link odor and pheromone signaling with reproduction.
The physiology of pheromone-controlled reproduction links what organisms eat to all energy-dependent biodiversity via the de novo creation of genes and gene activation that is biophysically constrained by the metabolism of food to pheromones which control the physiology of reproduction in all living genera.
See also: AMP-enabled FLT3-ITD detection

Independent and bidirectional probes are specifically optimized to detect internal tandem duplications (ITDs) of all sizes. The reads originating from these probes are bioinformatically assembled by Archer Analysis using a de novo assembler to form longer consensus sequences that span the ITD. These longer sequences are then aligned to the reference genome to identify the presence of even very large ITDs (> 250bp).^a
^a Only available on Illumina^® instruments

Use of a so-called “de novo assembler” eliminates any consideration of energy as information that must be used in the context of bioinformatics and the identify of reference genomes that are used to identify pathological gene variants that arise in the context of energy-dependent de novo gene creation. The link from Emmy Noethe’s theorems to the pseudoscientific nonsense about the “de novo assembler” may not be clear without examination of facts about the physiology of reproduction.
For example, see: Physiology is rocking the foundations of evolutionary biology

Perhaps the elegant mathematics and the extraordinary reputation of the scientists involved blinded us to what now seems obvious: the organism should never have been relegated to the role of mere carrier of its genes.

For information on Emmy Noethe’s reputation and her elegant mathematics, see:

The Mighty Mathematician You’ve Never Heard Of (2012)

She invented a theorem that united with magisterial concision two conceptual pillars of physics: symmetry in nature and the universal laws of conservation.

Noether’s brilliance was obvious to all who worked with her, and her male mentors repeatedly took up her cause…

A Fight for the Soul of Science (2015)

Silk accused these theorists of “moving the goalposts” of science and blurring the line between physics and pseudoscience. “The imprimatur of science should be awarded only to a theory that is testable,” Ellis and Silk wrote, thereby disqualifying most of the leading theories of the past 40 years. “Only then can we defend science from attack.”

See for comparison:

Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems April 10, 2014 by James V Kohl

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.

From my publications alert: What’s new for ‘microRNA’ in PubMed on July 26, 2017
Tiny RNAs and their voyage via extracellular vesicles: Secretion of bacterial small RNA and eukaryotic microRNA

MicroRNAs are small non-coding RNAs that bind to the 3′-untranslated region of target mRNAs and have transcriptional or translational inhibitory function in eukaryotes. Before microRNAs were widely known, bacterial non-coding small RNAs around 50-200 nt in length were discovered whose mechanism of action resembled that of microRNAs. Recently, RNAs that are of similar size to or smaller than microRNAs have been discovered in bacteria and indeed, this class of small RNAs have been found throughout all domains of life. Moreover, recent findings suggest that these tiny RNAs can be released via extracellular vesicles (such as exosomes in eukaryotes and outer membrane vesicles in bacteria), which in turn heralds a new field of research, interkingdom communication. This review discusses two similar classes of small RNAs in evolutionarily distinct eukaryotes and bacteria. In addition to their biogenesis and regulation, we discuss small RNA vehicles and their secretion. Impact statement The possible endogenous functions of small RNAs such as regulatory small RNAs in bacteria and microRNAs in eukaryotes have been extensively studied since they were first discovered. However, their powerful functions should not be seen as limited to their cells of origin. Recently, several papers have demonstrated that small RNAs function as signaling molecules between cells. This is possible because small RNAs can be shuttled around after being incorporated into environmentally protective extracellular vesicles. It is now clearly plausible that secreted small RNAs can regulate other types of cells through biofluids. Given their “common molecule” status, the role of small RNAs in mediating bacteria-human crosstalk is an emerging and competitive area of genetic research. This review provides insight into the function of small RNAs in intercellular and even interkingdom communication.

Energy-dependent microRNA biogenesis

May 4, 2017

by James Kohl with No Comment Adaptations Ecology Human Pheromones Model Organisms RNA Directed RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression Variations

Published May 3, 2017 Genetic variation and RNA structure regulate microRNA biogenesis

…primary sequence determinants and RNA structure are key regulators of miRNA biogenesis.

