Biology to a Physicist

Abiogenesis vs microRNA biogenesis

Summary: The pseudoscientific nonsense about abiogenesis that has been touted by Karo Michaelian and others like him has caused the unnecessary suffering and premature death of millions to billions of people by placing the pathogenic consequences of deregulated miRNAs into the context of ridiculous theories.
See for comparison: Structural diversity of supercoiled DNA and the parody from the same research group:
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Abiogenesis (2017)
Microscopic dissipative structuring and proliferation at the origin of life (Oct 13, 2017)

Some fundamental molecules of life are suggested to have been formed, proliferated, and evolved through photochemical microscopic dissipative structuring and autocatalytic proliferation under the UV-C/UV-B solar environment prevalent at Earth’s surface throughout the Archean. Evidence is given in the numerous salient characteristics of these, including their strong absorption in this spectral region and their rapid non-radiative excited state decay through inherent conical intersections. The examples of the dissipative structuring and dissipative proliferation of the purines and of single strand DNA are given. UV-C and UV-B-induced stationary state isomerizations and tautomerizations are shown to be crucial to the formation of the purines from hydrogen cyanide in an aqueous environment under UV-C light, while UV-C induced phosphorylation of nucleosides and denaturing of double helix RNA and DNA are similarly important to the production and proliferation of single strand DNA. This thermodynamic dissipation perspective provides a physical-chemical foundation for understanding the origin and evolution of life.

The suggestion is ridiculous. No serious scientist would claim that some fundamental molecules of life formed, proliferated, and evolved in the context of thermodynamic dissipation after the UV-C induced phosphorylation of nucleosides and denaturing of double helix RNA and DNA.
The functional structure of supercoiled DNA is energy-dependent.
All serious scientists start with the link from the sun’s anti-entropic virucidal energy on contact with water to the creation of ATP synthase; the creation of microRNAs; the creation of all other enzymes; the creation of all receptors; the creation of all hormones. That’s how serious scientists link microRNA biogenesis to all biophysically constrained food energy-dependent pheromone-controlled morphological and behavioral diversity on Earth.
MicroRNA biogenesis (2018)

The tipping point of 72,000 indexed published works that mention microRNAs was reached on 4/18/18
See: microRNA
Example: Arthropod viruses and small RNAs (2013)

Understanding the role of small RNAs in arthropod host-virus molecular interactions will facilitate manipulation of these pathways for both management of arthropod pests of agricultural and medical importance, and for protection of beneficial arthropods such as honey bees and shrimp. This review highlights recent research on the role of small RNAs in arthropod host-virus interactions with reference to other host-pathogen systems.

Example: MicroRNAs as mediators of insect host-pathogen interactions and immunity (2014)

In this review, we will discuss the latest developments in regards to the role of microRNA in insect host-pathogen interactions and provide some insights into this rapidly developing area of research.

Example: miRNA regulation of innate immunity (2018)

MicroRNAs (miRNAs) are small noncoding RNA and are pivotal posttranscriptional regulators of both innate and adaptive immunity. They act by regulating the expression of multiple immune genes, thus, are the important elements to the complex immune regulatory network. Deregulated expression of specific miRNAs can lead to potential autoimmunity, immune tolerance, hyper-inflammatory phenotype, and cancer initiation and progression. In this review, we discuss the contributory pathways and mechanisms by which several miRNAs influence the development of innate immunity and fine-tune immune response. Moreover, we discuss the consequence of deregulated miRNAs and their pathogenic implications.

The pseudoscientific nonsense touted by Karo Michaelian and others like him has caused the unnecessary suffering and premature death of millions to billions of people by placing the pathogenic consequences of deregulated miRNAs into the context of ridiculous theories.
See for comparison: Structural diversity of supercoiled DNA and the parody from the same research group:

See also: Michaelian K
and Retraction: Oligoarginine peptides slow strand annealing and assist non-enzymatic RNA replication (Nov 23, 2017)
The life’s works of all those who have ever touted their ridiculous claims about abiogenesis can now be placed into the context of the eternal significance of microRNAs. The energy dependent de novo creation of microRNA flanking sequences has repeatedly been linked from the physiology of pheromone-controlled reproduction to biophysically constrained viral latency and sympatric speciation in all living genera.
See: 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)
See also: Cytosis (for ages 10+)

Players take turns placing workers on available organelles within a human cell in order to collect resources (such as Carbohydrates or ATP!) or take actions (such as purchasing Cell Component cards or translating mRNA into Proteins!)

Players use their resources to build Enzymes, Hormones, and Hormone Receptors and also to help detoxify the cell – all of which score health points. The player with the most health points at the end of the game wins!

See for comparison: DNA Denaturing through UV-C Photon Dissipation: A Possible Route to Archean Non-enzymatic Replication (2014)

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.

On January 15, 2016 John Hewitt commented:  You have just described the founding principle and thermodynamic function of life
On April 17, 2018, I commented on the ridiculous claim this so-called science journalist made because he blocked me from seeing his tweets a few months ago.

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The MicroRNAome Strikes Back: A Sokalian hoax (8)

Defeating Diseases with Energy (January 9, 2018) is a thinly disguised attempt to help corporate giants continue to promote ridiculous neo-Darwinian theories. It features the works of Douglas C. Wallace, who failed to link the virus-driven degradation of messenger RNA to all pathology since he published: Neoplastic transformation is associated with coordinate induction of nuclear and cytoplasmic oxidative phosphorylation genes (1990).

Similar analysis of a cervical carcinoma (HeLa), fibrosarcoma (HT1080), and an Epstein-Barr virus (EBV)-transformed lymphoblastoid line (EBV-L) revealed that all three ANT isoforms were also expressed in these cells. Hence, changes in the expression of OXPHOS genes may be a common feature of transformed cells.

Did he not recognize the significance of the energy-dependent transformation of adenine (in the context of the adenine nucleotide translocator) and oxidative phosphorylation (OXPHOS) genes?
Did Douglas C. Wallace introduce the world to the pervasive nature of the first biologically-based Sokalian hoax, which was subsequently used to bastardize everything known to serious scientists about molecular epigenetics?
Is that how you become a corporate “Champion of Science?”
See for comparison: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)
Why isn’t Bruce McEwen a corporate “Champion of Science” in the context of his claims about the food energy-dependent creation of RNA via a type of “oxidative phosphorylation?”
When will so-called science journalists realize the difference between a serious scientist like Bruce McEwen and a pseudoscientist like Douglas C. Wallace?
Simply put, the difference is in their approach to explaining how biophysically constrained energy-dependent changes in base pairs are linked from fixation of RNA-mediated amino acid substitutions to the differentiation of all cell types. In all living genera, fixation of RNA-mediated amino acid substitutions occurs in the context of the physiology of pheromone-controlled reproduction, which links feedback loops to all biodiversity.
People like Douglas C. Wallace claim that “evolution did it.” Serious scientists put his ridiculous claim into the context of experimental evidence of biophysically constrained energy storage.
See: Long-range coherence and energy storage in biological systems  (1968)
Energy storage begins with the creation of energy and ends with the virus-driven degradation of messenger RNA that links mutations to all pathology. How many more victims of Sokalian hoaxes will there be? Who will help to prevent the next viral apocalypse? Will it be the “Trump Administration?”
I think that fact is obvious.
See: Double-layered protein nanoparticles induce broad protection against divergent influenza A viruses

The amino acid sequence of influenza matrix protein 2 ectodomain (M2e) is highly conserved among human seasonal influenza A viruses20.

