Plenty of Room at the Bottom

Environmental selection is natural selection (2)

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

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

Acknowledgments

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

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

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

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

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

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

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

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

5th-6th Sept 2018 Dublin, Ireland

Part 3: Light-controlled cell biology (revisited)

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

Out of Order: Undaunted 

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

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

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

See also: This Compound Can Reverse Aging in Mice. Will It Work in People? and Mitotic progression, arrest, exit or death is determined by centromere integrity and independent of de novo transcription

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

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

See also: PhD title: Fibrillation of proteins involved in neurodegenerative diseases: influence of mRNA

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

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

See also:

 More germane to DDNews, the most recent pattern I cannot seem to shake is discussion of the microbiome.

Neo-Darwinian theorists and Big Bang cosmologists seem to have no sense of pattern recognition in the context of Olfaction Warps Visual Time Perception

See for comparison: What Stephen Hawking’s Final Paper Says (And Doesn’t Say)

The claims in “Olfaction Warps Visual Time Perception” link the sense of smell in bacteria to our visual perception of energy and mass in the context of the space time continuum and biophysically constrained viral latency. Everything known to Hawking’s co-authors Roger Penrose and George FR Ellis has since been linked from what organisms eat to the physiology of reproduction via the creation of sunlight and biomolecules.

The difference between Hawking’s ridiculous theories and biologically-based facts will place the claims about his intelligence and insight into the historical context of how celebrity scientists have led to our unnecessary suffering and premature death. It’s ironic that Hawking could have been effectively treated with food energy-dependent microRNAs, but instead got stuck with a useless theoretical approach to life. I would not want that to happen to my children or grandchildren (if I had any). What are your children being taught to believe in: theories or experimentally established facts?.

5th-6th Sept 2018 Dublin, Ireland

Conceptual critique: Innateness vs the death gene (1)

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

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.

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)
 

An evolutionary theory killer

A reversible TCA cycle in a thermophile (3)

A pathway for mitotic chromosome formation

The combination of nested loops distributed around a helically twisted axis plus dense chromatin packing achieves the 10,000-fold compaction of chromatin into linearly organized chromosomes that is required for accurate chromosome segregation when cells divide.

The compaction of chromatin in the context of hydrophobicity is the topic of: Structural diversity of supercoiled DNA

Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

Differential recognition of proteins clearly involves this link from natural selection for energy-dependent codon optimality to the physiology of reproduction via RNA-directed DNA methylation.
See for comparison: DNA-Methylation: Master or Slave of Neural Fate Decisions?

The involvement of splicing as effector of changes in DNA methylation is an exciting new angle to pursue with more precise epigenetic engineering tools. Distinguishing essential from specific, and causal from secondary marks will be essential for neuro-epigenetics. New approaches promise to answer long outstanding questions and will likely facilitate the discovery that DNA modifications might have new unexpected roles in the brain.

Splicing is not the effector of changes in DNA methylation, energy-dependent changes in the microRNA/messenger RNA balance must be given first consideration. But, this article is part of the Research Topic: Epigenetic Mechanisms of Neurogenesis in the Developing Neocortex

The topic is an example of human idiocy for comparison to this report on alternative splicing, which was linked to energy-dependent biophysically constrained viral latency in the context of:

 Alternative splicing and the evolution of phenotypic novelty and the cell biology game: Cytosis

This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.

The origins of morphological diversity cannot be evaluated outside the context of the origins of energy-dependent behavioral diversity, which requires that RNA-mediated DNA methylation be linked to differences in cell fate in all tissues of all individuals of all species on Earth. Typically, serious scientists do this by linking the creation of the sun’s anti-entropic viral latency from  subatomic particles to creation of atoms and ecosystems in the context of human brain development via mitotic chromosome formation.

See for instance: The Excitable Mitochondria and The vibrational theory of olfaction for the win by John Hewitt.
If he did not believe that “evolution did it” after the emergence of energy, he would not have placed his bets on ridiculous theories and criticized my life’s history of publications and presentations, which he claimed were BS.
See for comparison to his claims: Correcting for Differential Transcript Coverage Reveals a Strong Relationship between Alternative Splicing and Organism Complexity
We placed the facts about alternative splicing and increasing organismal complexity into the context of our section on molecular epigenetics in From Fertilization to Adult Sexual Behavior

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans…

The sexual differentiation of all cell types in species from yeast to humans was presciently placed into the context of what was known about pre-mRNA mediated biophysically constrained viral latency in 1996. Food energy-dependent pre-mRNAs are now referred to as microRNAs (miRNAs). The creation of the miRNAs links the anti-entropic virucidal of the sun to all biodiversity via the physiology of reproduction,  and our details from 1996 have been extended across species via this recently published work:
Reproductive role of miRNA in the hypothalamic-pituitary axis

The hypothalamic-pituitary-gonadal (HPG) axis plays a critical role in regulating reproductive function. Gonadotropin-releasing hormone (GnRH), which is secreted by the hypothalamus, acts on pituitary gonadotrophs to stimulate luteinizing hormone (LH) and follicle-stimulating hormone (FSH) synthesis and secretion, ultimately affecting the animal’s fertility. MicroRNAs are small, non-coding RNAs that are widely expressed throughout the brain and can fine-tune gene expression post-transcriptionally. Recently, growing evidence has unveiled the central position of miRNAs within a key regulatory process involving GnRH secretion and subsequent activation in the pituitary. Although transcriptional regulation of reproduction has been well studied, the post-transcriptional processes are less well understood. In this review, we elaborate comprehensively on the critical role of miRNAs in the reproductive process, including both temporal and spatial aspects. A better understanding of how miRNAs impact the neuroendocrine system may improve our knowledge of reproduction and provide novel targets for therapeutic development.

For comparison, see: No Missing Link: Knowledge Predicts Acceptance of Evolution in the United States

Using a new demographically representative survey (N = 1100) that includes a detailed measure of evolution knowledge, we find that knowledge predicts level of acceptance, even after accounting for the effects of religion and politics. These results demonstrate that Americans’ views on evolution are significantly influenced by their knowledge about this theory and therefore might be amenable to change.

Reported as: Better knowledge of evolution leads to greater acceptance of the concept

…actual knowledge of the science seems to play a role, and we’ve documented that here for evolution for the first time in a representative population.”

If that claim was true, we would not see so many examples of people in other countries who have replaced the teaching of ridiculous evolutionary theories with facts that their students learn about ecological variation and ecological adaptations.
For example: Israeli Middle Schools School to Include Theory of Evolution (2014)

…learning about evolution is not the primary function of the decision, but rather to use it as a building block for students to learn more about their ecology.