Genetic variation aka primary sequence determinants are energy-dependent and RNA-mediated. Energy-dependent RNA methylation is an experience-dependent link from natural selection for energy-dependent codon optimality. Natural selection for energy-dependent codon optimality links ATP-dependent microRNA biogenesis to RNA biosynthesis.
Ridiculous attempts to portray energy-dependent top-down causation as if genetic variation came first may continue for another 52 years. But see this report from 1964 to help you recognize how much pseudoscientific nonsense has been touted since then.
See: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

Isolated thymus nuclei transport amino acids into an intranuclear pool by a process which seems to depend on energy from nuclear ATP synthesis (20).

If any experimental evidence of biophysically constrained RNA-mediated cell type differentiation was not linked from an anti-entropic energy source to nuclear ATP synthesis that experimental evidence might support the claims of pseudoscientists who think that mutations link natural selection to evolution of different species.
See for comparison: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The bias between codons or amino acids, and mRNA expression levels has been previously recognized across species and is thought to result from selection for efficient, accurate translation, and folding of highly expressed genes…

My translation: Natural selection for energy-dependent and energy-efficient protein folding chemistry links what organisms eat to the energy that they require for reproduction via the accurate translation and folding of highly expressed genes.
Alternatively, virus-driven energy theft links the degradation of messenger RNA to all pathology via conserved molecular mechanisms in all living genera. Simply put, the molecular mechanisms of healthy longevity and biodiversity are nutrient energy-dependent and pheromone-controlled.

The fact that population geneticists have ignored what us known to all serious scientists about the controlled molecular mechanisms that link metabolic networks to genetic networks has led to the unnecessary suffering and premature death of millions to billions of people. If you are not willing to join those who are Combating Evolution to Fight Disease, you probably will be asked why you decide to ignore everything known about the energy-dependent de novo creation of genes. If you did not recognize your ignorance, try to find experimental evidence in the works of evolutionary theorists who did not start after the energy-dependent de novo creation of genes.

So far as I know, all pseudoscientists still consistently place the facts about de novo gene creation, which refute their nonsense about mutation-driven evolution, into the context of their published works. Those works will continue to cause the unnecessary suffering and premature death of millions to billions of people.

The fact that experience-dependent genetic variation does not create itself is a thorn in the side of all theorists who now recognize and must ignore the facts about RNA-mediated cell type differentiation. The facts link the energy-dependent RNA-mediated fixation of amino acid substitutions to all biodiversity.

The facts also link mutations to all pathology, which means the facts have always been evolutionary theory killers. The facts haven’t changed since Thomas Hunt Morgan presciently linked them to chromosomal inheritance and Schrodinger presciently linked the anti-entropic virucidal energy of sunlight to RNA-mediated DNA repair.

See also: Exiqon “Genome Web” This link opens the pdf for microRNA target identification by RNA pull down with biotinylated microRNA mimics

Approximately one in five microRNA interactions with mRNAs occur through non-canonical binding sites. Although of functional relevance these microRNA targets are not predicted by bioinformatics tools. Improved RNA pull-down techniques with biotinylated microRNA mimics open new possibilities to identify microRNA targets experimentally.

Download the tech note

My comment: Although I have repeatedly mentioned works that link energy-dependent changes in the microRNA/messenger RNA balance to cell type differentiation and healthy longevity, I had not seen any mention of biotinylation, until today.

In biochemistry, biotinylation is the process of covalently attaching biotin to a protein, nucleic acid or other molecule. Biotinylation is rapid, specific and is unlikely to perturb the natural function of the molecule…

I do not know any theorists who are biochemists and suspect that all the ridiculous theories of pseudoscientists include nothing that is known about biotinylation. That may be why I did not hear the term mentioned, until today. What would happen if I heard it and failed to learn what it meant? God forbid, I might still be a biologically uninformed theorist
See for example: The landscape of sex-differential transcriptome and its consequent selection in human adults

This work provides a comprehensive overview of the sex-differential transcriptome and its importance to human evolution and human physiology in health and in disease.