Reported as: Researchers Develop Universal Vaccine To Protect Against Influenza A Viruses

“Vaccination is the most effective way to prevent deaths from influenza virus, but the virus changes very fast and you have to receive a new vaccination each year,”

See also: Lung-derived exosomal miR-483-3p regulates the innate immune response to influenza virus infection

Exosomes regulate cell-cell communication by transferring functional proteins and RNAs between cells. Here, to clarify the function of exosomes during influenza virus infection, we characterized lung-derived exosomal microRNAs (miRNAs).

For comparison see this Sokalian hoax: Comparison of miRNA evolution and function in plants and animals

MicroRNAs (miRNAs), as a major player in post-transcriptional regulation of gene expression, have been reported to regulate a broad variety of key biological processes, including growth, development and stress responses in both plants and animals. While the biogenesis and regulatory abilities of miRNAs have been extensively studied, the evolutionary history of miRNAs still needs more exploration. So far, several models explain the origination of plant and animal MIRNA (MIR) genes. Both inter-species and intra-species conservation and divergence of miRNAs exhibits functional adaptation to changing environments in evolution. Here we summarize recent progress in how these similarities and differences contribute to the characteristic features of miRNA evolution in the two kingdoms.

MicroRNAs do not have an evolutionary history. They link the creation of the sun to the creation of ATP to the creation of RNA. ATP did not evolve. RNA did not evolve. Amino acids did not evolve. Viruses do not evolve.
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.

See the NIH report: Flu infection study increases understanding of natural immunity
Natural immunity did not evolve!
For a historical perspective on the ridiculous claims about evolution, see: Neo-Darwinism has failed as an evolutionary theory (May, 1995) by Brian Goodwin

To understand why organisms look the way they do we need models that involve physical forces as well as biological variables, organised to produce organisms with specific morphologies, as described in my book, How the Leopard Changed its Spots.

See: Brian Goodwin:

In a critical review, biologist Catherine S. C. Price noted that although he had succeeded in providing an alternative to mutation as the only source of variation, he failed to provide an alternative to natural selection as a mechanism of adaptation.[7]

That claim has been echoed in the literature published by pseudoscients and so-called science journalists for more than two decades. Natural selection for food energy-dependent codon optimality has repeatedly been linked from the pheromone-controlled physiology of reproduction to all biophysically constrained biodiversity and ecological adaptation since the time we published The Scent of Eros: Mysteries of Odor in Human Sexuality (first published in May, 1995)
Helen Fisher said this about The scent of eros: mysteries of odor in human sexuality (by Kohl and Francoeur 1995): “This is science at its best, with adventure, ideas, and lots of facts.”
Reviewed by Mark Sergeant
Reviewed by Ralph Underwager, Institute for Psychological Therapies
Reviewed by Jan Peregrine
See also: 6 Amazon.com customer reviews
No experimental evidence of biologically-based cause and effect supports the ridiculous claims that Catherine S. C. Price, and others like her, seem to think link mutations to the molecular mechanisms of adaptation via natural selection. That fact explains why theorists must invent new theories and claim to be reconceptualizing their past pseudoscientific nonsense.
See: Theme issue ‘Re-conceptualizing the origins of life’ compiled and edited by Sara Walker and George Cody
For example: Review article: Exploring astrobiology using in silico molecular structure generation
See for comparison: Jerry Fodor Held High Ground to Evolution’s Militant Fundamentalists

Astrobiology doesn’t exist. What are its laws?

See also: The First Virus Communication Signals

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.

Enzyme-constrained interethnic biodiversity (3)

Excerpt: Understanding a “correlational mechanism” is like understanding mutation-driven evolution. You have a mutation. You have evolution. Thus, you understand the simple-minded magic of the correlation. No energy-dependent molecular mechanisms are required.
For comparison: Enzyme-constrained interethnic biodiversity is exemplified in Amish populations in the United States of America. Obviously, interethnic difference in genes matter.
See: Low cancer incidence rates in Ohio Amish (2009) Why Don’t The Amish Get Cancer? (2016)
See also: A null mutation in SERPINE1 protects against biological aging in humans (2017)
Reported as: An Internal Fountain of Youth: Why These Amish Live Longer And Healthier

Amish with this mutation also have significantly less diabetes and lower fasting insulin levels.

“The findings astonished us because of the consistency of the anti-aging benefits across multiple body systems,” said Dr. Douglas Vaughan, the lead author of the paper who has been studying PAI-1 for almost 30 years.

See also: Diabetes and Alzheimer’s correlation mechanism understood!
Understanding a “correlational mechanism” is like understanding mutation-driven evolution. You have a mutation. You have evolution. Thus, you understand the simple-minded magic of the correlation. No energy-dependent molecular mechanisms are required.
For comparison, see: Aerobic Glycolysis in the Human Brain Is Associated with Development and Neotenous Gene Expression
The article links imaging to the required molecular mechanisms of behavioral development. Finally,  all serious scientists can move forward as they should have been doing for more than a decade since Panksepp et al (2002) published Comparative approaches in evolutionary psychology: molecular neuroscience meets the mind. His group won the same award that my group won for publication in 2001 of: Human pheromones: integrating neuroendocrinology and ethology.
Comparative approaches start with the creation of quantized energy and link it to aerobic glycolysis. Clearly, all serious scientists have been following the experimental evidence that led to publication of: Redefining neuroendocrinology: Epigenetics of brain-body communication over the life course (November 15, 2017) by Bruce McEwen and Loss of APOBEC1 RNA-editing function in microglia exacerbates age-related CNS pathophysiology (November 24, 2017), which was co-authored by Bruce McEwen.
Brain-body communication is food energy-dependent. The obvious link from the virus-driven degradation of messenger RNA to mutations and all pathology via gene losses has since led to the end of the hunt for drugs to treat some neurodegenerative diseases. See Enzyme-constrained interethnic biodiversity (6)
Unfortunately, even though Bruce McEwen set the stage for achieving world peace in the context of interethnic biodiversity, he did not win the 2017 Nobel Peace Prize as I predicted he would.
See: Predicting who wins the 2017 Nobel Prizes

Bruce McEwen has since helped others to link nutrient-stress and social stress from the virus-driven degradation of messenger RNA to amino acid substitutions in the context of the physiology of pheromone-controlled reproduction. For example, the substitution of one amino acid in the cell types of mammals protects them from the virus-driven energy theft that links amino acid substitutions in viruses to all pathology. McEwen’s works are the only known works of a serious scientist who has continued to refute the pseudoscientific nonsense touted by neo-Darwinian theorists since before 1964.

Indeed, most people who are not yet dead, probably do not know how people like Bruce McEwen have linked food energy-dependent “Interethnic Genetic Similarities and Differences” to world peace.
But see: Living in a Genetic World: How Learning About Interethnic Genetic Similarities and Differences Affects Peace and Conflict
Reported as: For groups in conflict, genes matter 

“In conflict contexts, we often see attempts to emphasize genetic differences between groups. We saw that in Rwanda. We saw that in Bosnia,” Kimel said. “One thing we suggest in the paper is that groups like International Crisis Watch and Genocide Watch should go on heightened alert when they see this kind of rhetoric in conflict contexts.”

The paper also cites popular media reports on the genetic differences between groups with a history of conflict. Such articles are cause for concern, Kimel said, because they often fail to mention just how genetically similar humans are.

