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

Energy-dependent physical and biophysical constraints (2)

Summary: The mind does not exist in nature. It is a manifestation of how ecological variation must be linked to the creation of food energy-dependent pheromone-controlled ecological adaptations.
Energy-dependent physical and biophysical constraints (1)
The energy-dependent de novo creation of all receptors is biophysically constrained.
See: Channel opening and gating mechanism in AMPA-subtype glutamate receptors
This was reported as: Scientists capture first image of major brain receptor in action

Defects in glutamate receptors, or the processes they mediate, are implicated in neurodegenerative disorders such as Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, multiple sclerosis and glaucoma; psychiatric disorders such as anxiety, depression, schizophrenia, and drug use disorders; as well as in acute disorders such as brain trauma and stroke. The new structure of an active AMPA receptor and understanding of the activating mechanism create a solid platform for developing therapeutics to treat neurological disorders that are associated with glutamate receptor dysfunction.

The activating mechanism is energy-dependent and virus-driven energy theft is linked to all pathology via changes in the microRNA/messenger RNA balance. Search the PubMed database for “microRNA” and “glutamate receptor,” “Alzheimer’s,” “Parkinson’s,” “Huntington’s,” “multiple sclerosis,” “glaucoma,” “anxiety,” “depression,” “schizophrenia” and any other disorders.
For example: microRNA+glutamate+receptor 

MicroRNA in glutamate receptor-dependent neurological diseases

But wait… There’s more.
“Alzheimer’s,”
“Parkinson’s,”
“Huntington’s,”
“multiple sclerosis,”
“glaucoma,”
“anxiety,”
“depression,”
“schizophrenia”

See also:  Cytosis: A Cell Biology Board Game

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses! Energy is required to build the enzymes, hormones and receptors that protect organized genomes from the virus-driven degradation of messenger RNA, which links mutations to all pathology.

See also: Excerpt from update #16

We’ve had a ton more of you volunteer to playtest the Subatomic PnP than we expected, which is terrific.

I did have the PnP ready to send out… or so I thought. Somehow every time we’ve played Subatomic the past several weeks I’ve made significant changes. We’ll integrate a change into the rulebook, player mat, cards… and then we play again, and make another set of significant changes all over again.

I want to get a good handle on which of these changes will stay and which don’t work well over the long term before I send the PnP to you all. All that being said, I’m planning to get the link out to you in the next week or so.

As all serious scientists know, the changes that stay will link quantized energy from the subatomic particles to our visual perception of energy and mass in the context of Olfaction Warps Visual Time Perception and a series of articles that were published by young earth creationists.
See: Researchers identify ‘tipping point’ between quantum and classical worlds
The “tipping point” between quantum and classical worlds is energy-dependent and biophysically constrained via the anti-entropic virucidal effect of sunlight, which is linked to the physiology of food energy-dependent reproduction in all living genera.
See also: Subatomic Particles, Part 1: Leptons
Subatomic Particles, Part 2: Baryons, the Substance of the Cosmos
Subatomic Particles, Part 3: Mesons
Subatomic Particles, Part 4: Gauge Bosons, the Glue That Holds the Universe Together

We have seen the delicate balance between the four forces; each is perfectly designed to make life possible. We have explored the fleeting nature of so many subatomic particles. Yet the ones needed for atomic chemistry and life are stable. The masses and forces are precisely tuned. If the up quark were just slightly heavier than the down quark, all matter would decay into neutrons. Slightly change the charge of an electron or a quark and atoms could never form larger structures due to electric repulsion. It’s clear the universe is perfectly designed for life.

What then can be said about the virus-driven degradation of messenger RNA that links mutations to all pathology? What challenges to perfectly designed life would theorists like serious scientists to consider outside the context of food energy and human idiocy?
For example, this claim was reasserted in the June 2017 issue of Discover Magazine:

…energy may not be conserved “locally” — that is, in an arbitrarily small patch of space — but everything works out when the space is sufficiently large.

See for comparison: Food energy

Richard Feynman was a Nobel prize winning Theoretical Physicist who popularized physics… This snippet is taken from one of his lectures in the series “The character of Physical Law” where he complains about all the different units that are used to measure the single concept of Energy.
Claims that the local conservation of energy do not require conservation in the context of an ever-expanding time-space continuum are additional examples of human idiocy. The fact that theoretical physicists must return to the examination of a early 1900’s theory set forth by an uneducated layperson attests to the reason why even Richard Feynman ridiculed those from his discipline.
See also: A Neuroscientist Just Tricked 4 Dodgy Journals Into Accepting a Fake Paper on ‘Midi-Chlorians’

…a prominent neuroscientist has tricked four publications into accepting a totally fake paper about midi-chlorians – the entirely fictional life forms in Star Wars that make ‘the force’ possible.

See also: Dear Readers – Hiatus From Blog

For five years, I have written summaries of current scientific literature in subjects related to how mind exists in nature.

The mind does not exist in nature. It is a manifestation of how ecological variation must be linked to the creation of food energy-dependent pheromone-controlled ecological adaptations.
My comment to Jon Lieff.

Finally. By the time the “Cytosis” becomes available, everyone else will learn how much confusion you have contributed via your failure to integrate what is known about energy-dependent RNA-mediated cell type differentiation into a cohesive representation of biophysically constrained top-down causation that exists outside the context of your nonsense about 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!

I look forward to reviewing your book at the earliest opportunity to do so. See for example of a recent review: “How Can Physics Underlie the Mind?: Top-Down Causation in the Human Context (The Frontiers Collection)”

Cytosis

Epigenetic effects of stress by Bruce McEwen (2)

Summary:

…rapid mRNA turnover starts with the energy-dependent de novo creation of microRNAs and ends with the virus-driven degradation of messenger RNA, which links mutations to all pathology.
 
This was reported in the following context: “RNA molecules live short lives” July 12, 2017

See also: Epigenetic effects of stress by Bruce McEwen (1)

Summary:

In the early 1990’s, Bruce McEwen inspired my life’s works, which link the epigenetic effects of nutrient-stress and/or social stress to the fact that RNA biosynthesis is ATP-dependent. That fact helped all serious scientists link the virus-driven energy theft of quantized energy to the degradation of messenger RNA, which links mutations to all pathology.

Pseudoscientists refuse to accept that fact.

New research uncovers the secrets of photosynthesis that could help develop computer technology

Energy and charge transfer is what drives photosynthesis and any solar-to-chemical or electrical-to-chemical energy conversion.

That fact links the anti-entropic virucidal energy of sunlight from the de novo creation of microRNAs to all biodiversity. Bruce McEwen published on the role that microRNAs play in: Characterization of the vulnerability to repeated stress in Fischer 344 rats: possible involvement of microRNA-mediated down-regulation of the glucocorticoid receptor (2008)

We also identified that microRNA (miR)-18a inhibited translation of GR mRNA in cultured neuronal cells and that increased expression of miR-18a in the PVN was observed in F344 rats compared with SD rats. These strain differences in GR protein levels were not found in the hippocampus and prefrontal cortex, and the expression of miR-18a was much lower in these brain regions than in the PVN. Our results suggest that F344 rats could be a useful animal model for studying vulnerability to repeated stress, and that miR-18a-mediated down-regulation of GR translation may be an important factor to be considered in susceptibility to stress-related disorders.

See also: Early Life Stress Enhances Behavioral Vulnerability to Stress through the Activation of REST4-Mediated Gene Transcription in the Medial Prefrontal Cortex of Rodents (2010)

Figure 3.

