5th-6th Sept 2018 Dublin, Ireland

Polymaths and paradigm shifts: from Asimov to Bear (4)

by with No Comment AdaptationsDiseases & DisordersEcologyRNA Directed

Saying Goodbye to the RNA World Theory

RNA has a limited ability for catalysis compared to peptides, and would have struggled to maintain its catalytic activity under the changing temperature conditions of early Earth. Carter and Wills also argued that if an RNA world existed, it would have been unlikely for it to incorporate peptides later on.

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

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

The energy-dependent creation of ATP synthase has since been linked to this claim from McEwen et al., (1964):

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

By starting with the energy-dependent de novo creation of enzymes, others have linked Schrödinger’s claims from “What is Life” (1944)  to all biophysically constrained biodiversity.
Say Hello again to Schrödinger at 75 – The Future of Biology
Let Timothy J. Cunningham, who disappeared from the CDC last month, reintroduce you. See his publications on:
1)”Racial Disparities in Age-Specific Mortality”
2) “Sex-specific relationships between adverse childhood experiences”
3) “Associations between antioxidants and all-cause mortality”
and
4) “Health and Safety Issues for Travelers”
Serious scientists know that all racial/ethnic disparities are food energy-dependent, RNA-mediated, and pheromone-controlled  in the context of enymes, metabolism, and amino acid substitutions. Fixation of the RNA-mediated amino acid substitutions differentiates all cell types in all living genera — including sex differences in cell types.
See for examples our section on molecular epigenetics from this 1996 Hormones and Behavior review of RNA-mediated cell type differentiation. 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…

Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus…

See for comparison, this nonsense: Caenorhabditis elegans glia modulate neuronal activity and behavior

Introduction: a brief on evolution of neuroglia

“Nothing in biology makes sense except in the light of evolution”. — Theodosius Dobzhansky (1900–1975)

Evolution of the nervous system proceeded through an increase in number and complexity of the nervous elements and through their specialization into electrically excitable neurons connected through defined synaptic contacts and electrically non-excitable neuroglia forming networks through intercellular gap junctions. Intercellular chemical neurotransmission is, however, characteristic for both forms of the neural cells that express appropriate receptors and are capable of secreting neurotransmitters. The evolution of the nervous system was not a straight journey from less complex and accomplished networks to the more refined ones; at the turning point between invertebrates and vertebrates, a fundamental metamorphosis occurred that changed the overall structure of the central nervous system (CNS).

The difference in the energy of two photons has since been linked from the proton motive force to the creation of enzymes and metabolism of food. The pheromone-controlled physiology of reproduction in species from bacteria to humans has linked DNA methylation from the creation and fixation of RNA-mediated amino acid substitutions to viral latency and all biodiversity. Timothy J. Cunningham placed that fact into the context of his history of published works.
For comparison, see: On the Difference between Physics and Biology: Logical Branching and Biomolecules (2018) and The Large Scale Structure of Space-Time(1975) George FR Ellis was a coauthor of both published works.
He, and others like him, failed to link Physics and Chemistry from molecular epigenetics to what is known about energy-dependent RNA-mediated biophysically constrained cell type differentiation to all biodiversity on Earth. Framing what is known to all serious scientists about cell type differentiation in the context of what Ellis might think is a logical representation of biomolecules attests to his lack of logic across the time-space continuum of his life.
See for comparison: Olfaction Warps Visual Time Perception (2017).
See also Odor-induced mood state modulates language comprehension by affecting processing strategies (2016)
The 2016 citation to The impact of natural odors on affective states in humans can now be linked to the accurate representations of top-down biophysical constraints on food energy-dependent pheromone-controlled feedback loops. The feedback loops are required to biophysically constrain viral latency.
See: What is life when it is not protected from virus driven entropy (video)

The anti-entropic force of virucidal ultraviolet light links guanine–cytosine (G⋅C) Watson–Crick base pairing from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. For example, protection of DNA from permanent UV damage occurs in the context of photosynthesis and nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to DNA repair. In the context of thermodynamic cycles of protein biosynthesis and degradation, DNA repair enables the de novo creation of G protein coupled receptors (GPCRs). Olfactory receptor genes are GPCRs. The de novo creation of olfactory receptor genes links chemotaxis and phototaxis from foraging behavior to social behavior in species from microbes to humans. Foraging behavior links ecological variation to ecological adaptation in the context of this atoms to ecosystems model of biophysically constrained energy-dependent RNA-mediated protein folding chemistry. Protein folding chemistry links nutrient-dependent microRNAs from microRNA flanking sequences to energy transfer and cell type differentiation in the context of adhesion proteins, and supercoiled DNA that protects all organized genomes from virus-driven entropy.

See for comparison: Gay, Straight, and the Reason Why: The Science of Sexual Orientation (2011)

Still, even in fruit flies, other sensory input besides pheromones — acoustic, tactile, and visual stimuli — play a role in sexual attraction, and sex specific responses to these stimuli appear to be innate rather than learned by association [36.]. We simply don’t know where the boundary between prespecified attraction and learned association lie in our own species, nor do we have compelling evidence for the primacy of one sense over another. (pp. 210- 211)

See also: Gay, Straight, and the Reason Why: The Science of Sexual Orientation, 2nd edition (2016)
From the second edition of LeVay’s book:

… chemosignal enthusiasts point to a variety of studies in which sniffing body secretions or substances purified from secretions appears to have some psychological effect… (p. 115)

LeVay cites Kohl et al., (2001) Human pheromones: integrating neuroendocrinology and ethology.
He has never mentioned the fact that the effects of virus-driven entropy on cell type differentiation were linked human sexual orientation in The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002) and in the book chapter he cited in the first edition of Gay, Straight, and the Reason Why: The Science of Sexual Orientation.
See for comparison: Always follow your nose: the functional significance of social chemosignals in human reproduction and survival (2015) This article is part of a Special Issue “Chemosignals and Reproduction”
John Cacioppo, a Founder of Social Neuroscience, Dies

The University of Chicago psychology professor made fundamental contributions to understanding the neural mechanisms of social experiences.

My comment to The Scientist:

See also: Evolution of neuroarchitecture, multi-level analyses and calibrative reductionism (2012)

I hope John Cacioppo is remembered for this refutation of neo-Darwinian pseudoscientific nonsense:

Although peptide chemistry has been with us since amino acids first formed, the social role of oxytocin did not exist prior to the evolutionary sculpting of the vertebrate brain.

He may have been one of the first social scientists to recognize the fatal flaw that others continue to include in their works. All other serious scientists, like him, start with the energy-dependent creation of enzymes and amino acids. Only pseudoscientists still start with the evolution of the vertebrate brain.

I remember when he and his wife turned towards me and smiled — after I asked the speaker from Argentina about the role of oxytocin in a rodent model. No studies were being done for the obvious reason that few people knew where oxytocin came from.

I invited the speaker to lunch and we laughed a lot about the works that tried to link oxytocin to differences in behavior without linking the differences to altered  RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse

RIP John Cacioppo

See also: Multilevel integrative analyses of human behavior: social neuroscience and the complementing nature of social and biological approaches (2000)
Nothing published during that 12-year period and nothing published before or since then suggests the the neuroarchitecture of intelligent creatures somehow evolved.
For comparison, see: Human pheromones and nutrient chemicals: epigenetic effects on ecological, social, and neurogenic niches that affect behavior (2012) Presented at the Society for Social Neuroscience Annual Meeting 2012
See also: Neuroglia in C. elegans (2018)

The nematode C. elegans is one of the most important model organisms for understanding neurobiology. Its completely mapped neural connectome of 302 neurons and fully characterized and stereotyped development have made it a prototype for understanding nervous system structure, development, and function. Fifty-six out of C. elegans‘ total of 959 somatic cells are classified as neuroglia. Although research on worm glia has lagged behind studies focused on neurons, there has been a steep upswing in interest during the past decade. Information arising from the recent burst of research on worm glia supports the idea that C. elegans will continue to be an important animal model for understanding glial cell biology. Since the developmental lineage of all cells was mapped, each glial cell in C. elegans is known by a specific name and has research associated with it. We list and describe the glia of the hermaphrodite form of C. elegans and summarize research findings relating to each glial cell. We hope this lecture provides an informative overview of worm glia to accompany the excellent and freely available online resources available to the worm research community.