The similarities in all humans have been linked to interethnic differences in only two genes via publication of Brief report: Geographic variation in EGFR mutation frequency in lung adenocarcinoma may be explained by interethnic genetic variation. I reiterate: The full article can be downloaded from here:

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

Evolution outside the context of "the light of evolution"

Summary: The claim that two mutations led to the weekend resurrection of the bacterial flagellum cannot be supported with the claim that only one amino acid substitution differentiates the cell type of two different primate species (gorillas and humans) from two similar species (chimpanzees and humans). The fact that mutations are not amino acid substitutions can be supported in the context of food energy-dependent pheromone-controlled cell type differentiation in species from microbes to humans.
Nothing in Biology Makes Any Sense Except in the Light of Evolution (1973)

…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.

Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system (2015) with my emphasis. As a service to the community this article is available to view for free.

After 96 hours of incubation of AR2 and Pf0-2x at room temperature on SMM, two breakout mutations were visible, conferring first slow (AR2S and Pf0-2xS) and then fast (AR2F and Pf0-2xF) spreading over the agar surface (Fig. 1A). The AR2F strain produces flagella, but we could not detect flagella in electron microscopy samples for AR2S (Fig. 1B). Genome resequencing revealed a single-nucleotide point mutation in ntrB in strain AR2S, causing an amino acid substitution within the PAS domain of the histidine kinase sensor NtrB [Thr97→Pro97 (T97P)] (13). The fast-spreading strain AR2F had acquired an additional point mutation in the σ54-dependent EBP gene ntrC, which alters an amino acid (R442C) within the DNA binding domain (Table 1 and table S2).

The claim that two mutations led to the weekend resurrection of the bacterial flagellum cannot be supported with the claim that only one amino acid substitution differentiates the cell type of two different primate species (gorillas and humans) from two similar species (chimpanzees and humans). The fact that mutations are not amino acid substitutions can be supported in the context of food energy-dependent pheromone-controlled cell type differentiation in species from microbes to humans.
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model for comparison to: Mutation-Driven Evolution
The cell biology game “Cytosis” will help to end the neo-Darwinian pseudoscientific nonsense touted in the context of mutation-driven evolution.
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 virus-driven degradation of messenger RNA causes the mutations that all serious scientists have linked to all pathology. Protection from the virus-driven degradation of messenger RNA is food energy-dependent and pheromone-controlled. In Dobzhansky’s example, the alpha chains of hemoglobin differ “… in a single amino acid (out of 141) in the gorilla.” Pseudoscientists must now try to place that fact back into the context of their ridiculous theories without linking a single amino acid substitution in the organized genomes of all other species to all biodiversity on Earth, which is what some Young Earth Creationists (YEC) have done.
Watch as the pseudoscientists try and fail to account for more than 1200 nutrient-dependent pheromone-controlled hemoglobin variants in human populations.
The pseudoscientists must ignore the facts about the hemoglobin variants: Updates of the HbVar database of human hemoglobin variants and thalassemia mutations (2014) with my emphasis

Hemoglobinopathies are the commonest single-gene genetic disorders in humans, resulting from pathogenic genome variants in the human α-like and β-like globin gene clusters (reviewed in 1). Single nucleotide substitutions or indels [INsertions/DELetionS] can lead to several hemoglobin variants owing to amino acid replacements, while molecular defects in either regulatory or coding regions of the human HBA2, HBA1, HBB or HBD genes can minimally or drastically reduce their expression, leading to α-, β- or δ-thalassemia, respectively.

See for comparison: In the Light of Evolution

In this cross journal series, BMC Biology, BMC Evolutionary Biology and Biology Direct  bring together a collection of articles exploring how evolutionary principles applied across the spectrum of biology can shed light on a diverse range of topics from molecules to ecosystems, and with a particular emphasis on human genetics, interactions with the environment, and health and disease. Selected research articles will be included in addition to invited reviews and comment.

We will consider Research manuscripts of exceptional interest on the following topics (with my emphasis)
•    Evolution of morphological change
•    Understanding and treating disease in the light of evolution
•    Origins of evolutionary complexity
•    Human evolutionary biology in a post-genomic era
•    Anthropogenic effects on evolution
•    Evolutionary insights into genome variation, and vice versa
•    Host-parasite interactions
•    Evolutionary lessons from large-scale genomics
•    Insights from ancient DNA on human origins
•    Molecular mechanisms of evolution
•    Applied microbial evolution 
•    Evolutionary ecology
•    Genomics and the evolution of development

The only consideration of the nutrient energy-dependent pheromone-controlled physiology of reproduction that links RNA-directed DNA methylation from atoms to ecosystems via fixation of amino acid substitutions in organized genomes may be the articles about  Host-parasite interactions.  The interactions involve energy-dependent ecological adaptations or extinction. Virus-driven energy theft causes the extinctions via the theft oif quantized energy as information. Theft comes after the creation of virucidal light, which is the ultraviolet light that comes from sunlight. That fact, which indicates “agency” in the context of “creation” is not likely to be considered in the context of Insights from ancient DNA on human origins.
Clearly, Dobzhansky (1973) knew that all neo-Darwinian theorists were biologically uninformed science idiots and that they always would be. The fact that he placed the virucidal energy of ultraviolet light into his expressed “Creationist” views with a title that refuted all the pseudoscientific nonsense attests to his sense of humor, and the inability of theorists to “get the joke.”

…organic diversity becomes, however, reasonable and understandable if the Creator has created the living world not by caprice but by evolution propelled by natural selection. It is wrong to hold creation and evolution as mutually exclusive alternatives. I am a creationist and an evolutionist. Evolution is God’s, or Nature’s, method of Creation. Creation is not an event that happened in 4004 B.C.; it is a process that began some 10 billion years ago and is still under way.

There is no support for the ridiculous claim that Creation is a “process” that began some 10 billion years ago. There is a model that places all human biodiversity into the context of food energy-dependent ecological adaptations that protect all organisms from the virus-driven degradation of messenger RNA in the context of their pheromone-controlled physiology of reproduction.
Watch as the facts about Creation are removed from consideration because the focus of these articles is on support for ridiculous theories. Remember this:

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

  1. Dosage-sensitive genes in evolution and disease

    For a subset of genes in our genome a change in gene dosage, by duplication or deletion, causes a phenotypic effect. These dosage-sensitive genes may confer an advantage upon copy number change, but more typic…

  2. Q&A: Where did the Neanderthals go?

    Genomic evidence has demonstrated that humans and Neanderthals interbred. Today, the genomes of most individuals outside Africa contain 2–3% Neanderthal DNA. However, it is still hotly debated why the Neandert…
  3. Biological function in the twilight zone of sequence conservation

    Strong DNA conservation among divergent species is an indicator of enduring functionality. With weaker sequence conservation we enter a vast ‘twilight zone’ in which sequence subject to transient or lower cons…
  4. Examining non-LTR retrotransposons in the context of the evolving primate brain

    Researchers have long sought to understand the genetic basis of the cognitive differences between primates, with particular focus on the human brain. Although all mutational types have worked in concert with e…
  5. Q&A: What is human language, when did it evolve and why should we care?

    Human language is unique among all forms of animal communication. It is unlikely that any other species, including our close genetic cousins the Neanderthals, ever had language, and so-called sign ‘language’ i…
  6. Peto’s Paradox: how has evolution solved the problem of cancer prevention?

    The risk of developing cancer should theoretically increase with both the number of cells and the lifespan of an organism. However, gigantic animals do not get more cancer than humans, suggesting that super-hu…
  7. Non-model model organisms

    Model organisms are widely used in research as accessible and convenient systems to study a particular area or question in biology. Traditionally only a handful of organisms have been widely studied, but moder…
  8. Can a biologist fix a smartphone?—Just hack it!

