Electron cloud superimposed on the yin yang symbol

The "walking fish" walks straight from quantum physics to quantum souls (4)

January 3, 2018

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy base editing biophotonics Cytosis Diseases & Disorders Ecology 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 Epigenetic Heredity Variations

Excerpt: During the past 21 months, others have either learned nothing about microRNAs or they have ignored the fact that virus-driven energy theft is not the same as energy dissipation in the context of food energy (the quantized energy as information that is used by viruses to create the amino acid substitutions that stabilize their RNA and DNA).

The dark side of the new popularity of cryo-electron microscopy

…we need to stand together as a field, and support our colleagues by accepting to review their papers and grant applications in order to ensure a fair evaluation. In my opinion, we need to collaborate, support and acknowledge each other as best as we can so we can successfully move forward together into a bright future in cryoEM.

This invited review of nutritional epigenetics was returned without review. Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

Food energy-dependent changes in base pairs were linked to ecological adaptation in species from microbes to humans via methylation and the fixation of RNA-mediated amino acid substitutions. There is no dark side to cryo-electron microscopy (cryoEM), and Ariane Briegel knows that. See: Structure of bacterial cytoplasmic chemoreceptor arrays and implications for chemotactic signaling (2014)

…methylations confer adaptation on the system, modulating its response based on recent environmental conditions (Kleene et al., 1979; Toews et al., 1979; Lupas and Stock, 1989). The architecture of these membrane-bound chemoreceptor arrays is not specific to E. coli, indeed it is universal among bacteria (Briegel et al., 2009). The architecture of these arrays is likely key to the high sensitivity, wide dynamic range, cooperativity, and feedback control of this system…
Interestingly, while transmembrane arrays remain intact upon cell lysis, presumably due to the stabilizing effect of the membrane, cytoplasmic arrays fall apart unless molecular crowding agents are added. This suggests that cellular crowding contributes to the stability of the array and may be an important factor in assembly of these, and likely other, cellular structures (Ellis, 2001; Zhou et al., 2008; Zhou, 2013). We observe the same requirement for molecular crowding (mimicking the cellular environment) in our in vitro preparation from E. coli. This supports the idea that chemoreceptor interactions can be enhanced by membrane binding (Shrout et al., 2003), but in the absence of a membrane, this can be achieved by molecular crowding and sandwiching (Fowler et al., 2010).

Briegel et al., (2014) reestablished the facts from our 1996 review of biophysically constrained RNA-mediated cell type differentiation. See the molecular epigenetics section of From Fertilization to Adult Sexual Behavior.
Life on Earth exists within the confines of the energy that is required to maintain the functional structure of the cell membrane. The crowding of food energy-dependent microRNAs in the cell membrane is reduced by 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.

Bacteria become archaea and archaea become L-forms (with no cell wall).
See: L-form bacteria cohabitants in human blood: significance for health and diseases
That significance of L-forms was not placed into the context of this representation of how serious scientists will prevent or begin to effectively treat all virus-driven pathology in the context of what has been revealed by the cryoEM technology.
See: Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels
The circadian cycling of energy-dependent microRNA-mediated protein biosynthesis and degradation has been linked to healthy longevity via what is known about quantum physics and the link from quantized energy as information to quantum souls via hydrogen-atom transfer in DNA base pairs in solution that link microRNA flanking sequences in exosomes to RNA-mediated DNA repair.
See: Exosomes from human umbilical cord blood accelerate cutaneous wound healing through miR-21-3p-mediated promotion of angiogenesis and fibroblast function (Jan 1, 2018)

It has been shown that exosomes contain large amounts of miRNAs and can serve as vehicles to transfer miRNAs to recipient cells, where the exogenous miRNAs can alter the gene expression and bioactivity of recipient cells [28].

28. Au Yeung CL, Co NN, Tsuruga T, Yeung TL, Kwan SY, Leung CS. et al. Exosomal transfer of stroma-derived miR21 confers paclitaxel resistance in ovarian cancer cells through targeting APAF1. Nat Commun. 2016;7:11150

These data suggest that the malignant phenotype of metastatic ovarian cancer cells can be altered by miR21 delivered by exosomes derived from neighbouring stromal cells in the omental tumour microenvironment, and that inhibiting the transfer of stromal-derived miR21 is an alternative modality in the treatment of metastatic and recurrent ovarian cancer.

All experimental evidence of biophysically constrained viral latency links the food energy-dependent creation of microRNAs from the bioreactivity of recipient cells to healthy longevity via protection from the virus-driven degradation of messenger RNA, which all serious scientists have linked from mutations to all pathology.

See this presentation from a Precision Medicine virtual conference for review

Cryo-EM: More than a suggestion

October 24, 2017

by James Kohl with No Comment Adaptations Diseases & Disorders Ecology Variations

Cryo-EM imaging suggests how the double helix separates during replication October 23, 2017

Details in the structure not previously seen reveal how various protein subunits of the twin hexamers latch on to the double helix, via tiny loop-like structures.

What are the subunits of protein?

The subunits of proteins are called amino acids.

I will not stop saying that cryo-EM links what is known about energy-dependent changes in the microRNA/messenger RNA balance from electrons to ecosystems via fixation of amino acid substitutions in the context of the pheromone-controlled physiology of reproduction, which has been linked to all biophysically constrained viral latency and all biodiversity.

And, obviously, serious scientists are not going to stop confirming that fact.

See: Noguchi Y et al, “Cryo-EM structure of Mcm2-7 double hexamer on DNA suggests a lagging-strand DNA extrusion model” appears in Proceedings of the National Academy of Sciences the week of October 23, 2017.

From E. coli to monkeys and mankind: Theories vs models (2)

May 28, 2017

by James Kohl with One Comment Adaptations Alternative Splicings biophotonics Diseases & Disorders Ecology Light Energy Model Organisms Nutrigenomics Physics RNA Directed 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

Dedicated to Dr. Tom Jordan and Priscilla Jordan on the day of their retirement from the Baptist ministry, May 28, 2017. They always encouraged me to learn more about the “Laws of Biology” and link the Laws from energy as information to all biodiversity on Earth via the physiology of reproduction.

High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding (5/23/127)

…changes in observed association and dissociation, suggesting the possibility of kinetic and thermodynamic tuning of Cas9 behavior.