Reported as: Researchers identify 6,500 genes that are expressed differently in men and women

The detailed map of these genes, reported in BMC Biology, provides evidence that males and females undergo a sort of separate, but interconnected evolution.

I thank God, for not allowing me to believe that males and females are different mutants of the same species.
See for comparison: We are all mutants

Darwin is a god in evolution, so you can’t criticize Darwin. If you do, you’re branded as arrogant.

But any time a scientific theory is treated like dogma, you have to question it. The dogma of natural selection has existed a long time. Most people have not questioned it. Most textbooks still state this is so. Most students are educated with these books.

You have to question dogma. Use common sense. You have to think for yourself, without preconceptions. That is what’s important in science.

Common sense? Masatoshi Nei’s textbook Mutation-Driven Evolution was published on the same day as my 2013 review: Nutrient-dependent/pheromone-controlled adaptive evolution: a model, which is a refutation of mutation-driven evolution.

Excerpt:

…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.

Conclusion:

…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’.

See for comparison: John Deely, from the Point of View of Biosemiotics

Conclusion:

….his unlimited but judiciously applied enthusiasm, his sterling example as a scholar, and his inspirational support of semiotic colleagues, institutions, and the ongoing investigation into the reality of sign process at every level of life have been and will remain a force that both inspires and that sets the standard by which our colleagues continue with their important work.

My comment: The reality of sign process at every level of life is that it is energy-dependent, RNA-mediated, and biophysically constrained by the physiology of reproduction in species from archaea to humans.

Epigenetically-effected nucleosome repositioning sheds Dobzhansky's light on evolution

April 14, 2017

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

Crystal structure of the overlapping dinucleosome composed of hexasome and octasome

My summary: Nucleosomes are dynamic entities that are repositioned by energy-dependent links from sunlight to ATP and RNA biosynthesis that act on DNA during the chromatin remodeling, which is biophysically constrained by the pheromone-controlled physiology of reproduction during the transgenerational epigenetic inheritance of all morphological and behavioral phentoypes. processes.

Reported as: Unveiling how nucleosome repositioning occurs to shed light on genetic diseases

…an incomplete formation of overlapping dinucleosome may trigger abnormalities in the genetic switch, turning normal cells into tumor cells. Accordingly, understanding the atomic structure of the overlapping dinucleosome may provide valuable information for understanding how the abnormal dynamics of chromatin are related to cancer…

The atomic structure of the dinucleosome is energy-dependent. The atomic structure links the sun’s anti-entropic virucidal energy to all healthy longevity via endogenous RNA interference (RNAi). RNAi is is the nutrient energy-dependent link from atoms to ecosystems via what is known to all serious scientists about supercoiled DNA. Virus-driven energy theft causes the incomplete formation of the overlapping dinucleosome and all pathology in all living genera.
See for comparison my invited review of nutritional epigenetics: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

See also: Structural diversity of supercoiled DNA and the parody from the Zechiedrich lab.

Nothing in Biology Makes Any Sense Except in the Light of Evolution

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

Combating Evolution to Fight Disease

It’s time for biophysicists to tell theorists and pathologists how to differentiate between theories about the genesis of different cell types and the biological facts about the nutrient-dependent pheromone-controlled ecological adaptations that enable the genesis of different cell types in individuals of different species. Simply put, it’s time to stop trying to explain ecological adaptations in the context of mutations and evolution.

Feedback loops link odor and pheromone signaling with reproduction
Roles of differential expression of microRNA-21-3p and microRNA-433 in FSH regulation in rat anterior pituitary cells

Taken together, our results show that both miR-21-3p and miR-433 down-regulate FSHb expression and cause FSH secretion decreased. These findings provide insights into the effects of the regulatory mechanisms of miRNAs on the reproductive functions of the pituitary.