    Biological systems integrate multiscale processes and networks and are, therefore, viewed as difficult to dissect. However, because of the clear-cut separation between the software code (the information encode…
  9. Open questions: Tackling Darwin’s “instincts”: the genetic basis of behavioral evolution

    All of us have marveled at the remarkable diversity of animal behaviors in nature.
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

Pattern recognition vs evolutionary processes (revisited)

Summary: Recent findings suggest that polyphenols display the ability to reverse adverse epigenetic regulation involved in pathological conditions, such as obesity, metabolic disorder, cardiovascular and neurodegenerative diseases, and various forms of cancer.
That suggests the ignorance of pseudoscientists who fail to link pattern recognition from the food that organisms eat to the pheromone-controlled physiology of reproduction via microRNAs is the cause of all pathology.

From egg to the air: 21 days of bee development condensed into one mesmerising minute

After just three weeks of development, worker bees emerge from their brood cells fully formed, flying out to begin supporting their hive. In a stunning high-definition time-lapse video, the US photographer Anand Varma follows the bee’s stages of development from egg to larvae to pupa to worker bee, with a sprightly score to match the insects’ rather startling journey into being.

From Fertilization to Adult Sexual Behavior links the 21 days of bee development to food energy-dependent pheromone-controlled RNA-mediated biodiversity in all living genera via the molecular mechanisms detailed in Nutrient-dependent/pheromone-controlled adaptive evolution: a model.

This model details how chemical ecology drives adaptive evolution via: (1) ecological niche construction, (2) social niche construction, (3) neurogenic niche construction, and (4) socio-cognitive niche construction. This model exemplifies the epigenetic effects of olfactory/pheromonal conditioning, which alters genetically predisposed, nutrient-dependent, hormone-driven mammalian behavior and choices for pheromones that control reproduction…

The model is a refutation of neo-Darwinian pseudoscientific nonsense that linked atoms to ecosystems in Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems via food energy-dependent changes in microRNAs.

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.

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

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 innate ability to fend off attacking viruses links changes in chirality to autophagy and supercoiled DNA, which links the physiology of reproduction to the viral latency that protects all organisms from the virus-driven degradation of messenger RNA. The virus-driven degradation of messenger RNA is linked from mutations to all pathology by all serious scientists.
For example, see:Two new studies offer insights into gastrointestinal dysfunction in Parkinson’s patients

The GI distress has repeatedly been linked from the virus-driven degradation of messenger RNA in gut bacteria to all pathology via links from quantum physics to supercoiled DNA, which protects all organized genomes from virus-driven pathology. You need only look up “microRNA” in a search of the PubMed database to learn what theorists are not telling you about biologically-based cause and effect.

See also: Cell senescence is regulated by innate DNA sensing
The innate immune cells use a host of to sense and identify foreign parts of an invading pathogen, such as the DNA of a virus. DNA-sensing is accomplished through a two-receptor system comprising an enzyme called cGAS and an adaptor molecule called STING. Once activated, the cGAS-STING pathway triggers the production of inflammatory proteins that help fight off the pathogen.
The energy-dependent de novo creation of G protein-coupled receptors links the virus-driven degradation of messenger RNA to all pathology.  See: Olfaction Warps Visual Time Perception
For an example of someone who has failed to link pattern recognition to top-down causation and all biophysically-constrained biologically based-cause and effect, see: Discovering Hidden Temporal Patterns in Behavior and Interaction: T-Pattern Detection and Analysis with THEME™
Magnus S. Magnusson, who I sometimes describe as an atheistic hate-monger, claims that my model and all my comments to his FB page are:

“Ridiculously irrelevant. I may not be intelligent, but I give keynotes at international conferences in proteomics and mass spectroscopy and in a few weeks in nanotechnology. However, I have mostly worked on the biology of behavior and neuroscience especially regarding neuronal interactions in the brain with the University if Cambridge, UK.”

He won’t answer any questions about the role of energy-dependent receptor-mediated interactions that link the de novo creation of the receptors to all biologically-based cause and effect. He does not seem to grasp the fact that viruses steal the quantized energy that links the de novo creation of the receptors to healthy longevity, which may be why he cannot link virus-driven energy theft to all pathology.
See for comparison: Evolutionary processes shaping diversity across the Homo lineage

These results show that genetic drift, and, likely, small population sizes were important factors shaping the evolution of Homo and many of its novel traits, but that selection played an essential role in driving adaptation to new contexts.

When all else fails to convince any serious scientist, pseudoscientists will still have their “evolutionary processes.” For comparison, serious scientists will continue to link what organisms eat to the physiology of their pheromone-controlled biodiversity and use microRNA therapy to effectively treat or cure all pathology.
Study shows mango consumption has positive impact on inflammatory bowel disease
Facts about food consumption and ecological adaptations include links to the control of virus-driven messenger RNA degradation and control of inflammatory bowel disease. The facts make sense in the context of this model. Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

See also: Mango polyphenolics suppressed tumor growth in breast cancer xenografts in mice: role of the PI3K/AKT pathway and associated microRNAs
See also: Dietary polyphenols and chromatin remodeling
Recent findings suggest that polyphenols display the ability to reverse adverse epigenetic regulation involved in pathological conditions, such as obesity, metabolic disorder, cardiovascular and neurodegenerative diseases, and various forms of cancer.
See also: This brief exchange with Jay R. Feierman
James V. Kohl: “Evolution by natural selection cannot be the outcome if something is not first selected. Selection is always for nutrients. It is as simple as that.”
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.
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: New Research Shocks Scientists: Human Emotion Physically Shapes Reality!
1)

In the presence of negative emotions the DNA tightened. In the presence of positive emotions the coils of the DNA relaxed.

The scientists concluded that “Human emotion produces effects which defy conventional laws of physics.”

2)

The DNA was placed in a different room in the same building. Both the donor and his DNA were monitored and as the donor exhibited emotional peaks or valleys (measured by electrical responses), the DNA exhibited the IDENTICAL RESPONSES AT THE EXACT SAME TIME.

3)

The third experiment proved something pretty shocking!

Scientists observed the effect of DNA on our physical world.

Light photons, which make up the world around us, were observed inside a vacuum. Their natural locations were completely random.

Human DNA was then inserted into the vacuum. Shockingly the photons were no longer acting random. They precisely followed the geometry of the DNA.

Scientists who were studying this, described the photons behaving “surprisingly and counter-intuitively”. They went on to say that “We are forced to accept the possibility of some new field of energy!”

They concluded that human DNA literally shape the behavior of light photons that make up the world around us!

Until you link quantum physics to quantum souls via olfaction, you may not understand any claim about light-induced energy-dependent changes in the endogenous substrate of all cell types that links the creation of RNA from top-down causation to every aspect of energy-dependent RNA-mediated cell type differentiation.
Human DNA does not shape the behavior of light photons. The speed of light on contact with water links the anti-entropic virucidal energy of sunlight to the de novo creation of amino acids and supercoiled DNA via feedback loops. The experiments linked the feedback loops from behavior to changes in DNA, and biologically uninformed science idiots claimed that DNA shapes the behavior of light photons.
The idiots (people who have no professional expertise in any scientific discipline) claim that “…we are connected to our DNA beyond space and time.”
See for comparison: Olfaction Warps Visual Time Perception
At this level of examination, the researchers link the sense of smell in bacteria from quorum-sensing to the physiology of pheromone-controlled reproduction in all living genera via the honeybee model organism and our visual perception of energy and mass in the context of the space-time continuum via feedback loops. Nothing happens to us that is outside our ability to unconsciously perceive energy and mass. No magic exists in the context of facts like this: Feedback loops link odor and pheromone signaling with reproduction
See also: Roger Penrose On Why Consciousness Does Not Compute

…I asked him if he thinks there’s any inherent meaning in the universe. His answer surprised me. “Somehow, our consciousness is the reason the universe is here.” So does he think there’s intelligent life—or consciousness—somewhere else in the cosmos? “Yes, but it may be extremely rare.” But if consciousness is the point of this whole shebang, wouldn’t you expect to find some evidence of it beyond Earth? “Well, I’m not so sure our own universe is that favorably disposed toward consciousness,” he said. “You could imagine a universe with a lot more consciousness that’s peppered all over the place. Why aren’t we in one of those rather than this one where it seems to be a rather uncommon activity?

