physics Archives - Scent of Eros

Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

Polymaths and paradigm shifts: from Asimov to Bear (2)

March 14, 2018

by James Kohl with One Comment Adaptations Alternative Splicings Autophagy base editing biophotonics Cytosis Diseases & Disorders Ecology Light Energy microRNA editing Model Organisms Nutrigenomics Physics RNA Directed RNA editing RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity Subatomic What's in the News

Polymaths and paradigm shifts: from Asimov to Bear (1)
See also: Search results for virus-driven energy theft
Summary: The creation of enzymes, such as ATP synthase is energy-dependent. The energy biophysically constrains viral latency via the creation of microRNAs and RNA-mediated amino acid substitutions that differentiate the cell types of all living genera.
Modifying Other’s Originality without Quote is an Act of Piracy

A writer who does not cite the sources in h/h feature article is committing piracy. Piracy is plagiarism… high level quality requires originality and creativity… these inattentions…should be strongly condemned… Accordingly, the originally contributing author may preserve the honor worthily and endeavor to further contribution in scientific study.

See for comparison: Here’s how viruses inactivate the immune system, causing cancer

It’s no new news that viruses cause cancer.

The full text of the article is free: DNA Tumor Virus Regulation of Host DNA Methylation and Its Implications for Immune Evasion and Oncogenesis

…virus-associated cancers show highly increased levels of DNMT expression [75,76,77,85,94,95,96,97,98,99]. In HBV-associated hepatocellular carcinoma (HCC), DNMT expression is inversely correlated with levels of tumor suppressor microRNAs (miRNAs), including miR-152 targeting DNMT1 [97] and miR-101 targeting DNMT3A [99]. Virus-induced DNA hypermethylation is commonly found on several tumor suppressor genes…

RNA-directed DNA methylation links the energy-dependent microRNA-mediated creation of tumor suppressor genes to biophysically constrained viral latency via the proton motive force. The proton motive force links differences in the energy of photons from hydrogen-atom transfer in DNA base pairs in solution to the light-activated endogenous substrates of RNA-mediated DNA repair.
See also: “There is no honor among thieves” is a pithy saying that captures Solomon’s observation concerning the wicked and those who choose their company.
A Twitter search returned several interesting comments related to what is known to serious scientists about the proton motive force and the claim that “There is no honor among thieves.” For instance, writers who modify the claims and questions about the proton motive force are plagiarists and/or thieves. See:

Steven Bird‏ @stevenbird64 12 Sep 2010

What do proton motive force driven multidrug resistance transporters have in common?

2. Toya‏ @toyaj05 19 Jun 2010

The H+ gradient is called the proton-motive force. This force drives the H+ back across the membrane through H+ channels. ATP synthases aids

The creation of enzymes, such as ATP synthase is energy-dependent. The energy biophysically constrains viral latency via the creation of microRNAs and RNA-mediated amino acid substitutions that differentiate the cell types of all living genera.

Philip Ball‏ @philipcball Mar 2

This was filmed tonight, so you’ll soon get to see why Nick Lane thinks the key to the origin of life is not amino acids or RNA but proton gradients. (I think he may be right.)

See for comparison: snippet from our June 24, 2017 conversation about the claims of Philip C. Ball.

The origin of life

Dr Frankenstein aimed to create new life from inanimate parts. But how did life first arise on Earth? Join Nick Lane in conversation with Phil Ball as they discuss the latest ideas, from warm ponds to space rocks and hydrothermal vents.

Ask when Nick Lane and/or Philip C. Ball first learned about proton gradients. See how much longer it takes them to link the creation of sunlight from differences in the energy of photons to biophysically constrained viral latency and all biodiversity via the physiology of reproduction and this model: Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013)

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’.

Abstract:

This angstroms to ecosystems model of ecological adaptation links nutrient energy-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements via the physiology of reproduction in species from microbes to humans. 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 ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity. Species-specific pheromones link quorum-sensing in microbes from chemical ecology to the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection for codon optimality links nutritional epigenetics to the behaviors that enable ecological adaptations. All biodiversity is an ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. Simply put, olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of supercoiled DNA in the organized genomes of species from microbes to man during their development.

See for comparison: On the Difference between Physics and Biology: Logical Branching and Biomolecules

In my model, microRNAs are the biomolecules that link the creation of sunlight to all energy-dependent biophysically constrained viral latency. Viral latency is required to link the physiology of reproduction to all biologically-based diversity in all species.

Claims about proton gradients that link physics to biology without starting with the creation of sunlight are made by biologically uninformed theorists.

Subatomic: From thermophiles to humans (3)

February 13, 2018

by James Kohl with No Comment Adaptations Cytosis Diseases & Disorders Ecology microRNA editing Model Organisms Neuronal Plasticity Nutrigenomics RNA Directed RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated gene silencing RNA–Mediated Epigenetic Heredity Subatomic Variations

Summary: RNA-mediated cell type differentiation in species from insects to primates can be linked from claims about the lower percentage of food energy-dependent DNA methylation in Diet and cell size both affect queen-worker differentiation through DNA methylation in honey bees (Apis mellifera, Apidae) to the conclusion from “Cryo-electron tomography reveals that dynactin recruits a team of dyneins for processive motility.”
See also: Starfish reveal the origins of brain messenger molecules (February 9, 2016)

One of the neuropeptides found is similar to kisspeptin, a chemical that triggers the onset of puberty in humans.

The link from kisspeptin to GnRH helped to establish the link from food odors and pheromones to the RNA-mediated physiology of reproduction in all invertebrates and vertebrates.
Placing facts about neuropeptides into the context of human brain evolution thus seems to exemplify incredible ignorance of physics, chemistry, and molecular epigenetics.
See for comparison: The Importance of ncRNAs as Epigenetic Mechanisms in Phenotypic Variation and Organic Evolution
Conclusion:

The increasing number and diversity of these small and long ncRNAS in relation to the complexity and adaptability of living beings, explains that they have been paramount in complex biological processes and are not an evolutionary paradox.