The worm research community seems to be largely unaware of this fact: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes
The have failed to link food odors from the pheromone-controlled physiology of reproduction to ecological adaptatation manifested in morphological and in behavioral diversity.

Cytosis

Long-term adaptation replaces evolution (2)

by with No Comment AdaptationsAlternative SplicingsAutophagybiophotonicsCytosisDiseases & DisordersEcologyHuman BrainHuman PheromonesModel OrganismsNutrigenomicsPhysicsRNA-directed DNA methylationRNA-mediated gene silencingRNA–Mediated Epigenetic Heredity

The food energy-dependent “doubling up” on ‘junk DNA’ is biophysically constrained by the physiology of pheromone-controlled reproduction. The metabolism of food to species-specific pheromones links the conserved molecular mechanisms of RNA-mediated cell type differentiation in all individuals of all living genera to healthy longevity via what is known about amino acid substitutions in supercoiled DNA, which link energy-dependent changes in chirality to autophagy.

See: It’s all about that base

The virus-driven degradation of messenger RNA in bacteria links top-down causation to what happens to archaea and L-forms in the context of the viral hecatomb, which links the destruction of G protein-coupled receptors to all pathology because the de novo creation of G protein-coupled receptors links the creation of the sense of smell to all biodiversity.

Our ability to detect differences in amino acid substitutions in the blood has been linked to the ability of flies to find food and to reproduce via the physiology of food-energy-dependent pheromone-controlled reproduction.

See: A mammalian blood odor component serves as an approach-avoidance cue across phylum border – from flies to humans
See also:

Adaptive evolution by spontaneous domain fusion and protein relocalization

Phenotypic heterogeneity promotes adaptive evolution

My 2013 model of energy-dependent ecological adaptations: Nutrient-dependent/pheromone-controlled adaptive evolution: a model refuted neo-Darwinian pseudoscientific nonsense. That that model is being revisited each day that another publication is added to those that link the energy-dependent de novo creation of microRNAs to all biodiversity via hydrogen-atom transfer in DNA base pairs in solution. See: microRNA

For example:Recent advances in signal amplification strategy based on oligonucleotide and nanomaterials for microRNA detection-a review.

See also:

Overview of microRNA biology. Mohr AM et al. Semin Liver Dis. (2015)

MicroRNA Therapeutics: the Next Magic Bullet? Simonson B et al. Mini Rev Med Chem. (2015)

MicroRNAs in cancer: biomarkers, functions and therapy. Hayes J et al. Trends Mol Med. (2014)

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

Predicting who wins the 2017 Nobel Prizes (5)

by with No Comment AdaptationsAutophagybiophotonicsDiseases & DisordersEcologyLight EnergyModel OrganismsNutrigenomicsPhysicsSubatomic

Summary: If he was not still dead, the 1965 Nobel Laureate, Richard P. Feynman might claim that this year’s Physics Prize was awarded for “human idiocy.”
Nobel Prize in Physics Awarded to LIGO Black Hole Researchers

Einstein’s General Theory of Relativity, pronounced in 1916, suggested that matter and energy would warp the geometry of space-time the way a heavy sleeper sags a mattress, producing the effect we call gravity. His equations described a universe in which space and time were dynamic.
 

Other claims in this article appear to arise in the context of the emergence of energy from nothing with no mention of the biophysical constraints that link food energy from electrons to ecosystems via the pheromone-controlled physiology of reproduction in species from microbes to humans.

If he was not still dead, the 1965 Nobel Laureate, Richard P. Feynman might claim that this year’s Physics Prize was awarded for “human idiocy.”

See:

 
Facts about Einstein’s “General Theory” have since been validated with experimental evidence of biologically-based cause and effect. See: Olfaction Warps Visual Time Perception
 

The energy-dependent de novo creation of G protein-coupled receptors, such as odor receptors, links the sense of smell in bacteria to the physiology of pheromone-controlled reproduction, which links changes in chirality to autophagy. Autophagy links what organisms eat to cell type differentiation via amino acid substitutions that link our visual perception of energy and mass to the feedback loops that link what organisms eat to their behavior.

Experimental proof of concept might require the sacrifice of one mammal. If it can find a mass of energy that is biophysically constrained in a source of food, it must also eat the food and survive to reproduce. Foraging and reproduction occur in the context of facts presented in Feedback loops link odor and pheromone signaling with reproduction (co-authored by 2004 Nobel Laureate, Linda  Buck).

If an organism cannot find the food and eat it, entropy must clearly be linked to its death unless it is among the individuals of a species that mutated and evolved from a common ancestor. For comparison, theories about common ancestors can be linked to the billion dollar LIGO “black hole” project and to this year’s Nobel Laureates in Physics.

I encourage others who live on Earth to do that in the context of a money-saving effort to save all humanity from death that will be caused by the virus-driven entropy of organized genomes.

See for details: 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!

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

Optogenetics replaces fMRI but not pseudoscientific nonsense

by with No Comment Alternative SplicingsbiophotonicsDiseases & DisordersEcologyHuman BrainHuman PheromonesLight EnergyModel OrganismsNeuronal PlasticityNutrigenomicsPhysicsRNA DirectedRNA interferenceRNA methylationRNA-directed DNA methylationRNA-mediated epigenetic regulation of gene expressionRNA-mediated gene silencingRNA–Mediated Epigenetic HereditySubatomicVariations

Summary: The ability to evaluate spaciotemporal influences on health compared to virus-driven pathology must include a link from quantized energy to the creation of ATP and the creation of RNA. Hunting people down who are aware of that fact is difficult because most of them have ignored the facts from this 1964 publication.
Ed Boyden and Optogenetics: The Future of Neuroscience (video) (transcript)

What I’m trying to do now is see whether we can help people pilot crazy projects that don’t quite fit in. I started talking to people about the craziest things they could think of that wouldn’t ever get a government grant or pass peer review—when other people have to tell you whether they think it’s a good idea or not. There’s something to be said for trying to hunt those ideas down.

The ability to evaluate spaciotemporal influences on health compared to virus-driven pathology must include a link from quantized energy to the creation of ATP and the creation of RNA. Hunting people down who are aware of that fact is difficult because most of them have ignored the facts from this 1964 publication.
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: Cell diversity and network dynamics in photosensitive human brain organoids (2017)

…neuronal activity within organoids could be controlled using light stimulation of photosensitive cells, which may offer a way to probe the functionality of human neuronal circuits using physiological sensory stimuli.

See for comparison: Nonlinear cavity optomechanics with nanomechanical thermal fluctuations Reported as: Nanoscale motion sends light into overdrive

The higher harmonics of the produced light signals carry different kinds of information about the nanostring motion. For example, we demonstrated that they allow measuring the energy of the vibration with a high accuracy. This could potentially lead to direct observations of quantized energy in the string, as we would expect from the theory of quantum mechanics.