“So, yes, we want to see the purpose of it. I don’t know. Maybe it’s attributing the wrong word. Purpose—what does that mean?” He chuckled.

Evolution–who thinks that the purpose of life can be placed into the context of ridiculous theories about evolutionary processes.
See for comparison: Structural diversity of supercoiled DNA (and this parody). See also: Chemists Know and m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs
 

achiral-glycine

Energy-dependent microRNA biogenesis

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.

amino acid homeostasis

Energy-dependent pheromone-controlled entropy (4)

Solar-driven reforming of lignocellulose to H2 with a CdS/CdOx photocatalyst
Reported as: Scientists harness solar power to produce clean hydrogen from biomass
They claim that the rigid structure of nature’s equivalent to armored concrete evolved to protect plants and trees from degradation. They don’t make claims about what might cause the degradation.
They start with the likelihood that degradation automagically occurs. That led them to design a combination of catalyst and solution that mimics how the anti-entropic energy of sunlight is linked to the potential of hydrogen, which is referred to as pH. Their design allowed them to extract the potential of hydrogen in the context of naturally occurring hydrogen-atom transfer in DNA base pairs in solution. They placed their simple design into the context of the evolution of armored concrete.

Pieces of wood, paper and leaves were placed in test tubes and exposed to solar light.

Their sunlight-powered extraction technology reminds me Schrodinger’s (1944) inference. Schrodinger seemed to suggest that someone designed an anti-entropic force, when he attempted to support the answer to his question: “What is Life.”
Theosophically, the God of the Holy Bible and Schrodinger both seemed to be saying that God might have used “the force” as if it came from the “Star Wars” series of movies. The sun could be like other stars and brave souls used “the force” to protect other people from harm.
In the context of the movies series, God, Schrodinger, and all serious scientists have detailed every aspect of how the conserved molecular mechanisms of RNA-mediated protein folding chemistry protect all organized genomes from virus-driven energy theft and genomic entropy.
For comparison, their design enables the production of clean hydrogen from unprocessed biomass. They think they have created a viable alternative to high temperature gasification, which appears to be a renewable means of hydrogen production. It could be compared to God’s way of ensuring that food energy is linked to the physiology of reproduction via endogenous RNA interference and to all biodiversity via energy-dependent biophysically constrained supercoiled DNA. The supercoiled DNA is the linked to chromosomal rearrangements that protect organisms from evolving into something different than their ancestors.
However, their design runs in reverse. They are taking the hydrogen energy out instead of putting it into supercoiled DNA via what is known about quantum physics and how subatomic particles must be linked to the energy-dependent de novo creation of all biodiversity and/or the virus-driven energy theft that appears to be destroying it.

For comparison, this claim links the anti-entropic virucidal energy of sunlight on contact with water from the creation of nucleic acid precursors to all healthy longevity and biodiversity on Earth via the physiology of reproduction.
Virus decomposition provides an important contribution to benthic deep-sea ecosystem functioning

Viruses proliferate at the expense of their hosts. …approximately 25% of viruses released by lysed prokaryotic cells are decomposed at fast rates. We show that… virus decomposition provides a major source of labile organic compounds able to sustain the microbial food webs and nutrient cycling at a global scale.

If you are a theorist who still does not know where the anti-entropic force comes from that prevents virus-driven energy theft from destroying all life on earth, find out more about how the virucidal effect of sunlight feeds the world in the context of the nutrient energy-dependent pheromone controlled physiology of reproduction.
It may be too late for you to become a serious scientist, but at least you will not continue to be one of the pseudoscientists who had us outnumbered since the time neo-Darwinism was invented.
See for an example of a pseudoscientist:
7/25/13
Jay R. Feierman: Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.

Light-induced-conformer-intercoversion-of-hydrogen-bond

Energy-dependent pheromone-controlled entropy (2)

See also: Energy-dependent pheromone-controlled entropy (1)
Let’s make peer review scientific

…peer review is often biased and inefficient. It is occasionally corrupt, sometimes a charade, an open temptation to plagiarists. Even with the best of intentions, how and whether peer review identifies high-quality science is unknown. It is, in short, unscientific.


The androgynous baby-faced boy or girl pictured among those wearing pink “crotch” hats appears to representing others at the March for Women. The sign may also be representing the intent of one of the organizers whose support for terrorists became better known after this March.
Next comes the March for Science, where anyone whose photo appears can be asked what area of scientific expertise most interested them. Attempts will be made to learn more about what they did to link energy-dependent changes in angstroms from sunlight to ecosystems in all living genera via hydrogen-atom transfer in DNA base pairs in solution.

See for example: Quantifying Intracellular Rates of Glycolytic and Oxidative ATP Production and Consumption Using Extracellular Flux Measurements

Abstract excerpt:

Measurement of ATP use revealed no significant preference for glycolytic or oxidative ATP by specific ATP consumers. Overall, we demonstrate how extracellular fluxes quantitatively reflect intracellular ATP turnover and cellular bioenergetics.

The energy-dependent extracellular fluxes link pheromone-controlled entropy from cellular bioenergetics to the physiology of reproduction. Virus-driven energy theft compromises the conserved molecular mechanisms of cellular bioenergetics.
See for example: Endothelial cell tropism is a determinant of H5N1 pathogenesis in mammalian species

…our study demonstrates that endothelial cell tropism is a determinant of the high virulence associated with HPAI H5N1 infection in mammalian hosts. By utilizing endogenous miRNA mediated restriction of viral tropism, we demonstrate that H5N1 infection of endothelial cells results in increased cytokine production in the lungs and loss of endothelial barrier function, which culminates in vascular leakage in the lungs. In addition, extrapulmonary spread of H5N1 virus likely occurs via the hematogenous route by infection of endothelial cells.

They link virus-driven energy theft from microRNAs in bacteria to messenger RNA degradation in archaea and L-forms (cells without walls). They fail to link energy theft to the substitution of nutrient energy-dependent amino acid substitutions in viruses, which links viruses to pathology in all living genera.
See for example: Identification of amino acid substitutions supporting antigenic change of influenza A(H1N1)pdm09 viruses

In conclusion, substitutions in or near the RBS can influence the antigenic properties of A(H1N1)pdm09 viruses. Based on the current and previous studies of antigenic change of influenza A viruses (11, 12), it is probable that emerging antigenic variants of A(H1N1)pdm09 viruses will escape from population immunity because of substitutions in or near the RBS. However, our results also suggest that the presence of antibodies directed to epitopes on seasonal A(H1N1) and A(H1N1)pdm09 viruses in much of the population limits the number of antigenic variants that can emerge to cause new epidemics.