See also: Turkish schools to stop teaching evolution, official says (2017)
If you are willing to consider the facts about why many countries do not teach humans to believe in ridiculous theories, please see:
Subatomic: From thermophiles to humans (in prep)

 
 
 

5th-6th Sept 2018 Dublin, Ireland

Anti-entropic sunlight: Schrödinger’s Creationist Secret? (4)

Summary: Antagonists such as John Hewitt have exhausted my patience. Now see this:

The authors invented the term “phosphate steering”  in an attempt to obfuscate what has been known to all serious scientists about oxidative phosphorylation for more than 50 years.

See: “oxidative phosphorylation” microRNA  (105 entries); “oxidative phosphorylation” (21955 entries) and “phosphate steering” (1 entry)

Compare the nonsense about phosphae steering to facts in the context of Modern diversification of the amino acid repertoire driven by oxygen (2017)
Reported on February 1, 2018 as: Quantum chemistry solves mystery why there are these 20 amino acids in the genetic code
Conclusion:

…we could characterize oxygen as the author adding the very final touch to the genetic code,” stated Moosmann.

Also reported on Feburary 2, 2018 as: Origin of Life: Quantum Chemistry Solves One of Genetics’ Biggest Mysteries Using Amino Acids From Space

Moosmann and his colleagues created a quantum chemistry model that compared amino acids on Earth to amino acids from space that had arrived via meteorites.

Conclusion:

The newer aminos’ reactivity still didn’t account for their presence in the genetic tool box to begin with. The researchers conducted additional experiments which verified their theoretical results. They found that at least three of the newer aminos—methionine, tryptophan and selenocysteine—were included in response to the rising levels of oxygen in our atmosphere. Since oxygen encourages the production of toxic-free radicals, we needed additional, nimbler amino acids to react to those free radicals and help our cells repair themselves.

Last month I advised John Hewitt against attemptng to link the creation of selenocysteine to biodiversity outside the context of the biophysical constraints on viral latency. Hewitt and many other biologically uninformed science journalists like the idea of neo-Darwinian evolution.
See why: On the unique function of selenocysteine — Insights from the evolution of selenoproteins

These evolutionary studies stem from the realization that patterns of amino acid conservation and substitution in proteins may provide important functional information.

The magic of evolutionary studies is easy compared to understanding the functional structure of supercoiled DNA in the context of the report from 2009. Hewitt likes that simple-minded ignorance compared to the difficulty of placing the structure and function of supercoiled DNA into the context of my model from 2013.

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

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’.

But, I digress. My point is that no experimental evidence of biophysically constrained top-down causation suggests that amino acids from space arrived on Earth via transport in meteorites. The fact that the creation of the amino acids must be linked to biophysically constrained viral latency has repeatedly been reported at every level of examination by serious scientists.
See for instance: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
Reported as:Researchers may have solved origin-of-life conundrum

…the conditions that produce nucleic acid precursors also create the starting materials needed to make natural amino acids and lipids. That suggests a single set of [light activated] reactions could have given rise to most of life’s building blocks simultaneously.

John Hewitt’s claims can now be placed into the context of my model.
On February 3, 2018, John Hewitt tweeted:

“all the substitutions were figured out long ago by bacteria”

I replied:

Do you realize how ridiculous that sounds in the context of any other claims that you have accurately represented?

On February 4, 2018, John Hewitt wrote:

“slander me again James and you are blocked. those silly viruses were artificially engineered that way”

I’ve placed his comments about slander into the context of his past claims about viruses and energy.
1) MIT team genetically engineers a quantum virus for efficient energy transport (2015)

Although the virus has demonstrated the ability to capture and transfer light energy…

John Hewitt failed to put his reported fact about the capture of light energy into the proper context of my works. He has since been denigrating my model and peer-reviewed publications in a month-long escalation of “twitter” attacks.
Like others, he has resorted to attacks via social media, because that’s where the ignorance is. The ignorance of other theorists has typically been in his favor. But see two other news reports from John Hewitt.
2) The Excitable Mitochondria (2016) http://inference-review.com/article/the-excitable-mitochondria

By fine-tuning their fusion and fission rates, each cell maintains a large centralized mitochondrial syncytium that dispatches and recalls mitochondrial quanta to different parts of the cell.

John Hewitt joined the ranks of others who have claimed the fine-tuning is automagical. He removed consideration for the creation of  quantized energy and the virus-driven capture of quantized energy. That is how he bastardized everything known to serious scientists about energy-dependent biophysically constrained viral latency and healthy longevity in species from microbes to humans. But wait, he almost helped other serious scientists make progress.
3) The vibrational theory of olfaction for the win (2017)

In addition to these discoveries, Turin also just published a much more sweeping treatise on molecular recognition in olfaction in the journal Advances in Physics: X. In it, he and his co-authors delve into more of the specifics of olfactory receptors, including particular amino acid motifs, metal binding capacities, and disulphide bridge redox status. It turns out that amino acid side chains alone frequently pull off some rather interesting electron transfer effects without the need for fancy co-enzymes or prosthetic groups. Although there are only a few cases in which this has been proposed, we can take a brief anecdotal look at how this mechanism operates in other proteins.

John Hewitt likes Turin’s theory, but ignores my model, which links the creation of sunlight from the creation of quantized energy as information to the creation of ATP. Conserved molecular mechanisms in microbes link the creation of ATP to RNA-mediated cell type differentiation via the creation of amino-acid substitutions that stabilize the organized genomes of all living genera in the context of the physiology of reproduction.
See the the initial prescient support for the claims in my mode, which came from the first person who ever critiqued it:, Bruce McEwen.
Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

See also: Long-range coherence and energy storage in biological systems (1968) published in International Journal of Quantum Chemistry

The supplied [quantized] energy is thus not completely thermalized but stored in a highly ordered fashion.

Clearly, energy-dependent biophysical constraints on the well-ordered stability of organized genomes is required for the transgenerational epigenetic inheritance of all morphological and behavioral phenotypes.
Quantum chemistry solves mystery why there are these 20 amino acids in the genetic code makes that fact perfectly clear.
But see also: Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment (2003)
and Learning from Bacteria about Natural Information Processing (2009)
and Stability of the hybrid epithelial/mesenchymal phenotype (2016)

…higher levels of these PSFs may be predictive of poor patient outcome. Finally, based on these specific examples, we deduce certain network motifs that can stabilize the hybrid E/M phenotype. Our results suggest that partial EMT, i.e. a hybrid E/M phenotype, need not be ‘metastable’, and strengthen the emerging notion that partial EMT, but not necessarily a complete EMT, is associated with aggressive tumor progression.

If you looked only at the works published by the late Eshel Ben-Jacob and his group, you would learn the difference between all serious scientists and all biologically uninformed theorists and their idiot minions: the biologically uninformed science journalists.
But for another 50-year-old historical perspective see: Non-singular general-relativistic collapse (1968) as cited in Absorption and Scattering Cross Section of Regular Black Holes Journal of Gravity (2014)
Reported as: What If the Big Bang Wasn’t the Beginning? New Study Proposes Alternative December 5, 2017

There is no empirical evidence for bouncing cosmologies today,” he said. “But there is no evidence for the initial singularity as well.