Direct observations of quantized energy and the virus-driven energy theft that is linked from mutations to all pathology can be considered in the context of  Olfaction Warps Visual Time Perception
My summary: Biophysically constrained neural energy links multisensory inputs from quantum consciousness to quantum souls at subsecond scales via the sense of smell in bacteria.The claim that space-time is warped by the distribution of mass and energy is linked to the perception of time outside the context of optogenetics because chemotaxis is the first link from pH-taxis to phototaxis via the de novo creation of G protein-coupled receptors.
Boyden may not know that he must find someone who knows how to link the measurements from Cryo-ET and Cryo-EM to the light-activated endogenous substrate in all cell types that links the physiology of pheromone-controlled reproduction to all biodiversity via the energy-dependent de novo creation of G protein-coupled receptors.
Dr Topol:

Only this year, “microbiome,” “epigenome,” and “CRISPR” got in. The New Yorker had a big profile on optogenetics. That’s mainstream, in the New Yorker.

Phytoremediation was also added. I wonder who else realizes that phytoremediation is the link from the microbiome to the epigenome via CRISPR (the innate immune system of bacteria, which protects them from the virus-driven degradation of their messenger RNA).

"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.

Science vs Secularism: Molecular Mechanisms or Math?

by with No Comment AdaptationsCytosisDiseases & DisordersEcologyHuman PheromonesModel OrganismsNutrigenomicsPhysicsRNA DirectedRNA-directed DNA methylationVariationsWhat's in the News

Summary: An example from ancient knowledge of trigonometry links pattern recognition as the basis for the science of creationism, and pattern recognition also is the basis for molecular biology.
What form of virus-driven pathology would you most like to see eliminated from future consideration by serious scientists who know how energy-dependent RNA-mediated cell type differentiation occurs? In any case, a PubMed search for microRNA and your disease of choice will be enlightening. See for example: microRNA + Alzheimer’s or microRNA + fragile X syndrome; Parkinson’s disease; diabetes; cancer; malaria; and/or other human diseases
See:  Are scientists who speak out against religion hurting science? for discussion of Why religion is not going away and science will not destroy it

…science needs all the friends it can get. Its advocates would be well advised to stop fabricating an enemy out of religion, or insisting that the only path to a secure future lies in a marriage of science and secularism.

Serious scientists have met the enemies of science. One of them is the author of Quantum common sense

We don’t need a conscious mind to measure or look. With or without us, the Universe is always looking

More than 64,000 indexed publications on the PubMed site attest to the fact that the energy-dependent de novo creation of plant microRNAs is linked to all healthy longevity via the food energy-dependent pheromone-controlled physiology of reproduction in species from microbes to humans. Experimentally established facts about the virus-driven degradation of messenger RNA are linked to all pathology via changes in the microRNA/messenger RNA balance.

See: 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!

What form of virus-driven pathology would you most like to see eliminated from future consideration by serious scientists who know how energy-dependent RNA-mediated cell type differentiation occurs? In any case, a PubMed search for microRNA and your disease of choice will be enlightening. See for example: microRNA + Alzheimer’s or microRNA + fragile X syndrome; Parkinson’s disease; diabetes; cancer; malaria; and/or other human diseases
Role of miRNAs in development and disease: Lessons learnt from small organisms

MicroRNAs (miRNAs) constitute a class of small (18-22 nucleotides) non-coding RNAs that regulate gene expression at the post-transcriptional level. Caenorhabditis elegans, Drosophila melanogaster, and many other small organisms have been instrumental in deciphering the biological functions of miRNAs. While some miRNAs from small organisms are highly conserved across the taxa, others are organism specific. The miRNAs are known to play a crucial role during development and in various cellular functions such as cell survival, cell proliferation, and differentiation. The miRNAs associated with fragile X syndrome, Parkinson’s disease, Alzheimer’s disease, diabetes, cancer, malaria, infectious diseases and several other human diseases have been identified from small organisms. These organisms have been used as platforms in deciphering the functions of miRNAs in the pathogenesis of human diseases and to study miRNA biogenesis. Small organisms have also been used in the development of miRNA-based diagnostic, prognostic and therapeutic strategies. The molecular techniques such as genome sequencing, northern blot analysis, and quantitative RT-PCR, have been used in deciphering the functions of miRNAs in small organisms. How miRNAs from small organisms especially those from Drosophila and C. elegans regulate development and disease pathogenesis is the focus of this review. The outstanding questions raised by our current understanding are discussed.

See for comparison: Quantum Theory Rebuilt From Simple Physical Principles by Philip Ball

“What is needed is new mathematics that will render these notions scientific,” he said. Then, perhaps, we’ll understand what we’ve been arguing about for so long.”

I do not believe that new mathematics will end the arguments, and I do not believe anything Philip Ball claims. Does any intelligent person on Earth believe this claim? “We don’t need a conscious mind to measure or look. With or without us, the Universe is always looking”

For a historical perspective on the nonsense touted by theorists and so-called science journalists, like Philip Ball, see:

Secularism: This ancient Babylonian tablet may contain the first evidence of trigonometry

He and Wildberger concluded that the Babylonians expressed trigonometry in terms of exact ratios of the lengths of the sides of right triangles, rather than by angles, using their base 60 form of mathematics, they report today in Historia Mathematica. “This is a whole different way of looking at trigonometry,” Mansfield says. “We prefer sines and cosines … but we have to really get outside our own culture to see from their perspective to be able to understand it.”

When have serious scientists not gone outside our own culture to understand how the history of human behavioral development has been misrepresented by so-called experts.

See: 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.

Simply put, the harmful variants probably contribute to our relative lack of intelligence compared to the intelligence of our ancestors, unless you think that a single-celled organism is one of your ancestors. Obviously, however, even if that is the case, you are somewhat more intelligent that pond scum. But, let me apologize in advance for referring to you as a “biologically uninformed science idiot” — in the context of the definition of “idiot” as someone with no professional expertise. Apologists might use the term “fool” in the context of this passage from the Holy Bible:

“Thou fool, that which thou sowest is not quickened, except it die:”

Feynman used the term “human idiocy” in the context of representations made by theoretical physicists:

Prepare yourself to experience more insults from experts who have, during the past 5-10,000 years confirmed the links from energy to physics, chemistry, and molecular biology in the context of food energy and the biophysically constrained pheromone-controlled physiology of reproduction.

Apologetics:Indiana Banks and the Tablet of Trig

This story attracted my attention because it is yet more evidence against the Darwinian narrative of human history, which holds that we evolved from apes and have been steadily gaining in technology and science ever since. The reality is very different. The evidence often points to initial brilliance followed by decline, the pattern that creationists would expect. In this instance, extremely ancient people pioneered a form of trigonometry that is more exact than the form used by later Mesopotamian nations and by the Greeks, Romans, and later Western Civilization.

Pattern recognition is the basis for the science of creationism and pattern recognition is the basis for molecular biology.

See also: Olfaction Warps Visual Time Perception

In their concluding paragraph, the authors link irreverent representations of the space-time continuum (Hawking, 1988) to our visual perception of mass and energy. With no vague representations of untested theories, they suggest that neural energy represents multisensory input at subsecond scales.

If what they suggest is true, their published work is an unprecedented refutation of neo-Darwinian pseudoscientific nonsense and an unparalleled refutation of “Big Bang” cosmology. Simply put, they concurrently link the creation of energy to the energy-dependent creation of the sense of smell in bacteria. The sense of smell is linked to the pheromone-controlled physiology of reproduction in all living genera via representations that link neural energy from the epigenetic landscape to the physical landscape of supercoiled DNA.

For example, the sense of smell in bacteria is linked to the weekend resurrection of the bacterial flagellum.

See:Evolutionary Rewiring

Strong selective pressure can lead to rapid and reproducible evolution in bacteria.