Expression analyses of mRNAs of RE-1-containing genes and brain-enriched pre-microRNAs in the mPFC of the maternally separated rats. A, B, The expression of mRNAs (A) and pre-microRNAs (B) of a variety of RE-1-containing genes in the mPFC of AFR, HMS15, and HMS180 rats at P14 were quantified by Q-PCR (n = 6 for all groups). C, D, The expression of mature microRNAs in the mPFC of AFR, HMS15, and HMS180 rats at P14 were quantified by Northern blotting analysis (n = 5–6 for each group). E, The mRNA and pre-microRNA expression of RE-1-containing genes in the mPFC of adult AFR, HMS15, and HMS180 rats were quantified by Q-PCR (n = 6 for all groups). *p < 0.05.

Bruce McEwen subsequently linked what is known about energy-dependent changes in single nucleotide polymorphisms to effects of hormones on behavior in mice and humans via a food energy-dependent biophysically constrained amino acid substitution.

See: Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity (2015)

Excitatory amino acids play a key role in both adaptive and deleterious effects of stressors on the brain, and dysregulated glutamate homeostasis has been associated with psychiatric and neurological disorders. Here, we elucidate mechanisms of epigenetic plasticity…  In WT mice after CRS and in unstressed mice with a BDNF loss-of-function allele (BDNF Val66Met), we show that the epigenetic activator of histone acetylation, P300, plays a pivotal role in the dynamic up- and down-regulation of mGlu2 in hippocampus via histone-3-lysine-27-acetylation (H3K27Ac) when acute stressors are applied. These hippocampal responses reveal a window of epigenetic plasticity that may be useful for treatment of disorders in which glutamatergic transmission is dysregulated.

See also: Multiplexed gene control reveals rapid mRNA turnover (open access)

The rapid mRNA turnover starts with the energy-dependent de novo creation of microRNAs and ends with the virus-driven degradation of messenger RNA, which links mutations to all pathology.
 
This was reported in the following context: “RNA molecules live short lives” July 12, 2017
“Sometimes it is hard to believe that scientists could have unknowingly worked with methods that produce inconsistent results for almost 30 years”, says Becskei.
 
Becskei adds insult to the injury, unnecessary suffering, and the premature death caused by misrepresentations of biologically-based cause and effect. An accurate representation was reported in 1964 as: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” 
 

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

The fact that some researchers still do not know that the synthesis of RNA is energy-dependent makes it impossible for them to link virus-driven energy theft from the degradation of messenger RNA to mutations and all pathology in all living genera.

It will soon become “child’s play” for anyone over 10 years old. 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!

terrarium-eco-system

The emergence of light as energy from a life-giving star

The Sun – our steady, reliable companion – tells a very different story up close

“…a mesmerising, perspective-shaking glimpse at Earth’s life-giving star.” (video)

Questions:
1) Did the energy in this life-giving star create itself?
2) How is hydrogen-atom transfer in DNA base pairs in solution biophysically constrained.
3) Who created the feedback loops that link the solar analemma from the time-space continuum to representations of biophysically constrained life and free will in the Mobius strip.
4) Was Linda Buck the first Nobel Laureate to establish the link from the food energy-dependent pheromone-controlled physiology of reproduction to biodiversity in all living genera?
5) Are biologically uninformed theorists capable of answering any questions about the energy of life or how virus-driven energy theft causes the degradation of messenger RNA that links constraint-breaking mutations to all pathology?
The Mobius strip and the solar analemma exemplifie biophysical constraints on life history events.

The Mobius strip (above) is a visual aid for those who do not understand the concept of how free will is connected to the conserved molecular mechanisms of biophysically constrained energy-dependent RNA-mediated cell type differentiation in all living genera. If you cannot answer all 5 questions about energy in the context of the visual aid, which links the solar analemma to choices between quantized energy-dependent life and death, please search for microRNA on PubMed. The sun’s anti-entropic virucidal energy is biophysically constrained in microRNAs at every level of examination from angstroms to ecosystems.
If you cannot find the answers to any of the five questions about energy, ask a theorist to answer the first question. Alternatively, see: Computational identification of mutually homologous Zika virus miRNAs that target microcephaly genes

…ZIKV may modulate the action of various miRNAs, and miR-1304 in particular, resulting in microcephaly.

ZIKV – driven degradation of messenger RNA is linked to microcephaly. See also: Absolute Biophysical Characterization with Multi-Angle and Dynamic Light Scattering

A SEC-MALS-RI or UV with DLS system extends the characterization range of biomolecules to glycoproteins, PEGylated proteins, hydrophobic proteins, biopolymers, and other biomolecules.

My summary: The “Brownian” motion of molecules links dynamic light-scattering (DLS) from ecological variation to ecological adaptations via Ultraviolet-visible (UV-Vis) spectroscopy. Detection of energy as information has been placed into the context of virucidal light as energy.

Dynamic light scattering [DLS]

Dynamic light scattering (DLS) is a technique in physics that can be used to determine the size distribution profile of small particles in suspension or polymers in solution.[1] In the scope of DLS, temporal fluctuations are usually analyzed by means of the intensity or photon auto-correlation function (also known as photon correlation spectroscopy or quasi-elastic light scattering).

See also: Detection Limits of DLS and UV-Vis Spectroscopy in Characterization of Polydisperse Nanoparticles Colloids
My summary: Ultraviolet-visible (UV-Vis) spectroscopy links the the food energy-dependent pheromone-controlled physiology of reproduction to the weekend resurrection of the bacterial flagellum in P. fluorescens, which responds to the light-activated chemistry of life with fluorescence even after the “knock-out” of the gene for its mobility, which was resurrected over the weekend as reported in: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
The resurrection in this organism, links its fluorescence to quantized energy-dependent exosome-delivered microRNAs, which have been reported to be Ultraconserved Elements in the Human Genome. When theorists use terms like ultraconserved elements outside the context of the conserved energy in microRNAs, it is clear that theorists are attempting to obfuscate this fact: The energy-dependent de novo creation of microRNAs has been linked to all biodiversity in all living genera via the physiology of pheromone-controlled reproduction.
See for example: All in the (bigger) family I wrote:

The 2015 Society for Integrative and Comparative Biology (SICB) presenters may not recognize how much progress has been made since the 2013 ecological epigenetics symposium. For example, since then authors claimed “…ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.” http://dx.doi.org/10.1038/nature13400

Six months later, other authors traced signaling factors found in vertebrates to the origin of nerve cell centralization via the diffuse nerve net of animals like the sea anemone. http://dx.doi.org/10.1038/ncomms6536 That fact suggests ecological variation is linked to ecological adaptations in morphological and behavioral phenotypes via signaling protein concentrations that differentiate various cell types in body axes and the central nervous system.

Links across species from the epigenetic landscape to the physical landscape of DNA in organized genomes appear to have their origins in the conserved molecular mechanisms of RNA-directed DNA methylation and RNA-mediated protein folding. Two weeks after the publication that refuted ideas about independently evolved neural systems or muscle specification — and perhaps refuted the independent evolution of anything else, SICB presenters linked crustaceans to insects.

Apparently, they’ve learned that the same set of microRNAs controls expression of the genes for rate-limiting enzymes that control the hormone production of different hormones in insects and crustaceans.

Why were they left with any questions about how crustaceans and insects could all be part of one big family? They linked RNA-mediated cell type differentiation to what we described in our section on molecular epigenetics in our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior

See for comparison: Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

The interactions of these small noncoding RNAs in such primitive species have wide-reaching effects, from increasing viral and bacterial proliferation, better responses to stress, increased virulence, to manipulation of host immune responses…

The small non-coding RNAs are energy-dependent microRNAs, which are the same thing as Ultraconserved Elements in the Human Genome..
Here’s a way to make that fact perfectly clear. When it becomes available, play this game: 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!

Stop playing the ridiculous games of theorists who have failed to link the Creation of the sun’s quantized energy to all biodiversity on Earth. Theorists also failed to link the virus-driven degradation of messenger RNA from mutations to all pathology. Instead, they have used definitions of terms and definitions of species that are not limited to that fact that all organisms on Earth must eat or they fail to reproduce.
See for examples of pseudoscientific nonsense: New Research Problem of Species Definitions

Darwin first noted that there is no one definition of species, and not much has changed since then.

