humans Archives - Scent of Eros

MicroRNA-mediated denuclearization (2)

April 24, 2018

by James Kohl with No Comment Adaptations Autophagy base editing biophotonics Cytosis Diseases & Disorders Ecology microRNA editing Model Organisms Physics RNA Directed RNA editing RNA interference RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA–Mediated Epigenetic Heredity

Summary:
The virus-driven theft of quantized energy creates a cellular environment that promotes the survival and self-proliferation of viruses by encoding viral miRNAs or miRNA-like molecules. The viral miRNAs or miRNA-like molecules target different types of host cells.
The sun’s anti-entropic virucidal energy biophysically constrains viral latency in the context of global control of human ES cell differentiation via circRNAs derived from lncRNAs. That fact refutes all neo-Darwinian gene-centric pseudoscientific nonsense. That fact also attests to the link from Chinese philosophy to scientific creationism in South Korea.
Scientific creationism appears to have defeated communism in the context of the electron cloud superimposed over the yin yang symbol of constrained energy.
For scientific support of the claims that appear to have defeated communism, see:
Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

Surprisingly, circRNAs derived from long non-coding RNAs (lncRNAs) were found to account for a significantly larger proportion of transcripts from their loci of origin than circRNAs from coding genes.

CONCLUSIONS:

Our results suggest that during human ES cell differentiation, changes in circRNA levels are primarily globally controlled.

Global control of human ES cell differentiation via circRNAs derived from lncRNAs refutes neo-Darwinian gene-centric pseudoscientific nonsense. The level of control comes as no surprise to serious scientists who start with the energy-dependent creation of microRNAs and link the energy to the RNA-mediated creation from genome assembly to the creation of all cell types.

The global control-based refutation is merely one more example of pattern recognition.

See: Three invariant Hi-C interaction patterns: applications to genome assembly

We suggest that simultaneously considering all three invariant patterns may lead to better Hi-C-based genome assembly methods.

Schrödinger suggested that genome assembly was energy-dependent in 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.)

Examining virus-host cell interaction is important for elucidating mechanisms of virus proliferation in host cells. Viruses can create an environment that promotes their survival and self-proliferation by encoding miRNAs or miRNA-like molecules that target various host cell.

…fine-tuning of the base-pair stability at the cleavage site is essential for efficient processing of pri-miR156a at a low temperature and for reduced flowering sensitivity to ambient temperature changes.

…17-24 amino acid changes, specifically A87T, D96N, S213D, and S242N substitutions in G2 epitopes, were observed. These results suggest that multiple interspecies re-assortment events might have contributed to the emergence of G2P[4] rotaviruses in the post-vaccination era in South Korea.

Several amino acid mutations were identified in PB2, PB1, PA, BM2, and/or NS1 protein coding regions, and one concurrent lysine (K)-to-arginine (R) mutation in PA residue 338 (PA K338R) was found in both maVc_BR60 and maYm_WI01 viruses. When analyzed using reverse-genetically rescued viruses, it was shown that PA K338R alone could increase the pathogenicity of both IBVs in mice and viral replication property in the respiratory tracts of ferrets.

The energy-dependent fine-tuning of the base-pair stability in plants prevents the emergence of rotaviruses via multiple interspecies re-assortment events linked to healthy longevity in post-vaccination era South Korea.

See for comparison: Engineered virus has artificial amino acid allowing it to serve as a vaccine

A team of researchers at Peking University has developed a new type of vaccine that they claim may allow for a new approach to generating live virus vaccines which could conceivably be adapted to any type of virus. In their paper published in the journal Science, the team outlines the means by which they modified an influenza virus causing it to incite an immune response without a risk of infection.

Scientific creationists in South Korea have showed that the Chinese cannot protect themselves from a viral apocalypse via vaccinations. The viruses adapt too quickly.

Knowing that also allows the scientific creationists to create a virus that damages the DNA of specific human populations who are less well-adapted to their food energy-dependent pheromone-controlled ecological, social, neurogenic, and socio-cognitive niches.

Would you threaten nuclear war after you learn that the population of your country could be decimated by a genetically engineered virus produced in a neighboring country. Or, would you denuclearize and de-escalate the tensions as soon as you learned that all niche construction is food energy-dependent and that the pheromone-controlled physiology of reproduction biophysically constrains viral latency.

That fact cannot be placed back into the context of atheism or communism. It is a neo-Darwinian theory killer and is the most likely reason for denuclearization in a reasonable world.

The facts about biophysically constrained viral latency and energy-dependent life will be discussed during Schrödinger at 75 – The Future of Biology – September 2018

See for comparison: Organ-specific metastases obtained by culturing colorectal cancer cells on tissue-specific decellularized scaffolds

…lung and liver decellularized scaffolds retained their tissue-specific tropism when injected in mice.

Reported as: Scientists create better laboratory tools to study cancer’s spread

The hypothesis is this is caused by both ‘seed and soil’ – that the cancer cells have something in them that drive them to a particular organ, and the soil has to be right for them to grow. Most of the focus has been on studying the cancer cell, or the seed, and not as closely looking at the soil, which is the organs that they go to. Our models will help us understand to better understand the conditions of the soil that help promote cancer metastasis.

The use of Schrödinger’s sunlight-to-soil metaphor of degraded organic matter and biophysically constrained viral latency is not likely to be a coincidence. It also appears in the context of the energy-dependent weekend resurrection of the bacterial flagellum and in the context of the weekend Resurrection of Christ.

Scientific creationism in South Korea supposedly began with the support of the US government in their attempt to fight against communism and atheism. Pseudoscientists have not linked energy-dependent RNA-mediated biophysically constrained viral latency to all healthy longevity in the context of Communism and atheism.

For comparison, all serious scientists who understand the role that the creation of energy plays in the creation of supercoiled DNA have won the war against communism by combating evolution to fight disease.

All disease has been linked to the virus-driven energy theft that causes the degradation of messenger RNA, which has been linked to all pathology.

The energy-dependent creation of microRNAs has been linked from the creation of the innate immune system to all biophysically constrained behaviors via what is known about how the physiology of pheromone-controlled reproduction must be linked from soil bacteria to the growth of seeds and all food energy-dependent life on Earth.

Evolutionary theories of epigenetic drift

September 15, 2017

by James Kohl with No Comment Adaptations Diseases & Disorders Ecology Model Organisms RNA Directed RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing Variations

Testing Two Evolutionary Theories of Human Aging with DNA Methylation Data
My summary: Outside the context of food energy-dependent biophysically constrained pheromone-controlled viral latency, mutation accumulation (MA) and disposable soma (DS) provide possible explanations for the existence of human aging. For example, age-differentially-methylated sites across the genome showed significant MA-consistent increases in heritability with age or significant DS-consistent decreases in heritability. Their results supposedly show that both MA and DS play a role in explaining aging and aging-related changes but their results do not link food energy-dependent RNA-directed DNA methylation to de novo gene creation or the virus-driven degradation of messenger RNA that serious scientists have linked from mutations to all pathology in all living genera.
See also: Caloric restriction delays age-related methylation drift

Epigenetic information encoded by DNA methylation is tightly regulated, but shows a striking drift associated with age that includes both gains and losses of DNA methylation at various sites.

Reported as: Researchers uncover mechanism behind calorie restriction and lengthened lifespan

Dr. Issa’s team made their discovery after first examining methylation patterns on DNA in blood collected from individuals of different ages for each of three species – mouse, monkey, and human.