Natural selection for food energy-dependent codon optimality was linked to the ability of P. fluorescens to find food, which was linked to their pheromone-controlled physiology of reproduction by everything known about quorum sensing. But wait, that fact defies attempts to put the refutation of all theories into the context of something as simple-minded as this claim:

We don’t need a conscious mind to measure or look. With or without us, the Universe is always looking

For more information on the mutation-driven “dumbing down” of you and your ancestors play the game “Cytosis” when it becomes available later this month and watch for more information on the game “Subatomic.” It is less difficult now than it ever has been to link energy-dependent changes from atoms to ecosystems by what is known to serious scientists. But first, you may need to dismiss the pseudoscientific nonsense touted by theorists.

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

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.

See also: Protecting 4 billion people from virus-driven entropy September 8, 2016
See also: Recurrence-Based Information Processing in Gene Regulatory Networks

We also show that the readout layer can learn to decode the information stored in the reservoir via standard evolutionary strategies. Our work thus suggests that recurrent dynamics is a key element for the processing of complex time-dependent information by cells.

What evolutionary strategies led to the recurrent dynamics of time-dependent information processing and the use of trigonometry ~5000 years ago?
Learning from Bacteria about Natural Information Processing

It seems that bacteria have some sort of collective memory by which they keep track of how they handled their previous encounters with antibiotics. They know how to collectively glean information from the environment, “talk” with each other, distribute tasks, generate collective memory, and turn their colony into a “cybernetic system”—a massive “brain” that can perform natural distributed information processing, learn from past experience, and possibly alter the genome organization or even create new genes to better cope with novel challenges.8–13,17,18

Physiology is rocking the foundations of evolutionary biology

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

 
 
 

diseases-disorders

Your indifference is killing you and others

by with No Comment AdaptationsbiophotonicsCytosisDiseases & DisordersEcologyHuman PheromonesLight EnergyModel OrganismsNutrigenomicsPhysicsRNA DirectedRNA-directed DNA methylationRNA-mediated epigenetic regulation of gene expressionVariations

Summary: Coherence-inducing mechanisms is double-speak for mechanisms that are nutrient-dependent and pheromone-controlled.
Feedback loops link odor and pheromone signaling with reproduction has been presented in double-speak as Looplessness in networks is linked to trophic coherence

We are currently studying the entropy of the coherence ensemble we defined for this work. “In general, higher trophic coherence would be associated with lower entropy states, which means that if networks are more coherent than the random expectation there must indeed be some kind of negentropic process at work.” Johnson notes that the impact in this case relative to trophic coherence would be found in quantifying the extent to which different empirical networks have been driven from their maximum entropy state. “This might be the best way of discovering when there are coherence-inducing mechanisms at work, how much energy must be involved, and ultimately identifying the nature of such processes.”

Feedback loops link the sun’s anti-entropic virucidal energy from the food that organisms eat to the physiology of pheromone-controlled reproduction in all living genera. The virucidal effect of ultraviolet light biophysically constrains viral latency. Energy-dependent RNA-mediated amino acid substitutions in supercoiled DNA are fixed in organized genomes via the physiology of reproduction and supercoiled DNA protects all organized genomes from the virus-driven degradation of messenger RNA that links mutations to all pathology.
Coherence-inducing mechanisms is double-speak for nutrient-dependent and pheromone-controlled in the context of Nutrient-dependent/pheromone-controlled adaptive evolution: a model. 
Despite the validity of the model, it has not been accepted by neo-Darwinian theorists or “Big Bang” cosmologists. Ridiculous beliefs about emergence and evolution are pervasive and the pseudoscientific nonsense of their theories leads to claims about coherence-inducing mechanisms.
That is why I changed the FB page description at RNA-mediated after a series of posts (see below).

It took 20 years for others to realize that all life on Earth is food energy-dependent. Now, most people are indifferent to that fact. They refuse to learn anything about where the food energy comes from.

Differences in the energy of photons have been linked to quantized energy-dependent fixation of RNA-mediated amino acid substitutions. The substitutions biophysically constrain supercoiled DNA via the physiology of pheromone-controlled reproduction.

Virus-driven energy theft links the degradation of messenger RNA to mutations via amino acid substitutions in viruses. The substitutions in the viruses have been linked to all pathology via changes in the energy-dependent microRNA/messenger RNA balance.

For comparison, the pseudoscientific nonsense of neo-Darwinian theories links mutations from natural selection to the evolution of new species. In reality, light energy is quantized information. The information links physics, chemistry, and molecular epigenetics from the speed of light on contact with water and hydrogen-atom transfer in DNA base pairs in solution to learning, memory, and behavior via RNA-mediated events such as the energy-dependent creation of enzymes and the the de novo creation of G protein-coupled receptors such as olfactory receptor genes.

Top-down causation and de novo gene creation are exemplified by energy-dependent differences in the microRNA/messenger RNA balance that link natural selection for codon optimality to amino acid substitutions that link the physiology of reproduction to supercoiled DNA. Supercoiled DNA protects all organized genomes from virus-driven energy theft. That fact supports the beliefs of young earth creationists, which may be the only existing basis for discussion of quantum biology and refutations of neo-Darwinian theories that have linked olfaction to quantum souls. If there is another basis for the link from quantum physics to quantum souls, no one has detailed in in the context of top-down causation, which must include information about the creation of genes.

Most people seem unwilling to accept experimental evidence that attests to how genes are created or information that shows how virus-driven energy theft is linked to all pathology. Discussion of the energy-dependent paradigm shift would lead others away from pseudoscientific nonsense about emergence and/or beneficial mutations and evolution.

Only via discussion of facts about the paradigm shift will others learn what is currently known to serious scientists about the biophysically constrained nutrient energy-dependent chemistry of RNA-methylation and all biophysically constrained RNA-mediated protein folding chemistry. Simply put, the protein folding chemistry must be linked to all biodiversity by the physiology of energy-dependent pheromone-controlled reproduction in all living genera.

Your indifference to that fact is killing people.

See for comparison: Looplessness in networks is linked to trophic coherence (May 16, 2017)

Our theory correctly classifies a variety of networks-including those derived from genes, metabolites, species, neurons, words, computers, and trading nations-into two distinct regimes of high and low feedback and provides a null model to gauge the significance of related magnitudes. Because trophic coherence suppresses feedback, whereas an absence of feedback alone does not lead to coherence, our work suggests that the reasons for “looplessness” in nature should be sought in coherence-inducing mechanisms.

Reported August 14, 2017 as Trophic coherence explains why networks have few feedback loops and high stability

The researchers are also investigating whether negentropy – the opposite of entropy, and in which a physical, thermodynamic or biological process creates order – are affected by trophic coherence. “The modern concept of entropy,” Johnson points out, “comes from statistical physics and is a property of ensembles, as described above – that is, the entropy of an ensemble is simply a function of the number of elements it contains.” Moreover, he adds, graph ensemble entropy has proven to be a powerful tool for understanding various network properties. We are currently studying the entropy of the coherence ensemble we defined for this work. “In general, higher trophic coherence would be associated with lower entropy states, which means that if networks are more coherent than the random expectation there must indeed be some kind of negentropic process at work.” Johnson notes that the impact in this case relative to trophic coherence would be found in quantifying the extent to which different empirical networks have been driven from their maximum entropy state. “This might be the best way of discovering when there are coherence-inducing mechanisms at work, how much energy must be involved, and ultimately identifying the nature of such processes.”

See for comparison: Feedback loops link odor and pheromone signaling with reproduction

These studies also indicate that GnRH neurons are likely to influence numerous brain functions. They appear to transmit signals to as many as 30,000 or more neurons in 34 brain areas, consistent with previous studies showing GnRH+ fibers and GnRH receptors in multiple brain regions (Badr and Pelletier, 1987; Jennes et al., 1988; Jennes et al., 1997). BL+ neurons likely to receive synaptic input from GnRH neurons were seen in areas associated with numerous different functions, including odor and pheromone processing, sexual behavior, appetite, defensive behavior, motor programs, and the relay of information to higher cortical areas. These results may reflect a strategy wherein GnRH neurons can modify diverse functions in order to coordinate the internal state of the animal and its behavior with reproduction in order to optimize reproductive success.