The fact that miRNAs can be mobilized by the fluids of plants and animals, allows them to act at different distances to where they were transcribed, much like hormones or pheromones do. In addition, they can respond to environmental stimuli, favoring the adaptation of organisms through the modification of epigenetic marks and also a transgenerational inheredity and the evolution of species as part of a Neo-Lamarckian model.

There has never been a neo-Lamarkian model for the evolution of species. Lamarck put his observations into the context of Darwin’s “conditions of life.” If the conditions of life are met, ecological variation can be linked to food energy-dependent ecological adaptations. Only the bastardization of Darwin’s claims put natural selection for mutations first — when biologically uninformed theorist invented neo-Darwinian pseudoscientific nonsense.
SARCASM ALERT: Please do not tell anyone about this 2013 refutation of neo-Dawinism. Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Excerpt:

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.

Conclusion:

See for comparison. Others are making the same claims:
Modulation of miRNAs by Vitamin C in Human Bone Marrow Stromal Cells

…identification of vitamin C-dependent microRNA regulation is important for understanding the basic mechanisms underlying BMSC differentiation and tissue engineering.

All cell type differentiation in all tissues of all species with tissues is energy-dependent and RNA-mediated. That fact is consistently thrown into the political ring of nonsense touted by theorists who attack the President of the United States.
See: Trump: Tell us about your flu shot

Why are so few Americans getting the flu vaccine? And why isn’t the CDC doing more to change that?

The CDC can do nothing. Intelligent people know that the flu virus adapts each season. The CDC will abandon their claims about mutations, which were linked to evolution. More people will be angry when they learn that only a single amino acid substitution can cause an adaption.
Trump-hating liberals may be forced to repurpose their anger and use it to rid the academic swamp of their idiot minions — the so-called science journalists who refused to join the serious scientists who are Combating Evolution to Fight Disease
Most of the anger will be directed toward biologically uninformed science journalists who have failed to present the facts about all virus-driven pathology. For example see: The Quest to End the Flu (2013)

New pandemics don’t come out of the blue. They evolve from viruses that infect animals—typically birds.

Pandemics “evolve” from viruses? What kind of so-called science journalist makes a claim like that?
Is Most of Our DNA Garbage? (March 5, 2015)

…junk DNA isn’t a sign of evolution’s failure. It is, instead, evidence of its slow and slovenly triumph.

The triumph is not slow and slovenly. One base pair change and fixation of one amino acid substitution is all that is required to start the process of ecological adaptation.
See for comparison: It’s time to put America’s health first

While the CDC neglected its mission here, Obama committed billions to build labs and train health personnel in Africa during the Ebola scare. Billions for a disease that killed only one person in the United States — and even he got infected elsewhere.

The so-called science journalists who also are Trump-haters have contributed to more unnecessary suffering and premature death than most people can begin to imagine. They spread their ignorance and hatred across the country and across the world. It is the pathology of their ignorance that must be removed if ever we are to put America’s health first. The first thing we must do, is rid ourselves of the unethical so-called science journalists.

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

Elsevier fails to support the concept of autophagy

December 15, 2017

by James Kohl with No Comment Alternative Splicings Autophagy Diseases & Disorders Ecology Light Energy microRNA editing Nutrigenomics RNA interference RNA-mediated gene silencing Variations What's in the News

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

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

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

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

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

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

The bias between codons or amino acids, and mRNA expression levels has been previously recognized across species and is thought to result from selection for efficient, accurate translation, and folding of highly expressed genes (Ikemura, 1982; Akashi, 1994; Akashi & Gojobori, 2002; Drummond & Wilke, 2008; Kudla et al, 2009; Novoa & Ribas de Pouplana, 2012). The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

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

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

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

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

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

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

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

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

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

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

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

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

Mouse morphs and primate diversity in 50 years

December 7, 2017

Excerpt:

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

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

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

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

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

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

As climate warms, mice morph

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

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

Excerpt 1)

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

Excerpt 2)

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

All serious scientists know that food energy biophysically constrains the pheromone-controlled physiology of reproduction, which links the fixation of RNA-mediated amino acid substitutions to cell type differentiation in all living genera.

We have now arrived at the claims of biologically uninformed science idiots who tell us that two different species evolved in 50 years.

Excerpt 3)

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

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

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

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

Exposing the 2nd Law to more ridicule (1)

December 6, 2017

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy base editing biophotonics Cytosis Diseases & Disorders Ecology Human Brain Human Pheromones Light Energy microRNA editing Model Organisms Neuronal Plasticity Nutrigenomics Physics RNA Directed RNA editing RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity Variations What's in the News

Summary: Experiment demonstrates quantum mechanical effects from biological system

After 1944, Richard P. Feynman took a stand against the human idiocy, and lost. He was not killed, just ignored.

Ignorance prevails. It always has. The virus-driven degradation of messenger RNA ensures that organized genomes continue to become less organized and that biologically uninformed theorists continue to tout pseudoscientific nonsense.

New Genes and Functional Innovation in Mammals 21 July 2017

We identify several previously described cases of genes originated de novo from noncoding genomic regions, supporting the idea that this mechanism frequently underlies the evolution of new protein-coding genes in mammals. Finally, we show that most young mammalian genes are preferentially expressed in testis, suggesting that sexual selection plays an important role in the emergence of new functional genes.

Reported as: Genes identified that distinguish mammals from other animals 4 December 2017

They have also identified antimicrobial peptides, which participate in the body’s defence against pathogens.

The energy-dependent creation of “…antimicrobial peptides, which participate in the body’s defence against pathogens” already was linked from the sense of smell in bacteria to the physiology of pheromone-controlled reproduction and biophysically constrained viral latency, which protects all organized genomes from the degradation of messenger RNA. False assumptions about entropy for comparison to experimental evidence of the de novo creation of genes have been placed into the context of the “arrow of time.”