Energy as information is epigenetically linked from the food that organisms eat to the physiology of pheromone-controlled reproduction in all living genera by RNA-directed DNA methylation and amino acid substitutions that differentiate all cell types in all individuals.
All serious scientists have linked RNA-mediated amino acid substitutions from the differentiation of cell types in yeasts to the differentiation of cell types in primates.
Nothing in Biology Makes Any Sense Except in the Light of Evolution

…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.

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

In the mouse model, the diet of the mice determines their nutrient-dependent pheromone production and social interactions with other mice. The mouse model also reveals something that was not revealed in the context of dogs and wolves (Axelsson et al., 2013; Lord, 2013). The aversive human body odor associated with fish odor syndrome can be epigenetically controlled by reducing dietary choline intake. It can also be controlled through antibiotic use (citations in Li et al., 2013). This may be important in the context of chemical ecology and epigenetic effects of genetically predisposed nutrient-dependent pheromone-controlled human interactions (Martin et al., 2010; Preti & Leyden, 2010).

See also the section on “An epigenetic continuum of nutrient-dependent / pheromone-controlled adaptive evolution”

Nematodes

Differences in the behavior of nematodes are determined by nutrient-dependent rewiring of their primitive nervous system…

Insects

The honeybee is currently an accepted model organism of nutrient-dependent pheromone-controlled adaptive evolution of the brain and behavior that is consistent with what is known about neurogenic niche construction in nematodes…

Mammals

Species-specific health and reproductive fitness is associated with nutrient-dependent amino acid substitutions and with pheromone-controlled reproduction. Disease is associated with mutations exemplified in cancer where perturbations of the glucose-dependent thermodynamic/thermoregulatory equilibrium are equally clear (Locasale, 2012).

Humans

Two additional recent reports link substitution of the amino acid alanine for the amino acid valine (Grossman et al., 2013) to nutrient-dependent pheromone-controlled adaptive evolution. The alanine substitution for valine does not appear to be under any selection pressure in mice. The cause-and-effect relationship was established in mice by comparing the effects of the alanine, which is under selection pressure in humans, via its substitution for valine in mice (Kamberov et al., 2013).

See for comparison: Feynman on social science
See also:

Proof: Sunlight is energy as information

March 13, 2017

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

Hypothesis: Kallmann’s syndrome is proof that virus-driven energy theft causes all pathology in species from archaea to humans via the degradation of messenger RNA and the loss of one allele.

Thought experiment:

Step 1) The loss of one allele and the transgenerational epigenetic inheritance of Zika virus-damaged DNA can be compared to the degradation of messenger RNA in bacteria that is manifested in archaea and L-forms.

Step 2) The degradation of messenger RNA in primates differentiates healthy longevity from pathology via a single amino acid substitution in gorillas compared to chimpanzees and modern humans.

Discussion:

Unless someone shows how mutation-driven evolution leads to increasing organismal complexity in species from microbes to humans, the speed of light on contact with water clearly establishes the link from the de novo creation of microRNA flanking sequences to hydrogen-atom transfer in DNA base pairs in solution and all energy-dependent morphological and behavioral phenotypes.

Conclusion:

Unless there is another model for comparison to Kohl (2013), energy as information will be established as the link from endogenous RNA interference to all biodiversity. Until then, a natural law appears to link food odors and the pheromone-controlled physiology of reproduction from biophysically constrained RNA-mediated protein folding chemistry to feedback loops.

The feedback loops clearly link physics and chemistry to biodiversity from energy as information and food odors to pheromones that control the physiology of reproduction. Pheromones are the chemical signals that prevent virus-driven energy theft and genomic entropy in all living genera.

Wikipedia refutes theistic evolution

February 21, 2017

by James Kohl with No Comment Adaptations Alternative Splicings biophotonics Diseases & Disorders Ecology Human Pheromones Light Energy Model Organisms Neuronal Plasticity 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

RNA-Directed DNA Methylation

Besides RNA molecules, a plethora of proteins are involved in the establishment of RdDM, like Argonautes, DNA methyltransferases, chromatin remodelling complexes and the plant-specific Polymerase IV and Polymerase V. All these act in concert to add a methyl-group at the 5′ position of cytosines. In contrast to animals, cytosines at all sequence context (CG, CHG, CHH) may get de novo methylated in plants.

There is no such thing as de novo methylation. Methylation is energy-dependent. Virus-driven energy theft prevents methylation and links mutations to all pathology via everything known to young earth creationists, which some of them have been reporting since the late 1990’s. That fact explains why theorists were forced to change RNA-Directed DNA Methylation to RNA interference in a face-saving attempt. Many pseudoscientists have claimed the creationists cannot be scientists and their attacks on young earth creationists have been among the most vicious of all attacks. But now, the young earth creationists have this:

RNA interference (RNAi) RNA interference (RNAi) is a biological process in which RNA molecules inhibit gene expression or translation, by neutralizing targeted mRNA molecules. Historically, it was known by other names, including co-suppression, post-transcriptional gene silencing (PTGS), and quelling. Only after these apparently unrelated processes were fully understood did it become clear that they all described the RNAi phenomenon.

The so-called unrelated processes linked to RNAi phenomenon were place into the context of what was known about molecular epigenetics in our section on molecular epigenetics from this 1996 Hormones and Behavior review.
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). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

The alternative splicings are energy-dependent.
See also: Contribution of epigenetic mechanisms to variation in cancer risk among tissues

Because de novo modification appears to take place almost exclusively on CpG islands that are already silenced by polycomb in the normal tissue (8), we suggest that this modification works by preventing these genes from becoming activated, thereby inhibiting normal tissue differentiation, causing clonal selection for cells that may predispose to cancer (31). Indeed, many of these methylation targets have been shown to be “driver” genes in a number of different cell types (Fig. S6).

Virus-driven energy theft prevents what they claim are the de novo modifications and the energy theft links contraint-breaking mutations from viral latency to all pathology. Only biologically uninformed pseudoscientists have continued to portray energy-dependent changes in methylation as if the changes occurred in the context of de novo modification.
See for comparison. These creationists start with energy and link it to experience-dependent cell type differentiation via what is known about sensing and signalling in all living genera.
Multipurpose plant sensors startle scientists

Evolutionary scientists did not predict such elaborate sensory integration in a single protein system.

Sensing and signalling in all living genera is links the physiology of reproduction in soil bacteria to the phyisology of pheromone-controlled reproduction in all livng genera. See for example:
The genome of Chenopodium quinoa

The TSARL1 transcript was alternatively spliced in the sweet progeny of Kurmi and 0654. A SNP in the last position of exon 3 (G2078C) co-segregates with the presence of saponins in the Kurmi × 0654 progeny. The G2078C SNP alters the canonical intron/exon splice boundary (Fig. 4e), probably leading to the alternative splicing at an upstream cryptic splice site in the sweet lines (Fig. 4e). This alternative splicing of TSARL1 results in a premature stop codon…

Start codons are important to understand because they mark the beginning of a recipe for translating RNA into specific strings of amino acids (i.e., proteins).