All species-specific behavior is food energy-dependent and RNA-mediated cell type differentiation biophysically constrains it in the context of the physiology of pheromone-controlled reproduction in all living genera. Darwin presciently included that fact in his “conditions of life.” He warned others that they could not start with natural selection, but many others have consistently ignored Darwin’s warnings. They also ignore the consistency of biological facts that link what organisms eat to the survival of all species via the pheromone-controlled physiology of reproduction. That forces them to ignore the consequences of virus-driven energy theft.
See: Virus-mediated archaeal hecatomb in the deep seafloor

We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.

See for support of the fact that virus-archaea interactions play a central role in global biogeochemical cycles: Feedback loops link odor and pheromone signaling with reproduction
The feedback loops link natural selection for energy dependent codon optimality from RNA-mediated amino acid substitutions in supercoiled DNA to all biodiversity on Earth via the exosome-mediated delivery of microRNAs.
See also: The phylogenetic utility and functional constraint of microRNA flanking sequences

…the clear identity and easy alignment of these sequences makes them good candidates for estimating phylogeny, and they can reliably be found and identified across all members of a clade of interest. Their relatively slow evolution [3] also means that they can easily be identified in de novo assemblies of genomes.

The assembly of all organized genomes is food energy-dependent. Without food energy there is no energy for assembly of anything. Exosomes mediated the delivery of the food energy in microRNAs.
See also: Exosome Mediated Delivery of miR-124 Promotes Neurogenesis after Ischemia.

The intrinsic ability of neurogenesis after stroke has been proven weak, which results in insufficient repair of injury in the nerve system. Recent studies suggest multiple microRNAs (miRNAs) are involved in the neuroremodeling process. Targeted miRNAs delivery for amplification of neurogenesis is promising in promoting the prognosis after ischemia. Here, we showed that modified exosomes, with rabies virus glycoprotein (RVG) fused to exosomal protein lysosome-associated membrane glycoprotein 2b (Lamp2b), could efficiently deliver miR-124 to the infarct site. Systemic administration of RVG-exosomes loaded with miR-124 promoted cortical neural progenitors to obtain neuronal identity and protect against ischemic injury by robust cortical neurogenesis. Our study suggests that RVG-exosomes can be utilized therapeutically for the targeted delivery of gene drugs to the brain, thus having great potential for clinical applications.

The fact that “…multiple microRNAs (miRNAs) are involved in the neuroremodeling process…” makes the role of food energy-dependent RNA-mediated DNA repair perfectly clear to all serious scientists. For comparison, use of virus-assisted delivery has been linked to the predictable horror of gene editing technology.
See: Unexpected mutations after CRISPR-Cas9 editing in vivo
See for comparison: Cell proliferation in the subventricular zone by synthetic murine pheromones

The elucidation of the mechanisms by which specific compounds influence cell proliferation and neurogenesis, and eventually reproductive conditions in males and females should provide further insight as to how the odor environment controls and modulates the reproductive activities of animals.

See also: Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis
Clearly, researchers who use viruses to stimulate neurogenesis have not learned that all cell type differentiation is energy-dependent and controlled by feedback loops. Their use of viruses will continue ot link virus-driven energy theft from the degradation of messenger RNA to all pathology via the constraint breaking mutations the Masatoshi Nei, and many other biologically uninformed theorists have included in their stories about Mutation-Driven Evolution.

Exosome-delivered microRNAs modulate the inflammatory response to endotoxin 6/18/16

The functional relevance of exosomes in many different biological systems, including the immune system, is beginning to be demonstrated5,6,7,8,9,10,11.

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

…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution. The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, ; Duvarci, Nader, & LeDoux, ; Griggs et al., ; Monahan & Lomvardas, ) in adaptive evolution will certainly be discussed in published works that will follow.

See also: Humans Fit All Of The Government Criteria For ‘Endangered Species’ and Past 5,000 years prolific for changes to human genome
See for comparison: Independent and Stochastic Action of DNA Polymerases in the Replisome

It has been assumed that DNA synthesis by the leading- and lagging-strand polymerases in the replisome must be coordinated to avoid the formation of significant gaps in the nascent strands.

Reported as: Close-Up View of DNA Replication Yields Surprises

What looks like coordination is actually the outcome of a random process of starting, stopping and variable speeds. Over time, any one DNA polymerase will move at an average speed; look at a number of DNA polymerases synthesizing DNA strands over time, and they will have the same average speed.

See for comparison: The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity

…the metabolic enzyme, pyruvate kinase muscle (PKM), interacts with sub-pools of endoplasmic reticulum (ER)-associated ribosomes, exerting a non-canonical function as an RNA-binding protein in the translation of ER-destined mRNAs.

Metabolism is food energy-dependent. That fact should have eliminated all the pseudoscientific nonsense about the random process of starting, stopping and variable speeds. For example, autophagy is quantized energy-dependent and the energy from food protects all organized genomes from virus-driven energy theft and the degradation of messenger RNA that links mutations to all pathology.
See also: The evolution of ecosystem ascendency in a complex systems based model
Abstract conclusion:

Our findings support the validity of ecosystem ascendency as a meaningful measure of ecosystem organisation, which increases over evolutionary time scales and significantly drops during periods of disturbance. The results suggest a general trend towards both higher integrity and increased stability driven by functional and structural ecosystem coadaptation.

Ecosystem ascendancy is food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction in all living genera.
Attempts to model general trends towards the increased stability of functional and structural ecosystems without linking the anti-entropic virucidal energy of sunlight to the physiology of reproduction are examples of what Richard Feynman referred to as human idiocy.

Richard Feynman was a Nobel prize winning Theoretical Physicist who popularized physics with his entertaining lecture style. This snippet is taken from one of his lectures in the series “The character of Physical Law” where he complains about all the different units that are used to measure the single concept of Energy.
See also: Structural diversity of supercoiled DNA

Six decades after the elucidation of its double helical structure, DNA continues to surprise us by revealing new information. Our cryo-ET, biochemical, and computational studies show the astounding versatility and dynamism of DNA depending on the degree of supercoiling. DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases. Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

See for comparison:
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.
7/26/13
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 also:These groups are moderated by Robert Karl Stonjek, who is an example of human idiocy. He knows nothing about biophysically constrained energy-dependent cell type differentiation and consistently displays his ignorance by limiting ability to explain the role that the virus-driven degradation of messenger RNA plays in all pathology.
Psychiatry and Clinical Psychology
Neuroscience
Evolutionary Psychology News
Religion: Science and Psychology
Paleoanthropology Studies
Quantum Physics News
On his FB group for discussion of Sensescence on 6/16/17 I wrote:

All death is caused by trauma or the virus driven degradation of messenger RNA

On 6/17/17 Robert Karl Stonjek wrote (with my emphasis):

Or viruses, or bacteria, or degenerative disease, or genetic disease (there are many), or substance abuse (there are many), or obesity, or….the only one I can’t find in the regular literature is virus driven degradation of messenger RNA.

And then: Robert Karl Stonjek turned off commenting for this post. Can you die from old age?
The pervasive ignorance of those who moderate or censor the comments made by serious scientists via social media has overwhelmed all attempts to present what is known about the virus-driven degradation of messenger RNA, which causes the mutations that have been linked to all pathology.
See for comparison:

Theorists will cause the death of us all. Who will be the next of your loved ones to unnecessarily suffer and prematurely die from the ignorance of theorists?
America’s Dominance In The Scientific World Is shrinking

…while Chinese-born scientists who trained in the United States used to stay here to work, they are now going back to China after their education is over.
 