Scientists Experimentally Demonstrate the “Reversal of the Arrow of Time” 4 December 2017

Through a remarkable experiment, an international team of scientists has found that it is possible to reverse the arrow of time without violating the second law of thermodynamics.

Pseudoscientists need no longer consider anything that cannot be linked to this experimental evidence of top-down energy-dependent causation and biophysically constrained viral latency/genomic entropy. Thank God, nothing but experimental evidence of the anti-entropic virucidal energy of sunlight has ever been considered by those who have linked feedback loops from odors and pheromones to all biodiversity on Earth.
See: QuEBS workshop

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

Quantum effects in biological light-harvesting systems have been linked from the de novo creation of sunlight to answers about all biophysically constrained biodiversity via Schrodinger’s What is Life? (1944).

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)

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.

See also: What is life when it is not protected from virus driven entropy (video) 30 Mar 2016

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: On causal roles and selected effects: our genome is mostly junk December 5, 2017

The idea that much of our genome is irrelevant to fitness—is not the product of positive natural selection at the organismal level—remains viable.

Conclusion:

That is to say, many of our uniquely human traits are probably the contingent products of drift and historical accidents—they make us us, but were not selected to have that, or necessarily any, effect. So we are back to Ohno’s conundrum. If lungfishes have junk, or at the least extraordinarily weakly or diffusely functional DNA in their genomes, why is it that we think we do not?

The concept of “junk DNA” is inconsistent with anything known to serious scientists about energy-dependent biophysically constrained viral latency. Feedback loops link top-down causation to the pheromone-controlled physiology of reproduction via RNA-mediated fixation of amino acid substitutions in the organized genomes of all living genera.
See: Understanding and accounting for relational context is critical for social neuroscience
My comment: New data on how genetic predispositions are epigenetically linked to phenotypically distinct neuroanatomy and behaviors is provided in the honeybee model. Across-species comparisons from insects to vertebrates clearly show that the epigenetic influence of food odors and pheromones continues throughout the life of organisms that collectively survive whereas individuals do not. These comparisons also attest to the relative salience of sensory input from the rearing environment. For example, when viewed from the consistency of animal models and conditioned behaviors, food odors are obviously more important to food selection than is our visual perception of food. Animal models affirm that food odor makes food either appealing or unappealing. Animal models reaffirm that it is the pheromones of other animals that makes them either appealing or unappealing.
“Socioaffective neuroscience and psychology may progress more quickly by keeping these apparent facts in mind: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).”

— Kohl, JV (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors Socioaffective Neuroscience & Psychology 2012 http://www.ncbi.nlm.nih.gov/pubmed/24693349

George F R Ellis This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics. This is explored here: [Top-down causation: an integrating theme within and across the sciences?] http://rsfs.royalsocietypublishing.org/content/2/1.toc 25 Apr 2014 at 07:49am
See also: What Bacteria Can Tell Us About Human Evolution December 5, 2017

See for comparison: Learning from Bacteria about Natural Information Processing
The link from biological light-harvesting systems to the pheromone-controlled physiology of reproduction in species from microbes to humans exemplifies everything known to serious scientists about biophysically constrained viral latency, which links ecological variation to ecological adaptations in the context of physics, chemistry, and molecular epigenetics. The facts refute all neo-Darwinian nonsense and the nonsense touted by “Big Bang” cosmologists.
Sunlight is quantized energy as information and it is virucidal.
See also: Generation of photonic entanglement in green fluorescent proteins

…our prepared state is free from environmental decoherence because of the protective β-barrel structure that encapsulates the fluorophore in the protein. Our photonic entanglement generation and characterization indicate that the SFWM process in EGFP is a promising quantum process for developing quantum spectroscopic techniques and quantum-enhanced measurements in biological materials.

Reported as: Experiment demonstrates quantum mechanical effects from biological system

Nearly 75 years ago, Nobel Prize-winning physicist Erwin Schrödinger wondered if the mysterious world of quantum mechanics played a role in biology.

Schrödinger (1944) linked the anti-entropic virucidal energy of sunlight from the physiology of pheromone-controlled reproduction in soil bacteria to all biodiversity. He then began to suspect that his colleagues, who displayed human idiocy, would kill him.
After 1944, Richard P. Feynman took a stand against human idiocy, and lost. He was not killed, just ignored.

Ignorance prevails. It always has. The virus-driven degradation of messenger RNA ensures that organized genomes continue to become less organized and that biologically uninformed theorists continue to tout pseudoscientific nonsense.

See for comparison: Microbiome-Centric Human Health: A Call for Systems Biology
Stop calling for more microbiome-centric systems biology and link what is known about energy-dependent changes in electrons to ecosystems in all living genera via pheromone-controlled biophysically constrained viral latency.
See: [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)] 1994

A study of the influence of pheromone stressor(s) on proliferating germ and somatic cells was performed on laboratory lines of house mouse in the context of the physiological hypothesis of mutation process, proposed by M.E. Lobashev in 1947. Data from experiments are presented, and results obtained during last 10-15 years are discussed. The adaptive role of cytogenetic and other observed pheromonal effects is considered. The possible existence of interorganism systems of genetic regulation is discussed, the search for and study of which may help in more complete understanding of the regularities of functioning of genetic material.

Predicting who wins the 2017 Nobel Prizes

October 2, 2017

by James Kohl with 4 Comments Adaptations Diseases & Disorders Ecology Model Organisms Nutrigenomics Physics RNA Directed RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing Variations

The Nobel Prize in Physiology or Medicine 2017 will be announced on Monday 2 October, 11:30 a.m. at the earliest.
The Nobel Prize in Physics 2017 will be announced on Tuesday 3 October, 11:45 a.m. at the earliest.
The Nobel Prize in Chemistry 2017 will be announced on Wednesday 4 October, 11:45 a.m. at the earliest.
The Nobel Prize in Literature 2017 According to tradition, the Swedish Academy will set the date for its announcement later.
The Nobel Peace Prize 2017 will be announced on Friday 6 October, 11:00 a.m.