FSH secretion links the nutrient energy-dependent pheromone-controlled epigenetic effects on endogenous RNA interference to healthy longevity and biodiversity in all vertebrates via the substitution of achiral glycine in position 6 of the gonadotropin releasing hormone decapeptide.
See also: Gonadotropin releasing hormone and human sexual behavior (1991)

Targeting Gut Bacteria May Be The Key To Preventing Alzheimer’s (2/21/17)

…mice with Alzheimer’s have a different gut bacterial profile than those that do not have the disease.

RNA editing refutes theistic evolution

February 21, 2017

by James Kohl with One Comment Adaptations Alternative Splicings Autophagy base editing biophotonics Diseases & Disorders Ecology Light Energy Model Organisms Neuronal Plasticity Physics RNA Directed RNA editing RNA-directed DNA methylation RNA-mediated gene silencing RNA–Mediated Epigenetic Heredity Variations

Charge-altering releasable transporters (CARTs) for the delivery and release of mRNA in living animals January 9, 2017
Reported February 19, 2017 as A new way Forward for Gene Therapy

If you want an explanation of how mRNA works within a cell, check out the video above from the Khan Academy.

Unfortunately, the speaker seems to think that sickle-cell disease is caused by a mutation. All serious scientists know that the hemoglobin S variant is a biophysically constrained nutrient energy-dependent ecological adaptation that protects populations from virus-driven genomic entropy due to phages in the class of Sporazoa, which includes the parasite that causes malaria.
See also: HbVar: A Database of Human Hemoglobin Variants and Thalassemias
More than 1200 hemoglobin variants have been reported.
Here is more information on the known variants Dobzhansky (1964) reported that “Ingram and others found that hemoglobin S differs from A in the substitution of just a single amino acid, valine in place of glutamic acid in the beta chain of the hemoglobin molecule.”
If you want details about how energy-dependent changes in the microRNA/messenger balance link amino acid substitutions in supercoiled DNA to all healthy longevity compared to the fact that virus-driven energy theft is linked from mutations to all pathology, 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.

The papers by Jaeger (microbiology) and Noble (physiology) are strong steps forward in this regard. This is perhaps the area where most needs to be done, across the board in all domains. Areas where striking progress is being made in this regard are epigenetics [22] and social neuroscience [23]. These papers are in fact dealing with top-down causation: the way they provide experimental confirmation of this concept needs to be made more explicit.

What don’t pseudoscientists understand about the need to link energy-dependent RNA-mediated protein folding chemistry from metabolism in microbes to their nutrient-dependent pheromone-controlled physiology of energy-dependent reproduction before inventing more theories based on definitions and assumptions about interpretations of data?
Each example of RNA editing will continue to link chirality to autophagy and link endogenous RNA interference (RNA editing) to supercoiled DNA via amino acids in supercoiled DNA. If example of virus-driven energy theft are not sufficient to show that it is the cause of all pathology, someone will need to show what causes the mutations that are linked to all pathology.
See also: Genomic Energy Landscapes
Their perspective on the energy landscape theory asks the same old questions about chromosomal inheritance and provides no basis for linking experimental evidence of top-down energy-dependent causation from RNA-mediated protein folding chemistry to all biodiversity via the physiology of pheromone-controlled reproduction. It is another refutation of theistic evolution because it fails to link anything to anything else.
See for comparison: Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection (2014)

Comparing the details of the physical and information theoretic models has already suggested ways of improving the prediction of mutational effects on the stability of protein sequence/structure pairs.

Virus-driven energy theft causes mutations, which link messenger RNA degradation to genomic entropy in hosts because the energy is used for amino acid substitutions that stabilize the organized genomes of viruses. How much evidence of virus-driven energy theft and pathology can be viewed in the context of the fossil record compared to the frozen corpse of “the Tyrolean Iceman?”
See: miRNAs in ancient tissue specimens of the Tyrolean Iceman reported as: Otzi the Iceman: Researchers validate the stability of genetic markers

…microRNAs can remain stable even after 5,300 years.