That’s two strikes against “Big Bang” cosmology before serious scientists start.
See for comparison: Non-singular quantum-inspired gravitational collapse (2013)
Biologically uninformed journalists continue to display their epic failure to understand any aspect of pattern recognition. For example, all patterns appear to be energy-dependent and the energy appears to be physically constrained in the context of gravity and and biophysically constrained in the context of all  biodiversity.
I placed that fact into the context of part three of this series.
Anti-entropic sunlight: Schrödinger’s Creationist Secret? (3)
The fact that two articles published in 1968 attest to the facts about the energy-dependent creation of ATP and RNA in McEwen et al., (1964) , links claims about human idiocy to science journalists — with John Hewitt as the best example of idiocy.
But, two days later, In an attempt to support the nonsense touted by John Hewitt, Nik Willmore added:

Replying to @jvkohl @jhewitt123

Stringing together walls of general science buzzword salad as an excuse to hurl quack insults makes you the poster boy for Pink Floyd’s album The Wall.

My response: See Andrew Jones unpublished thesis on abiogenesis and the editor’s comments on his criticisms: “…subjected to standard peer review and the revised version was accepted by me after it had been accepted by both reviewers.” Find your friends on The Dark Side of the Moon.
People like @nikwillmore and @jhewitt123 might claim that they want to see “Science” only after peer review. Most of them do not want to see anything published that refutes the pseudoscientific nonsense of their ridiculous theories. But see also: Universal Alternative Splicing of Noncoding Exons
Compare claims that “…noncoding exons are functionally modular, with alternative splicing generating an enormous repertoire of potential regulatory RNAs and a rich transcriptional reservoir for gene evolution.” See: our section on molecular epigenetics From Fertilization to Adult Sexual Behavior

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism…

We did not forget to mention the emergence of energy, abiogenesis, and evolution.
All serious scientists dismiss ridiculous claims. For comparison, all pseudoscientists and biologically uninformed science journalists dismiss the experimental evidence of energy-dependent biophysically constrained viral latency as if the experimental evidence was optional. See:  Combating Evolution to Fight Disease.
See also: The real reason behind The Big Bang Theory’s ratings drop

So how come Big Bang isn’t popping the way it used to?

It’s getting eclipsed by Young Sheldon

As Cheers begot Frasier and Buffy begot Angel, The Big Bang Theory has spawned Young Sheldon. It chronicles the oft-spoken of adventures of Sheldon when he was a socially oblivious, one-of-a-kind, once-in-a-generation genius growing up in a small town with a family that didn’t understand him. Enjoying a lead-in from The Big Bang Theory, Young Sheldon was a hit right out of the gate.

This appears to be proof that most people would rather be entertained to death rather than examine the facts about the creation of the sun’s anti-entropic virucidal energy and biophysically constrained viral latency.
See also: “You are blocked from following @jhewitt123 and viewing @jhewitt123’s Tweets. Learn more”
I do not need to learn more: See: A Few Good Man “You Can’t Handle the Truth”
See also: 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… autophagy.

People like John Hewitt and Nik Willmore consistently test the patience of serious scientists until the ignorance of their ridiculous theories is exposed.
See also: Phosphate steering by Flap Endonuclease 1 promotes 5′-flap specificity and incision to prevent genome instability

Phosphate steering mutations could thus be the trans-modifiers of repeat expansions during either somatic, or intergenerational transmissions in human disease65. Moreover, as the basic residues implicated in phosphate steering are largely conserved in the 5′-nuclease superfamily, control over the +1 and −1 phosphates may be a superfamily-conserved mechanism.

The authors invented the term “phosphate steering”  in an attempt to obfuscate what has been known to all serious scientists about oxidative phosphorylation for more than 50 years.
See: “oxidative phosphorylation” microRNA  (105 entries)
“oxidative phosphorylation” (21955 entries) and “phosphate steering” (1 entry)
See for comparison: Gamma oscillations organize top-down signalling to hypothalamus and enable food seeking

Cortical cognitive processing9, 10 involves gamma oscillations11, 12, 13, 14, 15, which support memory16, 17, attention18, cognitive flexibility19 and sensory responses20. These functions contribute crucially to feeding behaviour by unknown neural mechanisms. Here we show that coordinated gamma (30–90 Hz) oscillations in the lateral hypothalamus and upstream brain regions organize food-seeking behaviour in mice.

Reported as: Gamma oscillations coordinate food seeking

“Preferential and selective control of feeding-related cells by rhythmic inputs to hypothalamus demonstrates a beautiful interaction of structure and function in the brain” says Alexey Ponomarenko. “Here we see how fast synchronization, combined with a precise information transfer between brain regions and cells types, drives behaviors crucial for survival.”

The behaviors linked to species survival can be viewed in the context of this report from 2005: Feedback loops link odor and pheromone signaling with reproduction
But first, serious scientists must start with the anti-entropic virucidal energy of sunlight, which is what Schrödinger did 75 years ago.

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.) (pp. 73 and 74)

This evolutionary tree shows the split between primate and rodent lineages about 90 million years ago, before the emergence of Alu elements in primates and B/ID elements in rodents. These short interspersed elements evolved independently in the two lineages to play the same role in gene regulation. Credit: Bronwyn Lucas

Read more at: https://phys.org/news/2018-01-convergent-evolution-gene-humans-mice.html#jCp

The MicroRNAome Strikes Back: A Sokalian hoax (1)

Summary: How can this not be a Sokalian hoax? The creation of sunlight is not linked to anti-entropic virucidal energy-dependent  cell-type-specific epigenetic modifications. The quantized energy-dependent epigenetic modifications include RNA-directed DNA methylation, histone modification, nucleosome remodeling and higher-order chromatin reorganization. Instead, the magic of non-cell autonomous DNA methylation in plants is placed into in the context of the cytosine residue in CG, CHG and CHH sequence contexts (where H represents A, T or C).
See for comparison: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants January 2013
Reported as: Past 5,000 years prolific for changes to human genome

The findings confirm their earlier work suggesting that the majority of variants, including potentially harmful ones, were picked up during the past 5,000–10,000 years.

The variants are food energy-dependent and biophysically constrained by the physiology of pheromone-controlled reproduction in the context of the transgenerational epigenetic inheritance of all morphological and behavioral phenotypes.
See also: The palaeolithic diet and the unprovable links to our past November 2014

The picture is rapidly emerging that genetics play a pretty minor role in determining the specifics of our diet. Our physical and cultural environment mostly determines what we eat.

That fact can be placed into the context of how the physical environment of plant growth determines what cattle eat and how the food energy-dependent microRNAome prevents the virus-driven degradation of messenger RNA in the context of the transgenerational epigenetic inheritance of healthy longevity.
See for instance: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression December 2014

In the last few decades, sperm have been reported to carry both RNA and microRNA to the fertilized zygote [17], [18]. MicroRNA (miRNA) are important regulators in translation, and their altered expression often leads to disease or cancer.