My Predictions

Wen Zhou wins the 2017 Nobel Prize in Physiology or Medicine

See: Why the First Drawings of Neurons Were Defaced by R. Douglas Fields

Even in this age of electron microscopy and nuclear magnetic resonance imaging, his drawings retain their power to inspire and inform. While I was at the institute, Toledano opened one of the black boxes of glass microscope slides and held up a histological section of human brain cut and stained by Cajal at the turn of the 20th century. “This one I used in my new paper on senile dementia,” he said with a smile.

See for comparison: Link to Little-known nerve may be secret to lust

“You take those facts and form a hypothesis, and that’s exactly where we are,” he said.

Fields has supporters, among them James Kohl, co-author of “The Scent of Eros,” a book on pheromones.

“He’s right on,” Kohl said. “We have known there is some physical link, but [nerve zero] really helps to define it. Maybe a lot of neuroscientists don’t know about it, but people who study the olfactory system and pheromones see that and say that’s really important.”

Here’s exactly where we are 10 years later: Olfaction Warps Visual Time Perception
My summary: The sense of smell in bacteria has been linked from their energy-dependent pheromone-controlled physiology of reproduction to our visual perception of energy and mass in the context of the time-space continuum. Their findings and the findings of all serious scientists suggest that neural energy represents a warped perception of time in the context of multisensory input at subsecond scales.
The reality of the weekend resurrection of the bacterial flagellum in P. fluorescens attests to the fact that all neo-Darwinian theories will be eliminated when Wen Zhou wins the 2017 Nobel Prize in Physiology or Medicine.

Gianmarc Grazioli wins the 2017 Nobel Prize in Physics

m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs
Reported as: DNA’s dynamic nature makes it well-suited to serve as the blueprint of life
By linking energy-dependent changes from physics and chirallity to the RNA-mediated stability of base pairs,Gianmarc Grazioli crossed the disciplines that Wen Zhou crossed to win her Nobel Prize in Physiology or Medicine.
See also: Chemists know (parody)
See also: RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly

Mutations that destabilize native P5abc decrease the assembly rate up to 100-fold.

Lynn Zechiedrich wins the 2017 Nobel Prize in Chemistry

See: Structural diversity of supercoiled DNA
Zechiedrich has linked the energy-dependent transfer of hydrogen atoms in DNA base pairs in solution from quantum physics to chemistry and the functional structure of DNA via RNA-directed DNA methylation and fixation of amino acid substitutions that differentiate all cell types in all living genera in the context of their pheromone-controlled physiology of reproduction.
See also: All about that base (parody)

Bruce McEwen wins the 2017 Nobel Peace Prize

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.

Bruce McEwen has since helped others to link nutrient-stress and social stress from the virus-driven degradation of messenger RNA to amino acid substitutions in the context of the physiology of pheromone-controlled reproduction. For example, the substitution of one amino acid in the cell types of mammals protects them from the virus-driven energy theft that links amino acid substitutions in viruses to all pathology. McEwen’s works are the only known works of a serious scientist who has continued to refute the pseudoscientific nonsense touted by neo-Darwinian theorists since before 1964.
He will receive the “Peace Prize” for helping to establish and reestablish the fact that all organisms must forage and find food or they do not become part of a species. And, no organism has ever mutated into an organism that became a member of another species. That fact will lead to world peace if all those who are ecologically adapted to life in their energy-dependent ecosystems eat the most nutritious foods they can find and avoid eating too much. Eating too much causes the virus-driven degradation of messenger RNA that links excess energy to the proliferation of viruses that typically is constrained by food and pheromones.
See for comparison: Dr. David Sinclair, Discoverer of Anti-aging NAD Fad, Speaks About Human Trials of NMN

DNA damage, if not repaired, is a significant cause of the diseases of aging such as declining energy levels, cancer, chronic inflammation and a host of other diseases. Unfortunately, our body’s natural DNA repair mechanisms decline with age. Boosting our DNA repair mechanisms could help us ward off the chronic illnesses of old age, such as flagging energy levels, chronic inflammation, and cancer. If NAD boosting with NMN supplementation repairs human DNA, it could be one of the greatest anti-aging and disease-preventing inventions of all time.

A conserved NAD+ binding pocket that regulates protein-protein interactions during aging NADH stands for “nicotinamide adenine dinucleotide (NAD) + hydrogen (H). The virus-driven theft of quantized energy has been linked from the degradation of messenger RNA to all pathology by serious scientists who do not make claims that the facts about energy-dependent healthy longevity have not been linked from viruses to all pathology. Serious scientists link hydrogen-atom transfer in DNA base pairs in solution to all biodiversity via the pheromone-controlled physiology of reproduction, which biophysically constrains viral latency.

Greg Bear wins the 2017 Nobel Prize in Literature

He predicted everything known about biophysically constrained viral latency in a series of novels that started with “Blood Music” (1985) and continued with “Darwin’s Radio” (1999), “Darwin’s Children” (2003) and Quantico (2006). The fact that he followed in the footsteps of the 1930 Nobel Prize winner in Literature, will be mentioned in the context of claims by Sinclair Lewis about viruses in bacteria that have since been linked to all pathology via the theft of quantized energy.
See also: Relating protein functional diversity to cell type number identifies genes that determine dynamic aspects of chromatin organisation as potential contributors to organismal complexity
See for comparison: From Fertilization to Adult Sexual Behavior

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995).