Antigenic variants that are biophysically constrained cannot “emerge.” Nutrient stress or social stress must first break the biophysical constraints or there would be no new epidemics. That fact means that nutrient-dependent pheromone-controlled neurogenesis links the physiology of reproduction to ecological adaptations in all cell types of all individuals of all living genera, including organisms with no brain. If you start from neurogenesis in the human brain without realizing that it is pheromone-controlled, you may never learn how food odors and pheromones link the physiology of reproduction to the transgenerational epigenetic inheritance of all morphological and behavioral diversity via conserved molecular mechanisms of endogenous RNA interference.
See also from 6 years ago: Reproduction: A New Venue for Studying Function of Adult Neurogenesis?

Recent studies disclose that SVZ neurogenesis is under regulation of reproductive cues like pheromones.

Some recent debate about this fact was published to the Discover Magazine blog site in the context of accurate claims that Ben Carson made about learning and memory. A anonymous character with the screen name “Neuroskeptic” caused me to voice some concerns about the intelligence of people who accused Ben Carson, a pediatric neurosurgeon, of being wrong about anything.
See: Ben Carson and the Power of the Hippocampus 3/10/17

See also: Social phobia: Indication of a genetic cause — reported on “medicalxpress”
Excerpt: The cause of genetic illnesses often lies in the SNPs.
My comment: The energy-dependent differences in the SNPs is RNA-mediated. In this case, the differences link RNA methylation from endogenous RNA interference to learning and memory via experience-dependent cell type differentiation during life history transitions.
For example, one amino acid substitution (COMT Val158Met) was already linked to differences in the behavior of adolescents and adults. When will Neuroskeptic and others admit that they need to learn more about biologically-based cause and effect before they attack people like Ben Carson.

My comment from 3/11/17
See also:Reproduction: A New Venue for Studying Function of Adult Neurogenesis?” (2011) Cell Transplant

Excerpt: …the number of dividing neurons in the hippocampus of female sheep increased robustly (43), which is accompanied with a sharp increase in circulating luteinizing hormone. Additionally, luteinizing hormone level and hippocampal neurogenesis were also upregulated by the soiled bedding. With the use of prolactin and leutinizing hormone receptor knock-out mice, it was confirmed that the hippocampal neurogenesis is due to the increase of the luteinizing hormone but not prolactin; in contrast, prolactin is the regulatory factor of SVZ neurogenesis (69).

Neuroskeptic displayed the ignorance of all theorists and left them with no excuse to say anything more about Ben Carson, or anyone else who intends to help the President of the United States “Make America Great Again.” Only biologically uniformed liberals will continue their attempts to stop President Trump. The anti-entropic effect of pheromones on GnRH and luteinizing hormone links food odors and pheromones from feedback loops to the physiology of reproduction in all vertebrates via the substitution of the achiral amino acid glycine in position 6 of the GnRH decapeptide.

With co-authors, Donald Pfaff did this in the context of autism. For example, substitution of the achiral amino acid glycine in position 6 of the GnRH decapeptide also links food odors and pheromones from stress-linked changes and feedback loops to sex-specific gene–environment interactions via the hypothalamic-pituitary-gonadal axis.
See: Sex-specific gene–environment interactions underlying ASD-like behaviors

…we found a significant three-way interaction on corticotropin-releasing hormone receptor-1 (Crhr1) gene expression, in the left hippocampus specifically, which co-occurred with epigenetic alterations in histone H3 N-terminal lysine 4 trimethylation (H3K4me3) over the Crhr1 promoter. Although it is highly likely that multiple (synergistic) interactions may be at work, change in the expression of genes in the hypothalamic–pituitary–adrenal/stress system (e.g., Crhr1) is one of them. The data provide proof-of-principle that genetic and environmental factors interact to cause sex-specific effects that may help explain the male bias in ASD incidence.

This was reported as: Study tests the ‘three-hit’ theory of autism

…the researchers looked for molecular changes within these rodents’ brains that might help to explain the differences in behavior. They found an increase in the expression of a gene that helps to kick off stress responses, in a brain region called the left hippocampus. With help from C. David Allis’s lab, they looked for chemical alterations in the packaging of DNA that might explain this uptick in gene activity. This effort revealed one particular chemical change in the nerve cell nucleus that encourages the expression of this stress-relevant gene.

The chemical alterations are energy-dependent and RNA-mediated via methylation, which alters gene activation to help ensure that all organisms of all living genera have the best opportunity to ecologically adapt. If they fail to adapt, they die. They do not mutate and become another species.
See: Every amino acid matters: essential contributions of histone variants to mammalian development and disease  (2014) by senior author C. David Allis.
Conclusion:

…numerous histone variants seem to be restricted to specific cell lineages or tissue types, yet it remains unclear how such expression patterns are maintained and what the consequences are of increasing or reducing combinatorial variant deposition across cell types. Aberrations in these processes result in detrimental phenotypic outcomes across numerous mammalian systems, including humans. Although we are clearly still in the infancy of this ever-expanding and diverse field, we imagine that future endeavours related to histone variant biology will hold great promise for human health and disease.

The tag-team of Pfaff and Allis will continue to prevent others from what is known to all serious scientists about epigenetically-effected gene-environment interactions among all living genera. The interactions are nutrient-energy-dependent and pheromone controlled by the physiology of reproduction.
I posted this question to the CRISPR Cas 9 FB group and to the miRNA & siRNA FB group

Does any experimental evidence of biologically-based cause and effect suggest that microRNA-mediated host-induced gene silencing is not linked from biophysically constrained viral latency to energy-dependent RNA-mediated cell type differentiation via amino acid substitutions in the cell types of all living genera?

For example, could host-induced gene silencing occur outside the context of natural selection for energy-dependent codon optimality and endogenous RNA interference and the physiology of reproduction?

See also: What’s Next for Diagnostic Patents After Ariosa v. Sequenom

…we should use language that highlights the inventive piece of the invention rather than the natural law underlying it.
 
The natural law underlying all links from ecological variation to ecological adaptation could be applied to the patent for RNA-Guided Human Genome Engineering. If so, the examiners will find that host-induced gene silencing is the obvious link from nutrient energy-dependent RNA methylation to the pheromone-controlled physiology of reproduction in all living genera via Kohl’s Laws of Biology.
 
Simply put, Kohl’s Laws includes two facts:
 
1) all organisms must eat or they die.
2) all species must reproduce or they become extinct.
 

Can you imagine what the value of future patents on drugs will be if researchers continue to deny what is known about those two natural laws?

Alternative splicing of pre-mRNA

Energy is information. Objections over ruled. You're fired!

Objection: In the law of the United States of America, an objection is a formal protest raised in court during a trial to disallow a witness’s testimony or other evidence which would be in violation of the rules of evidence or other procedural law.
Americanism (ideology) links the laws of United States of America to God’s “Laws of Biology.”  Pseudoscientists violated the rules of evidence that link Darwin’s “conditions of life” from God’s “Laws of Biology” to all nutrient energy-dependent biophysically constrained pheromone-controlled biodiversity on Earth.
Laws of biology: why so few? (2010)

…every biological decision is optimal in a given environmental context. However, due to complex nature of biological organization it is difficult to think of a universal law or a theory in biology connecting all the levels, from atoms to ecosystems.

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

  1. In Section One, the focus is on links between atoms and ecosystems via amino acid substitutions. In Section Two, the focus is on examples of links across a continuum of nutrient-dependent, pheromone-controlled, epigenetically-effected, receptor-mediated ecological adaptations via amino acid substitutions and changes in the microRNA/messenger RNA balance.
  2. Nutrient-dependent pheromone-controlled ecological adaptations exemplify how sensing nutrients and secreting the metabolites of nutrients accomplishes different tasks. Efficient circuits enable the functional flexibility that is required in ever-changing ecologies that cause species diversity. Biophysical constraints on ecological adaptations are exemplified in physical proof which suggests that Kohl’s Laws of Biology (Kohl’s Laws) represent what Darwin called ‘conditions of life.’