The anti-entropic virucidal efffect of sunlight (see: Schrodinger, 1944) on soil bacteria and plant growth is linked from the physiology of pheromone-controlled reproduction in soil bacteria to all biophysically constrained energy-dependent cell type differentiation in all living genera via changes in base pairs, microRNA editing, RNA editing and the hydrogen-atom transfer in DNA base pairs in solution, which is required for energy-dependent RNA-mediated DNA repair.
That fact led to another Sokalian-like hoax.  See for review The Sokal Hoax [quantum gravity]:The Sham That Shook the Academy

gravity, Sokal argued, was a fiction that society had agreed upon, and science needed to be liberated from its ideological blinders.

The original Sokal hoax about the obvious facts linked to gravity appears to have set the precedent for Nonomura’s monograph. In the context of word usage by Richard P. Feynman, this example of human idiocy can be used to show that nothing has changed in the world of biologically uninformed theorists. They still have not linked quantum physics to biophysically constrained life on Earth.
Nonomura indirectly argues that the quantized energy of virucidal light is not required to link sunlight from cell type differentiation in plants to all biophysically constrained biodiversity in animals.  He, like many others, provides details about the conserved molecular mechanisms of RNA-mediated cell type differentiation. But Nonomura, like Masatoshi Nei, in Mutation-driven evolution, starts with the pathways and asks that others ignore the facts about sunlight.
Sokal asked that others ignore the facts about gravity. Nonomura’s follow-up is brilliant!
Ignore sunlight! Ignore the link from sunlight to plant growth!  Ignore food energy! Display your level of human idiocy.

See how the hoaxes ridicule peer-review:  List of scholarly publishing hoaxes
The list of nonsense papers does not include cases of scientific misconduct. The intent

“…is typically to expose shortcomings in a journal’s peer review process or to criticize the standards of pay-to-publish journals.

See how it’s done: Small RNA pathways responsible for non-cell-autonomous regulation of plant reproduction

Especially in grass species, 21- and 24-nucleotide phasiRNAs are abundant in anthers during premeiosis and meiosis.

In the context of “non-autonomous regulation” microRNAs become small RNAs, which become small interfering RNAs (siRNAs) that become: trans-acting siRNA (tasiRNA) and phased secondary siRNA (phasiRNA) in the context of claims about the evolution of eukaryotic species to land plants. The land plants have somehow evolved a unique non-cell autonomous epigenetically-effected mode of reproduction that is not linked to the energy-dependent creation of the microRNAs.
The epigenetically-effected pathways of energy-dependent non-cell-autonomous regulation are placed into the context of automagical cell type differentiation via microRNA-mediated biophyiscally constrained viral latency until the time comes to claim that genetic and epigenetic regulation must differ between the germline and somatic companions. After that, the author tries to explain how the small RNAs (e.g., microRNAs, siRNAs, tasiRNA, phasiRNA) are linked from nutrient energy-dependent pheromone-controlled viral latency in my model. Every aspect of food energy-dependent RNA-mediated cell type differentiation in animals begins with the non-cell-autonomous regulation of somatic-to-reproductive cell communication in model plants.
What then, is non-cell autonomous regulation? Is it magic?

…sperm and egg cells develop as part of the multicellular gametophyte. Thus, the non-cell-autonomous regulation by somatic companions plays important roles in efficient reproduction, in addition to the cell-autonomous regulation. Epigenetic silencing of transposable elements is one of the central events by which the germline transmits the error-free genome to the next generation.

The transfer of the error-free genome to the next generation is food energy-dependent and the pheromone-controlled physiology of reproduction typically ensures transmission of the error-free genome to the next generation.
How can Nonomura’s most recent publication not be a Sokalian hoax? The creation of sunlight is not linked to anti-entropic virucidal energy-dependent cell-type-specific epigenetic modifications. The quantized energy-dependent epigenetic modifications include RNA-directed DNA methylation, histone modification, nucleosome remodeling and higher-order chromatin reorganization. Instead, the magic of non-cell autonomous DNA methylation in plants is placed into in the context of the cytosine residue in CG, CHG and CHH sequence contexts (where H represents A, T or C).
That magic extends to the magic of non-cell-autonomous cell type differentiation, which somehow defines all biophysically constrained cellular identities during the development of unicellular organisms or multicellular organisms.
But see for comparison from 1999 (First author is KI Nonomura): Organization of the 1.9-kb repeat unit RCE1 in the centromeric region of rice chromosomes.
The organization of chromosomes links everything known to serious scientists about the energy-dependent creation of supercoiled DNA to all biophysically constrained viral latency via the physiology of reproduction and energy-dependent microRNA-mediated mechanisms of recombination.
See: Mechanisms of Recombination conference 
See also: What should I do with my life? 
This is somewhat silly advice from the company that discovered how to epigeneticallly prevents activation of the death gene. Use the information from them to help drain the academic and to help drain the political swamp. Help yourself live a healthy life by helping the Trump administration make America great again. Limit the ability of others to make money from your unnecessary suffering and premature death,

"Evolution of Man. - Undoubtedly there once lived upon the earth races of men who were much lower in their mental organization than the present inhabitants.

Autophagy is the antiphage defense strategy (2)

2/15/17 Energy as information and constrained endogenous RNA interference (video)
The 6.46 minute-long technical presentation (above) from the Precision Medicine Virtual Conference is difficult to understand.Thus, 10 months later, Nik Willmore asked:

12/24/17 What are your insights into CRISPR and mTOR, for a young audience? I’m not mocking you…yet, Humpty Dumpty. What is the basis of your unifying principle? Vibration? Bohmian morphogenetic fields? Modified Darwin? God? –Nik Willmore 

12/25/17 Replying to

God created the anti-entropic virucidal energy of sunlight and all energy-dependent biodiversity via the physiology of pheromone-controlled reproduction. I co-authored a book about that for a young audience in 1995/2002, and a 6-part series for today.

1/1/18 Replying to

Do you understand any aspect of how to model biophysically constrained biologically-based energy-dependent top-town causation and bottom-up effects on cell type differentiation via the physiology of reproduction and autophagy? The “walking fish” walks straight from quantum physics to quantum souls (2)

1/9/18 Viral suppressors of RNAi employ a rapid screening mode to discriminate viral RNA from cellular small RNA

My paraphrased summary:

RNA interference (RNAi) is our indispensable antiphage defense mechanism. Viruses escape the defense system by the theft of quantized energy, which encodes RNAi suppressors that prevent elimination of viral RNAs. The suppressors ensure energy-dependent virus accumulation.