See my posts on Discovering Vismodegib in the Fight Against Skin Cancer: The First Approved Inhibitor of the Hedgehog Pathway
No one I know is likely to understand this link from the anti-entropic virucidal energy of sunlight to prevention of all pathology because they must first understand the fact that proteins do not create themselves. There is no need for this inhibitor of the Hedgehog pathway or inhibition of any other pathway if cancer is prevented. But most people are not willing to learn about prevention because they think they can rely on medical practitioners to effectively treat their diseases. Do you think that your physician knows anything about light scattering characterization of glycoproteins and their interactions with other proteins and antibodies?
Absolute Characterization of Glycoproteins and their Interactions with Proteins and Antibodies by Light Scattering
Light scattering can now be linked to the characterization of glycoproteins and their immune system interactions in all species on Earth. That suggests the speed of light on contact with water links energy as information to the de novo creation of the glycoproteins,
If so, the physiology of reproduction links pheromones to biophysical constraints on the creation of more glycoproteins in the context of morphological and behavioral differences in species from microbes to humans. That suggests the refutation of neo-Darwinism is complete, since the virus-driven degradation of messenger RNA has been linked to all pathology in bacteria that become archaea before virus-driven energy theft causes them to become L-forms.
Simply put, Carl Woese was wrong. There is only one domain of life and virus-driven energy theft is what destroys all life on Earth.

 

rp_amino-acid-homeostasis-300x300.jpg

Automagical protein creation sans energy

by with No Comment AdaptationsbiophotonicsCytosisDiseases & DisordersEcologyLight EnergyModel OrganismsPhysicsRNA DirectedRNA-directed DNA methylationRNA–Mediated Epigenetic Heredity

Summary:
The creation of the enzyme is linked to the evolution of all biodiversity via the creation of the enzyme and mutations. See for comparison: Neuronal-expressed microRNA-targeted pseudogenes compete with coding genes in the human brain. Listen to this song about Santa Claus and note that he sees you when you’re sleeping and somehow unconsciously determines if you’ve been good or bad. Santa Claus may know that the sense of smell has repeatedly been linked to effects on hormones and unconscious affects on behavior.

This enzyme enabled life to conquer a hostile earth

The first major step of photosynthesis is triggered by an enzyme known as Rubisco. Previous research suggested that Rubisco is likely the most abundant protein on Earth

The first major step of photosynthesis is the de novo creation of the sun’s anti-entropic virucidal energy. The energy must be linked from its creation to the Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
See for review: The role of quantum information in thermodynamics—a topical review
Excerpts:

1) If physical theories were people, thermodynamics would be the village witch.

2) In the early twentieth century, information theory was constructed as the epitome of detachment from physics [7].

3) But as it turned out, not all information was created equal.

I’m reading a book by Matthew Cobb that fails to resolve that problem. In the first part of the book, he fails to link Schrodinger’s claims about sunlight and negative entropy from energy as information to all biophysically constrained biodiversity on Earth, and complains that Schrodinger gets not credit for the concept of energy as information because he never used the word information. See: Life’s Greatest Secret: The Race to Crack the Genetic Code and Genes Before DNA: How geneticists around the world struggled to bring the foundation of life’s building blocks to light “… there are no direct links between Schrödinger’s lectures and the experiments and theories that were part of the decades-long attempt to crack the genetic code…”

4) In the past twenty years, the field of non-equilibrium statistical mechanics has seen a rapid development in the treatment of driven classical and quantum systems beyond the linear response regime. This has culminated in the discovery of various fluctuation theorems which relate equilibrium thermodynamic quantities to non-equilibrium ones, and led to a revision on how we understand the thermodynamics of systems far from equilibrium [20–24].

5) Entanglement and phase transitions in condensed matter. Entanglement is frequently used as an indicator of quantum phase transitions in condensed matter systems. We do not cover this particular setting but the interested reader may find a comprehensive review in [36].

[36] Entanglement in many-body systems can be compared to what is known about the Structural diversity of supercoiled DNA, and this playful representation of all biophysically constrained biologically-based cause and effect in this parody about energy-dependent base pairs.

The authors of Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree  ignore the fact that food energy as information must be linked to quantum entanglement via changes in base pairs in the context of the creation of amino acids and all protein-based biodiversity on Earth. Instead, they ignore biophysical constraints on energy-dependent base pairs that are linked to biophysically constrained viral latency via RNA-mediated fixation of amino acid substitutions in supercoiled DNA.
For instance, they start with the automagical creation of a protein. Then they link the automagical creation of the protein from the enzyme known as Rubisco to protein folding chemistry and to all biophysically constrained biodiversity on Earth.  In the context below, anything is possible. All that theorists need to do is remove the energy and focus on the math, which they now must link to ecological adaptations.

Ribulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO, or Rubisco) catalyzes a key reaction by which inorganic carbon is converted into organic carbon in the metabolism of many aerobic and anaerobic organisms…

Therefore, it is possible that the mutational enrichment periods between the Form III and Form I common ancestral sequences correspond to the adaptation of key oxygen-sensitive components of Rubisco prior to, or coincident with, the Great Oxidation Event.

It is equally possible that mathematical models of energy-dependent biophysically constrained biologically-based cause and effect could be used in representations like this: Quantum common sense

We don’t need a conscious mind to measure or look. With or without us, the Universe is always looking

For comparison: Listen to this song about Santa Claus and note that he sees you when your sleeping and somehow unconsciously determines if you’ve been good or bad.
For comparison to the Rubisco phylogenetic tree  see: The phylogenetic utility and functional constraint of microRNA flanking sequences
When pseudoscientists fail to link the quantized energy of sunlight as information from changes in base pairs to the creation of microRNAs and all biophysically constrained biodiversity, they typically proceed to tout ridiculous theories about mutations (e.g, mutational enrichment periods). They seem to not recognize the fact that the mutations are caused by the theft of quantized energy and the virus-driven degradation of messenger RNA.
The theft of quantized energy as information cannot lead to mutational enrichment periods outside the context of mathematical models. In this case, natural selection for energy-dependent codon optimality is no longer considered in the context of the Great Oxidation Event, which is placed into the context of a mathematical model. The creation of the enzyme is linked to the evolution of all biodiversity via the creation of the enzyme and mutations.

Post hoc, ergo propter hoc

The term refers to a logical fallacy that because two events occurred in succession, the former event caused the latter event.

The logical fallacy is exemplified above. Rubisco links an enzyme to catalysis via a key reaction that corresponds to the adaptation of key oxygen-sensitive components of Rubisco prior to, or coincident with, the Great Oxidation Event.

The ease of obfuscation (the former event caused the latter) links other logical fallacies to claims about mutation-driven evolution. Those ridiculous claims can be compared to accurate representations of energy-dependent top-down causation in the context of the pheromone-controlled physiology of reproduction. Nutrient-dependent/pheromone-controlled adaptive evolution: a model.

Anyone who thinks they can continue to tout theories instead of facts about energy-dependent ecological adaptations should be cast out of academia. Minimally, they will continue to be told to stop linking their ridiculous theories about enzymes to all biodiversity on Earth without claims about how the enzymes were created. But first, they should be forced to admit that they do not know where the energy for the creation of the protein, Rubisco came from.

Rather than admit that their theories are examples of human idiocy (see Food energy), biologically uniformed science idiots continue to serve as examples of the idiocy (Richard P. Feynman’s term). The “food energy” snippet comes from one of his lectures in the series “The character of Physical Law.” He complains about all the different units that are used to measure the single concept of Energy.