Denise Chen’s student, Wen Zhou did that. See: Olfaction Warps Visual Time Perception

Had she stayed in the United States, she would have been subjected to pseudoscientific nonsense like this:

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.” — Simon LeVay (2011) in his comments on my award-winning model – after it won a second award in 2007. See: The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences

See also:

… chemosignal enthusiasts point to a variety of studies in which sniffing body secretions or substances purified from secretions appears to have some psychological effect…” — Simon LeVay (2016)

He cited the review that won the first award (Kohl et al., 2001). Human pheromones: integrating neuroendocrinology and ethology

It does not surprise me that senior author Wen Zhou has since linked the sense of smell to the time-space continuum. She was the most promising student I ever met, and I was sad to see her return to China after developing her expertise in the context of what she learned from Denise Chen, who learned about olfaction and pheromones from Martha McClintock.
 
Earlier this year, Wen Zhou’s group showed that olfaction alters the perception of the space-time continuum, which also is warped by the distribution of mass and energy. She has helped to show how food energy and the pheromone-controlled physiology of reproduction are linked to energy-dependent subjective time. For comparison, theorectical physicists have failed to explain anything in the context of multisensory inputs. That is why I frequently refer to biologically uninformed theoretical physicists in the same context as the biologically uninformed neo-Darwinian theorists who have failed to link quantized energy to all healthy longevity and failed to link virus-driven energy theft from the degradation of messenger RNA to mutations and all pathology.
 
Simply put, the multisensory inputs link quantized energy as information from the epigenetic landscape to the physical landscape of DNA at subsecond scales via neural energy and RNA-mediated amino acid substitutions.
 

The subsecond scales links femtosecond blasts of UV light to DNA repair, which is required to link quantum physics to quantum souls. That is the topic of my next interview with J.A. Parker, who sent me the questions in advance, so that I could try to keep the jargon to a minimum.

Until I am sucessful, see: Analysis sheds light on how metaphors like ‘sheds light’ evolved

Words that originally had only concrete or external meaning have grown to also have meaning in the realms of the abstract and internal.

Who else besides Schrodinger in “What is Life? (1944) and J.A. Parker of Quantum Souls knew that Dobzhansky’s “light of evolution” would be traced back to “Let there be Light” in Biblical Genesis via what is known about the anti-entropic virucidal energy of sunlight?

Cytosis

God's shrinking role in salvation (3)

Summary: I believe there is a bipartisan trend that links conservative Republicans to survival of the species, but I don’t know for sure what will happen to the liberal Democrats. And, I can’t prove it!
 
Helicity and chirality https://www.facebook.com/ed.unverricht/videos/10155506720828729/

See also: God’s shrinking role in salvation (2)
A Theory of Reality as More Than the Sum of Its Parts

“Causal emergence is a way of claiming that your agent description is really real,” said Hoel, a postdoctoral researcher at Columbia University who first proposed the idea with Larissa Albantakis and Giulio Tononi of the University of Wisconsin, Madison. “If you just say something like, ‘Oh, my atoms made me do it’ — well, that might not be true. And it might be provably not true.”

For comparison, see also: How concepts of God have developed: God’s shrinking role. God’s survival. Conclusions.

The chances of a given person belonging to God’s “true” religious institution is rather small. Some people are willing to accept this conclusion. However, most are quite certain that their faith tradition is the one that is God’s. Sadly, many find it quite difficult to extend equal human rights to members of other religions. A few are quite capable of denying human rights to, and even killing, those that they consider to be infidels in order to further what they perceive to be their God’s wishes.

See also the historical perspective on the de novo creation of energy-dependent biophysically constrained cell type differentiation in species from microbes to humans. This must be manifested in the context of helicity, chirality, autophagy, and chromosomal inheritance.

From fertilization to adult sexual behavior (1996) and The zinc spark is an inorganic signature of human egg activation (2016)

The historical perspective links the creation of sunlight to injections of adenosine for repair of damaged DNA via a “minimal gene signature.”

See for example: Cross-species gene modules emerge from a systems biology approach to osteoarthritis

Consensus modules established between species

To establish concordance and divergence in the network organization across the two species, consensus modules, modules shared by both networks, were derived from each species network using the weighted average of the two correlation matrices. In all, there were six consensus modules (C1–C6), Figs. 1b and 2b and Supplementary Figs. 4b and 5b. Functional annotation of the consensus modules included: “muscle system process” (C1), “oxidative phosphorylation” (C2), “cell cycle” (C3), “system development” (C4), and “immune system process” (C5).

For comparison, most theorists have traditionally used inferences of top-down causation to establish a consensus, which they tout in simple-minded claims that “evolution is true.” Here is a fact about the pathology of osteoarthritis.

Reported as: Cross-species links identified for osteoarthritis

OA [osteroarthritis] is the destruction of the tissues of the joints and affects more than half of individuals over 65 years old; it is the leading cause of joint pain and disability in the UK.

Animal models are often used to replicate human disease; the relevance and similarity between animal models of joint disease and human osteoarthritis has not been fully evaluated.

Researchers from the University’s Institute of Ageing and Chronic Disease, led by Senior Lecturer in Orthopaedic Sciences Dr Simon Tew, examined molecular messages produced by cartilage cells in both humans and rats.

The molecular messages, which the researchers extended across species  also link the speed of light on contact with water to the energy-dependent de novo creation of all biodiversity on Earth.

See: New research explains hydrophobicity and A single ion impacts a million water molecules

See also: The interfacial structure of water droplets in a hydrophobic liquid, which was reported as: Water is surprisingly ordered on the nanoscale
Sunlight is also surprisingly ordered at the level of quantized energy. If it was not, serious scientists would not know how to link energy dependent changes from Ångströms to ecosystems in all living genera. Thank God, the information about water ordered on the nanoscale can now be linked from the color of the rainbow to all biodiversity on Earth via the physiology of reproduction.

Their surprising results have been published in Nature Communications. They pave the way to a better understanding of atmospheric, biological and geological processes.

Nanometric-sized water drops in the air as droplets or aerosols, in industrially produced medications,  within rocks and oil fields, and within supercoiled DNA interact with changes in temperature in their hydrophobic environment. Simply put, that is the concept of how theromodynamic cycles of protein biosynthesis and degradation are biophysically constrained by ecological adaptation to stress at different temperatures in different functional structures. At room temperature, water molecules at the surface of the droplets have stronger interactions than the water molecules in a normal water surface.

Does any of the above information surprise you? If so, see Water is surprisingly ordered on the nanoscale (discussion attempt)
Avishek Ghosh This is not at all surprising enough to be published in Nature!! There have been many publications by the Bakker group since 2003/2005. In fact my own publication in JACS, PRL discusses such a phenomena at lipid membrane interfaces back in 2007/8. Wonder what’s going on. And a fun fact, Sylvie and I were colleagues for a short while in AMOLF!!

James Kohl  The problem is hydrophobicity in supercoiled DNA. It’s energy-dependent and the anti-entropic energy comes from the sun. Add the fact that cryo-EM has linked hydrogen atom transfer in DNA base pairs in solution to all biophysically constrained biodiversity via the physiology of reproduction in species from microbes to humans. The Nature Publications Group must continue to tout pseudoscientific nonsense about emergence and evolution or rehash the ridiculous concepts until all neo-Darwinian nonsense is completely trashed. Help me. See RNA-mediated.com

James Kohl Non-radiative relaxation of photoexcited chlorophylls: theoretical and experimental study

Peer-review in the United States has prevented dissemination of facts like these, which link photosynthesis from the creation of ATP to the creation of microRNAs and all biodiversity or to the virus-driven degradation of messenger RNA, which links mutations to all pathology (e.g., not to evolution).

Radek Łoziński Maybe it was energized by some mighty magician!

How else could inorganic material be linked to the creation of all biodiversity via signal transfer in bacteria and the zink spark From Fertilization to Adult Sexual Behavior.


See also: Endogenous adenosine maintains cartilage homeostasis and exogenous adenosine inhibits osteoarthritis progression.