1/12/18 Human cytomegalovirus-encoded miR-UL112 contributes to HCMV-mediated vascular diseases by inducing vascular endothelial cell dysfunction

The significantly altered pathways mainly include the mitogen-activated protein kinase signaling pathway, cell adhesion molecules, chemokine signaling pathway, cytokine-cytokine receptor interaction, circadian rhythm-mammal, mineral absorption, protein processing in the endoplasmic reticulum, proximal tubule bicarbonate reclamation, vasopressin-regulated water reabsorption, and arachidonic acid metabolism. In conclusion, hcmv-miR-UL112 could serve as a potential biomarker, and the miRNA-mediated regulation of signaling pathways might play significant roles in the physiological effects of hcmv-associated diseases.

1/12/18 H5N1 influenza virus-specific miRNA-like small RNA increases cytokine production and mouse mortality via targeting poly(rC)-binding protein 2

We conclude that miR-HA-3p is the first identified influenza virus-encoded microRNA-like functional RNA fragment and a novel virulence factor contributing to H5N1-induced ‘cytokine storm’ and mortality.

Virus-encoded microRNA-like functional RNA fragments are not novel virulence factors. They link the virus-driven degradation of messenger RNA to all pathology in all living genera via the theft of quanitzed energy, which typically links the fixation of RNA-mediated amino acid substitutions to healthy longevity.
See: Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs
All serious scientists know what goes wrong in the context of host microRNA-mediated regulation of viruses. They also know how it goes wrong. See Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

The serious scientists do not claim that viruses evolve. Scientists who make claims about evolution  typically do not know how to link the creation of sunlight from ecological variation to food energy-dependent pheromone-controlled ecological adaptation via the physiology of biophysically constrained reproduction and biophysically constrained viral latency. Indeed, most pseudoscientists do not know the difference between a mutation and an RNA-mediated amino acid substitution.
See for comparison: Mechanisms of Recombination conference Start: Sunday, May 20, 9.00am Finish: Tuesday, May 22, 6.45pm

Description

Genetic recombination provides an important mechanism for the repair of chromosome breaks caused by DNA damage or replication fork demise. Defects in the recombination process have been linked to cancer predisposition, in particular breast cancers caused by mutations in BRCA1, BRCA2 and PALB2, and also acute leukemias associated with the rare genetic disease Fanconi anemia. Understanding precisely how recombination occurs is of interest to workers in the fields of meiosis, DNA repair, replication, chromosome architecture and interactions, and chromatin biology.

Download provisional conference program
Excerpts:

Douglas Bishop (University of Chicago, US)
A primary function of the ATPase activity of E. coli RecA is to prevent accumulation of a toxic form of the protein bound to undamaged chromosomal sites

Maria Jasin (Memorial Sloan Kettering Cancer Center, US)
Protecting the genome by homologous recombination

The energy-dependent microRNA-mediated creation of enyzmes protects all organized genomes from the virus-driven degradation of messenger RNA that links the theft of quantized energy from mutations to all pathology.  Pseudoscientists who do not start with the creation of energy, have bastardized Darwin’s claims. His claims were based on placing “conditions of life” before natural selection. Conditions of life are energy-dependent and biophysically constrained by the mechanisms of pheromone-controlled recombination, which have been linked to autophagy by all serious scientists since 1925.
See also my RNA-mediated Facebook page and/or my RNA-mediated Facebook group and other tweets @jvkohl
The number of my tweet impressions since December 21, 2017 has climbed to more than 68,000 as the number of published works that mention “microRNA” has climbed to nearly 69,000. See for comparison: The tipping point (revisited): 68,000 publications, which was published to my other blog site on December 21, 2017.
See also: What Darwinists Fail to Consider (discussion attempt)
See also, this discussion attempt about the “spark of life.”
See also: Noncoding RNA Helps Cells Recover from DNA Damage

“The most logical, simple explanation is that the [noncoding RNA] counteracts the protein encoding form…”

My comment to the Scientist:

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.

See also: Search Results for “autophagy”

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

Elsevier fails to support the concept of autophagy

Summary: Who lets biologically uninformed theorists make presumptions about evolution after all serious scientists have linked light-harvesting from energy-dependent changes in electrons to ecosystems in all living genera via natural selection for food energy-dependent codon optimality. Who lets them pretend not to know that the pheromone-controlled physiology of reproduction links autophagy to the transgenerational epigenetic inheritance of healthy longevity? Who is causing the unnecessary suffering and premature death of your loved ones?
Elsevier publishing supports the pseudoscientific nonsense touted by theorists by who publish articles like this:
Neurotransmitter Funneling Optimizes Glutamate Receptor Kinetics (open access) Published Online: December 14, 2017 (with my emphasis)

These studies suggest that neurotransmitter binding is a directed process for which kinetics have been optimized (presumably by evolution)…

Our experiments reveal a strikingly elaborate management of ligand transport by AMPA receptors, whereby flexible positive charges ensure that glutamate binding reactions are fast. The existence of these pathways is surprising, and the fact that they alter the kinetics of receptor activity indicates that the molecular mechanisms that determine the action of neurotransmitters at receptors are more complex than previously thought. R660 is conserved between AMPA and NMDA receptors; in kainate receptors, R660 and R661 are replaced by lysine residues (Figure S8). It is possible that these helix F interactions also coordinate ligand binding in kainate and NMDA receptors. Given that electrostatic interactions are also important for coordination in other neurotransmitter binding sites (McCammon, 2009), these principles of ligand funneling may be general.

They linked the lysine residues (i.e., amino acid substitutions)  from electrostatic interactions to RNA-mediated cell type differentiation in all living genera. Their studies do not link any experimental evidence from electrostatic interactions or optimized kinetics to evolution. Evolution cannot optimize any aspect of energy-dependent kinetics. Evolution cannot optimize any aspect of energy-dependent RNA-mediated cell type differentiation, which is biophysically constrained by the physiology of pheromone-controlled reproduction.
The nonsense about evolution was reported as: Scientists chart how brain signals connect to neurons (with my emphasis)

Scientists at Johns Hopkins have used supercomputers to create an atomic scale map that tracks how the signaling chemical glutamate binds to a neuron in the brain. The findings, say the scientists, shed light on the dynamic physics of the chemical’s pathway, as well as the speed of nerve cell communications.

See: Life is physics and chemistry and communication
All experimental evidence of top-down causation links quantized energy from the speed of light on contact with water to energy as information-dependent changes in electrons and all ecosystems via the physiology of pheromone-controlled reproduction, which biophysically constrains viral latency. The use of supercomputers led the researchers to report findings that eliminate everything known to serious scientists about energy-dependent RNA-mediated cell type differentiation. It is common for theorists to eliminate energy as information-dependent changes and replace facts with mathematical models.
See for comparison: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition (open access)

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 (Ikemura, 1982; Akashi, 1994; Akashi & Gojobori, 2002; Drummond & Wilke, 2008; Kudla et al, 2009; Novoa & Ribas de Pouplana, 2012). The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

This is not just an alternative perspective. It is a refutation of neo-Darwinian pseudoscientific nonsense that was reported as: Codon optimality at genome transition

Nucleotide triplets, or codons, designate specific amino acids for protein synthesis. However, that is not their only job. In yeast and bacteria, codons contribute to RNA stability, with “optimal” codons stabilizing RNAs and “suboptimal” codons destabilizing RNAs. This is possible because multiple codons can encode the same amino acid.