Evolution outside the context of "the light of evolution" (2)

September 13, 2017

by James Kohl with One Comment Adaptations Diseases & Disorders Ecology Model Organisms RNA Directed RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing Variations

See first: Evolution outside the context of “the light of evolution”

How many proponents of Intelligent Design never learned that Darwinian evolution was based on his “conditions of life?”

ch 4 IV. Natural Selection; or the Survival of the Fittest “IF under changing conditions of life…”

ch 5 http://www.bartleby.com/11/5002.html “…the greater variability of species having wider ranges than of those with restricted ranges, lead to the conclusion that variability is generally related to the conditions of life…”

“…we cannot tell how much to attribute to the accumulative action of natural selection, and how much to the definite action of the conditions of life.”

ch 6 http://www.bartleby.com/11/6001.html “By my theory these allied species are descended from a common parent; and during the process of modification, each has become adapted to the conditions of life…

How many biologically uninformed science idiots do not know that conditions of life are nutrient energy-dependent and controlled by the physiology of reproduction?

Intelligent Design – Science & Philosophy Discussion attempt:

https://lh3.googleusercontent.com/M3lHqwXQtKTjApLzM1L43lyjhKKtNHviQEu8EJvcvH2PwjUxJIfzFY4JsND9Nb2b2Uv1crMERBWlRBGu4FTOG837c1H1ULTAE8BPdG1NaPYK9tNYMMcJVdu-xFjUCz7I8FWHRVj1

Food energy-dependent RNA-directed DNA methylation alters the shifting of membrane helices. The alterations prevent the virus-driven degradation of messenger RNA and all pathology via fixation of amino acid substitutions in organized genomes. The physiology of reproduction and pheromone-controlled chromosomal inheritance link the fixation of amino acid substitutions in all cell types of all living genera to all biodiversity.

Andréia Silva James Kohl you won the Nobel prize for refuting evolution, correct?

Yoshinori Ohsumi won last year for doing that: A protein conjugation system essential for autophagy

This [energy-dependent] conjugation can be reconstituted in vitro and depends on ATP.

Ben Feringa also won last year: Dynamic control of chirality and self-assembly of double-stranded helicates with light

Did you not get the memo? They linked the speed of light on contact with water from energy-dependent changes in chirality to all biodiversity via ATP, which is required for the creation of RNA.

The link from self-assembly to autophagy includes a light-activated endogenous substrate that links the innate immune system of all species to protection from the virus-driven degradation of messenger RNA, which links mutations to all pathology.

All serious scientists are waiting for all pseudoscientists to realize the level of ignorance they have displayed for at least the past 50 years and take responsibility for the unnecessary suffering and premature deaths their ridiculous theories have caused.

Thank God, some serious scientists have taken the lead.

See: Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation

Pathway analyses found a significant enrichment for “xenobiotic metabolism signaling” and “PXR/RXR activation” pathways. Our H3K27ac ChIP-seq identified 9,514 peaks that are PenStrep responsive. These peaks were enriched near genes that function in cell differentiation, tRNA modification, nuclease activity and protein dephosphorylation. Our results suggest that PenStrep treatment can significantly alter gene expression and regulation in a common liver cell type such as HepG2, advocating that antibiotic treatment should be taken into account when carrying out genetic, genomic or other biological assays in cultured cells.

Reported as: Common use of antibiotics in cells grown for research could distort tests

“…we treat cells with antibiotics all the time in cell culture and nobody’s looked at how this might affect gene expression and gene regulation,” said Ahituv.

Admitting that you and your colleagues once were biologically uninformed science idiots is the first step towards recovery. The antibiotic treatment caused the constraint-breaking mutations that all serious scientists have linked to all pathology. Food energy and the pheromone-controlled physiology of reproduction link biophysically constrained viral latency to healthy longevity.

The worst part of all this is that it clearly indicates Carl Woese was wrong. There is one domain of life and the virus-driven degradation of messenger RNA links the theft of quantized energy from the creation of bacteria to the creation of archaea.

Virus-driven energy theft also links the creation of humans to the creation of non-human primates via the same molecular mechanisms that link the food energy-dependent pheromone-controlled physiology of reproduction in bacteria to healthy longevity in species from microbes to humans.

My antagonists will continue to hate me for revealing that fact, but it was first revealed in Biblical Genesis. If I link the virus-driven theft of quantized energy to the creation of L-forms, I may be martyred.

But wait, I already did that and so did Paul in 1 Corinthians 15:36. I’m not quoting scripture, even though it parallels facts from what some people might call the book of “nature” even though there is only one book about that.

"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?

September 7, 2017

by James Kohl with No Comment Adaptations Cytosis Diseases & Disorders Ecology Human Pheromones Model Organisms Nutrigenomics Physics RNA Directed RNA-directed DNA methylation Variations What'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.

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.

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.

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.

The Origin of Information (3)

August 3, 2017

by James Kohl with One Comment Adaptations Cytosis Ecology Model Organisms Nutrigenomics RNA Directed RNA-directed DNA methylation RNA–Mediated Epigenetic Heredity Variations

Summary: I presented two poster sessions during the Labroots virtual conference “Neuroscience,” March 16-17, 2016
One linked sunlight to energy as the origin of information. The other linked energy as information to biophysically constrained viral latency via the pheromone-controlled physiology of reproduction in all living genera.
Additional experimental evidence of top-down causation has since confirmed that the creation of sunlight can be linked from energy as information to all biodiversity via its anti-entropic virucidal effects. The direct quantitative measurement of top-down causation supports the claims made by all serious scientists, and also refutes all the claims made by evolutionary theorists and “Big Bang” cosmologists.
See: The Origin of Information (1) 7/28/16 From hydrogen atom transfer in DNA base pairs to ecosystems

The Origin of Information (2) 7/28/16 RNA mediated molecular epigenetics and virus driven entropy (working title: The Origin of Information)

A good model predicts. See also: Direct quantitative measurement of the C═O⋅⋅⋅H–C bond by atomic force microscopy

The direct measurement of the interaction with a hydrogen atom paves the way for the identification of three-dimensional molecules such as DNAs…

Reported on 7/31/17 as: Scientists Decode DNA; See and Touch the Force That Gives Us Life
My summary: Hydrogen (H) t is the most abundant energy source in the Universe. It is also an indispensable source of the energy that is required for life. The energy links nucleic acids (DNA, RNA) and proteins to the creation of life via hydrogen bonds between molecules.
Energy as information is crucial for encoding the secrets of life. Those who cannot understand the concept of energy as information cannot understand anything about the energyd-dependent creation of life or the energy-dependent physiology of pheromone-controlled reproduction, which links energy as information to all biodiversity.
For instance, the biodiversity of all morphological and behavioral phenotypes is food energy-dependent. Richard Feynman put that fact into the perspective of something that many people are intuitively able to understand.