His prescient perspective on human idiocy can now be viewed in the context of sunlight as the quantized energy of information. In the latest rendition of pseudoscientific nonsense, quantized energy as information has since been eliminated from the creation of an enzyme. Then, the protein, Rubisco is linked to ecological adaptation and all energy-dependent biodiversity on Earth (and perhaps even on other planets).

To place that pseudoscientific nonsense into the context of life and death on Earth, see: Olfaction Warps Visual Time Perception

The altered human visual perception of mass and energy was placed into the context of the space time continuum via links to the food energy-dependent pheromone-controlled physiology of reproduction in bacteria.

See: Neuronal-expressed microRNA-targeted pseudogenes compete with coding genes in the human brain

…several studies report active target RNA-directed degradation of miRNAs, rather than passive ‘sponging’ activities.7 Together, this calls for re-inspection of the evolutionary, global in vivo impact, directionality and specificity of the competition between PSGs and protein-coding genes (PCGs) in the human brain.

Re-inspection of the evolutionary, global in vivo impact et al., in the context of the virus-driven degradation of messenger RNA will link the energy-dependent de novo creation of olfactory receptor genes to healthy longevity via biophysically constrained viral latency. The viral latency is manifested in pseudogenes. Humans have more pseudogenes than other mammals because more viruses were biophysically constrained.  The biophysical constraints are food energy-dependent.

So far as I know, you cannot get to altered perception without the energy-dependent de novo creation of microRNAs and G protein-coupled receptors such as olfactory receptor genes. However, altered perception has been linked to social behavior via pheromones and de novo gene creation as well as the creation of pseudogenes that biophysically constrain human behavior in the context of neurogenesis and a potential cure for all neurodegenerative diseases.

See: Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis

The neurodegenrative diseases have been linked to suicide and to suicide prevention via expertise is pharmacogenetics.

See: Formulation and evaluation of anti-suicidal nasal spray of Thyrotropin releasing hormone

The role that the de novo creation of energy-dependent microRNAs plays in the prevention of all pathology is clear to all serious scientists.

See also: MicroRNAs-based therapy: a novel and promising strategy for cancer treatment

The role of microRNA-based therapies (microRNA and disease) extends across the space time continuum to the formulation of the anti-suicidal nasal spray via the formulation of human pheromone-enhanced products. That fact is not being examined by anyone I know about.

The role that mutations and natural selection play in the automagical creation of all energy-dependent biodiversity has captured the attention of pseudoscientists and other biologically uninformed science idiots who have attacked me for more than 20 years. The question remains: When is enough, enough? Even friends are beginning to attack.

See: 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!

Without the anti-entropic virucidal energy of sunlight, enzymes cannot be built and hormones and receptors cannot be linked From Fertilization to Adult Sexual Behavior via published works like this: Feedback loops link odor and pheromone signaling with reproduction or by any other serious scientists who are Combating Evolution to Fight Disease.

My comment to Science:

Darwin probably anticipated the insemination of population genetics that led to the bastardization of his detailed observations in the “Modern Synthesis.” He politely insisted that ‘conditions of life’ be considered before natural selection.

There are two ‘conditions of life.’ It is nutrient-dependent and pheromone-controlled. Rosenberg and Queitsch now note the work with Dobzhansky’s rarely acknowledged claim: “I am a creationist and an evolutionist.” They also declare the need for “Deep understanding of the mechanisms that generate variation at the molecular level…”

Deep understanding of the ‘conditions of life’ does not come from theory.

Problems with the “modern synthesis” now lead us back to the facts about biologically-based cause and effect that Darwin and Dobzhansky approached with humility, which are the same biological facts that evolutionists approached with ignorance about behavioral affects and the arrogance that accompanies that ignorance. Rosenberg and Queitsch echo the sentiments of those who have been subjected to academic suppression.

Clearly, however, “nothing in evolution makes sense except in the light of biology” is not an exaggeration. It is a common sense statement about the biologically plausible genesis of functional cell types. Population genetics and evolutionary theories abandoned the biophysical constraints of ecological variation and the physiology of reproduction, which enable epigenetically-effected nutrient-dependent pheromone-controlled receptor-mediated ecological adaptations and species diversity via the complexities of protein folding and niche construction.

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

See also: Protein folding: Much more intricate than we thought: Scientists are still uncovering all the players that help keep proteins folded inside cells—and all the ways the process can go wrong

The sequence of amino acids in a protein is sufficient to determine its three-dimensional structure.

Natural selection for energy-dependent codon optimality is the link from the physiology of reproduction to fixation of the amino acid substitutions that differentiate all cell types in all individuals of all living genera. That fact has now been placed, once again, into the context of this pseudoscientific nonsense.
See: Scientists Uncover That Humans Have A ‘Magnetic 6th Sense’ to Detect Something We Can’t Even See

Inspired by articles written by Collective-Evolution and Science Alert.

Kirschvink was able to discover in one of his experiments that when the magnetic field itself is rotated counterclockwise around a patient, their neutrons responded with generating a spike in electric activity.

See also: Joseph Kirschvink et al., “A Magnetotactic Origin for the Mitochondria (and Organelle-bearing Eukaryotes) at ∼2ga: In The Aftermath of the Cyanobacterial Radiation and the Great Oxygenation Event, Causing the End Of The Lomagundi-jatuli Carbon Isotope Excursion and Paving the Way for the Rest of Proterozoic Time” (paper presented at 34th International Geological Congress Unearthing our Past and Future—Resourcing Tomorrow, Brisbane, Australia, 5–10 August, 2012). — cited in “The Excitable Mitochondria” by John Hewitt
For attacks on my model by friends,  see: MicroRNA: A novel target of curcumin in cancer therapy (Discussion attempt)
I do not think that any family members and/or most of my friends want the cure for cancer and all other pathology to be revealed — unless the cure cannot be linked to healthy longevity from my model of food energy-dependent pheromone-controlled RNA-mediated biodiversity.
“A Magnetotactic Origin for the Mitochondria” divorces the origin of the mitochondria from the energy-dependent de novo creation of G protein-coupled receptors that link pH-taxis to chemotaxis and phototaxis.
All energy-dependent taxis/movement is biophysically constrained by the anti-entropic virucidal energy of sunlight in the context of the physiology of pheromone-controlled reproduction. The claims that linked human pheromones to our “sixth sense” have nearly been removed from consideration during the past two decades. See for instance this review of See What I’m Saying: The Extraordinary Powers of Our Five Senses

The goals of the book are threefold: (1) to reveal that you have extraordinary perceptual skills of which you are largely unaware;(2) to show that by becoming aware of these skills and how they work, you can actually enhance how to use them; and (3) to convey that these skills illustrate some of the most important recent developments in perceptual science.

The most important recent developments in perceptual science link food odors and pheromones from the sense of smell in bacteria to the physiology of reproduction, which biophysically constrains viral latency. That prevents the virus-driven degradation of messenger RNA that would otherwise reduce all of creation to examples of archaea and L-forms that Carl Woese claimed should be placed into the context of different domains of life.
See:
Cellular versus viral microRNAs in host–virus interaction
Viral and cellular messenger RNA targets of viral microRNAs
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.