See also: Codon optimality controls differential mRNA translation during amino acid starvation (2016)
They help to make the fact clear that all organisms must eat.
See also:Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition (2016)
They make it clear that the bias between codons or amino acids, and mRNA expression is the link from natural selection for energy as information that links the selection of food to efficient, accurate translation, and folding of expressed genes. Simply put, the energy-dependent amino acid optimality code differentiates between theories of evolution and facts about how ecological variation must be linked to ecological adaptation via the physiology of pheromone-controlled energy-dependent reproduction and supercoiled DNA in all living genera.
Obviously, pseudoscientists who cannot link energy-dependent changes in codon optimality have indirectly been responsible for all virus-driven pathology because they failed to link the viral hecatomb from archaea to the transgenerational epigenetic inheritance of Zika virus-damaged DNA or to all other pathology, including cancer and degenerative diseases.
Thank God, Bill Gates and President Trump are among the billionaires who have decided to help others who have been combating evolutionary theorists to fight disease for several decades.
See also: Combating Evolution to Fight Disease

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

Dobzhansky 1973 and precision medicine (3)

January 25, 2017

by James Kohl with One Comment Adaptations Alternative Splicings biophotonics Diseases & Disorders Ecology Light Energy Model Organisms Neuronal Plasticity RNA Directed RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA–Mediated Epigenetic Heredity Variations

Dobzhansky 1973 and precision medicine
Dobzhansky 1973 and Precision Medicine (2)
How Do Bacteria Help Cancer

Studying bacterial effects on cancer are very complex, because there is no one clear mechanism

Jon LIeff has again obfuscated the clarity of facts about energy-dependent conserved molecular mechanisms. These are the facts:
1) Closed feedback loops link nutrient energy-dependent pheromone-controlled quorum sensing in bacteria to supercoiled DNA in all living genera.
2) Virus-driven energy theft causes the degradation of messenger RNA in bacteria that is manifested in the morphology and behavior of so-called archaea.
3) Archaea are bacteria with less supercoiling in their DNA. (For comparison to bacteria the so-called archaea are less well-adapted. They must struggle harder to avoid extinction.)
4) Negative supercoiling in the organaized genomes of bacteria has been linked to communication among viruses.
5) Viral signaling pits energy theft against the nutrient energy- dependent signaling that links quorum sensing from ecological variation to ecological adaption in all cell types of all individuals of all species on Earth.
Healthy longevity is linked from the nutrient-dependent pheromone-controlled physiology of reproduction in bacteria to supercoiled DNA, which prevents the transgenerational epigenetic inheritance of Zika virus-damaged DNA.
To his credit, this is the first time I have seen Jon Lieff attempt to distance himself from ridiculous theories about evolution.
He concludes:

All of these interactions are based on the natural communications between bacteria and human cells.

…Sorek reports in the journal Nature that his team has found the protein that viruses used to communicate. His team has called the protein arbitrium, which is Latin for “decision.”

They conclude with this ridiculous claim about viruses as a primitive life form instead of realistically linking virus-driven energy theft from mutations to all pathology.

Even though viruses are the most primitive form of life, they infect and harm millions of people every year. The possibility of tapping into viral communication has many scientists excited, because it offers new ways to build drugs that could defeat viruses.

Quorum sensing in bacteria is the nutrient energy-dependent pheromone-controlled link from the innate immune system of all living genera to the physiology of reproduction. Ecological variation must be linked to ecological adaptation via conserved molecular mechanisms of RNA-mediated protein folding chemistry in the context of the physiology of reproduction. If the physiology of reproduction is not biophysically constrained by the availability of nutrients, you are left with a ridiculous theory about mutation-driven evolution.
See also: Alternative RNA Splicing in Evolution (2012)
On 10/27/13 Jon Lieff wrote:

I very much appreciate your comments on pheromone communication and its rapid and critical link to the olfactory brain. I look forward to any current references and future work to help understand the immune brain connection as well as communication in general.

That comment was edited, and now appears as:

Thanks for the current article and information. I very much appreciate your important information and will try to learn more about it.

Another pertinent current article was published in May 2016
See: Spliceosomal intronogenesis
Unfortunately, Jon Lieff and many others have tried to link alternative RNA splicings to the evolution of morphological and behavioral phenotypes outside the context of the energy-dependent physiology of reproduction. Attempts to make viruses the cause of evolution are even more ridiculous, since virus-driven energy theft is the cause of all pathology.
See for comparison: Stromal cues regulate the pancreatic cancer epigenome and metabolome

…these studies raise the possibility that microenvironmental context broadly influences the epigenetic state of tissue-resident cell types under physiological and pathological conditions.

They refuse to admit that the epigenetic state is energy-dependent and RNA-mediated. They must not reveal that virus-driven energy theft is the cause of all pathology. Instread, they claim that “…the mechanistic underpinning of this crosstalk remains poorly understood.”
See for comparison: Communication between viruses guides lysis–lysogeny decisions
Reported as: Do you speak virus? Phages caught sending chemical messages

If you had a molecule that could drive viruses into complete latency, it would be a good drug.

Viral latency is nutrient energy-dependent and it is controlled by the physiology of reproduction. There is no need for a good drug until virus-driven energy theft causes the accumulated mutations that all serious scientists have linked to all pathology. For comparison, all pseudoscientists have linked the mutations to evolution.
Pseudoscientists abandoned every aspect of nutrient energy-dependent healthy longevity and focused on drug development. For a track record of pseudoscientific nonsense, see:
Masatoshi Nei and Naruya Saitou (1986) Genetic relationship of human populations and ethnic differences in reaction to drugs and food

…variant alleles at the pseudocholinesterase locus seem to be maintained by the balance between mutation and weak selection.

Naruya Saitou, JC Stephens and Masatoshi Nei (1985) Methods for computing the standard errors of branching points in an evolutionary tree and their application to molecular data from humans and apes

The DNA sequence data suggested that the chimpanzee is the closest and that the gorilla is the next closest to the human species.

Naruya Saitou and Masatoshi Nei (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees

A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data.

29 years later we have:
IA Babarinde and Naruya Saitou (2016) Genomic locations of conserved noncoding sequences and their proximal protein-coding genes in mammalian expression dynamics

CNS-flanking genes were often found in evolutionarily conserved genomic neighborhoods. ChIP-Seq signal and gene expression patterns also suggested that CNSs regulate nearby genes. Interestingly, genes with more CNSs have more evolutionarily conserved expression than those with fewer CNSs. These computationally obtained results suggest that the genomic locations of CNSs are important for their regulatory functions. In fact, various kinds of evolutionary constraints may be acting to maintain the genomic locations of CNSs and protein-coding genes in mammals to ensure proper regulation.

Conserved non-coding sequences, which are typically reported as microRNA flanking sequences, are reported as CNS-flanking genes. Two decades after we reported how alternative splicings of pre-mRNA were linked from RNA-mediated cell type differentiation to biodiversity via sexual differentiation of cell type in species from yeasts to mammals, the experimental evidence forced Masatoshi Nei’s 1985 co-author to admit that the statistical evidence matches the facts. At first glance, it mght appear that Saitou and Nei never heard about virus-driven energy theft in the context of neo-Darwinian evolution. But wait, instead, they chose to ignore what they knew.
See: Naruya Saitou and Masatoshi Nei (1986) Polymorphism and evolution of influenza A virus genes
See also: Naruya Saitou and Masatoshi Nei (1986) The number of nucleotides required to determine the branching order of three species, with special reference to the human-chimpanzee-gorilla divergence

When these five different tree-making methods, as well as Fitch and Margoliash’s method, are applied to the mitochondrial DNA data (1834 bp) obtained by Brown et al. and by Hixson and Brown, they all give the same phylogenetic tree, in which human and chimpanzee are most closely related. However, the trees considered here are “gene trees,” and to obtain the correct “species tree,” sequence data for several independent loci must be used.

Simply put, they admitted that the nonsense about minimal mutational difference could not be used for comparison to the data from sequencing which now links natural selection for energy-dependent codon optimality to all biodiversity.
See also: Switching off the brain: Study implements an optogenetic tool that inhibits neural activity

In optogenetics, neurons are genetically modified to express light-sensitive ion channels (proteins that conduct electricity), such that light exposure may be used to activate or inhibit electrical activity.