Feynman also presciently placed the measurement of energy into its current context. He somehow knew that technological advances would someday allow serious scientists to measure the energy in a hydrogen atom and link what organisms eat to all biodiversity.
See also: Hydrogen bonds directly detected for the first time

The measured forces and distances between the oxygen atoms at the tip of the atomic force microscope and the propellane’s hydrogen atoms… show that the interaction clearly involves hydrogen bonds. The measurements mean that the much weaker van der Waals forces and the stronger ionic bonds can be excluded.

The fact that experimental evidence established the primacy of the hydrogen bond in the interactions that link energy-dependent changes from chirality to autophagy and from angstroms to ecosystems in all living genera can be placed into the context of the food energy-dependent physiology of reproduction for comparison to: Mutation-Driven Evolution, which was published on the same day in 2013 as Nutrient-dependent/pheromone-controlled adaptive evolution: a model
The good news is that neo-Darwinian theories have been replaced with Darwin’s energy-dependent “conditions of life.” That is bad news for all theorists.
For example, yesterday, Jay R. Feierman again threatened to ban me from participation on the Human Ethology Yahoo Group. Our history of friction began in 1995 but it was amplified in 2013, when I wrote:

Evolution by natural selection cannot be the outcome if something is not first selected. Selection is always for nutrients. It is as simple as that.

Feierman responded:
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.
As first author of the award-winning review Human pheromones: integrating neuroendocrinology and ethology, I may be the only former member of the International Society for Human Ethology (1) who still participates on the yahoo group they own (2). See also their FB page (3).

The International Society for Human Ethology (ISHE) promotes ethological perspectives in the scientific study of humans worldwide. We aim to achieve this goal through:
- Encouraging empirical research in the field of human behavior, using the full range of methods developed in biology and the human behavioral sciences, and operating within the conceptual framework provided by evolutionary theory.
- Promoting the exchange of ethological knowledge and opinions with the other empirical sciences of human behavior.
The International Society for Human Ethology (ISHE), http://www.ishe.org/, a not-for-profit scientific organization, is the owner of this listserv, whose purpose is to facilitate communication among persons interested in human ethology and to attract new persons to the field. The language is English. The current moderator is Jay R. Feierman.
The International Society for Human Ethology (ISHE) aims at promoting ethological perspectives in the scientific study of humans worldwide. ISHE encourages empirical research in all fields of human behavior.

If I am the only person who has detailed the facts about the Origin of Information, and Jay R. Feierman bans me from participation in the ISHE’s group, he will help to eliminate discussion of empirical research such as Feedback loops link odor and pheromone signaling with reproduction.
There are a few other people like Jay R. Feierman, who have helped prevent the dissemination of accurate information about the Origin of Information and all biodiversity in the context of our visual perception of energy and mass, which has been placed into the context of everything known about the space-time continuum. See: Olfaction Warps Visual Time Perception.
But, to my knowledge, no one besides Jay R. Feierman has claimed that “Variation is not nutrient availability and the something that is doing the selecting is not the individual organism.” According to Feynman, Jay R. Feierman exemplifies “human idiocy.”
But, see also this comment from James Gray (August 1, 2017):

Jay,

I just want you to note my support for your warning to Jim Kohl. Too bad that his attempts at comments are so incomprehensible.

After Feierman blocked another one of my posts to the group, I wrote:

It can only get worse from here, Jay. Even if you will not admit to the fact that you were dead wrong, others will learn that you caused the death of their loved ones via your ignorance and arrogance.

You are an example of what Feynman’s referred to as human idiocy.

https://www.youtube.com/watch? v=roX2NXDUTsM

Feierman responded (to the group)

This is warning #1. Say something equally offensive again to me in a personal email or on the group and you will be permanently banned from the Yahoo Human Ethology Group.

Sadly, no one ever responds to your posting because they are incomprehensible. I post them out of human compassion for you. But that does not give you license for being rude and flaming.

I’m copying this to the human-ethology group as well, so other members will know why you are gone from the group, if your flaming re-occurs.

Jay

Jay R. Feierman, Moderator Yahoo Human-Ethology Group

See for comparison: http://www.odedrechavilab.com/About.aspx

Our principle aim in the lab is to attack scientific dogmas. Mainly, we aim to use powerful genetic tools to discover novel biological principles by which RNA affects formation and inheritance of complex traits. While linking rare Mendelian traits to specific sequence variations has been accelerated, the genetic basis of many common diseases is not understood despite the undertaking of many genome wide association studies. It appears that our current genetic models fall short of faithfully explaining the inheritance of most complex traits.

Replaced by: Laboratory for radical science
See also: Principles of Transgenerational Small RNA Inheritance in Caenorhabditis elegans

…how these modifications regulate RNAi or small RNA inheritance was until recently unclear. Integrating the very latest literature, we suggest that changes to histone marks may instigate transgenerational gene regulation indirectly, by affecting the biogenesis of heritable small RNAs. Inheritance of small RNAs could spread adaptive ancestral responses.

The changes to histone marks are energy-dependent and they link hydrogen-atom transfer in DNA base pairs to the food energy-dependent fixation of RNA-mediated amino acid substitutions in supercoiled DNA, which prevents virus-driven energy theft from causing the degradation of messenger RNA that links mutations to all pathology.