Simply put, the technology didn’t work. That’s a problem for CRISPR/Cas9 advocates (see the incessant barrage of CRISPR/Cas9 promotion on the closed FB group CRISPR Cas9).

Advocates will be forced to accept the fact that natural selection for energy-dependent codon optimality has always been the link from ecological variation to ecological adaptation via food odors and pheromones.

Suggesting the possibility of kinetic and thermodynamic tuning is akin to telling all serious scientists that, until now, the innate immune system of bacteria and the CRISPR Cas technology has not been examined inside the context of the Laws of Physics and the Basic Principles of chemistry. The Laws and the Basic Principles must link RNA-mediated protein folding chemistry from the physiology of reproduction to all food energy-dependent pheromone-controlled behavior in species from microbes to humans via amino acid substitutions in supercoiled DNA.

That fact separates the serious scientists from the pseudoscientists who have refused to examine other facts about biologically-based biophysically constrained protein folding chemistry. The facts start with the sun’s anti-entropic virucidal energy as information and the energy as information has been linked to all cell type differentiation by these researchers.

See: Mechanism of transmembrane signaling by sensor histidine kinases (5/18/17)

Reported as: Scientists investigate how the sense of smell works in bacteria

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.

My summary of the signalling mechanism, which links subatomic particles to cell type differentiation in all living genera via the sense of smell in bacteria:

The active and inactive signaling states link energy-dependent changes from angstroms to ecosystems via slight variations at the nitrate-binding site. When the ion binds to the sensor, a change in 0.5-1 angstroms (approximately one fifth of the size of the ion itself) causes a change in the protein that links input from the sensor to a change in the output that varies by as much as 7 angstroms.

In the context of what is known about food energy-dependent pheromone-controlled quorum sensing in bacteria, the change in 0.5-1 angstroms can be linked from the changes in 7 angstroms to base pair changes and amino acid substitutions that stabilize the organized genomes of species from E. coli to primates in the context of all energy-dependent interactive ecosystems, which appear to have existed from the dawn of Creation.

For example, the link from energy-dependent changes in angstroms to ecosystems in all vertebrates is mentioned in the title of this published work: The zinc spark is an inorganic signature of human egg activation.

The spark that links inorganic material to organic life was placed into the context of our 1996 Hormones and Behavior review of RNA-mediated cell type differentiation. See our section on molecular distance in: From Fertilization to Adult Sexual Behavior.

Molecular distance. As measured in centimorgans, human and other species’ male and female chromosomes, including the autosomes, tend to have different lengths in various segments. To some extent, this suggests a correlation with physical distance but instead the differing lengths are based upon rates of recombination; although sections of most female chromosomes are longer than their homologous counterparts in male chromosomes, in some segments of various chromosomes opposite length-difference occurs, with males having larger centimorgan values than females in those regions (Lawrence, Collins, Keats, Hulten, and Morton, 1993; Murray, Buetow, Weber, Ludwigsen, Scherpbier-Heddema, Manion, Quillen, Sheffield, Sunden, and Duyk, 1994; Straub, Speer, Luo, Rojas, Overhauser, Ott, and Gilliam, 1993). While ramifications of these centimorgan sexual dimorphisms are not yet clearly established, in recent years cis- and trans-acting factors contributing to these recombination length differences have been reported for a specific part of the murine major histocompatibility complex (MHC) (Shiroishi, Sagai, Hanzawa, Gotoh, and Moriwaki, 1991).

Simply put, the cited works linked energy-dependent changes from angstroms to ecosystems via the innate immune system of bacteria, which was linked to sex differences in chromosomes. Note the difference between our accurate representation of biophysically constrained energy-dependent chromosomal inheritance and the claims in: Sex chromosome evolution: historical insights and future perspectives

Conclusion:

…a direct experimental test of the steps in sex chromosome evolution constitutes more robust evidence than a comparative study, especially considering the new manipulative possibilities opened up by the CRISPR/Cas9 system [105]. In any case, the field of sex chromosome evolution seems likely to remain active and dynamic for many years to come.

Reported as: Knowledge gap on the origin of sex

The review shows that the significance of ecology has not been sufficiently noted. Therefore, the biologists in Lund call for more research on how the living environment of a population affects the development and evolution of sex chromosomes. This could include factors such as access to food, age variations within a population or the consequences for sex chromosomes when populations that have lived separately meet and mix.

The fact that others still claim that the origin of sex has not already been linked from factors such as access to food, age variations within a population or the consequences for sex chromosomes attests to the ignorance of theorists. The fact that theorists want to attempt to evoke aspects of the CRISPR Cas9 technology in attempts to explain sexual differentiation attests to the ignorance of those who think more research is required to link energy-dependent changes from angstroms to ecosystems in all living genera via the physiology of pheromone-controlled reproduction and chromosomal inheritance.

Energy-dependent changes were linked from angstroms to ecosystems in all living genera in this published work: Structural diversity of supercoiled DNA (10/12/15) and in this parody from 12/10/14.

The hope is that a theory akin to our other theories in fundamental physics might one day emerge to explain the phenomenon of life, and in turn finally permit solving its origins.

See for comparison: The Chirality Of Life: From Phase Transitions To Astrobiology

A key missing piece is the origin of biomolecular homochirality: permeating almost every life-form on Earth is the presence of exclusively levorotary amino acids and dextrorotary sugars.

Watch as Jeremy England eliminates any discussion of light activated endogenous substrates in the context of microRNAs linked to the energy-dependent creation of exclusively levorotary amino acids and dextrorotary sugars.

A New Physics Theory of Life

You start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant.

If another ridiculous theory emerged, will it explain anything outside the context of experimental evidence that links energy as information to biophysically constrained cell type differentiation via the physiology of reproduction in all living genera? For example, what theory might emerge to explain how an infection in the throat is linked to mental disorders in adults.

See: Streptococcal throat infection linked to mental disorders

The researchers found that the risk of any mental disorder was increased for individuals with a positive streptococcal test compared to those without a streptococcal test…

Watch a biologist fail to link physics and chemistry from the strep infection to brain development via the innate immune system and molecular epigenetics as he explains CRISPR at 5 different levels of his ignorance. 5/24/17

The speaker is a co-author of: Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis 3/5/15

In all of these experiments, the effect of mutations on primary tumor growth positively correlates with the development of metastases. Our study demonstrates Cas9-based screening as a robust method to systematically assay gene phenotypes in cancer evolution in vivo.