 
 

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

Sunlight, phytochemicals, microRNAs and cancer

by with No Comment AdaptationsbiophotonicsCytosisDiseases & DisordersEcologyLight EnergyModel OrganismsPhysicsRNA DirectedRNA-directed DNA methylationRNA–Mediated Epigenetic HeredityVariations

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!
Summary: If the creation of the uranium isotopes was not biophysically constrained in the context of hydrogen-atom transfer in DNA base pairs in solution, the sun’s anti-entropic virucidal energy would be a less effective treatment for cancer than radiation therapy.
The link from the anti-entropic virucidal energy of sunlight to the de novo creation of microRNAs and prevention of all pathology will become clearer each day until the cell biology game “Cytosis” is available for play by anyone ten years old or older.
Jay R. Feierman continues his attempts to obfuscate that clarity. He failed to post three comments to the Human Ethology Yahoo Group and sent me three private messages: All three claim: “You can only post one message a day as you keep saying the same thing over and over again.”
This research was published yesterday.
Role of phytochemicals in the modulation of miRNA expression in cancer (published in Food & function)

…phytochemicals play an important role in the modulation of miRNA expression, which is related to changes in oncogenes, tumour suppressors, and cancer-related protein expression. Hence, phytonutrients can suppress tumour development, prevent metastasis, reverse the EMT, and improve drug sensitivity via the modulation of miRNA expression.

The research supports what I have been saying since the time I learned that Schrodinger (1944) stated it clearly:

“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.)”

People like Feierman must prevent others from learning facts about the anti-entropic virucidal energy of sunlight. The facts are neo-Darwinian evolutionary theory killers becasue Darwin’s claims began with food energy-dependent “conditions of life.”
See for comparison:
Jay R. Feierman wrote: You can only post one message a day as you keep saying the same thing over and over again. —In human-ethology@yahoogroups.com, he wrote :

Re: This claim is above my level of expertise to refute. — Jay R. Feierman

My response: It is unfortunate that the comment by James Gray about Jay’s understanding cannot be found in this series, and that no one seems interested in discussion of facts that attest to Jay’s claim.

Others who cannot refute the claim that “DNA Begins As a Quantum Wave” may continue to link the anti-entropic virucidal energy of sunlight to mutations, natural selection, and evolution despite my history of published works that led Jay to claim:

7/26/13
“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.” 

We may never know why others, like Jay, would make claims about random mutations without knowing the origin of DNA, which links energy as information to the biophysically constrained physiology of reproduction in my model of all biologically-based diversity.
Jay R. Feierman wrote: You can only post one message a day as you keep saying the same thing over and over again.

He blocked this comment:

Journal article abstract excerpt: “…isotopic analyses of individuals amino acids offer the opportunity to further examine this hypothesis.”

Food energy-dependent RNA-mediated amino acid substitutions link ecological variation to ecological adaptations in species from microbes to humans in the context of the physiology of pheromone-controlled reproduction. That fact led to a counter-claim by Jay R. Feierman, and he has since limited all discussion of my model.

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. 

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

MODERATOR NOTE: I’m not going to post more from Kohl until he answers the very direct and simple question posed to him by anon, which is whether he (Kohl) believes that RNA splicing can change DNA.]

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

My attempts to discuss facts about food energy-dependent RNA-mediated cell type differentiation have consistently been placed into the context of attempts to discuss beliefs by a moderator who has consistently supported claims that link random mutations from natural selection to the evolution of biodiversity.

Jay R. Feierman wrote: You can only post one message a day as you keep saying the same thing over and over again.
He blocked this comment:

Genes Before DNA

How geneticists around the world struggled to bring the foundation of life’s building blocks to light.

Excerpt: “Information” was about to enter science, but had not done so when Schrödinger gave his lectures. Without that conception of the content of the code, Schrödinger’s insight was merely part of the zeitgeist, a hint of what was to come rather than a breakthrough that shaped all subsequent thinking.

My comment: In 1944, Schrödinger stated: 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)

The fact that quantized energy is information seems to have escaped the grasp of many theorists, but virtually all the medical professionals I have encountered realize that organisms die if they do not find some form of quantized energy as information to eat.

Addendum: Arguably, Feierman is right. I do repeat myself. He forces me to repeatedly present my claims about energy as information by ignoring them. Instead, he makes ridiculous claims about mutations, natural selection, and evolution. That is what all pseudoscientists do.
USDA Emails: Don’t Use “Climate Change”

The news report suggested these were political moves to fall in line with the newly installed Trump administration.

The truth is that these moves are consistent with the claims that Schrodinger (1944) made in “What is Life” and the claims made in Role of phytochemicals in the modulation of miRNA expression in cancer.
Weather extremes link changes in the microRNA/messenger RNA balance in soil bacteria to healthy longevity or from the virus-driven degradation of messenger RNA to all pathology. Climate change is comparatively ambiguous, since it does not link the anti-entropic virucidal energy of sunlight to healthy longevity.
The biophysically constrained energy of sunlight also helps to reduce greenhouse gases and to sequester carbon, which links the de novo creation of energy as information to all life on Earth by building organic material in soil.  For example, sunlight has been linked from the metabolism of bacteria to the biophysically constrained creation of uranium isotopes.
See: Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits
If the creation of the isotopes was not biophysically constrained in the context of hydrogen-atom transfer in DNA base pairs in solution, the sun’s anti-entropic virucidal energy would be a less effective treatment for cancer than radiation therapy.

Can protein folding chemistry be understood by theorists?

by with No Comment AdaptationsAlternative SplicingsAutophagybiophotonicsCytosisDiseases & DisordersEcologyHuman PheromonesLight EnergyModel OrganismsNeuronal PlasticityNutrigenomicsPhysicsRNA DirectedRNA interferenceRNA methylationRNA-directed DNA methylationRNA-mediated epigenetic regulation of gene expressionRNA-mediated gene silencingRNA-mediated toxicityRNA–Mediated Epigenetic HeredityVariations

Excerpt: The researchers believe their discovery dovetails with their research on how tumor viruses and cancer mutations change a cell’s DNA structure and organization to cause uncontrolled cell growth.
Aye group discovers avenue for precision cancer treatment

One challenge is that multiple variations, or isoforms, of the same protein can all catalyze the same cellular function, “but the nuances of biology rest in how individual isoforms are regulated,” Aye said.

Natural selection for energy-dependent codon optimality regulates the creation of isoforms and all biodiversity via links from RNA-mediated amino acid substitutions in supercoiled DNA to chromosomal inheritance.

Protein folding: Much more intricate than we thought

All protein folding chemistry is energy-dependent and RNA-mediated. It must link chirality to autophagy and the physiology of pheromone-controlled reproduction or it cannot link quantum physics to quantum souls via what organisms eat in the context of niche construction.
See also: New Imaging Technique Overturns Longstanding Textbook Model of DNA Folding

The researchers believe their discovery dovetails with their research on how tumor viruses and cancer mutations change a cell’s DNA structure and organization to cause uncontrolled cell growth.

Energy-dependent protein folding chemistry is no more intricate than it was when we detailed everything known about RNA-mediated cell type differentiation in this 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior

See also: 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.

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

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction.

See also: Olfaction Warps Visual Time Perception

See for comparison: What the ctenophore says about the evolution of intelligence

The ctenophore was already known for having a relatively advanced nervous system; but these first experiments by Moroz showed that its nerves were constructed from a different set of molecular building blocks – different from any other animal – using ‘a different chemical language’, says Moroz: these animals are ‘aliens of the sea’.

Moroz tries and fails to recover from decades of touting the pseudoscientific nonsense of neo-Darwinian evolution.  See: Independent origins of neurons and synapses: insights from ctenophores

The possibility of secondary loss of neurons and synapses in the Porifera/Placozoa clades is a highly unlikely and less parsimonious scenario.