The fact that femotosecond blasts of virucidal UV light have been linked from quorum-sensing in bacteria to repair of virus-driven DNA damage in species from archaea to humans, suggests the understanding of optogenetics has moved far beyond what was specific to neuronal activation.

See for example: Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein

By varying the time between two pulses of light, serious scientists saw how the structure of the protein morphed over time. They did not extend the time to millions of years and suggest that protein evolution had occurred during that time because they are serious scientists, not pseudoscientists.

See: Dobzhansky 1973 and precision medicine (4) in prep

Epigenetics and autophagy vs mutations and evolution (2)

November 11, 2016

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy Diseases & Disorders Ecology Neuronal Plasticity Physics RNA Directed RNA-directed DNA methylation Variations

Plants send light to roots to ‘see’ underground
My comment: Sending light requires an energy-dependent link from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects all organanized genomes from virus-driven energy theft and genomic entropy.
See Schrodinger (1944)
Excerpt:

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)

Ongoing confirmations of facts have escaped the attention of most theorists.

My comment: The physics of life is the same as the physics that underlies inorganic chemistry. There is no such thing as chemoautotrophic or chemoheterotrophic metabolism. Metabolism is energy-dependent. Chemosynthesis and symbiogenesis are energy-dependent and controlled by the physiology of reproduction, not by the magic of evolution.
How can anyone not understand the link from information transfer in the context of physics or not link quantized energy from chemistry to RNA-mediated cell type differentiation in species from microbes to humans via the physiology of reproduction.
If the anti-entropic virucidal effects of UV light did not cause RNA-mediated DNA repair in soil bacteria, plants could not grow. Instead, sunlight is the link from the nutrient-dependent pheromone-controlled physiology of reproduction in soil bacteria to all biodiversity via the conserved molecular mechanisms of epigenetics that we first detailed in our 1996 review.
See: From Fertilization to Adult Sexual Behavior
Excerpt:

Filtering light through a prism to identify tissue type

Hydrogen-atom energy in DNA base pairs

September 19, 2016

by James Kohl with One Comment Adaptations biophotonics Diseases & Disorders Ecology Light Energy Model Organisms Neuronal Plasticity Physics RNA Directed RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity Variations

Hydrogen atom transfer (HAT) reactions are ubiquitous and play a crucial role in chemistries occurring in the atmosphere, biology, and industry.

My comment: The link from physics to chemistry and the conserved molecular mechanisms of biologically-based RNA-mediated cell type differentiation has been the focus my works for more than 20 years, even before I knew what I would need to explain about the energy-dependent links from angstroms to ecosystems via hydrogen-atom energy in all living genera.
See also: For first time, researchers see individual atoms keep away from each other or bunch up as pairs
Excerpt:

Different configurations of electrons give rise to specific elements, making carbon atoms, for instance, distinct from hydrogen atoms.

My comment: Without the different configurations of electrons, energy-dependent changes in angstroms could not be linked from hydrogen-atom transfer (HAT) in DNA base pairs in solution to all biodiversity in all ecosystems. Simply put, the sun’s biological energy must be linked from atmospheric chemistry to biophysically constrained protein folding chemistry on Earth.
When these interactions are seen for the first time the experimental evidence must confirm theories. Otherwise physicists will try to come up with new untestable theories to stall scientific progress. Serious scientists make progress when experimental evidence is accepted. Chemists typically know what to accept. So do molecular biologists.
What do evolutionary theorists or other social scientists know about physics, chemistry, or molecular epigenetics? How do pseudoscientists known what to accept when they already have accepted only theories?
For comparison, serious scientists know that angstroms measure distance, and every angstrom is dynamic in the context of energy-dependent RNA-mediated cell type differentiation. How can any serious scientist understand the claims of theorists made in the context of articles like this:
Humans and Neanderthals had sex. But was it for love? An investigation
Excerpt:

We know for sure humans and Neanderthals had sex because of a Swedish scientist named Svante Pääbo, who “more or less invented the field of paleogenetics,” Elizabeth Kolbert wrote in a terrific New Yorker article in 2011.

My comment: Elizabeth Kolbert lied and used Svante Pääbo’s works to support her ridiculous claim:

We know for sure humans and Neanderthals had sex…

Serious scientists know that Svante Pääbo is the senior author of two articles. The two articles linked Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees and Loss of Olfactory Receptor Genes Coincides with the Acquisition of Full Trichromatic Vision in Primates.
Natural selection for the de novo creation of olfactory receptor genes and the loss of genes is not an indicator that humans and Neanderthals had sex. It is an indicator that natural selection for energy-dependent codon optimality occurred in the context of the physiology of reproduction in all primates. For contrast, all serious scientists know that members of two different species do not have sex. Chromatin remodeling and chromosomal rearrangements limit fertility among species via their nutrient-dependent pheromone-controlled physiology of reproduction and their behavior. The behavior is linked to energy-dependent codon optimality via the physiology of reproduction, not by sex between consenting humans and Neanderthals.
Is is silly to ask questions about sex for love without consideration of fertility, since the sexual interactions must be linked to survival of the species via biophysically constrained RNA-mediated protein folding chemistry in the context of the physiology of reproduction. The biophysical constraints are energy-dependent, but the theorists’ and journalists’ preference for fiction is clear.
Excerpt:

Robert Sawyer is a science fiction author who won the Hugo Award — one of sci-fi’s highest honors — for his 2002 book Hominids, a story that imagines a parallel world where Neanderthals survived and we didn’t. In the book (which spawned a trilogy), a Neanderthal physicist opens up a rift between the worlds and falls in love with a human.

For comparison, see this presentation text about Greg Bear’s novels in which he detailed for his non-technical audience how the nutrient energy-dependent pheromone-controlled physiology of reproduction is linked from RNA-amino acid substitutions to all cell type differentiation in all individuals of all species. The Darwin Code
See also: Structural and Functional MRI Differences in Master Sommeliers: A Pilot Study on Expertise in the Brain
Excerpt:

This study identified enhanced structural and functional patterns in the olfactory network of sommeliers. These findings are consistent with the learning they undergo in achieving the status of Master Sommelier. Furthermore, the volume of a region of the brain involved in olfactory memory was associated with experience, suggesting that the continued training results in morphological changes of the brain. These results speak to the plasticity of the adult brain in response to sensory expertise.

Reported as: Smelling Lots Of Wine Makes Your Brain Alzheimer’s Resistant

Overall, these differences suggest that specialized expertise and training might result in enhancements in the brain well into adulthood,” the study states. “This is particularly important given the regions involved, which are the first to be impacted by many neurodegenerative diseases.

See also: What Sensory Receptors Do Outside of Sense Organs
My comment to the Scientist (I have posted: 361 comments so far)

20 years ago, we published: From Fertilization to Adult Sexual Behavior, which was a review of RNA-mediated cell type differentiation. We included a section on molecular epigenetic in the Hormones and Behavior review.