Reported as: In vivo CRISPR-Cas9 screen sheds light on cancer metastasis and tumor evolution

The results highlighted some well-known tumor suppressor genes in human cancer, including Pten, Cdkn2a, and Nf2, but included some genes not previously linked to cancer. Unexpectedly, the screen also implicated several microRNAs — small RNA segments that are functional in the cell.

Neville E Sanjana, has now linked his ignorance from 2015 to assays that link energy-dependent microRNAs to healthy longevity or from virus-driven energy theft to all pathology. Kaveli Kull attests to the fact about what loser must do, when facts replace their ridiculous theories about genome editing.

Kalevi Kull: Censorship & Royal Society Evo Event

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

Anyone who has tried to explain what humans are made of without linking energy from the light activated endogenous substrate that links ATP to the creation of RNA via microRNAs in the context of what is now being referred to as endogenous RNA interference may not recognize how desperate evolutionary theorists have become in their attempt to make others think that all neo-Darwinian theorists are not losers.

See (link opens .pdf) Participation of glycolysis, and the citric acid cycle, in nuclear adenosine triphosphate synthesis (1963)

…thymus nuclei appear to have an endogenous substrate, and some experiments are presented which suggest that this substrate is probably not glycogen or glucose.

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

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

What is life without sunshine?

April 19, 2017

by James Kohl with No Comment Adaptations Alternative Splicings biophotonics Cytosis Diseases & Disorders Ecology Light Energy Model Organisms Nutrigenomics Physics RNA Directed 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

Summary: It seems likely that Schrodinger’s anti-entropic virucidal effect of sunlight will be linked to the RNA-mediated de novo creation of all organized genomes and the maintenance of the “spotless epigenome” in this presentation later today. If so, even theorists and other pseudoscientists who planned to “March for Science” will finally be seen in the context of Dobzhansky’s claims about the “…light of evolution.”

Erasing Epigenetic Marks: Eternal Sunshine of the Spotless Epigenome

Topics to be covered:

The variety of epigenetic modifications and their influence on gene expression
How editing or erasing epigenetic marks might be used in a therapeutic manner

Topics already covered elsewhere: IP3-mediated gating mechanism of the IP3 receptor revealed by mutagenesis and X-ray crystallography was reported as: Atomic structure reveals how cells translate environmental signals
The team identified an amino acid sequence in the leaflet that is conserved in parasites, suggesting structural insights that may assist in drug discovery for these devastating conditions.
Case for the genetic code as a triplet of triplets was reported as: Reading the genetic code depends on context
University of Utah biologists now suggest that connecting amino acids to make proteins in ribosomes, the cell’s protein factories, may in fact be influenced by sets of three triplets – a “triplet of triplets” that provide crucial context for the ribosome.
Placing the atomic structure of any functional protein into the context of energy-dependent changes in RNA-mediated amino acid substitutions links natural selection for energy-dependent codon optimality to all biodiversity. That fact about natural selection refutes neo-Darwinian theories by making the link from virus-driven energy theft to the degradation of messenger RNA the obvious link from mutations to all pathology.
It seems likely that the virucidal anti-entropic effect of sunlight will be linked to the creation and maintenance of the spotless epigenome in this presentation later today. Hopefully, they will mention that femtosecond blasts of UV light appear to biophysically constrain energy-dependent protein folding chemistry. For instance, see also: UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair

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

Energy-dependent pheromone-controlled entropy (2)

March 12, 2017

by James Kohl with One Comment Adaptations Diseases & Disorders Ecology Human Brain Human Pheromones Model Organisms Neuronal Plasticity Nutrigenomics Pharmacogenomics Physics RNA Directed 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

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

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

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

Abstract excerpt:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

…we should use language that highlights the inventive piece of the invention rather than the natural law underlying it.

The natural law underlying all links from ecological variation to ecological adaptation could be applied to the patent for RNA-Guided Human Genome Engineering. If so, the examiners will find that host-induced gene silencing is the obvious link from nutrient energy-dependent RNA methylation to the pheromone-controlled physiology of reproduction in all living genera via Kohl’s Laws of Biology.

Simply put, Kohl’s Laws includes two facts:

1) all organisms must eat or they die.

2) all species must reproduce or they become extinct.

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

More refutations of neo-Darwinian nonsense

December 23, 2016

by James Kohl with One Comment Adaptations Alternative Splicings Autophagy Diseases & Disorders Ecology Model Organisms Neuronal Plasticity Nutrigenomics Physics RNA Directed 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

New CRISPR–Cas systems from uncultivated microbes

In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet identified. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in E. coli. Interrogation of environmental microbial communities combined with in vivo experiments allows access to an unprecedented diversity of genomes whose content will expand the repertoire of microbe-based biotechnologies.

They discovered that energy-dependent RNA-mediated DNA methylation is the link from autophagy to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.

There results were reported as: Compact CRISPR systems found in some of world’s smallest microbes

The team also found the first CRISPR-Cas9 system in some of the world’s smallest microbes: a nano-scale member of the archaea, which is a sister group to the bacteria.

‘Sister group’ is a term used by theorists to label what they believe appears to be the closest relatives in an evolutionary tree. The authors of the article used the term domain. Carl Woese divided the close relatives into the life forms called archaea, bacteria, and eukaryote. Woese suggested that archaea and bacteria arose separately from a common ancestor.
He also suggested that the common ancestor had poorly developed genetic machinery. Initially, Woese used the term “kingdom” to name what the news report on the experimental evidence refers to as a sister group despite the fact that archaea, bacteria, and eukaryotes have been referred to in the context of three different domains of life since 1990.
Substituting the term sister group for domain clearly indicates that something has gone horribly wrong with the theories about different domains of life. By using the term domain, the researchers from Berkeley seem to be suggesting that everything reported by others who have made claims about mutations and evolution must now be revised. Use of term “sister group” is an example of how the media tailors the claims of researchers in attempts to fit back into the context of ridiculous theories.
Carl Woese claimed that archaea and bacteria were different domains of life. The media changed his claim to make archaea a sister group of bacteria. That suggests the literature from Berkeley’s domain must change all the claims to include what it known about energy-dependent ecological adaptation, which links the physiology of reproduction from autophagy to supercoiled DNA.