See also: Human GW182 Paralogs Are the Central Organizers for RNA-Mediated Control of Transcription Elsevier — Cell Reports (August 15, 2017)

Nuclear RNAi, regardless of whether it is controlling splicing, transcription, or some other nuclear process, would have distinct advantages as a mechanism for evolution, because it would expand sequence-specific control of gene expression by miRNAs.

No experimental evidence of biologically-based cause and effect suggests that microRNAs evolved to control sequence-specific gene expression. The authors linked TNRC6, MED14, NAT10, and WDR5 to RNA-mediated gene activation. They inadvertently linked the energy-dependent de novo creation of microRNAs to Trinucleotide Repeat Containing (TNRC) 6A expression.  See: miR-26a-5p Regulates TNRC6A Expression and Facilitates Theca Cell Proliferation in Chicken Ovarian Follicles
The anti-entropic virucidal energy of sunlight links the creation of microRNAs and multiple codons to the creation of differences and similarities in the same amino acid. That fact has been ignored.
See also: MicroRNAs recruit eIF4E2 to repress translation of target mRNAs

There is increasing evidence indicating that translation initiation is a major target of miRNA repression…

…we provide evidence indicating that TNRC6A, the core component of RISC, can directly recruit eIF4E2 to target mRNA to repress translation.

They provided evidence that the energy-dependent de novo creation of microRNAs represses the expression of the mutations that cause all pathology.
See for example: Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention
Reported as: New Study Finds That Most Cancer Mutations are Due to Random DNA Copying ‘Mistakes’

John Hopkins Kimmel Cancer Center scientists report data from a new study providing evidence that random DNA copying “mistakes” account for nearly two-thirds of the mutations that cause cancer. Their research is grounded on a novel mathematical model based on DNA sequencing and epidemiologic data from around the world.

This was reported in the context of the “bad luck” theory of cancer (video).
For comparison see:  Why Is This Bacterium Hiding in Human Tumors?

 “The whole idea of bacteria in tumors is fascinating and unexpected,” said Dr. Bert Vogelstein, a colon cancer researcher at Johns Hopkins.

See for comparison: QuEBS: Workshop on Quantum Effects in Biological Systems  has established itself as an outstanding stage to present the research in the intersection of physics, chemistry and biology. This field has… established excitons in biology as the “must-talk-language” when describing the quantum effects in biological light-harvesting systems.
All serious scientists have linked the anti-entropic virucidal energy of sunlight from physics and chemistry to biophysically constrained viral latency via the de novo creation of microRNAs and the physiology of pheromone-controlled reproduction, which links autophagy to fixation of amino acid substitutions that stabilize the organized genome of all living genera in the context of autophagy.
Only biologically uniformed researchers, like Bert Vogelstein are surprised to find bacteria in tumors, because all serious scientists have link the viruses in bacteria from the degradation of messenger RNA in bacteria to the degradation of messenger RNA that causes all pathology in all living genera.
 
 
 

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.

Mouse morphs and primate diversity in 50 years

Excerpt:

Analysis of the crystal structure of deer mouse Hb at 1.8 Å resolution (24, 25) revealed that each of the eight rHb mutants is characterized by a unique constellation of hydrogen bonds within and between subunits (Table 2 and fig. S2). Additional hydrogen bonds between subunits of the same αβ dimer are formed in the presence of β128Ser (an L-type residue; fig. S2), which contributes to the observed epistasis between allelic α- and β-chain variants.

———————————
Energy-dependent RNA-mediated biophysically constrained viral latency (i.e., silencing of viral elements) protects all organized genomes from the degradation of messenger RNA that links mutations to all pathology. The mutations are caused by nutritional stress and/or social stress. That fact has been known to all serious scientists for at least 50 years. But see:
Silencing of viral elements: A cure for schizophrenia? ARTICLE Provisionally accepted

1. The problem.
Scientific evidence for various infectious agents as cause for psychosis in schizophrenia is not robust. Many pathogens that influence brain development might play a role in disease causation. It has been shown that influenza exposure before birth(Brown, 2012), exposure to herpes simplex during birth(Brown et al., 2011) or exposition to Toxoplasma gondii and other pathogens (Arias et al., 2012) increases risk for schizophrenia and/or compromises cognition. During psychosis viral and also ancient retroviral elements become may activated in the brain(Karlsson et al., 2001; Perron et al., 2012). The implication of this research for use in clinical practice is ambiguous, because a robust virus test is lacking.

Examples of human idiocy are the problem. See for comparison:

QuEBS workshop has established itself as an outstanding stage to present the research in the intersection of physics, chemistry and biology. This field has been developed in Lithuania for more than 20 years already. The beginnings could be associated with a series of “Light-harvesting Physics” international conferences, which were held in Lithuania (in Preila, 1992 and 1994, and in Birštonas, 1996). During these conferences, discussion of notable scientists and pioneers of Quantum Biology, such as Graham R. Fleming, Shaul Mukamel, Rienk van Grondelle, Richard Cogdell, Alfred Holzwarth and others, established excitons in biology as the “must-talk-language” when describing the quantum effects in biological light-harvesting systems.

Every aspect of biophysically constrained energy-dependent RNA-mediated life on Earth has refuted the pseudoscientific nonsense about emergence and evolution.

As climate warms, mice morph

Biologists document changes in teeth and skull structure in two species in southern Quebec over past 50 years

The ridiculous claim that the fixed amino acid substitutions were adaptive mutations proves how little the authors understand about biophysically constrained viral latency.

Excerpt 1)

“Biologists document changes in teeth and skull structure in two species in southern Quebec over past 50 years

Excerpt 2)

“These changes may be related to a dietary shift caused by climate change, combined with competition for food resources between the two species of mice, according to the researchers.”

All serious scientists know that food energy biophysically constrains the pheromone-controlled physiology of reproduction, which links the fixation of RNA-mediated amino acid substitutions to cell type differentiation in all living genera.
 
We have now arrived at the claims of biologically uninformed science idiots who tell us that two different species evolved in 50 years.
 

Excerpt 3)

“One question that remains to be settled is whether the changes are genetic, and will be passed on to future generations — actual evolution — or whether they represent “plasticity,” the capacity of some species to adjust to rapid environmental change.”

The facts about the transgenerational epigenetic inheritance of healthy longevity for comparison to virus-driven pathology have been exquisitely detailed. All serious scientists have dispensed with the nonsense that questions the capacity of some species to adjust to rapid environmental change. Ecological variation must be linked from the physiology of pheromone-controlled reproduction in all living genera via the conserved molecular mechanisms of RNA-mediated cell type differentiation that link fixation of amino acid substitutions to the morphological and behavioral phenotypes of all individuals and all species on Earth.