Natural selection for nutrient energy-dependent codon optimality is exemplified in species from archaea to humans. See for example: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition (2015)

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.

That perspective on sequence changes between paralogs in evolution and human disease placed endogenous RNA interference into the context of Intelligent Design after Darwin and all other serious scientists had linked it from sunlight to all biodiversity on Earth via their observations and experimental evidence of biologically-based cause and effect.
See for example: 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’.

See for comparison: Membrane Patterns Carry Ontogenetic Information that is Specified Independently of DNA
Reported as: Peer-Reviewed Paper: Development Needs Ontogenetic Information that Cannot Arise from Neo-Darwinian Mechanisms

Wells recognizes that various well-established processes like alternative splicing and RNA editing often determine the amino acid sequence of proteins.

Like all pseudoscientists before him, Wells failed to recognize the most important fact of all. That fact was expressed in the context of the fact that gene expression is energy-dependent in 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.

The pseudoscientists that failed to acknowledge that fact are among the losers that were placed into the following perspective:
Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge.Kalevi Kull (2016)
The losers can now be recognized in the context of the failure to provide the free delivery of God’s “billion dollar baby” to  healthcare practitioners. Simply put, many healthcare professionals were not told how to link energy from endogenous RNA interference (RNAi) to healthy longevity in all living genera. They were not told that natural selection for energy-dependent codon optimality and endogenous RNAi have always linked angstroms to ecosystems in all living genera via RNA-mediated amino acid substitutions in supercoiled DNA. Why didn’t all medical practitioners learn that supercoiled DNA protects all organized genomes from virus-driven energy theft and genomic entropy.
See for examples of what was missing:
Get Well in the RNAi Way-RNAi, A Billion Dollar Baby in Therapy

RNAi has targeted exogenous genes in models of viral infection…

RNA-triggered gene silencing (1999)
RNA-Guided Human Genome Engineering (2015)

Repetitive elements or endogenous viral elements can be targeted with engineered Cas+gRNA systems in microbes, plants, animals, or human cells to reduce deleterious transposition or to aid in sequencing or other analytic genomic/transcriptomic/proteomic/diagnostic tools (in which nearly identical copies can be problematic).

Alnylam Pharmaceuticals: RNAi Failure Could Catch Monsanto Investors Off Guard ? (2016)

The other technology besides CRISPR gene editing, which is the subject of this post is called RNAi technology. See link in references below as to the differences between CRISPR & RNAi technologies.

…something went horribly wrong, they don’t really know what it was other than it failed, caused death of some patients and so they discontinued the experimental drug. This has an uncanny similarity to and is reminiscent of the Tryptophan disaster – GM Potato & Árpád Pusztai affair & the GM pea causes allergic reactions to name a few.

“Deep inside its labs, Monsanto is learning how to modify crops by spraying them with RNA rather than tinkering with their genes”

Spraying crops with RNA causes RNA interference in the same way that the CRISPR/Cas9 technology replaced virus-altered RNA interference via use of other viruses that caused the innate immune response to link amino acid substitutions to DNA repair if the missing amino acids were again made available. It is like fighting fire with fire, which sometimes works to extinguish the life of one fire that is out of control but does not prevent other fires from emerging and destroying other properties, or the same property at a later date. The ominous prophecies from the Holy Bible now loom larger if, like all other prophecies, they are correct. Those who survive the next viral apocalypse seem likely to live long enough to die a fiery death that clearly will be linked to the sun’s biological energy from the protection of supercoiled DNA that once helped to ensure our healthy longevity.

See for comparison:  A Christian Worldview & Mental Health (2011)

Christian concern for the whole person includes both mind and body, so this volume encourages readers to think about theoretical and spiritual issues within Christian mental health care. Views are collected from various disciplines such as ethics, psychology, theology, counseling, and psychiatry. In its consideration of a Seventh-day Adventist spiritual identity in mental health theory and practice, this text will prove very valuable to mental health education.

The Christian worldview links what organisms eat to natural selection for energy-dependent codon optimality and healthy longevity, which links supercoiled DNA from the physiology of reproduction to all morphological and behavioral diversity in species from microbes to humans. The Christian worldview has typically been one in which peaceful coexistence is the desired goal. That goal is based on what is known about energy-dependent symbiosis and homeostasis in species from microbes to humans. The atheistic worldview is shared by proponents of Intelligent Design and others who are biologically uninformed. They seem to think that Darwin replaced the Laws of Biology, when what he repeated asserted was that “conditions of life” come first. Only pseudoscientists have continued to link mutations from natural selection to the evolution of one species from another across millions of years.
The pseudoscientists have organized a “March for Science” in an attempt to keep forcing their pseudoscientific nonsense on the biologically uninformed masses in the United States of American who were taught that they could break any of God’s Laws that they chose to break, after the Laws were broken by those who chose to believe in, and to teach, their ridiculous theories to several generations of children that grew up to become liberals.
But wait, here are a few more claims that can be placed into the context of the Laws of Biology, but not into the context of mutation-driven evolution.
Worm gene could be key to developing obesity treatment
Nutrient energy-dependent changes in the microRNA/messenger RNA link endogenous RNA interference to biophysically constrained biodiversity in nematodes that is exemplified in differences between C. elegans and P. pacificus, a predatory nematode with teeth. The physiology of reproduction is controlled by pheromones in all living genera and the pheromones link microRNAs from supercoiled DNA to chromosomal inheritance in different species.
See also from 2013: Extracellular Regulation

During Caenorhabditis elegans development, the hermaphrodite-specific neurons (HSNs) migrate and then extend axons toward their functional targets. Posttranslational modification of heparan sulfate proteoglycans are important for HSN development, and so Pedersen et al. (p. 1404) tested the effect of disrupting or reducing chondroitin and heparan sulfate synthesis during C. elegans development. The results suggest that proteoglycan biosynthesis is tightly regulated by a microRNA pathway to shape the cell surface glycosylation architecture required to direct neuronal migration.

Females More Prone to Disease Due to Key Immunological Difference
This means the sex difference in cell types can be linked to the advent of sexual reproduction in yeasts via the conserved molecular mechanisms we detailed in the molecular epigenetics section of our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior
See for comparison: Today on Darwin Day, Trey the Explainer Sends a Gift. He Power Owns Dr. Ben Carson! (Video)
The “Explainer” dismisses facts about energy-dependent endogenous RNA interference and pretends that the variants in the fossil record support the ridiculous theories of neo-Darwinian theorists. There is no way to explain his ignorance, or why he flaunts it.
See also: Team develops tool that maps functional areas of the genome to better understand disease

…sections of DNA called “enhancers” dictate where and when the gene information is read out.
 

Energy as information dictates gene expression in the context of established links from chirality to autophagy in species from microbes to humans.

See: Light Could Propel Nanorobots on a “Fantastic Voyage” Through the Human Body

“Light is a more effective option to communicate between the microscopic world and the macroscopic world,” said Tang.
 

All pathology is caused by virus-driven energy theft. The barrage of misinformation you are being subjected to is increasing each day.