If they don’t make the changes, they will continue to look even more foolish than they have during the past twenty years. All serious scientists know that supercoiled DNA protects all organized genomes from virus-driven entropy.
See also: Virus-mediated archaeal hecatomb in the deep seafloor

Their evidence of virus-driven pathology links bacteria to archaea, without claims about sister groups or different domains of life. They make it clear that virus-driven energy theft in bacteria causes the bacteria to degenerate into archaea. That fact makes it clear that nutrient-dependent pheromone-controlled autophagy in bacteria causes the change in bacteria that become eukaryotes.

See for comparison: Obama Advisers Urge Action Against CRISPR Bioterror Threat

For the past two decades, the government has focused its biodefense efforts on a list of known pathogens—such as anthrax, smallpox, and Ebola—declared by the Department of Health and Human Services and Department of Agriculture to have the “potential to pose a severe threat to public health and safety.” Government-funded research on these pathogens receives special scrutiny, and the National Institutes of Health limits researchers from conducting experiments that could make certain germs, like influenza, more dangerous.

A similar process is also at work in molecular evolution and helps us understand how a feature that is absolutely necessary for survival can be modified by natural selection for a different function if it is duplicated. For example, globin is a truly ancient protein. Billions of years old, it was present in the common ancestor of bacteria, plants, animals, and fungi. Globin performed an essential job: binding and carrying oxygen. You might imagine that natural selection would lock globin into that one job; however, through duplication and divergence, different copies of the globin molecule were adapted for different roles. Vertebrates rely on several different globin genes: hemoglobin carries oxygen to body tissues (though a separate globin performs this function in fetuses), myoglobin keeps a reserve supply of oxygen for muscle cells to use, and neuroglobin and cytoglobin do jobs that we don’t yet fully understand. Multiple globin genes are found all across the tree of life. In fact, some globins in deep-sea-dwelling worms are adapted for carrying both oxygen and hydrogen sulfide.

Peter Berean and other theorists consistently fail to mention that ~1200 human hemoglobin variants link energy-dependent RNA-mediated amino acid substitutions to all cell type differences in all individuals of all primate species by as little as one base pair change and fixation of one nutrient energy-dependent amino acid substitution. Peter Berean has gone one step further towards obfuscation than most pseudoscientists have been willing to take. He invented the term “bio-functional information” which is the weasel word way to compare energy as information in the context of what is known to serious scientists.

The researchers from Berkeley and elsewhere who are touting the CRISPR technology as if it could lead to beneficial microbe-based biotechnologies have already missed the direct link from energy-dependent RNA-mediated amino acid substitutions to the prevention of all virus-driven pathology. The energy-dependent natural selection for codon-optimality that links fixation of RNA-mediated amino acid substitutions in supercoiled DNA via the physiology of reproducition is the only protection any organized genome has against virus-driven pathology.

Our results corroborate the prevalence of non-canonical splice-sites and a tendency towards unidirectionality of gene orientation in dinoflagellates. We identified a surprisingly large repertoire of proteins involved in molecule transfer in dinoflagellates, but also highlight enrichment of domains involved in the transport of carbon and nitrogen in the Symbiodinium lineage. We also find evidence for substantial differences of these domains between Symbiodinium species, which may provide a genomic basis to explain physiological differences and contribute to host-symbiont specificity. The large amount of intraspecific gene duplications in Symbiodinium putatively represents an alternate mechanism to increase transcript and protein levels in the absence of strong transcriptional control of gene expression.

It is refreshing to see that some researchers now report that nutrient energy-dependent alternative splicings of RNA link the pheromone-controlled physiology of reproduction to the physiological differences that contribute to host-symbiont specificity. Each time serious scientists fail to make a claim about mutations and evolution everybody is one step closer to eliminating the pseudoscientific nonsense of neo-Darwinian theory from any further consideration whatsoever.
See for comparison, the most recent obfuscation of facts that are make to fit the misrepresentations of theorists:
Discovery of short linear motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome

The intrinsically disordered regions of eukaryotic proteomes are enriched in short linear motifs (SLiMs), which are of crucial relevance for cellular signaling and protein regulation; many mediate interactions by providing binding sites for peptide binding domains. The vast majority of SLiMs remain to be discovered highlighting the need for experimental methods for their large-scale identification. We present a novel proteomic peptide phage display (ProP-PD) library…

Motif-mediated interactions is the “Weasel Word Way” (WWW) to obfuscate the fact the RNA-mediated protein folding chemistry is the energy-dependent link to the biophysically constrained order of eukaryotic proteomes.
I think I coined the term “Weasel Word Way” above, since I have not seen anyone else use it to describe how claims are made by theorists. Weasel words are words or phrases used in an ambiguous manner. Motif-mediated interactions makes it appear that the interactions are not energy-dependent and biophysically constrained by the physiology of reproduction.
See for comparison from 2002: An integrated vector system for cellular studies of phage display-derived peptides

Library construction and screening is performed using an optimized type 3 phage display vector, mJ(1), which is shown to accept peptide libraries of at least 23 amino acids in length.

I’ve tried to explain how the peptide libraries of amino acids link biophysically constrained RNA-mediated protein folding chemistry to energy-dependent changes in the microRNA/messenger RNA balance and amino acid substitutions, supercoiled DNA and cell type stability. Few people seem willing to accept the fact that virus-driven energy theft causes all pathology.
When I find an article like this, which was published in 2002, I realize the situation may be hopeless. You cannot explain facts about RNA-mediated cell type differentiation to theorists, even after physicists, chemists, and molecular biologists have already linked energy as information to all biodiversity. Theorists believe in mutation-driven evolution, and nothing is likely to change their ridiculous beliefs.
AXM mutagenesis: an efficient means for the production of libraries for directed evolution of proteins
Proteins do not evolve. Evolve is a WWW to claim that biodiversity is not energy as information-dependent
Use of micro-emulsion technology for the directed evolution of antibodies
Anti-bodies do not evolve. Energy as information is the key to ecological adaptation in all living genera. No species evolves into another species. All species adapt to virus-driven energy theft via nutrient uptake and the physiology of reproduction, or the species becomes extinct leaving only the fluorescence in its DNA to link the cause of extinction to virus-driven energy theft.

Here, they reported that two RNA-mediated amino acid substitutions were mutations so they could link virus-driven energy theft to evolution instead of linking energy as information to ecological adaptation.

Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

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

Controlled amino acid treatment of all pathology

November 22, 2016

Amino acid studies.com
Excerpt:

One of the cancer treatments that seems to be proving effective over time is CAAT: Controlled Amino Acid Treatment. CAAT works by restricting certain amino acids from the diet to combat the growth and reproduction of the cancerous cells.

Excerpt:

doctors can now actively battle cancers, using the best weapons possible, natural amino acids, which are actually designed to make changes in the body.

The trick has been to understand which changes are beneficial to cancer (or disease) sufferers, and which are not.

The trick is to understand how energy-dependent RNA-mediated protein folding chemistry is linked to biophysically constrained supercoiled DNA, which prevents virus-driven energy theft from causing all pathology. That understanding has not been made possible because it undermines the mutually supportive associations between politics and academia.
The Real War on Science(1) has gone virtually unnoticed by anyone who is not already (2) Combating Evolution to Fight Disease

(1) Excerpt:

The Left’s most rigid taboos involve the biology of race and gender, as the Harvard psychologist Steven Pinker chronicles in The Blank Slate. The book takes its title from Pinker’s term for the dogma that “any differences we see among races, ethnic groups, sexes, and individuals come not from differences in their innate constitution but from differences in their experiences.” The dogma constricts researchers’ perspective—“No biology, please, we’re social scientists”—and discourages debate, in and out of academia.

(2)

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

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

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

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

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

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

Let’s start with sex as a biological variable, shall we? Addressing sex as a biological variable
Which amino acid substitutions stabilized the sex differences in cell types at the advent of sexual reproduction in yeasts? What happened to stabilize the organized genomes of all living genera that sexually reproduce? What else besides the nutrient-dependent pheromone-controlled physiology of reproduction in bacteria could be used as a basis for the required links from energy-dependent changes in angstroms to ecosystems that do not seem to be caused by virus-driven energy theft and mutations?
See also: From Fertilization to Adult Sexual Behavior

See also: Gender-Specific Association of Galanin Polymorphisms with HPA-Axis Dysregulation, Symptom Severity, and Antidepressant Treatment Response
See also: Single-nucleotide polymorphism rs948854 in human galanin gene and multiple sclerosis: a gender-specific risk factor
Controlled amino acid treatments will take advantage of everything known to serious scientists about energy-dependent links from angstroms to ecosystems via RNA-mediated cell type differentiation. Most of what is known has only recently confirmed the works that led to the 1933 Nobel Prize in Physics (Schrodinger and Dirac) and the Prize in Physiology or Medicine (Morgan).
See for example: Fluorescence Correlation Spectroscopy — Going Beyond the Diffraction Limit
Excerpt:

In the simplest possible case, employing only one excitation wavelength, the sequence consists first of an excitation laser pulse (blue), followed by a slightly delayed STED laser pulse (red). The non-quenched emission light can then be collected, leading to a fluorescence decay obtained under STED conditions. The second part of the sequence features only the excitation pulse and the resulting decay curve is thus collected under confocal conditions.

Conclusion:

Furthermore, following the gradual changes in diffusion coefficient as a function of observation area size can provide insights into the organization and dynamics of the cell membrane beyond the diffraction limit. The method can be expanded for studies involving more than one fluorescent species by, for example, adding more excitation lasers to the PIE pulse pattern. In addition to cell membrane investigations, PIE-STED-FCS can also be applied to any research area where precise observation of the diffusion times of fluorescent species with high lateral resolution is desirable or required, such as membrane permeability or protein mobility studies.

Femtosecond blasts of ultraviolet light have already been linked to energy-dependent DNA repair. See: UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair
Energy-dependent RNA-mediated DNA repair is clearly linked from the physiology of reproduction to supercoiled DNA and healthy longevity. Virus-driven energy theft is linked to all pathology. Researchers are on the verge of learning which viruses are causing the pathology linked from negative supercoiling to species-specific tissue type-specific pathology in all cell types of all individuals of all living genera.
But you will still hear claims from theorists that not enough is known about how to prevent all pathology. Once everyone else learns how to prevent all pathology via controlled amino acid treatments, the claims of theorists will be exposed as the most ignorant of all claims since the Nobel Laureates from 1933 exposed the pseudoscientific nonsense touted by those who invented neo-Darwinism.
See also: Using light to map the circuitry of the brain

“This allows the image to be mapped to different frequency bands – like tuning a radio,” explains Zhou. “The delay separates the images for the light to detect different optical frequencies at the same time.”

My comment: It will allow all serious scientists to examine a detailed model of how energy-dependent RNA-mediated protein folding chemistry links base pairs from SNPs and species-specific nutrient-dependent pheromone-controlled cell type differentiation from fertilization to adult sexual behavior during life history transitions.
See for example: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

Energy-dependent purifying selection / autophagy (5)

November 21, 2016

by James Kohl with One Comment Adaptations Alternative Splicings Autophagy Diseases & Disorders Ecology Nutrigenomics RNA Directed RNA methylation RNA-directed DNA methylation Variations

See: Energy-dependent purifying selection / autophagy (4)

If we can pinpoint the genetic mutations that cause a particular disease, we can associate those mutations with specific proteins, and then design drugs to block or activate those proteins. We can also measure the activity of proteins identified in this manner to diagnose diseases more accurately, which is a major goal of precision medicine.

In: Histone Acetylome-wide Association Study of Autism Spectrum Disorder the same senior author admits this:

Acetylome aberrations in ASD were not attributable to genetic differentiation at cis-SNPs and highlighted genes involved in synaptic transmission, ion transport, epilepsy, behavioral abnormality, chemokinesis, histone deacetylation, and immunity.

That fact forced them to correlate energy-dependent epigenetically-effected histone acetylation with genotype and the discovery of what they refer to as >2,000 histone acetylation quantitative trait loci (haQTLs) in human brain regions, which include “…four candidate causal variants for psychiatric diseases.” Their failure to discover any direct links from genes to behavior forced them to report their findings in the context of neo-Darwinian pseudoscientific nonsense instead of what is known about biophysically constrained energy-dependent biologically-based cause and effect.

They have been forced to report their findings in terms of epimutations and try to link mathematical models of QTLs to brain development in hopes that no one will notice that everything is epigenetically effected at the level of energy-dependent changes in cell type differentiation.