See for instance, on the same day that my 2013 refutation of Nei’s pseudoscientific nonsense about Mutation-driven evolution was published, this also was published: Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin

Epistasis is food energy-dependent. The energy must be biophysically constrained in the context of the physiology of pheromone-controlled transgenerational epigenetic inheritance. The creation of energy in a hydrogen atom was linked from the anti-entropic virucidal effect of sunlight to the stability of the organized genome of mice by hydrogen-atom transfer in DNA base pairs in solution and differences in the hemoglobin molecule of ecologically adapted species.

Analysis of the crystal structure of deer mouse Hb at 1.8 Å resolution (24, 25) revealed that each of the eight rHb mutants is characterized by a unique constellation of hydrogen bonds within and between subunits (Table 2 and fig. S2). Additional hydrogen bonds between subunits of the same αβ dimer are formed in the presence of β128Ser (an L-type residue; fig. S2), which contributes to the observed epistasis between allelic α- and β-chain variants.

See also:

…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 fact that every Angstrom is dynamic and the fact that energy-dependent changes in the microRNA/messenger RNA balance have been linked to biophysically constrained viral latency and all biodiversity was placed into the context of this parody:

 See also:


The Mechanical Properties of DNA are food energy-dependent and RNA-mediated

The elastic properties of the DNA molecule determine how it supercoils during replication, how it packs into confined biological structures and how it interacts with proteins during gene expression.

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

Nutrient-dependent atomic-level changes may determine the nucleotide changes in a specific base pair. The nucleotide changes appear to link nutrient-dependent single nucleotide polymorphisms (SNPs) from the availability of fruits and vegetables or fermented milk products to individual differences and to species differences in the need for certain vitamins. For example, cell type determination and differentiation are associated with the nutrient-dependent 3D distribution of amino acid substitutions as they accumulated during a history of ecological adaptations [32] in flies [9] and in humans [33]. Sex differences in behavior also appear to arise from the single-molecule and single cell levels in flies, which suggests that adaptive changes in behavior can be explained in the context of nutrient-dependent pheromone-controlled genome-environment interactions that alter circuit plasticity via amino acid substitutions [34].

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

The companion papers [162-163] told a new short story of ecological adaptations. In the context of climate change and changes in diet, the story began with what probably was a nutrient-dependent base pair change and a variant epiallele that arose in a human population in what is now central China. Apparently, the effect of the epiallele was adaptive and it was manifested in the context of an effect on sweat, skin, hair, and teeth. In another mammal, such as the mouse, the effect on sweat, skin, hair, and teeth is probably due to a nutrient-dependent epigenetic effect on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. The pheromones appear to control the nutrient-dependent epigenetically-effected hormone-dependent organization and hormone-activation of reproductive sexual behavior in mammals such as mice and humans, but also in invertebrates and in microbes as previously indicated.

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

See for comparison: The evolution of H2
Biohydrogen production from hyperthermophilic anaerobic digestion of fruit and vegetable wastes in seawater: Simplification of the culture medium of Thermotoga maritima
Mechanism of Nitrogenase H2 Formation by Metal-Hydride Protonation Probed by Mediated Electrocatalysis and H/D Isotope Effects
The claims that energy emerged or that differences in hydrogen and differences in species evolved outside the context of the energy-dependent creation of enzymes are among the most ridiculous examples of human idiocy that any serious scientist has ever encountered.
Claims about the emergence of life were again retracted on November 23, 20-17 and reported on December 5, 2017.

”Definitely embarrassing:” Nobel Laureate retracts non-reproducible paper in Nature journal

See: Comment awaiting moderation.

James V. Kohl December 7, 2017 at 4:35 am
The Science Behind the Game “Cytosis,” pits the collaborative efforts of 20 serious scientists against the pseudoscientific nonsense touted by theorists. The serious scientists know how energy-dependent RNA-mediated cell type differentiation occurs.
Resources (e.g., mRNA, ATP) are used to build enzymes, hormones, and/or receptors. Health points accumulate to show why food energy must be linked from the physiology of pheromone-controlled reproduction to biophysically constrained viral latency.
For comparison, Szostak and other theorists have been stuck with their ridiculous misrepresentations of emergence and neo-Darwinian evolution, which failed to consider Darwin’s “conditions of life.”
“Conditions of life” are energy-dependent. The energy is Schrodinger’s anti-entropic virucidal energy. It comes from sunlight and is epigenetically “trapped” in food via the physiology of reproduction.
Board Game:
Cytosis: A Cell Biology Game
Title:
Cytosis – The Science Behind the Game https://boardgamegeek.com/filepage/155090/cytosis-science-behind-game
See also: Two retractions of human idiocy
See also: Routing gene therapy directly into the brain

Once the genetically-engineered HSCs are transplanted into the brain’s ventricles, the crucial enzyme they contain helps to metabolize the materials that were previously building up and causing tissue damage.

A new lineage of cells descended from the transplanted HSCs — a type of cell called a myeloid — begin to scavenge and consume the excess material that is responsible for neurodegeneration.

The pheromone-controlled differentiation of these cell types was predicted in the context of claims that pheromones biophysically constrain all pathology in the mouse to human model, which has been thoroughly detailed since 1994.
See: [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)
See also: Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis

See also: Researchers Discover Key to Diseases in Mitochondrial DNA Mutations

Because the primary job of the mitochondrion is to produce energy, most of its genes are involved in pathways in the energy production process. Although it has a small genetic code, mtDNA contains the blueprints for building many of the enzymes and proteins that are needed to function in those pathways.
 
The virus-driven theft of quantized energy as information links the degradation of messenger RNA from mutations to all pathology in all living genera. The speed of light on contact with water has been linked to all energy-dependent RNA-mediated DNA repair in the context of the physiology of reproduction and the transgenerational epigenetic inheritance of healthy longevity.
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

Reporting new scientific truths is not allowed in the USA (2)

Summary: Genetic mutations do not drive evolution.  Energy-dependent RNA-mediated fixation of amino acid substitutions links the physiology of reproduction to biophysically constrained viral latency.
With minimal effort, you can peruse the science news each day to see how many pseudoscientists report their findings outside the context of food energy-dependent pheromone-controlled biophysically constrained RNA-mediated cell type differentiation.
See for example:
Type 2 diabetes has hepatic origins

The researchers are now working on identifying the endogenous ligand produced by the body, or on developing molecules that could mimic its function.

Clearly, they are aware of the fact that they must link food energy to the endogenous substrate without claiming that gene activation and the creation of the protein automagically occur.
Diabetes, obesity behind 800,000 cancers worldwide: study

“Our study shows that diabetes—either on its own or combined with being overweight—is responsible for hundreds of thousands of cancer cases each year across the world.”