From the same first author: The missense of smell: functional variability in the human odorant receptor repertoire
The variability of single odorant receptors is clearly linked from energy-dependent changes in base pairs to the microRNA/messenger RNA balance. The balance links SNPs to natural selection for energy-dependent codon optimality.
Codon optimality links single amino acid substitutions from RNA editing to nutrient-dependent pheromone-controlled adaptations. That fact links natural selection from ecological variations to ecological adaptations. The energy-dependent adaptations obviously occur in species from microbes (including viruses) to man. If the adaptations did not occur in all living genera, the microRNAs could not have been linked to genetic markers in the ancient tissue specimens via RNA editing.
See also: Contribution of epigenetic mechanisms to variation in cancer risk among tissues

…the risk of cancer in any given tissue would be correlated with the number of abnormally methylated precancer cells in that cell type. Because de novo modification appears to take place almost exclusively on CpG islands that are already silenced by polycomb in the normal tissue (8), we suggest that this modification works by preventing these genes from becoming activated, thereby inhibiting normal tissue differentiation, causing clonal selection for cells that may predispose to cancer (31). Indeed, many of these methylation targets have been shown to be “driver” genes in a number of different cell types (Fig. S6).

Once again we see that serious scientists know the difference between energy-dependent polycombic ecological adaptations and the virus-driven hecatombic evolution of all pathology, but they clearly do not know how to express what they know in terms that are meaningful to those who know how to link angstroms to ecosystems in all living genera.

George Church refutes theistic evolution

February 9, 2017

by James Kohl with 3 Comments Adaptations Alternative Splicings biophotonics Diseases & Disorders Ecology Human Brain Light Energy Model Organisms Neuronal Plasticity Nutrigenomics Physics RNA Directed RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity Variations

Wednesday Afternoon Lecture Series (WALS) – The future of genetic codes and BRAIN codes

The NIH Director’s Wednesday Afternoon Lecture Series, colloquially known as WALS, is the highest-profile lecture program at the NIH.

The future of genetic codes and BRAIN codes (video)
My comment on the video: Biophysically constrained genetic codes are brain codes. They link the epigenetic landscape to the physical landscape of supercoiled DNA via metabolic networks, which link energy as information to all cell type differentiation in all individuals of all living genera.
Virus-driven energy theft is linked from “gene vandalism” to epigenetically effected nutrient energy-as-information dependent RNA-mediated DNA repair.
Synthesis of nucleic acids became a “bigger deal” when Sutherland’s group showed that ultraviolet light was linked to the simultaneous de novo creation of nucleic acid precursors, which are the starting materials needed to make natural amino acids and lipids.
See: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
They showed that a single set of light-activated reactions gave rise to most of life’s building blocks simultaneously. Simply put, that fact refutes every aspect of neo-Darwinian nonsense. It also eliminates consideration of any theories proposed by “big bang” cosmologists.
The irony of this is that not one of the young earth creationists I know would fail to link the hydrogen-atom energy-dependent de novo creation of nucleic acid precursors to all biodiversity on Earth via the physiology of biophysically constrained cell type differentiation.
For example, see: Multipurpose Plant Sensors Startle Scientists
Even if a young earth creationist knew nothing about energy-dependent cell type differentiation, he or she would not be likely to link minimal mutational differences, called mutations to the mutation-driven evolution of all biodiversity.
As you can see in the video, George Church has been forced to abide by the rules of serious scientists.
Here is an unavoidable rule: Kalevi Kull: Censorship & Royal Society Evo Event

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

George Church has, until yesterday, focused his efforts on exogenous RNA interference rather than what is known about endogenous RNA interference, which links supercoiled DNA to the prevention of all virus-driven pathology in all living genera. Most people will not recognize what President Trump has forced the NIH to do before the theistic evolutionist, Francis Collins is replaced. They may read this, but not understand what it means.
Obama Advisers Urge Action Against CRISPR Bioterror Threat