Old earth creationists and atheists have one thing in common. If they look at the experimental evidence of energy-dependent biologically-based cause and effect they are forced to put it into the context of their ridiculous theories. They must use definitions of meaningless terms like quantitative trait loci (QTL). QTLs are are energy-dependent changes that must be linked to ecological adaptation or they must be linked from virus-driven energy theft to all pathology.

See: Energy-dependent purifying selection / autophagy (6 )

Epigenetics and autophagy vs mutations and evolution (4)

November 11, 2016

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy biophotonics Diseases & Disorders Ecology RNA Directed

“Tobacco mosaic virus (TMV) is a positive-sense single stranded RNA virus that infects a wide range of plants, especially tobacco and other members of the family Solanaceae. The infection causes characteristic patterns, such as “mosaic”-like mottling and discoloration on the leaves (hence the name). TMV was the first virus ever to be discovered. Although it was known from the late 19th century that an infectious disease was damaging tobacco crops, it was not until 1930 that the infectious agent was determined to be a virus.”
My comment: In 1933 Thomas Hunt Morgan won the Nobel Prize in Physiology or Medicine for linking chromosomal inheritance to all biodiversity and Yoshinori Ohsumi won the 2016 prize for linking autophagy to all biodiversity.

See also: “Autophagy is a self-degradative process that is important for balancing sources of energy at critical times in development and in response to nutrient stress. Autophagy also plays a housekeeping role in removing misfolded or aggregated proteins, clearing damaged organelles, such as mitochondria, endoplasmic reticulum and peroxisomes, as well as eliminating intracellular pathogens.”

My comment: The intracelluar pathogens include human endogenous retroviruses that must be biophysically constrained by energy-dependent changes in organized genomes that link angstroms to ecosystems in all living genera via the physiology of reproduction. All serious scientists know that, and all pseudoscientists seem to be completely unaware that their ridiculous theories started to be removed from consideration by serious scientists more than 80 years ago.

See also: The Darwin Code
Excerpt:

…the closer we look at DNA, RNA, genes, and non-gene mechanisms, the less we find random change in a dominant role.

Polycombic ecological adaptation as a science, not a theory (2)

November 1, 2016

by James Kohl with 3 Comments Adaptations Alternative Splicings Autophagy biophotonics Diseases & Disorders Ecology Human Brain Human Pheromones Light Energy Model Organisms Neuronal Plasticity Nutrigenomics Pharmacogenomics Physics RNA Directed 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

Evolutionary Constraints in the β-Globin Cluster: The Signature of Purifying Selection at the δ-Globin (HBD) Locus and Its Role in Developmental Gene Regulation

Conclusion:

… the results here presented indicate that purifying selection is driving not only HBD evolution but also its neighbor pseudogene, HBBP1. In the light of recent advances in the characterization of the β-globin cluster, we propose that the complex patterns of diversity observed in this genomic region arose from distinct functional constraints related with the intricate process of chromatin and protein interactions coordinating the differential expression of genes at the β-globin cluster during development.

My comment: No experimental evidence of biologically-based cause and effect suggests that any locus of genes or any pseudogene has ever evolved. Purifying selection cannot drive evolution. Only energy-dependent variations can can be linked to polycombic ecological adaptation, and only virus-driven energy theft has been linked to the creation of pseudogenes in the context of biophysical constraints on viral latency.

See for comparison: microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection

Excerpt:

miRNA function is generally limited to cytokine levels in response to RNA viruses

Reported as: Mount Sinai Researchers Use Cellular miRNA-Elimination Tool to Study Viral Infection Dynamics

Excerpt:

…while the loss of miRNAs had a negligible impact on the cell’s immediate reaction to a virus or the short-term biology of the cell, sustained depletion had dramatic results on gene expression that was coupled to a burst of cytokines. The researchers concluded in the paper that miRNA function is limited to modulating the biology of the cell over long periods of time.

My comment: In my model, energy-dependent changes in the microRNA/messenger RNA balance link nutrient energy-dependent changes to all healthy longevity and virus-driven energy theft is linked to all pathology. Over long periods of time, autophagy is the link to polycombic ecological adaptation or virus-driven hecatombic evolution of pathology via energy-dependent biophysically constrained RNA-mediated protein folding chemistry. For example, fixation of amino acid substitutions differentiates all cell types in all individuals of all living genera in the context of the physiology of reproduction. For comparison, virus-driven hecatombic pathology is linked from mutations to all pathology.

Simply put, in my model of polycombic ecological adaptation, differential gene expression is nutrient-dependent and controlled by the physiology of reproduction.

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

Conclusion:

…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

My comment: Claims about RNA-mediated polycombic ecological adaptation were first placed into the context epigenetic imprinting in our 1996 review.

See: From Fertilization to Adult Sexual Behavior

Excerpt:

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

My comment: Polycombic ecological adaptation appears to link energy-dependent epigenetic effects on hormones (i.e., proteins) to chromatin structure in telomeric regions, which links the effect on transcription and silencing of various genes to hormone-organized and hormone-activated affects on behavior. The hormone-organized and hormone-activated behaviors link the epigenetic landscape of yeasts to the physical landscape of supercoiled DNA in species from bacteria to invertebrates and all vertebrates via the de novo creation of G protein-coupled receptors, which link chemotaxis and phototaxis to all biodiversity.

For comparison, see: Mutation-Driven Evolution

Excerpt:

Mutation… includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc.

My comment: The definition above links mutations to any change in any genome.

See for comparison: Updates of the HbVar database of human hemoglobin variants and thalassemia mutations

Excerpt:

Single nucleotide substitutions or indels [insertions/deletions] can lead to several hemoglobin variants owing to amino acid replacements, while molecular defects [mutations] in either regulatory or coding regions of the human HBA2, HBA1, HBB or HBD genes can minimally or drastically reduce their expression, leading to α-, β- or δ-thalassemia, respectively.

My comment: The facts about nutrient energy-dependent amino acid substitutions link hemoglobin variants from ecological adaptation to healthy longevity and the facts also link molecular defects from mutations to the pathology of α-, β- or δ-thalassemia, respectively. It would be difficult to include facts about biophysically constrained energy dependent cell type differentiation in the context of any other model that links amino acid substitutions to healthy longevity and links mutations to all pathology in all living genera.

See for example: Criticisms of the nutrient-dependent pheromone-controlled evolutionary model

Excerpt:

…James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research.