Unfortunately, few people realize that natural selection for energy-dependent codon optimality links the de novo creation of genes from the creation of G protein-coupled receptors to chemotaxis and to phototaxis before biophysically constrained energy-dependent biodiversity via RNA-mediated protein folding biochemistry can be linked to all biodiversity by amino acid substitutions.
When others report that mutations are linked to pathology, they seem to miss the fact that virus-driven energy theft causes the mutations. Nutrient-energy dependent viral latency has gone missing from explanations that would otherwise link what is known about biologically-based cause and effect from physics to chemistry and everything known about molecular epigenetics.
See also: Olfactory organ of Octopus vulgaris: morphology, plasticity, turnover and sensory characterization
My comment: Pseudoscientists could challenge representations like this if they had experimental evidence for comparison. They don’t. They have only their ridiculous theories, which they report in the story about sex between modern humans and Neanderthals. It is unadulterated pseudoscientific nonsense and nothing more than an unsubstantiated fictional account. It is not science fiction. The theorists claims are not scientifically based.
See for comparison: Role of olfaction in Octopus vulgaris reproduction and Two fatty acyl reductases involved in moth pheromone biosynthesis
Both articles cite Kohl (2013) Nutrient-dependent/pheromone-controlled adaptive evolution: a model
See also: The Ancient Origins of Consciousness: How the Brain Created Experience
Excerpt:

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

My comment: Chemical ecology is the main driver of energy-dependent ecological adaptations. It is not not the driver of mutation-driven evolution, and so far there is no other model for comparison to my model of chemical ecology. I deliberately used the term adaptive evolution to see if someone would take the bait and offer another model for comparison. No one did.
See also: How Psychiatrist Jon Lieff Turned an Interest in Cellular Intelligence into Award-Winning Blogging!
My comment: Lieff still presents cellular intelligence in the context of evolution. He ignores what is known about hydrogen-atom energy in DNA base pairs in solution. That shows how successful a blogger can be if they simply fail to address what is known about biophysically constrained RNA-mediated cell type differentiation. His focus is on evolution! That means he does not need to explain anything about how evolution occurs, or explain what he thinks cellular intelligence is or where it came from!
See for comparison: Direct interrogation of the role of H3K9 in metazoan heterochromatin function
Reported as: Tight DNA packaging protects against ‘jumping genes,’ potential cellular destruction
Tight DNA is supercoiled DNA and it protects the orgnaized genomes of all living genera from virus-driven energy theft and genomic entropy. Simply put, supercoiled DNA biophysically constrains virus-driven energy theft, which is the only way to establish a link from ecological variation to ecological adaptation without inventing another ridiculous theory.

“… viral latency is responsible for life-long pathogenesis and mortality risk…”

Nutrient energy-dependent microRNAs are the obvious link from olfaction to biophysically constrained RNA-mediated protein folding chemistry, plasticity, and prevention of all pathology.
See for example: Olfactory organ of Octopus vulgaris: morphology, plasticity, turnover and sensory characterization

Supercoiled DNA is the link to viral latency, which is the link to healthy longevity.

See also, from the Neuroscience FB group “As simple as random can be”
See also: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
My comment: There is no experimental evidence of biologically-based cause and effect that links anything except energy or energy theft to the species-specific COMT Val158Met amino acid substitution during life history transitions and the development of morphological and behavioral phenotypes.

COMT val158met polymorphism and molecular alterations in the human dorsolateral prefrontal cortex: Differences in controls and in schizophrenia
Excerpt:

…the COMT val158met polymorphism is not found in species other than humans (Palmatier et al., 1999).

My comment: That fact makes the COMT val158met polymorphism a “smoking gun” in the context of energy-dependent de novo gene creation and virus-driven energy theft that links gene losses to loss of function via differences in G protein-coupled receptors.
Dopamine Neuron-Specific Optogenetic Stimulation in Rhesus Macaques
G protein-coupled receptor kinases as regulators of dopamine receptor functions
Subsecond Regulation of Synaptically Released Dopamine by COMT in the Olfactory Bulb
Programmable RNA-binding protein composed of repeats of a single modular unit
Excerpt from the conclusion:

… Pumby may present a simplified context in which to insert Pumilio modules to study how specific amino acids contribute to the emergent properties of modular RNA binding, independent of position-specific effects.

Food supplement or licensed immunostimulant?

August 10, 2016

by James Kohl with No Comment Adaptations Alternative Splicings 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

Glucan from Food Supplement to a Licensed Drug

Excerpt:

“…β-glucan possesses a significant immunostimulating activity in a wide variety of species, including earthworms, shrimp, fish, chicken, rats, rabbits, guinea pigs, sheep, pigs, cattle, and, last but not least, humans. Based on these results, it has been concluded that β-glucan represents a type of immunostimulanting molecule that is actively spanning full evolutionary spectrum. Some experiments also show that β-glucan can help even in the protection of plants. β-Glucan is therefore not only a biologically active polysaccharide with strong immunomodulating effects, but is also considered to be an evolutionary very old stimulant of a variety of defense immune reactions.”

My comment: Lenski’s group removed the context of neo-Darwinian ‘old stimulants’ and linked natural selection from codon usage to RNA-mediated protein folding biochemistry via the de novo creation of G protein-coupled receptors and the innate immune system, albeit apparently without the biophysically constrained links from the physiology of reproduction to supercoiled DNA.

In ‘Tempo and mode of genome evolution in a 50,000-generation experiment,‘ they cited:

8. Wichman, H. A., Badgett, M. R., Scott, L. A., Boulianne, C. M. & Bull, J. J. Different trajectories of parallel evolution during viral adaptation. Science 285, 422–424 (1999).

12. Kvitek, D. J. & Sherlock, G. Whole genome, whole population sequencing reveals that loss of signaling networks is the major adaptive strategy in a constant environment. PLoS Genet. 9, e1003972 (2013).

The two citations make it much more difficult to claim that evolution occurs across millions of years. Loss of receptor-mediated signaling networks is linked to viral latency via adaptation to viruses and virus-driven energy theft is linked to all pathology. Only nutrient energy-dependent microRNA flanking sequences link ecological variation to ecological adaptation via supercoiled DNA, which protects all organized genomes from virus-driven entropy.

Others have started to link my model of nutritional epigenetics and RNA-mediated cell type differentiation in their publications, albeit without a full understanding of why they have been forced to do that by the Laws of Physics, Basic Principles of Chemistry, and everything known to serious scientists who have linked energy-dependent changes from angstroms to ecosystems in all living genera.

My model: Nutrient-dependent/pheromone-controlled adaptive evolution: a model published on 6/14/13

8/6/13 Epigenetics: a new link between nutrition and cancer

9/17/13 Nutritional epigenomics: a portal to disease prevention

My invited review of nutritional epigenetics

4/11/14 Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

Abstract excerpt:

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.

My comment: Lynette R. Ferguson was one of two guest editors who requested my review of nutritional epigenetics for inclusion in the Special Issue Nutritional Epigenetics. My submission was returned without review, but her co-authored text and conclusion came from it.

See: 1/30/15 The Interaction between Epigenetics, Nutrition and the Development of Cancer

Conclusion:

“…it is imperative to understand the implications of diet on epigenetic modifications, and the effect of those modifications on the development of cancer today and in future generations. Such an understanding and an appropriate resultant response would help decrease the level of risk in future generations.”

Abstract excerpt:

The epigenetic modifications investigated include DNA methylation, histone modifications and the influence of microRNAs.

See also from Ferguson, Lynnette R. et al., (2015)

Genomic instability in human cancer: Molecular insights and opportunities for therapeutic attack and prevention through diet and nutrition

Abstract excerpt:

Genomic instability arises from many different pathways, such as telomere damage, centrosome amplification, epigenetic modifications, and DNA damage from endogenous and exogenous sources, and can be perpetuating, or limiting, through the induction of mutations or aneuploidy, both enabling and catastrophic.

My comment: Like others who are biologically uninformed, these researchers failed to mention anything about virus-driven energy theft. If I had mentioned anything more than this in my invited review, they would have undoubtedly also used that information without attribution.

For example, nutrient-dependent ecological niche construction leads to pheromone-controlled social niche construction via the nutrient-dependent pheromone-controlled physiology of reproduction. The nutrient-dependent origin of amino acid substitutions in viruses (Bedford et al., 2014; Gong, Suchard, Bloom, & Pascual, 2013; Kohio & Adamson, 2013; Yamada et al., 2010), which also are manifested in plant and animal interactions, exemplifies a continuum of biological plausibility and ecological validity in the context of Laws of Biology.