See:How evolution alters biological invasions
also reported as:

Superspreader phages transfer drug resistance
Lucky for us, bacteriophages infect bacteria, not humans. That doesn’t mean they don’t have profound effects on us, however. A new report in the journal mBio from researchers at the University of Miami and the National Cancer Institute describes “superspreader” bacteriophages that promote DNA transfer from one bacterium to another – and some of this DNA codes for antibiotic resistance genes.

Does life have a purpose?
 

Alternative splicing of pre-mRNA

Dobzhansky 1973 and Precision Medicine (2)

What Did Neanderthals Leave to Modern Humans? Some Surprises

A few years ago, the Swedish geneticist Svante Paabo received an unusual fossilized bone fragment from Siberia. He extracted the DNA, sequenced it and realized it was neither human nor Neanderthal.

Savante Paabo co-authored this refutation of neo-Darwinian nonsense in 2003.Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees

It links natural selection for energy-dependent codon optimality from the pheromone-controlled physiology of reproduction in species from archaea to humans via what is known to serious scientists about the de novo creation of olfactory receptor genes. He also co-authored this article: Loss of Olfactory Receptor Genes Coincides with the Acquisition of Full Trichromatic Vision in Primates It links the virus-driven energy theft to the mutation-driven loss of G protein-coupled receptors in all cell types of all individuals of all living genera.

John Anthony Capra, the expert on what Neanderthals left to modern humans is probably aware of this fact: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

One energy-dependent RNA-mediated amino acid substitution was linked from G protein-coupled receptors to differences in morphological and behavioral phenotypes and the “personality” difference in human adolescents compared to adults. Dobzhansky (1973) put that fact into the context of other facts that link fixation of amino acid substitutions to all cell type differences in all individuals of all living genera.

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 problem with this fact manifests itself in attempt by pseudoscientists to ignore it. At the same time, all serious scientists have place the facts into their perspectives on hemoglobin variants such as the hemoglobin S variant.

Genetic Variations: Heroes or Villains

Variations have not only been associated with diseases like cancer, turner syndrome, sickle cell anaemia, cystic fibrosis etc., but some of them have even been proved to be beneficial in certain cases like for increasing bone density, lowering down cholesterol level, and for developing malaria resistance.

Many pseudoscientists did not learn that there are now more that ~1200 hemoglobin variants, or that sickle cell anemia is an example of an ecological adaptation. Some have learned not to refer to variants as mutations in the context of mutation-driven evolution. But past claims about mutations and evolution have become a nightmare scenario for anyone who has ever made them.

What Did Neanderthals Leave to Modern Humans? Some Surprises (revisited)

But I received racist inquiries, too. I got calls from all over the world from people who thought that since Africans didn’t interbreed with Neanderthals, this somehow justified their ideas of white superiority.

What happens next will be more interesting. As people like John Anthony Capra and Svante Paabo try to extricate themselves from the muck of ridiculous theories, which they nearly let engulf them, they will be forced to start naming names. The people who taught them to believe in pseudoscientific nonsense about mutations and evolution will be reviled instead of revered for their expertise.  Ultimately, works by people like Masatoshi Nei will be viewed as if they were published by people who were biologically uninformed.

See for example: The neighbor-joining method: a new method for reconstructing phylogenetic trees(1987)

For comparison, see: Genomic locations of conserved noncoding sequences and their proximal protein-coding genes in mammalian expression dynamics (2016)

Naruya Saitou is the first author of the 1987 revised theory and the senior author of the accurate representations of biologically based cause and effect from 2016.

His co-author Masatoshi Nei published Mutation-driven evolution on the same day in 2013 that my review of everything known to serious scientists about biologically-based cause and effect was published. Nutrient-dependent/pheromone-controlled adaptive evolution: a model

See also: We are all mutants

Every part of our body is controlled by molecules, so you have to explain on a molecular level. That is the real mechanism of evolution, how molecules change. They change through mutation. Mutation means a change in DNA through, for example, substitution or insertion [of nucleotides]. First you have to have change, and then natural selection may operate or may not operate. I say mutation is the most important, driving force of evolution.

The changes are nutrient energy-dependent and RNA-mediated in the context of chromosomal rearrangements and the pheromone-controlled physiology of reproduction.

See for confirmation: Spliceosomal intronogenesis

The group II intron-derived features are likely to have degenerated over time, leading to a necessity for the development of the pre-mRNA splicing machinery composed of trans-acting snRNAs and trans-acting protein factors (11, 18). Within this context…
 
Every aspect of energy-dependent RNA-mediated life on Earth occurs “within this context.” Life is energy-dependent and biophysically constrained by the pre-mRNA splicing machinery in the context of the physiology of reproduction and chromosomal rearrangements.
See also: From Fertilization to Adult Sexual Behavior (1996)

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

The sex difference in cell types have since been linked via conserved molecular mechanisms to all differences in all cell types of all individuals in all living genera.

Virus-driven energy theft was rarely considered since the time of our 1996 review. It has now been linked from communication among viruses to nutrient-dependent pheromone-controlled ecological adaptation in species from archaea to humans. Archaea and Zika virus-damaged DNA of human infants exemplify how virus-driven energy theft links degenerated mRNA from failed DNA repair to differences in species of bacteria and difference between non-human primates and modern humans.

See also: Quantum leap: Physicists can better study the quantum behaviour of objects on the atomic scale.

…quantum behaviour: a microscopic mirror in a quantum superposition, created through interaction with a photon, would involve about 1014 atoms. And, letting their imaginations run wild, researchers have proposed a method to do the same with small biological structures such as viruses.

The quantum leap has never been imaginary. Schrodinger recognized that it was energy-dependent and many others have linked energy-dependent changes in angstroms to ecosystems. Theorists have been left with no excuses for their ignorance, which is still displayed in video representations such as this one.

See also:

See also: The tipping point? 50, 000 publications

Did Dobzhansky see the UV light of creation?

ALPHA GENOMIX

Conclusion from 2): “The ability to recognize endogenous RNAs within complex mixtures with high affinity and in a programmable manner paves the way for direct transcript detection, analysis and manipulation without the need for genetically encoded affinity tags.”

That ability to recognize endogenous RNAs within complex mixtures shows up in Alpha Genomix testing, which represents a quantum leap forward from what many experts inaccurately attribute to mutations, natural selection, and evolution. Instead, Alpha Genomix is leading the way by incorporating what is currently known about RNA-directed DNA methylation and RNA-mediated events that link enzymes to amino acid substitutions that differentiate cell types.

Evolving DNA before RNA

Any discovery that links a chain of evolutionary events to anything  known about gains and losses of abilities attributed to biologically-based cause and effect would be remarkable. So far, not even one evolutionary event has been described. Thus, linking the dawn of life to the food on our tables via evolutionary theory would represent a quantum leap from a ridiculous theory to what is known about biological facts by serious scientists.

For example, quantum physics is linked to quantum biology via a light-induced amino acid substitution that links cell type differentiation in plants from ecological variation in light-dark cycles to RNA-directed DNA methylation and RNA-mediated amino acid substitutions.

Order and disorder: Ecological adaptations not mutations

A microRNA (abbreviated miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides). Thus, the quantum leap from biophysically constrainted light-induced amino acid substitutions to the nutrient-dependent microRNA/messenger RNA balance that controls genome stability via epigenetically-effected amino acid substitutions is replaced with the concept of epigenetically-effected mutations, which are called epimutuations.

By mixing the theory of mutation-initiated natural selection and the evolution of biodiversity with biological facts about how ecological variation leads to epigenetically-effected ecological adaptations manifested in biodiversity, the senior author of the “epimutations” article sets the stage for his claim to be “the first” to find something new and important.