The virus-driven degradation of messenger RNA has been linked to the secondary loss of G protein-coupled receptors that link multisensory input from the sense of smell in bacteria to our visual perception of mass and energy in the context of the space-time continuum.
See also: Viral Genome Junk Is Bunk

So, where do viruses come from that essentially share the same sequences as those found in their host genomes? Perhaps the evolutionists have placed the cart before the horse on this issue, as proposed by several creationist scientists.4,6 In fact, in an ironic twist, the evidence mentioned above indicates that viruses likely arose from their hosts and not the other way around. As molecular biologist and biochemist Peter Borger notes, “The most parsimonious answer is: the RNA viruses got their genes from their hosts.”6

The possibility that the virus-driven degradation of messenger RNA causes the secondary loss of neurons and synapses in the Porifera/Placozoa clades is the most likely and most parsimonious scenario. Neo-Darwinian theorists and others who have failed to link the sun’s anti-entropic virucidal energy to the biophysically constrained physiology of reproduction and all biodiversity via the chemistry of protein folding are forced to continue to ignore all experimental evidence of biologically-based cause and effect. Their only alternative is to invent new terms for “microRNA,” since energy-dependent changes in the microRNA/messenger balance have linked the physiology of reproduction from chromosomal rearrangements to viral latency and all biodiversity.
See also:  Gut viruses tied to potentially deadly complication of bone marrow transplant

…the onset of GvHD appeared to trigger the late awakening of these covert viruses, laying to rest a longstanding chicken-and-egg debate: which comes first, viral infection or GvHD? The researchers conclude that much of the viral flare they saw is due to reactivation of latent gut infections following transplantation.

The link from gut bacteria to reactivation of latent gut infections following transplantation links a change in the energy-dependent microRNA/messenger RNA balance to hematopoiesis and.cell type differentiation in all vertebrates and vertebrates.
 See also:
Mysterious children’s neurological disease is traced to a single error in one gene

The researchers found in all patients the same spontaneously occurring, non-inherited genetic change in a gene (named “UBTF”) responsible for ribosomal RNA formation.
 

The de novo creation of RNA is energy-dependent. No disease can be traced to a single gene outside the context of the virus-driven degradation of messenger RNA that causes the pathology.

See: Oligogenic basis of isolated gonadotropin-releasing hormone deficiency

The deficiency links the virus-driven degradation of messenger RNA from a single gene to every aspect of vertebrate morphology and behavior via GnRH.

The de novo energy-dependent creation of RNA has been linked to GrRH since 1964.

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

I reiterate:  Next we will learn that “Nothing in Biology Makes Sense…” outside the context of food energy-dependent pheromone-controlled RNA-mediated ecological adaptations.

NgAgo Paper Retracted

“[W]hen it comes to biology, answers are often not definitive. And when it comes to replication studies, the one thing we know is that it takes time,” it says. “In the case of NgAgo, the time has come and the data have spoken.”

Earlier today, I mentioned to my friend, Jo Rockafellor, that Bruce McEwen told me, in 1992, my model could not be validated without starting from gene activation in gonadotropin releasing hormone (GnRH) neurons. After learning from Donald Pfaff that Robert L. Moss might know something important, “Bob” Moss and I became friends. He once told me, “you know how it works, write the book.”
 
If you think I am name-dropping, you are right. These are the people that others must learn from or they are not likely to learn anything about energy-dependent biophysically constrained RNA-mediated cell type differentiation.
 
Another line of experimental evidence links publication of The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002), from Martha McClintock’s works to the claim made by Denise Chen when she introduced me to Wen Zhou.

Denise claimed that my book was responsible for her interest in the study of olfaction, and Wen Zhou has since linked quantum physics to quantum souls.

When someone like Moroz claims that “The possibility of secondary loss of neurons and synapses in the Porifera/Placozoa clades is a highly unlikely and less parsimonious scenario.” he attests to the ignorance of several generations of pseudoscientists who failed to ask how and when the energy-dependent de novo creation of RNA occurred. Instead, they link the virus-driven degradation of messenger RNA to all biodiversity via mutations and natural selection.

That, is foolish. See: 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!

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

Evolutionary congruence (losers) vs ecological adaptation (winners)

by with No Comment AdaptationsAlternative SplicingsAutophagybase editingbiophotonicsCytosisDiseases & DisordersEcologyLight EnergyModel OrganismsPhysicsRNA DirectedRNA editingRNA-directed DNA methylationRNA-mediated epigenetic regulation of gene expressionRNA–Mediated Epigenetic HeredityVariations
This is the first DNA-sequence based phylogeographic assessment of Salvadora in the world. Sequence based phylogeographic assessment of tropical tree species is a relative rarity and in India, such investigations are almost non-existent.
 

Kalevi Kull: Censorship & Royal Society Evo Event

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

In a rapidly changing world of post-censorship, the losers tout “DNA-sequence based phylogeographic assessment.” All serious scientists have linked energy-dependent RNA-mediated protein folding chemistry from changes in angstroms to ecosystems via supercoiled DNA, which protects all organized genomes from the virus-driven degradation of messenger RNA.

Each time you see a term like evolutionary congruence, ask for a definition that links it to what is currently known to all serious scientists about biophysically constrained energy-dependent RNA-mediated biologically based cause and effect.

You will learn There is no such thing as an evolutionary congruence. Molecular Phylogeography is not examined (e.g., by serious scientists) outside the context of the anti-entropic virucidal energy of the sun.

The virucidal energy links the creation of microRNAs in plants to the food energy-dependent creation of microRNAs in animals and all biophysically constrained biologically-based cause and effect on Earth via the physiology of pheromone-controlled reproduction in bacteria.
See: The phylogenetic utility and functional constraint of microRNA flanking sequences

See also: Cystosis

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

Food energy links the de novo creation of microRNA flanking sequences to the creation of enzymes, hormones and receptors that link ecological variation to ecological adaptation via the physiology of pheromone-controlled reproduction in species from microbes to humans. The pheromone-controlled physiology of reproduction biophysically constrains the transgenerational epigenetic inheritance of virus-driven energy theft, which has been linked from mutations to all pathology –except by Greg Bear, who linked biophysically constrained viral latency to the pheromone-controlled creation of a new human subspecies.

See: The Darwin Code by Greg Bear

Bacteriophages–phages for short–can either kill large numbers of host bacteria, reproducing rapidly, or lie dormant in the bacterial chromosome until the time is right for expression and release. Lytic phages almost invariably kill their hosts. But these latter types–known as lysogenic phages–can actually transport useful genes between hosts, and not just randomly, but in a targeted fashion.

See for comparison: A Crack in Creation review – Jennifer Doudna, Crispr and a great scientific breakthrough

Jennifer Doudna’s work began with organisms even further out on the Palin scale: bacteriophages, tiny viruses that prey on bacteria.

Conclusion: The difference between the works of science fiction novelist Greg Bear, and people like Jennifer Doudna, is clear. Greg Bear’s works (and the works of the late Eshel Ben-Jacob) predicted that, if viral latency was not biophysically constrained, the virus-driven degradation of messenger RNA would be linked to all pathology.
The works of biologically uninformed researchers tout the benefits of the virus-driven degradation of messenger RNA, which is used in their gene-editing technology, as if the concept of gene-editing exemplified a “Crack in Creation.” For comparison, natural selection for energy-dependent codon optimality links the pheromone-controlled physiology of reproduction from energy-dependent changes in chirality to autophagy, which protects all organized genomes from the virus-driven degradation of messenger RNA that Doudna and others have linked to all pathology.
See also: 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 (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.

See also:
The Origin of Information (3) If they do not know where the quantized energy in a hydrogen atom came from, they cannot discuss a Crack in Creation in the context of the virus-driven degradation of messenger RNA that is their key to gene editing.
See also: NgAgo Paper Retracted

[W]hen it comes to biology, answers are often not definitive. And when it comes to replication studies, the one thing we know is that it takes time,” it says. “In the case of NgAgo, the time has come and the data have spoken.

Next we will learn that “Nothing in Biology Makes Sense…” outside the context of food energy-dependent pheromone-controlled RNA-mediated ecological adaptations.