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 also: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
The likelihood that NIH funding will be used for any studies that do not link prevention from the National Microbiome Initiative to the Precision Medicine Initiative via the microRNAome and energy-dependent microRNA expression can be placed into the context of failed mathematical models, which have not addressed any aspect of energy-dependent biologically-based cause and effect.
Let me help others decipher the content of George Church’s claims in: The future of genetic codes and BRAIN codes
The question (at 54:22) about teratomas is answered with a classic attempt to obfuscate what is known about virus-driven energy theft and all pathology.
How organs assemble in the context of virus-driven energy theft has been placed into the context of energy-dependent viral latency since the time that Sinclair Lewis published “Arrowsmith” in 1925 and Thomas Hunt Morgan won the 1933 Nobel Prize in Physiology or Medicine for his works on chromosomal inheritance.
At 59.00 the question about natural selection for energy-dependent codon optimality leads to another attempt to obfuscate what is known about top-down causation.
At 1:00 he begins to talks about adding a built-in sequencer in your phone. At this point, you may need some comic relief, which Jon Stewart provided with his question about whether the new technology would be integrated with a camera. See: Jon Stewart interviews Greg Bear.
At 1:04, the question and answer about Alzheimer’s vs cognitive enhancement can be placed into the context of Greg Bear’s works, which were published in 1999 and 2003. They were reviewed by Michael A. Goldman in “Nature.”
Evolution rising from the grave
Living with the Neanderthals
See also: Newly found mechanism for protecting neurons could underlie brain disease

The neurons expel large (4- micron diameter) membrane-bound vesicles (dubbed “exophers”) that are filled with clumped protein and damaged cellular organelles including mitochondria.

The only mention of exopher in the extant literature indexed on PubMed is in the article published yesterday, C. elegans neurons jettison protein aggregates and mitochondria under neurotoxic stress. The authors seem to be trying to make everything known to all serious scientists appear to be new information about the biophysically constrained RNA-mediated transgenerational epigenetic inheritance of morphological and behavioral phenotypes.
This is roughly the equivalent of inventing de Vries 1902 term “mutation,” which was used by theorists to dismiss Darwin’s “conditions of life.”
For comparison, there are now 58,887 indexed articles on PubMed that mention microRNA. For example, see: MCMDA: Matrix Completion for MiRNA-Disease Association prediction
If you do not object to the level of obfuscation that is required for pseudoscientists to continue touting their ridiculous theories, you may not be allowed to join those who are Combating Evolution to Fight Disease.
What career goals will you pursue after the Trump administration ensures that pseudoscientific nonsense is no longer funded?
Activity-dependent spatially-localized miRNA maturation in neuronal dendrites
Reported as: Bright Spots in Brain Cells

Thanks to Anna Di Cosmo for calling attention to more detailed facts about cell type differentiation that link energy-dependent changes in fluorescence from the weekend resurrection of the bacterial flagellum to endogenous RNA interference and the maturation of brain cells in rats.
Everything known appears to link the conserved molecular mechanisms of nutrient-dependent pheromone-controlled physiology of reproduction in species from archaea to humans.
In any case, no one is challenging the perspective that serious scientists like Anna Di Cosmo have added to what is known about everything that links quantum physics to quantum consciousness via energy-dependent “bright spots in brain cells.”
And there is still no other model for comparison to this model of biologically-based cause and effect. Nutrient-dependent/pheromone-controlled adaptive evolution: a model
A good model predicts, and people who understand the need for a good model of biologically-based cause and effect predictably make the most scientific progress.
In 2013 I wrote:

“…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.”

In 2015, Role of olfaction in Octopus vulgaris reproduction, Anna Di Cosmo’s group concluded:

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). The knowledge of the nature of the factor released by the optic gland could shed light on the role played by this gland in the reproduction: is it a gonadotropin or a trophic factor? Intriguingly, even though the mechanisms and molecules regulating reproduction are the same in both male and female, O’Dor and Wells (1978) observed mature sperms in young O. vulgaris males independently from optic gland hypertrophy.

Scent of Eros

Posts tagged: amino acids