For comparison, the excerpt is from Genomic instability in human cancer: Molecular insights and opportunities for therapeutic attack and prevention through diet and nutrition:

“…vitamins, minerals, and antioxidants, such as vitamin D, vitamin B, selenium, and carotenoids, as well as nutraceuticals, such as resveratrol, have shown remarkable plasticity in elucidating antitumor responses. In addition to alleviating genomic instability, these compounds are known to inhibit proliferative signaling [353], [354], [355], attenuate oncogenic metabolism [268], [338], [364], [383], [384], [385], [386], and block inflammation [354], [391], [392], [393], [394], [395], [396], [397], [398], [399], [400], [401], [402], [403], [404].

My comment: What does Genomic instability in human cancer: Molecular insights and opportunities for therapeutic attack and prevention through diet and nutrition tell us about the cause of the proliferative signaling, which has been linked to all pathology?

Others have since linked virus-driven energy theft to oncogenic metabolism, but they seem very unsure of how to link angstroms to ecosystems in all living genera.

See: The Evolution of Epigenetics: From Prokaryotes to Humans and Its Biological Consequences

Excerpt:

The virus reprograms the host’s epigenetic machinery, which permanently affects the host cells.94 One study has demonstrated that cells that have been exposed to EBV experience hypermethylation at CpG islands when compared to cells that have not been exposed to the virus.94 Some of these methylations affect the transcription of genes, which may increase the tumorigenic capabilities of the host cells and lead to the development of cancer.

See for comparison to their video representation (below):

Like many other groups, this one is stuck with neo-Darwinian theories, which means they must place their claims into the context of pseudoscientific nonsense. They have discovered nothing new about energy-dependent cell type differentiation or virus-driven energy theft, which already has been linked to all pathology.

For comparison to what the future holds for researcher in this group, see: A comparative perspective on epigenetics

Excerpt:

She also reviews how olfactory imprinting can be inherited epigenetically by subsequent generations – although the mechanism of transmission is yet to be determined.

Excerpt from the conclusion:

Hoppeler says, ‘I really hope that the awareness of the possibility that epigenetic mechanisms modify the situation of a species under certain conditions is providing a better understanding of how a phenotype can be morphed and may morph over several generations’.

My comment: Any researcher who continues to make claims about evolution across more than several generations is stuck with the horrid failure of ridiculous attempts to link the 1902 definition of “mutation” to assumptions about how many accumulated mutations might be required for one species to evolve into another. Researchers like that are evolutionary dead-ends.

None of their ridiculous claims will be known to serious scientists of the future. For example, in only one generation, Richard Lenski — who was reported to be The Man Who Bottled Evolution — has been caught holding experimental evidence of how ecological variation is linked to ecological adaptation in all living genera via their nutrient energy-dependent physiology of reproduction, and supercoiled DNA.

The supercoiled DNA protects all living genera from virus-driven pathology and genomic entropy. But Pennisi, reporting in Science, starts with the headline: “Richard Lenski’s 25-year experiment in bacterial evolution shows no signs of running out of surprises about how mutation and selection shape living things.”

SURPRISE! The bacteria never evolved. They adapted. There was no mutation and selection. There was only selection for energy-dependent codon usage in the context of RNA-mediated cell type differentiation, which links ecological variation to biophysically constrained ecological adaptation via protein folding chemistry and DNA repair. Virus-driven energy theft prevents DNA repair.

Conclusion:

The results of this study suggest that at least some of the subcellular mechanisms by which damaged hair bundles are repaired were conserved in evolution.

My comment: How does DNA repair occur in the context of “evolution?”

Reported as: Sea anemone proteins repair damaged mouse cochlear hair cells

Conclusion:

…mice produce many proteins that are closely related to the sea anemone repair proteins, suggesting that it may be possible to mobilise the same repair mechanisms in mammals with damaged hearing. Watson hopes that this ground-breaking discovery will eventually lead to a treatment for patients with hearing loss. However, he acknowledges that this research is in its infancy and is keen to discover the mechanism that could eventually allow sea anemones to restore our hearing.

My comment: Research that links energy-dependent RNA-mediated DNA repair to viral latency is not in its infancy and it does not link conserved molecular mechanisms of biophysically constrained protein folding chemistry to “evolution.” All experimental evidence of biologically-based cause and effect links energy-dependent changes from angstroms to ecosystems and virus-driven energy theft to all pathology in the context of ecological variation and ecological adaptation. If you let them, theorists will continue to claim that serious scientists do not know how to link cause and effect from the innate immune system to supercoiled DNA in all cell types of all individuals of all living genera.

Excerpt:

She also reviews how olfactory imprinting can be inherited epigenetically by subsequent generations – although the mechanism of transmission is yet to be determined.

My comment: The molecular mechanisms of biophysically constrained RNA-mediated protein folding chemistry were detailed in From Fertilization to Adult Sexual Behavior. See our section on molecular epigenetics and tell theorists to stop pretending they don’t know how to link ecological variation to ecological adaptation except via the magic of “evolution.”

Bringing RNA back to epigenetics (20 years later)

February 19, 2016

by James Kohl with No Comment Adaptations Diseases & Disorders Ecology Model Organisms Nutrigenomics Pharmacogenomics Physics RNA Directed RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity Variations

Has Contemporary Academia Outgrown the Carl Sagan Effect? [Subscription required]
Excerpt (with my emphasis):

[Sean Carroll] offered 13 pieces of advice…: “Do good research; Make an impact in the field; Bring in grant money… Don’t be too well known outside the field; Don’t write a book; Choose your hobbies wisely.” Carroll argued that academics look askance at colleagues that have too high of a public profile. Not out of envy—but because they worry that public scientists care more about their media presence than about discovery.

Excerpt:

…institutions must find new incentives for dissemination, and the Royal Society has recommended the implementation of “a more effective support system” and “the introduction of significant departmental rewards” (Royal Society, 2006) for those who communicate. These are worthwhile goals, but more pressing perhaps is the need to overcome lingering ambivalence toward engagement in public discourse.

My comment: The book I wrote and published in 1995 with co-author Robert T. Francoeur is available here in an updated paperback from 2002. See: The Scent of Eros: Mysteries of Odor in Human Sexuality. With other co-authors, I subsequently linked the nutrient-dependent physiology and behavior of species from microbes to humans via RNA-mediated events.
Metabolic networks and genetic networks are RNA-mediated. The networks link atoms to ecosystems in all living genera via the physiology of reproduction. Supercoiled DNA in organized genomes protects all genera against virus-driven pathology. Examples that link virus-driven pathology from bacteria to plants and animals have since repeatedly confirmed the links from atoms to ecosytems in the context of energy-dependent hydrogen-atom transfer in DNA base pairs in solution that link nutrient energy-dependent reproduction to RNA-mediated amino acid substitutions and all biomass and all biodiversity.
For comparison, see:
RNA Epigenetics January 1, 2016

MicroRNA-mediated RNA epigenetics January 4, 2016

New RNA letter regulates gene expression: Discovery brings RNA to the fore of epigenetics February 16, 2016
My comment: RNA has been at the fore of epigenetics since our 1996 Hormones and Behavior review. In our section on molecular epigenetics, we wrote:

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.

Among other published works, we cited:

Adler, B. K., and Hajduk, S.L. (1994). Mechanisms and origins of RNA editing. Curr. Opin. Genet. Dev. 4, 316-322.