On August 1, 2017 Jay R. Feierman wrote: 88186 “A genetic correlate of attachment and personality”

This is not a genetic correlate. The COMT VaL158Met amino acid substitution exemplifies the facts detailed in the context of: Hydrogen bonds directly detected for the first time The facts about hydrogen-atom transfer in DNA base pairs in solution have since been linked to all energy-dependent pheromone-controlled biodiversity in: Principles of Transgenerational Small RNA Inheritance in Caenorhabditis elegans

The changes to histone marks are energy-dependent and they link hydrogen-atom transfer in DNA base pairs to the food energy-dependent fixation of RNA-mediated amino acid substitutions in supercoiled DNA. The substitutions prevent virus-driven energy theft from causing the degradation of messenger RNA that links mutations to all pathology.

See for comparison: How to teach evolution when students hold creationist views

Teaching evolution is pointless.

See: Cytosis

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

Anyone ten years old or older will learn that natural selection for energy-dependent codon optimality is the key to healthy longevity and that the virus-driven degradation of messenger RNA links mutations to all pathology.

God's shrinking role in salvation

June 13, 2017

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

God’s shrinking role in salvation can temporarily be placed into the context of what serious scientists are reporting for comparison to the claims of pseudoscientists.
See: Quantum Simulation (free download)

It presents several examples of experiments using both density and momentum imaging and quantum gas microscopy to study the motion of atoms in optical lattices.

The energy-dependent motion of atoms must be linked to ecosystems by the physiology of pheromone-controlled reproduction in all living genera. That fact requires extended consideration of helicity, chirality, autophagy, and hydrophobicity in supercoiled DNA
Helicity – the projection of the spin onto the direction of momentum. ie. spin direction depends on direction of motion;
Chirality – not identical to its mirror image, ie. left-handed vs right-handed;
Cool animation of a particle where the Helicity matches the Chirality.

I’m not sure how to start an attempt to finalize ongoing comments on what has been learned during the past century about energy-dependent RNA-mediated cell type differentiation, which is manifested in the complexity of the animation. I would like to move forward without the redundancy of explaining everything each time a new finding links quantized energy from physics to chemistry and the facts link molecular epigenetics to the biologically-based energy-dependent creation of microRNAs and RNA-mediated cause and effect.
The energy-dependent creation of microRNAs is missing in this representation of energy-dependent internal motion in DNA.
DNA Internal Motion Likely Accelerates Protein Target Search in a Packed Nucleoid

The internal motions of DNA appear to be governed by strong internal forces arising from being crowded into the small space of the nucleoid.

God’s shrinking role in salvation can be placed into the context of works published by those who fail to link the creation of energy as information to the packed nucleoid via DNA internal motion in the context of the creation of microRNAs.
See for example: microRNA
Everything known to serious scientists about the creation of microRNAs links the sun’s anti-entropic virucidal energy from the solar analemma to representations of the time-space continuum in a Mobius strip and to this solution to the grandfather paradox, which is based on quantum entanglement, which includes quantum entanglement in DNA.
The solution to the grandfather paradox links quantized energy from quantum entanglement to energy-dependent changes in the structure and function of supercoiled DNA, which helps to ensure the survival of individuals and species, but only if the anti-entropic virucidal energy of sunlight was created before anything else.
The creation of quantized energy also must be biophysically constrained by the physiology of reproduction in all living genera.
See: Light Modulates the Biosynthesis and Organization of Cyanobacterial Carbon Fixation Machinery through Photosynthetic Electron Flow, which was reported as: Illuminating the inner ‘machines’ that give bacteria an energy boost
See also: Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes, which was reported as: Nanotechnology reveals hidden depths of bacterial ‘machines’ and subsequently placed into the context of the nonsense touted by theorists on June 8, 2017 as Revealing the Structure of Bacterial Machines
The structure and function of the bacterial machines depends on the innate ability of the species to find enough food. If an organism fails to find food, it cannot adapt to ecological variation and reproduce in the context of the pheromone-controlled physiology of reproduction. For example, this species finds food that it metabolizes to create a uranium isotope.
See: A new twist on uranium’s origin story, by CSU scientists

…using new techniques including synchrotron radiation-based spectroscopy and isotope fingerprinting. They found that up to 89 percent of the uranium from their 650-foot-deep samples wasn’t crystalline uraninite at all, but rather, a non-crystalline uranium that was bound to organic matter or inorganic carbonate. Most of the uranium they found in that unmined site is estimated to be 3 million years old, and formed via reduction by microorganisms – microbes that respire not on oxygen, but on uranium.

The energy-dependent creation of the isotope exemplifies how the energy of sunlight is biophysically constrained in the context of quantum physics and the physiology of energy-dependent reproduction, which Richard Feynman linked to the creation of the atomic bomb — even though he did not know where the energy in a hydrogen atom came from. I have asked others where the energy came from, but the question has not been answered.
The estimate that the uranium was formed by bacteria 3 million years ago is based on pseudoscientific nonsense touted by neo-Darwinian theorists and “Big Bang” cosmologists. Taken together those who are biologically uninformed are now attempting to separate everything known to serious scientists about the energy-dependent creation of all life on Earth from the quantized energy required for creation and the physiology of reproduction.
If quantized energy is not information, the loss of energy from the sun via thermal entropy could create life and all biodiversity, at least in theory. But who believes in theories that are this ridiculous?
See: Information entropy and thermal entropy: apples and oranges

…the change of information entropy and the related change of thermal entropy can be separated in space and time leading to the break of Brillouin’s negentropy principle. iv) The information entropy can increase without triggering any change of the thermal entropy indicating that information erasure does not necessarily require energy dissipation.
v) There is no case where Landauer’s principle of erasure dissipation is even seemingly valid because erasing of the memory does not yield change in the information entropy. vi) The information entropy can violate the Third Law of Thermodynamics.