Who did not know that?
New study finds mycobacteria can sense presence of proteins that cause disease

The transcription factor regulates the levels of the protein cargo transported by the machinery. When the bacteria sense the machinery is absent, the levels of the protein substrates are reduced.

Fat distribution in women and men provides clues to heart attack risk

“We hypothesized that there are gender-based differences in body composition and ectopic fat depots and that these could be associated with gender-specific risk profiles for diseases like diabetes, heart disease and stroke,” said lead author Miriam A. Bredella, M.D., radiologist at Massachusetts General Hospital and associate professor of radiology at Harvard Medical School in Boston.

Sex-differences in cell types link the food energy-dependent pheromone-controlled physiology of reproduction to RNA-mediated cell type stability in all living genera.
Women may be more vulnerable to concussions because of ‘leaner’ nerve fibers

The paper shows us that there is a fundamental, anatomical difference between male and female axons,” Smith said. “In the male axon, there are a great number of microtubules, which make the entire structure stronger, whereas in female axons, it’s more of a leaner type of architecture, so it’s not as strong.

This representation of energy-dependent RNA-mediated cell type differentiation is sexist. If researchers claimed there were racial differences in biophysically constrained cell type differentiation, the claim would be racist.

That’s the problem that all pseudoscientists have with cryo-EM. It makes everything that will be reported in the context of energy-dependent links from electrons to ecosystems appear to be racist in the context of A Civic Biology: Presented in Problems (New York, 1914)

Whole-transcriptome brain expression and exon-usage profiling in major depression and suicide: evidence for altered glial, endothelial and ATPase activity

Exploratory whole-exome analysis revealed higher expression of humanin-like 8 (MTRNR2L8, or HN8) in both suicide and depression (Figure 1, Supplementary Table 2). MTRNR2L8 is an isoform of the humanin gene (HN) (), a newly discovered mitochondrial-derived 24 amino acid peptide (), which is coded by nuclear DNA.

See also:

These effects appear to be driven primarily by depression, with the exception of genes involved in ‘DNA-dependent ATPase activity’, which appear to be greater in suicide but not depression. Results suggest cortical gene expression related to microglial, endothelial and glial cell functions may contribute toward or be altered in MDD and suicide, and identify the putative genes and pathways which may play a functional role in these disorders.

This claim makes it obvious that the researchers do not know the difference between an epigenetic effect on hormones and the affect of hormones on behavior. That explains their failure to link energy-dependent epigenetic effects from ATPase activity to changes in the microRNA/messenger RNA balance. That means they cannot link RNA-mediated differences in the cell types that protect organized genomes from the virus-driven degradation of messenger RNA to mutations and all pathology.

Heat, Hydrogen, and Togas

Ther­mo­to­gae are strict an­aero­bes and gram ne­ga­ti­ve. Their pep­ti­do­gly­can is uni­que in hav­ing as much D-ly­sine as the usu­al L-ly­sine. And, no LPS (or, at least, no LPS-ma­king en­zym­es), de­spi­te be­ing gram-ne­ga­ti­ve.

The stability of all organized genomes is energy-dependent and biophysically constrained by the fixation of amino acid substitutions in organized genomes. The amount of D-ly­sine compared to the amount of L-ly­sine links the dynamic control of chirality to the quantized energy-dependent creation of supercoiled DNA, which protects all organized genomes from the virus-driven degradation of messenger RNA that links mutations to all pathology.

 

The fact that hydrogen-atom transfer in DNA base pairs in solution links quantized energy as information from the creation of sunlight to the quality of RNA, which must be linked to energy-dependent DNA repair, seems to have escaped the attention of theorists.

Chemists reveal one mechanism of dihydrogen production by nitrogenase (with my emphasis)

There are 2 types of hydrogens in the catalytic cofactor (called FeMo-co): one located in a bridging position where it binds to two iron atoms (a bridging hydride), and one on a nearby sulfur atom ligands (basically a protonated sulfur atom: S-H). It turns out that during H2 evolution, the latter is the active partner. The S-H bond breaks and the resulting H+ moves toward the bridging hydride and protonates it forming H2: The calculations provide an explanation of the experimental observation that only one hydrogen is “active,” while the other is a mere spectator waiting for the arrival of its partner.
 

Can anyone help to link the calculations to the evolution of the two types of hydrogens in the context of Feynman’s claims about food energy and human idiocy?

A correspondent wrote:

Interesting chirality issues, however I know of no biological system where light directly changes polymer helicity, and this paper is not a biological system. Vines can change their macroscopic helicity, incredibly, just by single amino acid substitutions in different cytoskeltal monomer proteins.

Thanks. A single amino acid substitution at position 6 of the GnRH decapeptide in all vertebrates links the sense of smell in bacteria to the pheromone-controlled physiology of reproduction and all biophysically constrained biodiversity via achiral glycine. 

See also: Photoinduced charge transfer occurs naturally in DNA
Scientists identify the segmentation and consolidation mechanism of long-term memories

According to the research, published in the scientific journal Current Biology, the brain identifies context changes as “frontiers” in the flow of our experience and uses them to fragment the course of events into small units of memory that can be stored long-term. The study shows that this process takes place during the identification of a boundary event thanks to the rapid reactivation of the flow of information that precedes it.

The flow of information is energy-dependent and serious scientists have link the energy-dependent changes from RNA-methylation to RNA-directed DNA methylation and all biodiversity via the pheromone-controlled physiology of reproduction.
The article does not mention RNA-methylation, which means it is a compilation of pseudoscientific nonsense.
See for comparison: Experience-Dependent Accumulation of N6-Methyladenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice

The differential effects of m6A may depend on distinct cis-acting elements that are present on the RNA molecule which may interact with m6A, including micro-RNAs (Alarcón et al., 2015; Chen et al., 2015).

When physics gives evolution a leg up by breaking one

Genetic mutation may drive evolution, but not all by itself.

Genetic mutations do not drive evolution.  Energy-dependent RNA-mediated fixation of amino acid substitutions links the physiology of reproduction to biophysically constrained viral latency.
See Schrodinger (1944): and link the anti-entropic virucidal energy of sunlight to all biodiversity via the creation of RNA and the physiology of pheromone-controlled reproduction.

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 the reprint edition with the forward by Roger Penrose.
“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)
‘Mind’s eye blink’ proves ‘paying attention’ is not just a figure of speech

Mind’s eye blink is closely related to “attentional blink” that has been studied by Cornelius Vanderbilt Professor of Psychology David Zald and Professor of Psychology René Marois. Attentional blink is a phenomenon that occurs when a person is presented with a rapid series of images. If the spacing between two images is too short, the observer doesn’t detect the second image. In 2005, Zald determined that the time of temporary blindness following violent or erotic images was significantly longer than it is for emotionally neutral images.

Olfaction spontaneously highlights visual saliency map
Fear-related chemosignals modulate recognition of fear in ambiguous facial expressions
Global Sensory Impairment Predicts Morbidity and Mortality in Older U.S. Adults