Clemson, C. M., and Lawrence, J. B. (1996). Multifunctional compartments in the nucleus: Insights from DNA and RNA localization. J. Cell. Biochem. 62, 181-190.

Green, M. R. (1991). Biochemical mechanisms of constitutive and regulated pre-mRNA splicing. Annu. Rev. Cell Biol. 7, 559-599.

Guthrie, K. M., Anderson, A. J., Leon, M., and Gall, C. (1993). Odor-induced increases in c-fos mRNA expression reveal an anatomical “unit” for odor processing in the olfactory bulb. Proc. Natl. Acad. Sci. USA 90, 3329-3333.

Schneider-Gadicke, A., Beer-Romero, P., Brown, L. C., Mardon, C., Luoh, S. W., and Page, D. C. (1989). Putative transcription activator with alternative isoforms encoded by human ZFX gene. Nature 342, 708 -711.

Our focus was on sex differences in cell types. Others have since linked RNA-mediated events from the epigenetic landscape to the physical landscape of DNA in all living genera via the physiology of reproduction.
See for example:

See also: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
My comment: Science news outlets appear to be following my series of more that 600 blog posts and my FB group posts at RNA-mediated. If I were following reports from other news services I would not already have linked: Watson–Crick Base Pairing Controls Excited–State Decay in Natural DNA, which was reported as: Base-pairing protects DNA from UV damage, from microbes to mammals.
See for example: Applying humanized mouse models to immune therapy research
Excerpt:

Mouse models have been a mainstay in biomedical research for decades. As these models have become more sophisticated, their application has grown and now includes a wide variety of immunodeficient strains that can be used to examine the in vivo growth of human tumors and to test new cancer treatments.

My comment: I linked the mouse model organism to humans via one base pair change and one amino acid substitution in my 2013 review: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Excerpt:

The recently detailed mouse model (Li et al., 2013) builds on what is known about olfactory/pheromonal communication in species from microbes to man and incorporates works from mammals that elucidate the molecular mechanisms that are clearly involved. Sex-dependent production of a mouse ‘chemosignal’ with incentive salience appears to have arisen de novo via coincident adaptive evolution that involves an obvious two-step synergy between commensal bacteria and a sex-dependent liver enzyme that metabolizes the nutrient chemical choline.

Excerpt:

They identified a link between VTE and three variants in a chromosome — rs2144940, rs2567617, and rs1998081 — associated with decreased expression of thrombomodulin, a protein that regulates clotting. Approximately 36 percent of American Americans have at least one of these variants, however, these variants were found in much lower frequency in other ethnicities from previous studies.
“This study not only brings us closer to understanding the cause of VTE in African Americans,” Perera said in a statement, “it demonstrates the importance of conducting populations-specific research in precision medicine.

My comment: Do neo-Darwinian theorists think that these variants are mutations? Are they claiming that 36 percent of African Americans are mutants? If so, what are they claiming about the other 64 percent of African Americans who do not have these three variants in a chromosome?
See also: Transposons, and why you should love them

Although TEs can have deleterious effects, in higher animals they have become essential contributors to evolution, and have been described as the “motors of evolution”. By carrying out processes such as gene rearrangement, mutation of gene and regulatory sequences, genomic recombination, gene duplication, and other types of rearrangements, TEs have provided the adaptive benefit of increased genetic diversity and plasticity for their host species. TEs and their hosts have been forced to coevolve, and have achieved a fine balance between the potentially damaging and potentially beneficial effects of TEs.

My comment: They seem to be claiming that mutants co-evolved with organisms that ecologically adapted in the context of their nutrient-dependent physiology of reproduction, which is linked to the supercoiled DNA that protects all organisms from virus-driven entropy. Others have yet to link the virucidal effects of sunlight from hydrogen-atom transfer in DNA base pairs in solution to the physiology of nutrient-dependent pheromone-controlled RNA-mediated cell type differentiation in soil microbes to the cancer treatment “taxol.” When someone else finally does that, their report will be a follow-up to this one: Discovery brings RNA to the fore of epigenetics.
Until then, see: Delving into dark matter
Excerpt:

Bhardwaj added, “The ncRNAs in cancers where odd RNAs were being activated and transcribed had unusual patterns that were similar to some pathogens, and this causes them to stimulate an innate immune response.”
“All in all, we believe these ncRNAs may play a significant role in mediating immune responses against cancer, but much work remains to describe their precise interactions,” said Greenbaum. “If we could characterize the ncRNA and link it with specific pathways, we could understand its role in the tumor environment and determine how it can be utilized for patient therapy.”

My comment: They fail to recognize the difference between nutrient-dependent microRNAs and viral microRNAs, which is why they cannot categorize the difference in pathways that lead to nutrient-dependent healthy longevity, which could be compared to virus-driven pathology. Instead, most researchers are still trying to determine how what they once called “Junk DNA” and now call “dark matter” links metabolic networks from genetic networks to supercoiled DNA that typically protects all organized genome from virus-driven entropy.
A new kind of periodic table
Conclusion:

According to Marsh, researchers are still very interested in trying to understand the evolutionary pathways of protein complexes, in particular heteromeric complexes. “We are currently doing some work on how the assembly pathways of heteromers are related to their evolution. Now that I’ve started my own research group in Edinburgh, one of my main focuses is on understanding how pathogenic mutations can disrupt the assembly of protein complexes, and how protein complex assembly and quaternary structure can influence the phenotypic impacts of mutations.”

See also: How to Build Life in a Pre-Darwinian World Perhaps chemistry played a more instrumental role in the origin of life than scientists thought.

Conclusion: Hud and his collaborators propose that RNA and proteins evolved in tandem, and those that figured out how to work together survived best. This idea lacks the simplicity of the RNA world, which posits a single molecule capable of both encoding information and catalyzing chemical reactions. But Hud suggests that facility might trump elegance in the emergence of life. “I think there’s been an overemphasis on what we call simplicity, that one polymer is simpler than two,” he said. “Maybe it’s easier to get certain reactions going if two polymers work together. Maybe it’s simpler for polymers to work together from the start.”

My comment: They fail to link sunlight and gravitational waves from hydrogen-atom transfer in DNA base pairs in solution and claim emergence and evolution. Since our 1996 review brought RNA to the fore of epigenetics, please return to this blog site to find information that others may still be missing during the next 20 years, or if I gave up trying to tell them anything more about about the obvious links from angstroms to ecosystems.

Excerpt:

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

See for comparison: Evolution silences harmful mutations
Excerpt:

…researchers looked more closely at four synonymous but costly mutations in the gene for a ribosomal protein. They observed that the main problem with these mutations was that they caused a decrease in production of the mutated ribosomal protein. The cells entered into a vicious circle in which low protein levels resulted in defective ribosomes that in turn caused further problems with protein synthesis. By allowing these low fitness bacteria to grow for many generations it was possible to see that evolution solved the problem of synonymous mutations by creating compensatory mutations that restored the level of ribosomal protein to normal. In this way, the researchers have gained a greater understanding of why silent mutations might reduce fitness was and how bacteria could compensate for them.

My comment: Organisms that have enough food can reproduce. Successful reproduction links nutrient-dependent pheromone-controlled ecological adaptations to supercoiled DNA in species that control the replication of viruses and virus-driven genomic entropy.

Excerpt:

They identified a link between VTE and three variants in a chromosome — rs2144940, rs2567617, and rs1998081 — associated with decreased expression of thrombomodulin, a protein that regulates clotting. Approximately 36 percent of American Americans have at least one of these variants, however, these variants were found in much lower frequency in other ethnicities from previous studies.
“This study not only brings us closer to understanding the cause of VTE in African Americans,” Perera said in a statement, “it demonstrates the importance of conducting populations-specific research in precision medicine.