…adenosine, acting at A2AR, is an important homeostatic regulator of chondrocytes and cartilage and adenosine repletion may represent a novel approach to treating OA (Fig. 6).

Reported as: Rodents with trouble walking reveal potential treatment approach for most common joint disease

Important to the study’s implications, adenosine is derived from adenosine triphosphate (ATP), the molecule that stores the energy needed by the body’s cells until they break it up to use it. Scientists have known that both inflammation and aging lead to diminished ATP production (and so lower adenosine levels) in chondrocytes. Until now, they had not linked diminished adenosine levels to osteoarthritis, the commonplace, “wear-and-tear” form of arthritis.
The underlying gene regulatory mechanisms in osteoarthritis link injections of adenosine from A-to-I RNA editing via what is known about femtosecond blasts of UV light, which have been linked to the repair of DNA.  Simply put, the injecting adenosine is like an injection of virucidal ultraviolet light.

These consensus modules (in reverse order) support the link from the anti-entropic virucidal energy of sunlight to:

“muscle system process” (C1),

“oxidative phosphorylation” (C2),

“cell cycle” (C3),

“system development” (C4),

and

“immune system process” (C5).

The energy-dependent de novo creation of the innate immune system is the only way to link the other consensus models from angstroms to ecosystems in all living genera via the functional structure of supercoiled DNA.

Others have helped to establish the consensus models by starting with the obvious link from the innate immune system in E. coli, which is a model organism of nutrient-dependent pheromone-controlled ecological adaptation. This model organism also links the weekend resurrection of the bacterial flagellum in P. fluorescens to all biophysically constrained biodiversity on Earth via the sense of smell.

But, first see for comparison: Environment determines evolutionary trajectory in a constrained phenotypic space (2017)
reported as: Genetic mutation trade-offs lead to parallel evolution
In our 1996 Hormones and Behavior review of energy-dependent RNA-mediated cell type differentiation, we included a section on molecular epigenetics and stated this:

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.

One generation (~21 years) later, other serious scientists linked energy-dependent changes from angstroms to ecosystems in all living genera via what is known about biophysically constrained physiology of reproduction.
This journal report on parallel evolution preceded, but the news report on the evolutionary trajectory of genetic mutations, followed the publication of  Mechanism of transmembrane signaling by sensor histidine kinases,  which as reported as: Scientists investigate how the sense of smell works in bacteria. That is how, after-the-fact, the sense of smell in bacteria was placed back into the context of mutation-driven evolution.
This excerpt removed mutation-driven evolution from any further consideration by serious scientists.

…the signaling and inactive states differ only very slightly at the nitrate-binding site – by 0.5-1 angstroms, which is approximately one fifth of the size of the ion itself (1 angstrom is 10-10 meters). However, when this ion binds to the sensor, it causes huge changes in the protein: The helices of different monomers begin to move in different directions, like pistons. These “pistons” transmit the small change of 0.5-1 angstroms through the membrane, and their outer ends shift by approximately 2.5 angstroms in different directions. Inside the cell, in the HAMP domain, these shifts are converted into the rotation of two parts of NarQ relative to each other. Ultimately, the positions of the output helices change by as much as 7 angstroms, thus completing the signal transmission.

Serious scientists can compare the pseudoscientific nonsense about mutations and evolution to the accurate representation of how the sense of smell in bacteria links nutrient-dependent pheromone-controlled ecological adaptations from microbes to humans via signal transmission and an inorganic signature of human egg activation.
You can learn more about the energy-dependent spark that links the inorganic signature of gene activation in the human egg to adult sexual behavior in all living genera by learning more about cell biology,
You can learn more about the ignorance displayed by pseudoscientists who failed to learn anything about biophysically constrained energy-dependent RNA-mediated cell type differentiation by reading this article, which was co-authored by researchers I met during presentations at meetings of the Association for Chemoreception Sciences. Johan Lundström and
Mats Olsson are among the most biologically uninformed researchers I have encountered during those meetings. They demonstrate that fact by placing their recent study results into the context of neo-Darwinian nonsense.
See: Behavioral and neural correlates to multisensory detection of sick humans (subscription required)

A superadditive effect of olfactory–visual integration of sickness cues was found in the intraparietal sulcus, which was functionally connected to core areas of multisensory integration in the superior temporal sulcus and orbitofrontal cortex. Taken together, the results outline a disease-avoidance model in which neural mechanisms involved in the detection of disease cues and multisensory integration are vital parts.

If serious scientists attempt to tell people like this that God’s role in their salvation is clearly exemplified by the facts presented in Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants, the people would walk away as quickly as they have done when they passed by my poster sessions. Many other researchers have done that, and some professors have literally dragged their students away (lest they be unduly influenced by facts).
See for instance: 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.

See also: Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over? (1995)

If substitutions at 10% of all nucleotide sites have selection coefficients within this range with the mean 10(-6), an average individual carries approximately 100 lethal equivalents. Some data suggest that a substantial fraction of nucleotides typical to a species may, indeed, be suboptimal. When selection acts on different mutations independently, this implies too high a mutation load. This paradox cannot be resolved by invoking beneficial mutations or environmental fluctuations. Several possible resolutions are considered, including soft selection and synergistic epistasis among very slightly deleterious mutations.

If natural selection for energy-dependent codon optimality did not link what organisms eat to the de novo creation of receptors that link the metabolism of food to the pheromones the biophysically constrain energy-dependent biodiversity via the physiology of reproduction and chromosomal inheritance, all life on Earth would have dies 100 times over.
See for example: 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!

Ultimately you must start with a link from the speed of light on contact with water and the: Hydrogen bonding ability of the amide group

See also: How Politics Is Changing Conversations Between Therapists And Patients

 
If substitutions at 10% of all nucleotide sites have selection coefficients within this range with the mean 10(-6), an average individual carries approximately 100 lethal equivalents. Some data suggest that a substantial fraction of nucleotides typical to a species may, indeed, be suboptimal. When selection acts on different mutations independently, this implies too high a mutation load. This paradox cannot be resolved by invoking beneficial mutations or environmental fluctuations. Several possible resolutions are considered, including soft selection and synergistic epistasis among very slightly deleterious mutations.
Natural selection for energy-dependent codon optimality fits into the context of Darwin’s “conditions of life,” and biophysically constrained viral latency via the pheromone-controlled physiology of reproduction. That suggests all neo-Darwinists are among the “walking dead” who may or may not be here after the forthcoming viral apocalypse. They are not prepared to meet their Maker because they believe energy emerged and then they evolved from nothing, which automagically became everything from the inorganic to the organic.
 
For comparison, I believe there is a bipartisan trend that links conservative Republicans to survival of the species, but I don’t know for sure what will happen to the liberal Democrats. And, I can’t prove it!
Alternative splicing of pre-mRNA

From E. coli to monkeys and mankind: Theories vs models

Hard Science: The Measure of All Things Natural w/Dr. J Michael Bailey (video) Published on 24 May 2017

First in a series of interviews DocAmitay had with Dr. J. Michael Bailey, controversial researcher who dares to ask questions that most do not dare to ask and that many do not want answered. The next few videos present a candid look at the man behind “the monster” created by Trans advocates, the media and those who oppose critical thinking and scientific inquiry when the results do not conform to their own ideologies, wishes or needs. Please stay tuned for Parts 2 and beyond, coming soon!

Critical thinking and scientific inquiry are not linked by ideologies. The human condition is energy-dependent, RNA-mediated, and biophysically constrained by the physiology of pheromone-controlled reproduction. My experience with the ideologies of Dr. J. Michael Bailey, and many others like him, led me to attack his claims about critical thinking and others have since shown that he lacks any critical thinking skills.