My comment: The claims of a biologically uninformed undergraduate student reviewer were placed into the context of modern evolutionary theory, which involves Masatoshi Nei’s simple-minded revision of neo-Darwinian pseudoscientific nonsense. Nei does not compare his theory of mutations to the facts about nutrient energy-dependent fixation of amino acid substitutions in supercoiled DNA. The problem appears to be the use of the term “mutation” in the textbook published on the same day as my 2013 review was published.

I linked the energy-dependent fixation of amino acid substitutions to all healthy longevity. Nei’s textbook misrepresentations did not link anything to healthy longevity, but linked mutations to what I claimed are nutrient-dependent pheromone-controlled polycombic ecological adaptations.

I failed to include what is known about energy-dependent codon optimality in the context of polycombic ecological adaptations because there was no experimental evidence of biologically-based cause and effect to support those claims at the time of our 1996 review or my 2013 review. For comparison, there has never been any experimental evidence of biologically-based cause and effect to support claims about mutation-driven evolution. Simply put, nothing known to serious scientists about cell type differentiation suggest that mutation-driven evolution can occur.

For comparison, see: New analysis of big data sheds light on cell functions
Excerpt:

With today’s technology, scientists are able to generate data about a cell’s or organism’s complete set of genes, proteins, RNA profiles, metabolites and much more—known as omic data. Using omic data, scientists can model complex biological interactions and gain a more holistic view of different cellular processes.

See also: Research Topic Multi-omic Data Integration

Excerpt:

Stable, predictive biomarkers and interpretable disease signatures are seen as a significant step towards personalized medicine. In this perspective, integration of multi-omic data coming from genomics, transcriptomics, glycomics, proteomics, metabolomics is a powerful strategy to reconstruct and analyse complex multi-dimensional interactions, enabling deeper mechanistic and medical insight.

My comment: Glycomics, transcriptomics, proteomics, metabolomics and genomics have established fact about the biological basis of complex multi-dimensional interactions that link the nutrient-dependent pheromone-controlled physiology of reproduction in bacteria from quorum sensing to the molecular mechanisms that enable deeper mechanistic and medical insight in the context of the National Microbiome Initiative and Precision Medicine Initiative.

See for example: ‘Oming in on RNA–protein interactions

Excerpt:

…the interactions between pre-mRNA and proteins fine-tune alternative splicing in a manner that can gradually create new protein functionalities without the need to create additional genes and without affecting existing proteins [4-6].

See for comparison: From Fertilization to Adult Sexual Behavior

Excerpt:

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…. That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

My comment: Detailed examples of how the interactions between pre-mRNA and alternative splicings create new genes in the fine-tuned energy-dependent functional structure of supercoiled DNA explain how all cell types of all individuals of all living genera are protected from virus-driven energy theft. Energy-dependent RNA-mediated amino acid substitutions are fixed in organized genomes via the physiology of reproduction, which helps to prevent the transgenerational epigenetic inheritance of nearly all pathology by linking innate immune system to supercoiled DNA.

For comparison, viruses steal the energy that is required for cell type differentiation, which is how mutations are linked to all pathology. All differences between healthy longevity and virus-driven human pathology can be explained in the context of how nutrient energy-dependent microRNAs. The nutrient energy-dependent microRNAs are carried by erythrocytes in species with circulating blood.

See: Pitfalls of analysis of circulating miRNA: role of hematocrit

MicroRNAs are are delivered to the cell types on an as needed basis. When too few nutrient energy-dependent microRNAs are available, viruses use the existing energy they steal from cells to replicate. Eventually, the replication of the viruses causes the mutations, which are linked to all pathology. That’s why it is important to revisit the facts presented in the context of this article, which was published on 10/26/16

See: Multi-omic data integration enables discovery of hidden biological regularities
I reported this here as: Polycombic ecological adaptation as a science, not a theory for comparison to Biological evolution as a philosophy, not a science.
Despite several attempts to discuss the difference between science and philosophy, no progress was made.
See for example: Evolutionary assumptions (revisited)
See also the impasse that was reached in this attempt to discuss the anti-entropic virucidal energy of the sun.
It is worth joining The Battlefield FB group to see that others would rather hold on to their theories and opinions despite the overwhelming amount of experimental evidence that I have used to support my claims. For me, it is time to move forward and focus on the rediscovery of hidden biological regularities.
Finally, others have discovered that small intranuclear proteins generate alternative splicing techniques of pre-mRNA, which is how microRNAs link hydrogen-atom transfer in DNA base pairs in solution to the conserved molecular mechanisms of energy-dependent cell type differentiation, and to all cell type differences in all individuals of all living genera.
For comparison, this is an example of how virus-driven energy theft is linked viral replication and to virulence:
Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

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

For an example of how nutrient energy-dependent RNA-mediated amino acid substitutions are linked to healthy longevity via the physiology of reproduction, see:

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).”

My comment: The facts stated above have forced theorists to invent evolutionary cell biology.
See Evolutionary cell biology: Two origins, one objective
Reported as: Why some junk DNA is selfish, but selfish genes are junk
Excerpt:

“A commonly held but incorrect stance is that essentially all of evolution is a simple consequence of natural selection.” They point out, for example, that many pathways to greater complexity of both genomes and cells don’t confer any selective fitness.

My comment: Greater complexity requires a link from ecological variation to polycombic ecological adaptation, which links supercoiled DNA to protection from the virus-driven hecatombic evolution of all pathology.
My comment: New theories are worthless if they do not include information on the role of energy in cell type differentiation or the role of virus-driven energy theft in all pathology.
See for comparison the facts about: Detection of hemoglobinopathies and thalassemias using automated separation systems
See also: In vivo correction of anaemia in β-thalassemic mice by γPNA-mediated gene editing with nanoparticle delivery
Excerpt:

The combination of nanoparticle delivery, next generation γPNAs and SCF treatment may offer a minimally invasive treatment for genetic disorders of the blood that can be achieved safely and simply by intravenous administration.

My comment: That fact suggests all suffering and death caused by hemoglobin variants is caused by neo-Darwinian theorists who do not know how the variants link ecological variation to polycombic ecological adaptation.

Reported as: Scientists edit gene mutations in inherited form of anemia
Excerpt:

The researchers found that the technique corrected the mutation to such a degree that the mice no longer had symptoms of thalassemia. After 140 days, they tested hemoglobin levels in the animals and found them to be normal.
“The fundamental result here is that with nanoparticles containing PNAs, along with template DNA, and simple IV infusion of molecules, we achieved enough gene editing to effectively cure the anemia in mice that had thalassemia,” Glazer said.