Embryos in a particular phylum of the animal kingdom tend to most resemble one another at a stage in the middle of embryogenesis known as the phylotypic period; a transcriptional analysis of embryogenesis from single embryos of ten different phyla reveals that the transcripts expressed at the phylotypic stage (or mid-developmental transition) differ greatly between phyla, and a ‘phylum’ may be defined as a set of species sharing the same signals and transcription factor networks during the mid-developmental transition.

My comment: All development transitions are nutrient-dependent and RNA-mediated. Other variants in chromosomes are reported in terms that link energy-dependent hydrogen-atom transfer in DNA base pairs to phenotypic changes in the mouse model that clearly are linked from amino acid substitutions to morphological and behavioral phenotypes via the physiology of nutrient-dependent phermone-controlled reproduction.
Again, see: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

Two additional recent reports link substitution of the amino acid alanine for the amino acid valine (Grossman et al., 2013) to nutrient-dependent pheromone-controlled adaptive evolution. The alanine substitution for valine does not appear to be under any selection pressure in mice. The cause-and-effect relationship was established in mice by comparing the effects of the alanine, which is under selection pressure in humans, via its substitution for valine in mice (Kamberov et al., 2013).

These two reports (Grossman et al., 2013; Kamberov et al., 2013) tell a new short story of adaptive evolution. The story begins with what was probably a nutrient-dependent variant allele that arose in central China approximately 30,000 years ago. The effect of the allele is adaptive and it is manifested in the context of an effect on sweat, skin, hair, and teeth. In other mammals, like the mouse, the effect on sweat, skin, hair, and teeth is due to an epigenetic effect of nutrients on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. The pheromones control the nutrient-dependent hormone-dependent organization and activation of reproductive sexual behavior in mammals such as mice and humans, but also in invertebrates as previously indicated. That means the adaptive evolution of the human population, which is detailed in these two reports, is also likely to be nutrient-dependent and pheromone-controlled, since there is no other model for that.

Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees
Functional characterisation of a SNP in the ABCC11 allele—Effects on axillary skin metabolism, odour generation and associated behaviours
Odor perception between heterosexual partners: its association with depression, anxiety, and genetic variation in odorant receptor OR7D4
Excerpt:

Genetic variants in OR7D4 receptor can modify the detection of the steroids androstenone and androstadienone, two pheromones that have the potential to evoke behavioral changes in many mammals, including humans, including mood changes (Kohl et al., 2001) and inter-sex communication (Kohl et al., 2001).

Excerpt:

…it was observed that the rating of partner odor was significantly associated with rs8109935 genotypes suggesting that genetic variability in the OR7D4 might have a role in the odor perception between partners. In fact, the data of this study replicate, for the first time, the results of Keller et al. (2007) about the influence of genotype variations in OR7D4 on odor perception.

The difference in pollinator communities between regions may indicate that different pollinators select for differences in floral scent chemicals, but further experiments would be required to test this theory. Nonetheless, the authors state their study is the first to find consistent regional differences in selection on floral scent, showing that this could be one mechanism behind geographical floral chemical scent divergence.
Karin Gross notes: “The observed regional differences in selection are an important evolutionary force contributing to divergence in floral fragrances. Other traits such as plant height were also affected by selection, but in a more uniform way.”

My comment: The changes in the orchid’s scent link ecological variation in the soil bacteria to the nutrient-dependent pheromone-controlled physiology of reproduction in mammals.
Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin
Repeated elevational transitions in hemoglobin function during the evolution of Andean hummingbirds
Evidence from cyclostomes for complex regionalization of the ancestral vertebrate brain
Reported as: Reported as: Jawless fish brains more similar to ours than previously thought
See also: Distinct Circuits for the Formation and Retrieval of an Imprinted Olfactory Memory
Reported as: Neuroscience of Early-Life Learning in C. elegans
See also: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
The information that connects all of the above from ecological variation to ecological adaptation in all living genera via hydrogen-atom transfer in DNA base pairs in solution arrives so quickly that biologists must look at conference abstracts to stay current and they must also pay attention to advice like this:
Biologists urged to hug a preprint
Excerpt:

Both Vale and Vosshall think that preprints will become widely accepted only if the life-sciences community develops a consensus that preprint publication establishes a priority for any discovery.

See my invited review of nutritional epigenetics, which was published as a preprint when it was returned without review. Note, however, that Vosshall has referred to all my works as pseudoscience that she will not address. Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems. I would value her opinion if I thought she was a serious scientist. Instead, she is trying to genetically engineer mosquitoes to prevent the transmission of pathogens. Obviously, she doesn’t know enough about RNA-mediated cell type differentiation to predict that the pathogens will adapt faster than the organisms she genetically engineers.

Supercoiled DNA constrains virus-driven genomic entropy

October 13, 2015

by James Kohl with One Comment Adaptations Diseases & Disorders Ecology Light Energy Model Organisms Physics RNA Directed RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing Variations What's in the News

1) Genes linked with malaria’s virulence shared by apes, humans and
2) Supercoiled DNA is far more dynamic than the ‘Watson-Crick’ double helix were reported today.
One report (1) links viruses to the evolution of biodiversity in chimpanzees and humans compared to gorillas.
The other report (2) links nutrient energy-dependent base pair changes to RNA-mediated amino acid substitutions and DNA repair.

Both reports are linked to open access publications:

See 1) Ape parasite origins of human malaria virulence genes
Excerpt:

This Laverania species diversity provides an unprecedented opportunity to study the origins of genomic features that previously seemed unique to P. falciparum, such as the var gene family encoding erythrocyte membrane proteins. Here we show that various aspects of the multi-scale modularity of these loci can be recognized in diverse Laverania species, with the implication that a var or var-like gene family already existed in their last common ancestor.

My comment: The implication that gene families already existed in a last common ancestor are linked to the theoretical ghosts of the evolution industry. Despite a century of scientific progress, the ghosts are still linked to the gene-centric views of population geneticists. They used de Vries (1904) definition of “mutation” as the basis for assumptions about how long it would take for all extant or extinct biomass to automagically arise from a primodial soup. Sometime during that time apes evolved from microbes and became modern humans.
See also 2): Structural diversity of supercoiled DNA
Conclusion:

Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

My comment: The data that links small molecules, such as microRNAs, from metabolic networks to genetic networks, makes the claims of neo-Darwinian theorists the theme of this parody. It is an accurate representation of how nutrient-dependent base pair changes link ecological variation to ecological adaptation and all biomass on earth via what is currently known to serious scientists about base pair changes and RNA-mediated DNA repair.

Last week, I recorded a less technical representation of biologically-based cause and effect that placed squirrel-centric evolution into the context of current philosophy (we don’t know how species evolved) and claims of evolutionary theorists (random mutations and natural selection led to the theoretical basis of the “walnut crush” phenomenon). Sarcasm alert: Creationist claims are vaguely presented with no experimental evidence to support the idea that the walnuts grew on and fell from trees.

Obviously, no one can be perfectly sure that what is known about RNA-mediated epigenetic regulation of gene expression and RNA-mediated gene silencing link base pair changes to all extant biodiversity, or if de Vries definition of “mutation” and theories are the best approach to understanding the pathology of malaria. However, the 2015 Nobel Prize winners in Physics, Chemistry, and Physiology and/or Medicine have linked neutrinos to mass and the speed of light on contact with water from the light’s virucidal properties to the effective treatment of malaria via a water-based chemical extraction procedure described 1600 years ago.