See for example: Clinically Actionable Genotypes Among 10,000 Patients With Preemptive Pharmacogenomic Testing
The critical thinking skills of serious scientists linked different SNPs to risk factors among human populations that confer risk for inefficacy or toxicity among African Americans, Asians, Hispanics and other populations. For comparison, this problem appears to be common to all social scientists.
See: The general form of Hamilton’s rule makes no predictions and cannot be tested empirically

In this formulation, which has been called “exact and general” by its proponents, Hamilton’s rule can “predict” only the data that have already been given.

Simply put, social scientists take everything known about the human condition and predict that it evolved to be manifested as differences in African Americans, Asians, Hispanics and other populations. Serious scientists must take exact and general formulations and support their claims with experimental evidence of biologically based cause and effect.
The problem that serious scientists have in any attempts to discuss anything with social scientists is that all social scientists are pseudoscientists. See: Feynman on social science and Feynman Chaser – The Key to Science
Social scientists  have not learned enough about life on Earth to link physics and chemistry from molecular epigenetics to energy-dependent biophysically constrained cell type differentiation. In a fight for the soul of science, pseudoscientists are unarmed opponents of established facts.
See also: A Fight for the Soul of Science

…one year after George Ellis and Joe Silk, two white-haired physicists now sitting in the front row, called for such a conference in an incendiary opinion piece in Nature. One hundred attendees had descended on a land with a celebrated tradition in both physics and the philosophy of science to wage what Ellis and Silk declared a “battle for the heart and soul of physics.”

The “heart and soul” of biologically-based behavior cannot be considered outside the context of energy-dependent changes in angstroms to ecosystems. Anyone who claims to be able to think critically should start by asking the question: “Where did the energy come from?”
They must then use their critical thinking skills to link energy-dependent changes from angstroms to ecosystems in all living genera and to also explain why entropy has not caused the death of all life on Earth. One way to do that is via a model of biophysically constrained cause and effect that pits the snake-centric theory of human brain evolution against nutrient-dependent pheromone-controlled ecological adaptation.
The following review of 5 publications allows comparison of a model of top-down causation, which links energy-dependent changes from angstroms to ecosystems in E. coli to non-human primates, for comparison to a theory of how past selection for snake detection links monkeys to mankind.
Snake-centric theory
Pulvinar neurons reveal neurobiological evidence of past selection for rapid detection of snakes 2013

Compared with three other categories of stimuli (monkey faces, monkey hands, and geometrical shapes), snakes elicited the strongest, fastest responses, and the responses were not reduced by low spatial filtering. These findings integrate neuroscience with evolutionary biology, anthropology, psychology, herpetology, and primatology by identifying a neurobiological basis for primates’ heightened visual sensitivity to snakes, and adding a crucial component to the growing evolutionary perspective that snakes have long shaped our primate lineage.

With no experimental evidence of biologically-based cause and effect snake-centric theory was extended to the concept of the evolution of the social brain
Social and asocial prefrontal cortex neurons: a new look at social facilitation and the social brain 2017

Two populations of neurons were discovered: “social neurons”, preferentially active under social presence, and “asocial neurons”, preferentially active under social isolation. The activity of these neurons correlated positively with performance only in their preferred context (social neurons under social presence; asocial neurons under social isolation), thereby providing a potential neuronal mechanism of social facilitation. More generally, the fact that identical tasks recruited either social or asocial neurons depending on the presence or absence of a conspecific also brings a new look at the social brain hypothesis.

Simply put, they discovered social neurons in monkeys that other theorists predicted might be found in the context of snake-centric theory. For comparison, here is a model of biophysically constrained biologically based energy-dependent cell type differentiation in species from microbes to monkeys.
Nutrient-dependent/pheromone-controlled adaptive evolution: a model 2013
In the context of the model, the molecular mechanisms of energy-dependent cell type differentiation in E. coli can be linked to the mind of the monkey.
See for comparison: Mechanism of transmembrane signaling by sensor histidine kinases 2017

One of the major and essential classes of transmembrane (TM) receptors, present in all domains of life, is sensor histidine kinases (HKs), parts of two-component signaling systems (TCS). The structural mechanisms of transmembrane signaling by these sensors are poorly understood. We present here crystal structures of the periplasmic sensor domain, the TM domain and the cytoplasmic HAMP domain of the Escherichia coli nitrate/nitrite sensor HK NarQ in the ligand-bound and mutated ligand-free states. The structures reveal that the ligand binding induces significant rearrangements and piston-like shifts of TM helices. The HAMP domain protomers undergo lever-like motions and convert the piston-like motions into helical rotations. Our findings provide the structural framework for complete understanding of TM TCS signaling and for development of antimicrobial treatments targeting TCS.

Understanding the two-component signaling system that links what organisms eat from multisensory perception to their biophysically constrained pheromone-controlled physiology of reproduction in E.coli and in other bacteria links ligand-receptor binding to choices for healthy longevity via transgenerational epigenetic inheritance, or sickness and all pathology in humans.
For an example of how researchers express their inability to understand the complexities of systems biology that link the behavior of microbes to the behavior of humans, see:
Behavioral and neural correlates to multisensory detection of sick humans (2017)

In the perpetual race between evolving organisms and pathogens, the human immune system has evolved to reduce the harm of infections.

In the ridiculous misrepresentations made by these researchers who have studied human olfaction, they failed to link energy-dependent RNA-mediated cell type differentiation in any other species to energy-dependent RNA-mediated cell type differentiation in humans. The magic and pseudoscientific nonsense of neo-Darwinian theories does not require pseudoscientists to do anything except make claims that are based on the claims of other pseudoscientists who failed to include anything known about energy as the anti-entropic source for all biodiversity.
See for comparison:

See also: This 2016 publication eliminates the evolutionary perspective from any further consideration whatsoever in all model organisms. One of the co-authors is a co-author of the already outdated 2015 publication.The origin and evolution of social insect queen pheromones, which antagonist Jay R. Feierman introduced to the ISHE’s human ethology group this morning. I will continue to mention that his antagonism has caused the death of millions to billions of people during the past two decades because he insists on reintroducing the pseudoscientific nonsense of the past each time new experimental evidence of biophysically constrained cause and effect refutes another aspect of his neo-Darwinian pseudoscientific nonsense.
See for comparison: Expression of key components of the RNAi machinery are suppressed in Apis mellifera that suffer a high virus infection
Endogenous RNA interference protects all organized genomes from the virus-driven energy theft that causes the degradation of messenger RNA, which links mutations to all pathology
To place that fact into the context of the honeybee model organism, see: MicroRNAs in Honey Bee Caste Determination
See also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution. The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, 2012; Duvarci, Nader, & LeDoux, 2008; Griggs et al., 2013; Monahan & Lomvardas, 2012) in adaptive evolution will certainly be discussed in published works that will follow.”

It makes no difference whether or not you accept the facts about energy-dependent changes in microRNAs, unless you speak only to other theorists. This exemplifies how theorists speak to each other.
Nuclear codon reassignments in the genomics era and mechanisms behind their evolution
The nuclear codon reassignments are food energy-dependent and they control the physiology of reproduction, which links chromosomal inheritance to all biodiversity on Earth. There is no experimental evidence of biologically-based cause and effect that supports claims that molecular mechanisms evolved to control nuclear codon reassignments, or that anything else evolved to link biophysically constrained RNA-mediated cell type differentiation from angstroms to ecosystems in species from microbes to humans.
If you ignore everything known to all serious scientists about energy as information, you can continue to link mutations to evolution until everyone else on Earth is laughing at you, whether or not you live to see that day.
Until then, see also: How to make a sterile helper
Metaphorically, theorists make sterile helpers out of those who would rather believe in ridiculous theories that provide no Earthly good to humanity.  To avoid arguments from metaphors, serious scientists publish articles like this.
Serum microRNA signatures as “liquid biopsies” for interrogating hepatotoxic mechanisms and liver pathogenesis in human
At an appointment with a primary care physician yesterday, I discussed the fact that microRNA signatures have rapidly become the most predictive test of pathology. Nutrient energy-dependent microRNAs can be compared to viral microRNAs. The viral microRNA content of fluids and tissues is a measure of DNA damage. That damage must be repaired to restore healthy longevity at the level of hydrogen atom transfer in DNA base pairs in solution. Damage repair is energy-dependent. Viruses steal that energy, which is why the mutations that virus-driven energy theft causes cannot be linked to the evolution of anything except more hecatombic pathology. The physician is an exceptionally talented triathlete. I do not know anyone who knows how, when, or where the abilities of triathletes evolved.
Sarcasm alert: Perhaps, they evolved from behaviors in E. coli that linked the fear of snakes in monkeys to the evolution of similar structures in primate brains.

fruit-dove

Food energy-dependent epigenetic adaptation (3)

Food energy-dependent epigenetic adaptation (2)

On 5/24/17 I attempted to post this to the ISHE’s human ethology group in response to the post on How concepts of God have developed: God’s shrinking role. God’s survival. Conclusions.