My comment: The ability to correct the mutation requires a link from energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solutions such as blood. That’s how their IV therapy works. It changes the microRNA/messenger RNA balance and that forces the innate immune system to repair the damaged DNA.
See also: Two novel loci, COBL and SLC10A2, for Alzheimer’s disease in African Americans
Excerpt:

Two SNPs at novel loci, rs112404845 (P = 3.8 × 10−8), upstream of COBL, and rs16961023 (P = 4.6 × 10−8), downstream of SLC10A2, obtained genome-wide significant evidence of association with the posterior liability.

Reported as: Study Identifies Two New Genes Responsible for Alzheimer’s in African Americans
Excerpt:

In 2013, a genome-wide association study of AD in more than 5,500 African Americans identified two genetic risk factors for AD. This study looked at genetic variants across subjects’ entire genome and compared their frequency in cases versus controls.
By doing so they were able to identify two new genes (COBL and SLC10A2) associated with risk of AD in African Americans.

My comment: The author’s study results link hydrogen-atom transfer in DNA base pairs in solution to energy-dependent changes in the microRNA/messenger RNA balance. The neuroscience news report claims they identified two new genes. The neuroscience news report then links the genes — instead of the energy-dependent changes — to the disease in a human population. Many African Americans are examples of how ecological variation has been linked to polycombic ecological adaptation via hemoglobin variants. The adaptations include amino acid substitutions linked to the stability of organized genomes in populations where malaria is endemic. Failed adaptations are included in examples of virus-driven energy theft linked to mutations and the pathology of Alzheimer’s disease.

My comment: The ability to edit out gene mutations clearly links RNA-mediated amino acid substitutions to supercoiled DNA and all biodiversity.
See also: Inventing neo-Darwinism
See also: Pioneering Geneticist Explains Ambitious Plan to “Write” the Human Genome

Many Edits, All at Once

Excerpt:

…he notes that with an editing tool like CRISPR, one base out of many can be altered, but with a synthesis approach, a hundred edits could be made. This sort of change, he tells JAMA, could make a cell resistant to multiple viruses.

My comments: All the changes in base pairs may already have been linked from natural selection for codon optimality and energy-dependent changes in RNA-mediated cell type differentiation to supercoiled DNA, which links the physiology of reproduction from the innate immune system to fixation of the amino acid substitutions that differentiate the cell types of all living genera. If so, what might happen to an organized genome when a hundred edits are made?

Will anyone be able to stop the hecatombic evolution of pathology via the polycombic ecological adaptation, which links autophagy to healthy longevity via protection of organized genomes from virus-driven entropy?

See also: Yale scientists edit gene mutations in inherited form of anemia Genetics & Genomics

A new gene therapy is being tested for its ability to treat thalassemia, a form of anemia caused by genetic mutations. So far, scientists have successfully corrected gene mutations causing the disease in mice, and now researchers are interested in seeing if the same approach will work effectively in humans.
“The fundamental result here is that with nanoparticles containing PNAs, along with template DNA, and simple IV infusion of molecules, we achieved enough gene editing to effectively cure the anemia in mice that had thalassemia. We demonstrated we have extremely low off-target effects.”

See for comparison:

Product Development Pipeline

Excerpt:

Each microRNA mimic in our pipeline is designed to replicate the activity of a single tumor suppressor miRNA and regulate the expression of key oncogenes across multiple oncogenic pathways which can prevent proliferation and induce apoptosis in cancer cells.

See also: VACRC Projects

Excerpt: Future Projects

The Influence of Carbon Dioxide Enhancement on Plant Growth

Thermoregulation in Honey Bees

Biochemistry and Taxonomy in Pine Trees

The Formation of Multiple Tree Rings in Bristlecone Pine Trees

The VACRC suddenly seems willing to take everything I have claimed about RNA-mediated cell type differentiation during the past twenty years and begin to investigate the claims. This would have been a desirable outcome 20 years ago, but now it might prevent progress via use of my model. The model links energy-dependent changes from angstroms to ecosystems in all living genera, it and links virus-driven energy theft to all pathology.

The Pacific Yew Tree and production of taxol is an example of how the physi0logy of reproduction in soil bacteria can be linked from plant growth to the honeybee model organism of thermoregulation and behavior, which must be linked to the biochemistry and taxonomy of all species. That becomes meaningful via the explanatory power of a model that links RNA-mediated amino acid substitutions to all energy-dependent biodiversity via the conserved molecular mechanisms of polycombic ecological adaptation we detailed in our 1996 review.

However, when others wait too long to accept a model that may already have led to a paradigm shift, they may also realize it. That fact was addressed by Kaveli Kull in the context of next week’s meeting of the Royal Society.

See: Kalevi Kull: Censorship & Royal Society Evo Event

Excerpt:

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

My comment: Some work by young earth creationists has been at the cutting edge since 1996, as indicated here: Where do viruses come from?

Excerpt:

‘Viruses tend to keep nutrients away from the big stuff and keep them going around in the little stuff,’ says Fuhrman. If so, viruses have shaped the entire structure of the ecosystem.”9

My comment: 9 is Holmes, B. (1996) Who Rules the Waves? New Scientist 152(2054):8-9, supp I have not read it in its entirety but the claim fits into the context of everything else I have learned about physics, chemistry, and conserved molecular mechanisms of RNA-mediated cell type differentiation, which appears to be biophysically constrained in all living genera via their nutrient-dependent pheromone-controlled physiology of energy-dependent reproduction.

Scent of Eros

Posts tagged: energy-dependent changes

The "walking fish" walks straight from quantum physics to quantum souls (4)

Cryo-EM: More than a suggestion

From E. coli to monkeys and mankind: Theories vs models (2)

What is life without sunshine?

Erasing Epigenetic Marks: Eternal Sunshine of the Spotless Epigenome

Energy-dependent pheromone-controlled entropy (2)

More refutations of neo-Darwinian nonsense

Controlled amino acid treatment of all pathology

Energy-dependent purifying selection / autophagy (5)

Epigenetics and autophagy vs mutations and evolution (4)

Polycombic ecological adaptation as a science, not a theory (2)

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