When theorists are allowed by others who are biologically uninformed to tout the amount of pseudoscientific nonsense contained in this excerpt (above), everyone who believes that the Laws of Thermodynamics can be violated is an example of what Feynman claimed is a form of human idiocy.

See also, from 2-3 years ago in the science news:

The first ever photograph of light as both a particle and wave 3/2/15

Scientists see ripples of a particle-separating wave in primordial plasma 6/10/15

Scientists find genetic basis of brain networks seen in imaging studies 6/11/15
Cell density remains constant as brain shrinks with age 6/12/15
This Nifty Infographic Is a Great Introduction to Neuroplasticity and Cognitive Therapy
New immunoregulation and biomarker 6/12/15

Cell type stability is receptor-mediated and biophysically constrained.

DNA data explosion lights up the Bronze Age 6/10/15

Quantized energy-dependent amino acid substitutions are still being reported as if they are mutations.

See for comparison: The Molecular Nutrition of Amino Acids and Proteins, 1st Edition

See also: The Ancient Origins of Consciousness: How the Brain Created Experience 3/25/16
See also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model 6/14/13 My review is cited in the context of:

12. Plotnick, Dornbos, and Chen (2010). Others who advocate smell-first are Lucia Jacobs (Jacobs, 2012), who says the building of smell maps of environmental space came first and James Kohl (Kohl, 2013), whose model says chemical ecology is the main driver of adaptive evolution. — p. 263

The concept of smell-first was linked from energy-dependent changes in angstroms to ecosystems in all living genera.
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.

The signal transmission was linked from the physiology of reproduction in soil bacteria to fertility in mammals via changes in the bull sperm microRNAome. See: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
Outside the context of the creation of quantized energy and the de novo creation of genes linked to increasing organismal complexity, there is no need to discuss God’s shrinking role in salvation. You can, instead, link the Stepwise Evolution of a Buried Inhibitor Peptide over 45 My from the de novo evolution of genes and the novel proteins they encode to the innovations that automagically contribute to the diversity of life via The evolution of social behavior in microorganisms.
See also: Metabolism and the evolution of social behavior

…using experimental evolution, we followed the joint evolution of the genome, the metabolome and the social behavior as swarming re-evolved. New variants emerged spontaneously with mutations that reorganized the metabolome and compensated in distinct ways for the disrupted metabolic prudence. These experiments with a unicellular organism provide a detailed view of how metabolism—currency of all physiological processes—can determine the costs and benefits of a social behavior and ultimately influence how an organism behaves towards other organisms of the same species.

Simply put, the quantized energy of the smell-first model of energy-dependent ecological adaptation in species from microbes to humans can be compared to the metabolism-first theory of de novo gene evolution. Both can be compared in the context of the joint evolution of the genome, the metabolome and the evolution of social behavior, which is portrayed as swarming in the bacterium Pseudomonas aeruginosa. The swarming behavior re-evolved in an evolution experiment.
The re-evolved ability to swarm can be compared to the report on the weekend resurrection of the bacterial flagellum in Pseudomonas fluorescens.
See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
The weekend resurrection of the bacterial flagellum suggests that virtually any change in an organized genome can be linked to the pheromone-controlled the physiology of reproduction. If not, the claims about evolution can be linked from the wrong choice of food to the virus-driven degradation of messenger RNA, which links mutations to all pathology. But claims about the virus-driven degradation of messenger RNA are rarely made by theorists.
When the missing information about the virus-driven degradation of messenger RNA is placed into the context of the the solar analemma, a Mobius strip, and the solution to the grandfather paradox, quantum entanglement appears to link all changes in the amount of quantized energy that comes from sunlight to biophysically constrained energy theft and viral latency, which prevents pathology.
For comparison, see: A New RNA Synthesis of Cells: A Possible End of Birth Defects

…an estimation of these two above elements [nitrogen and phosphorus] as a chemical compound leads a human’s birth defect to have the correct amino acid sequence as previously mentioned and then become a normal trait. With the correct calculation of the compound of nitrogen and phosphorous for an unstable RNA messenger, which is traced to a birth defect, a researcher can discover the ideal growth rate for its stability as an RNA messenger and then its end as a birth defect.

The quantized energy-dependent biosynthesis of RNA is food energy-dependent and pheromone-controlled in species from microbes to humans and virus-driven energy theft appears to cause the degradation of messenger RNA, which has been linked to all pathology. The report of the evolutionary resurrection of flagellar motility clearly exemplifies how energy-dependent changes in RNA-mediated amino acid substitutions are linked to survival of the species outside the context of the “magic traits.” The “magic traits” do not link nutrient-dependent pheromone-controlled cell type differentiation to all biodiversity in reports like this one: Magic traits in speciation: ‘magic’ but not rare?
The “magic traits” have been linked to rapid speciation in bacteria and vertebrates
See: Extraordinarily rapid speciation in a marine fish

We evaluated different possible evolutionary scenarios under the approximate Bayesian computation framework and estimate that the speciation process started in allopatry ∼2,400 generations ago, following the colonization of the Baltic by the demersal lineage. This is faster than most known cases of ecological speciation and represents the most rapid event of speciation ever reported for any marine vertebrate.

Reported as:“Evolution on the fast lane—One flounder species became two” May 30, 2017

“The answer may lay in so called magic traits, meaning traits that are under selection which at the same time cause reproductive isolation as a byproduct. In theory, selection on such traits could play a central role in rapid speciation events. The mating strategies and reproductive traits of the two flounder species could act as magic traits,” clarifies Momigliano.

Quantum Physics News (see for discussion on this group)
The Quantum Physics News was created by Robert Karl Stonjek, whose atheistic pseudoscientific nonsense is pervasively distributed among several other Facebook groups and yahoo groups. His influence has caused the unnecessary suffering and premature death of millions of people who think God’s shrinking role in salvation can best be viewed in the context of the “magic traits” of neo-Darwinian theorists.