For comparison, see the expanding role of anti-entropic virucidal energy that theorists claim automagically emerged to sustain all evolved biodiversity.

I included a link to:


I also included a link to:

The moderator of the group responded quickly: Jay R. Feierman wrote:

What you are posting has nothing to do with the thread article.

See also: 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. 

My summary of past interactions with Jay R. Feierman:

He refuses to accept the fact that conditions of life are energy-dependent. He refuses to accept the fact that other biologically uninformed science idiots and many anonymous fools have consistently removed Darwin’s ‘conditions of life’ and replaced them with ridiculous theories about mutations and evolution.

At a conference we both attended in 1995, Jay R. Feierman was the first to challenge the entirety of the model I presented with the question “What about birds?”

He has continued to prevent dissemination of accurate representations of energy-dependent biologically-based cause and effect since then. He exemplifies the impact that one biologically uninformed science idiot can have across an entire generation of unsuspecting anonymous fools who are likely to believe that the creation of energy has nothing to do with the claims in: How concepts of God have developed: God’s shrinking role. God’s survival. Conclusions.

See also: The general form of Hamilton’s rule makes no predictions and cannot be tested empirically

Hamilton’s rule asserts that a trait is favored by natural selection if the benefit to others, B, multiplied by relatedness, R, exceeds the cost to self, C. Specifically, Hamilton’s rule states that the change in average trait value in a population is proportional to BR−C. This rule is commonly believed to be a natural law making important predictions in biology, and its influence has spread from evolutionary biology to other fields including the social sciences. Whereas many feel that Hamilton’s rule provides valuable intuition, there is disagreement even among experts as to how the quantities B, R, and C should be defined for a given system. Here, we investigate a widely endorsed formulation of Hamilton’s rule, which is said to be as general as natural selection itself. We show that, in this formulation, Hamilton’s rule does not make predictions and cannot be tested empirically. It turns out that the parameters B and C depend on the change in average trait value and therefore cannot predict that change. In this formulation, which has been called “exact and general” by its proponents, Hamilton’s rule can “predict” only the data that have already been given.

Simply put, the authors attest to the fact that every aspect that has ever been included in mathematical models of natural selection cannot link natural selection to anything that could not be predicted by what is known about how food energy must be linked from ecological variation to ecological adaptation by the sense of smell in all living genera. The sense of smell predictably links what is known about natural selection for energy-dependent codon optimality to biophysically constrained viral latency via publication in 2005 of Feedback loops link odor and pheromone signaling with reproduction.

There has never been any experimental evidence of biologically based cause and effect that link anything but olfaction, food odor, and pheromones directly to the survival of all species. Yet Feierman’s claim continues to be echoed in the claims of all others who are biologically uninformed:

Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. — Jay R. Feierman

See for comparison: Scientists investigate how the sense of smell works in bacteria

…the signaling and inactive states differ only very slightly at the nitrate-binding site – by 0.5-1 angstroms, which is approximately one fifth of the size of the ion itself (1 angstrom is 10-10 meters). However, when this ion binds to the sensor, it causes huge changes in the protein: The helices of different monomers begin to move in different directions, like pistons. These “pistons” transmit the small change of 0.5-1 angstroms through the membrane, and their outer ends shift by approximately 2.5 angstroms in different directions. Inside the cell, in the HAMP domain, these shifts are converted into the rotation of two parts of NarQ relative to each other. Ultimately, the positions of the output helices change by as much as 7 angstroms, thus completing the signal transmission.

 

Alternative splicing of pre-mRNA

Food energy-dependent epigenetic adaptation (2)

Due to the overwhelming support for my model of top-down causation and all energy-dependent biophysically constrained biodiversity on Earth, I will replace
Food energy-dependent epigenetic adaptation (2)
with the more appropriately titled
God’s shrinking role in your salvation
See: Food energy-dependent epigenetic adaptation
and God’s shrinking role in your salvation (in prep)
before proceeding to the rest of this series on epigenetic adaptation.
 

rp_tumblr_ngykp0yfND1r5gzz6o1_500.jpg

Energy-dependent epigenetic translation to mRNA stability (3)

Energy-dependent epigenetic translation to mRNA stability (2)

Energy-dependent epigenetic translation to mRNA stability (2)


See for comparison this treatise on climate change packaged as information on the evolution of a flying snake.
Fossil ‘winged serpent’ is a new species of ancient snake

At the time that Zilantophis dwelled there, the site was a sinkhole surrounded by forest, attracting a variety of animals. The local fauna included ancient representatives of familiar North American creatures such as bears, beavers and salamanders. Others were more exotic, including unique species of rhinoceros, alligator and the site’s famous red panda.

“This is a time when the world was moving in the direction of a modern climate and modern fauna,” Jasinski said.

For information on the evolution of the flying snake’s behavior see Robert Sapolsky: The biology of our best and worst selves

How can humans be so compassionate and altruistic — and also so brutal and violent? To understand why we do what we do, neuroscientist Robert Sapolsky looks at extreme context, examining actions on timescales from seconds to millions of years before they occurred. In this fascinating talk, he shares his cutting edge research into the biology that drives our worst and best behaviors.

I did not learn anything about cutting edge research from this TED talk. I learned that Robert Sapolsky believes in the evolution of human behavior. That surprised me because Robert Sapolsky is one of the most famous students of Bruce McEwen, who linked a single amino acid substitution (BDNF Val66Met) from nutrient energy-dependent biophysically constrained biologically-based top-down causation to behavior in the dramatically different pheromone-controlled ecosystems of mice and humans.
See: Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity

in unstressed mice with a BDNF loss-of-function allele (BDNF Val66Met), we show that the epigenetic activator of histone acetylation, P300, plays a pivotal role in the dynamic up- and down-regulation of mGlu2 in hippocampus via histone-3-lysine-27-acetylation (H3K27Ac) when acute stressors are applied. These hippocampal responses reveal a window of epigenetic plasticity that may be useful for treatment of disorders in which glutamatergic transmission is dysregulated.

See also: Correction for McEwen, Brain on stress: How the social environment gets under the skin

The authors note that on page 17184, right column, first paragraph, line 4, “effect” should instead appear as “affect.”

Until Robert Sapolsky helps others to make sense of how the energy-dependent pheromone-controlled de novo creation of olfactory receptor genes is linked to differences in epigenetic effects that link sensory stimuli from hormones to the affects of hormones on animal behavior, his lectures will be of little use to those who study the biology of behavior.
In all vertebrates, the study of behavior begins with the epigenetic effects of food odors and pheromones on gene activation that link changes in microRNAs from gonadotropin releasing hormone to the physiology of reproduction. In the early 90’s, Bruce McEwen told me that my model of biologically-based cause and effect could not be validated unless I found experimental evidence that could be linked to gene activation in gonadotropin releasing hormone (GnRH) neurosecretory neurons.
The late Robert L. Moss provided preprints from his group that now link everything known about energy-dependent RNA-mediated cell type differentiation in all vertebrates to the pheromone-controlled physiology of reproduction in mice and in humans via amino acid substitutions.
The early gene expression of cFos has since linked the Fos protein to proof of the concept that links food odors and pheromones to all receptor-mediated behavior in all living genera via what is known about vertebrate GnRH.
See: Induction of FOS immunoreactivity in central accessory olfactory structures of the female rat following exposure to conspecific males
See: A hypothalamic circuit that controls body temperature

…we used cFos staining to identify neurons that are activated by a thermal challenge and found induced expression in subsets of neurons…

See: Researchers discover neuronal targets that restore movement in Parkinson’s disease model

The research group used optogenetics, a technique that turns genetically tagged cells on and off with light.

See also: Hypothalamic microRNAs flip the switch for fertility
See also our section on molecular epigenetics in: From Fertilization to Adult Sexual Behavior
More than 60,000 published works on microRNAs link cutting edge research to energy-dependent healthy longevity or from virus-driven energy theft and the degradation of messenger RNA to all pathology. Who is discussing that fact?
See for comparison: Behave: Why do we do the things we do?

Over a decade in the making, this game-changing book is Robert Sapolsky’s genre-shattering attempt to answer that question as fully as perhaps only he could, looking at it from every angle. Sapolsky’s storytelling concept is delightful but it also has a powerful intrinsic logic: he starts by looking at the factors that bear on a person’s reaction in the precise moment a behavior occurs, and then hops back in time from there, in stages, ultimately ending up at the deep history of our species and its genetic inheritance.

And so the first category of explanation is the neurobiological one. What goes on in a person’s brain a second before the behavior happens? Then he pulls out to a slightly larger field of vision, a little earlier in time: What sight, sound, or smell triggers the nervous system to produce that behavior? And then, what hormones act hours to days earlier to change how responsive that individual is to the stimuli which trigger the nervous system? By now, he has increased our field of vision so that we are thinking about neurobiology and the sensory world of our environment and endocrinology in trying to explain what happened.

Sapolsky keeps going–next to what features of the environment affected that person’s brain, and then back to the childhood of the individual, and then to their genetic makeup. Finally, he expands the view to encompass factors larger than that one individual. How culture has shaped that individual’s group, what ecological factors helped shape that culture, and on and on, back to evolutionary factors thousands and even millions of years old.

The result is one of the most dazzling tours de horizon of the science of human behavior ever attempted, a majestic synthesis that harvests cutting-edge research across a range of disciplines to provide a subtle and nuanced perspective on why we ultimately do the things we do…for good and for ill. Sapolsky builds on this understanding to wrestle with some of our deepest and thorniest questions relating to tribalism and xenophobia, hierarchy and competition, morality and free will, and war and peace. Wise, humane, often very funny, Behave is a towering achievement, powerfully humanizing, and downright heroic in its own right.

See also: CRISPR kills HIV and eats Zika ‘like Pac-man’. Its next target? Cancer

Researchers paired proteins with a process that amplifies RNA which could be used to detect cancer cells

One of the most fascinating things that I have repeatedly encountered is the failure to link CRISPR from the nutrient-dependent pheromone-controlled physiology of reproduction to the biophysically constrained viral latency that links ecological variation to ecological adaptation via natural selection for energy-dependent codon optimality in all living genera.
It’s as if the gene-editing technology could not be understood in the context of femtosecond blasts of virucidal UV light and RNA-mediated DNA repair, which has been linked to the prevention of all pathology until stress overwhelms the immune system.
 

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.

terrarium-eco-system

Draining the academic swamp of parasites

National Academies Revise Conflict of Interest Policy

The proposed changes follow revelations in recent years that committee members preparing reports for the Academies did not disclose industry relationships.

By Ashley P. Taylor | May 3, 2017
Excerpt: They are also thinking about including not only current activities and relationships, as they do now, but past ones when determining whether or not a committee member has a COI.
See for comparison: Ian Hodder: Çatalhöyük, Religion & Templeton’s 25%
My comment: Past funding from the Templeton Foundation virtually guarantees results and recommendations that are tailored to fit into the context of neo-Dawinian pseudoscientific nonsense. But Ian Hodder concludes:

The Templeton Foundation has never put any pressure on me to define religion in any particular way or to come up with any particular results about religion. It’s been entirely pressureless as far as I’m concerned.

My comment: No pressure? 2004 Templeton Prize winner George FR Ellis published a book, which I reviewed here How Can Physics Underlie the Mind? Top-Down Causation in the Human Context.

Others linked the sun’s anti-entropic virucidal energy from energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.

After George Ellis failed to link anything he knew about my peer-reviewed published works from energy-dependent top-down causation to healthy longevity or from virus-driven energy theft to all pathology, Susan Mazur helped attest to the importance of energy-dependent RNA-mediated cell type differentiation in a book which I reviewed here: Royal Society: The Public Evolution Summit.
Now see this: Surprising link between blood sugar and brain cancer found
Excerpt: “This may suggest that the tumor itself affects blood glucose levels or that elevated blood sugar or diabetes may paradoxically be associated with a protective factor that reduces brain tumor risk,” Schwartzbaum said.
My comment: Serious scientists do not make suggestions outside the context of what is known about biophysically constrained biologically-based cause and effect. The protective factor is energy-dependent RNA-mediated DNA repair. The conserved molecular mechanisms of repair link an endogenous substrate in all cell types to healthy longevity in all living genera until virus-driven energy theft links the degradation of messenger RNA to all pathology via mutations.
The mutations arise at the level of hydrogen-atom transfer in DNA base pairs in solution, which typically links energy as information to all biodiversity via the physiology of reproduction. If you see anyone who has ever been funded by the Templeton Foundation report findings in the contest of energy-dependent healthy longevity or virus-driven energy theft linked to all pathology via the degradation of messenger RNA, you will have evidence that support for the findings comes from an unbiased source.

See these three articles that come from researchers in China. Individually and collectively the researchers make it clear that nutrient energy-dependent microRNAs are the link from apoptosis and autophagy to healthy longevity and that the virus-driven degradation of messenger RNA is the link to all pathology.

MicroRNA-17-5p mediates hypoxia-induced autophagy and inhibits apoptosis by targeting signal transducer and activator of transcription 3 in vascular smooth muscle cells.

Associations between prediagnostic blood glucose levels, diabetes, and glioma

Identification of miRNA-7 by genome-wide analysis as a critical sensitizer for TRAIL-induced apoptosis in glioblastoma cells

See for comparison: A New Generation Overthrows Gender

I think we’re seeing a new gender revolution,” says clinical psychologist Diane Ehrensaft. “It’s erased boxes and created gender infinity instead.

This is what all serious scientists expect to see come from pseudoscientists who know nothing about how ecologically derived biophysically constrained RNA-mediated energy-dependent sex differences in cell types are controlled by feedback loops that link food odors and pheromones to the physiology of reproduction in all living genera.

Feedback loops link odor and pheromone signaling with reproduction

See also: Commensal bacteria and essential amino acids control food choice behavior and reproduction

Reported as: Gut bacteria tell the brain what animals should eat

…the notion that microbes might also be able to control behavior seems a big conceptual leap. Yet that’s what the new study shows.

See the big conceptual leap from 2013: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

Warning: This ecological model was reported to be a refutation of neo-Darwinian pseudoscientific nonsense in: Criticisms of the nutrient-dependent pheromone-controlled evolutionary model

The editor dismissed the criticisms, and only recently was my model linked to another ecological model.

See: Variable habitat conditions drive species covariation in the human microbiota

Reported as: Resource availability drives person-to-person variations in microbes living in the body

Ecological model reveals relationships between resource availability and microbe species abundance

Simply put, ecological models must link what organisms eat from the physiology of reproduction to biophysically constrained energy-dependent RNA-mediated biodiversity via what is known to all serious scientists about supercoiled DNA and chromosomal inheritance.