Food energy-dependent epigenetic adaptation

By: James V. Kohl | Published on: May 24, 2017

Mechanism of transmembrane signaling by sensor histidine kinases, was reported as Scientists investigate how the sense of smell works in bacteria

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

The researchers from Russia link energy-dependent changes in angstroms to ecosystems in all living genera. See this parody for fun.
Listen for her to repeat the claim that “,,,every angstrom is dynamic from the 5 prime to the three…”
See also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013) and see this invited review of nutritional epigenetics from 2014: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
All adaptive evolution is epigenetically-effected ecological adaptation. In my model, adaptive evolution equates with epigenetic adaptation for claims that can be compared to claims about mutations and evolution. In 2013, I placed my claims into the context of adaptive evolution because many people did not realize that organized genomes must be protected from virus-driven energy theft at the level of energy-dependent changes in the microRNA/messenger RNA balance.
Other researchers have since begun to realize that virus-driven energy theft causes the degradation of messenger RNA. Every level of examination links the loss of quantized energy from angstroms to ecosystems via mutations, which are linked to all pathology. If my invited review had not been returned without review, other researchers probably would have linked the peer-reviewed publication from 2013 and virus-driven energy theft from the hecatombic evolution of pathology in archaea to all pathology via the degradation of messenger RNA and negative supercoiling of DNA.

See for example: Structural Dynamics and Mechanochemical Coupling in DNA Gyrase

Gyrase is a molecular motor that harnesses the free energy of ATP hydrolysis to perform mechanical work on DNA. The enzyme specifically introduces negative supercoiling in a process that must coordinate fuel consumption with DNA cleavage and religation and with numerous conformational changes in both the protein and DNA components of a large nucleoprotein complex. Here we present a current understanding of mechanochemical coupling in this essential molecular machine, with a focus on recent diverse biophysical approaches that have revealed details of molecular architectures, new conformational intermediates, structural transitions modulated by ATP binding, and the influence of mechanics on motor function. Recent single-molecule assays have also illuminated the reciprocal relationships between supercoiling and transcription, an illustration of mechanical interactions between gyrase and other molecular machines at the heart of chromosomal biology.

It has also become clear that no experimental evidence links the degradation of messenger RNA from mutations to evolution via natural selection or any other claims that have been made by biologically uninformed theorists. No experimental evidence that supports evolution via natural selection has been published in a peer-reviewed journal.
Natural selection for energy-dependent codon optimality is the experimental evidence-based link to healthy longevity and all biodiversity. Theorists might complain that their absence of experimental evidence is not evidence of absence. But that is how theorists try to keep serious scientists waiting for pseudoscientists to make a contribution to what is known about energy-dependent biologically-based cause and effect. Theorists are pseudoscientists who cannot do that.
For instance, and for an example, in the conclusion of Mutation-Driven Evolution, which was published on the same day as my 2013 review, Masatoshi Nei suggested that other theorists and everyone else should simply ignore the need to consider teleological elements.
Teleology is the philosophical attempt to describe things in terms of their apparent purpose, directive principle, or goal. For instance, in 2012, Thomas Nagel proposed a neo-Darwinian account of evolution that incorporates impersonal, natural teleological laws to explain the existence of life, consciousness, rationality, and objective value.
So far as I know, Nei is still biologically uninformed and Nagel is still looking for his Darwin. See: Awaiting a New Darwin
For comparison, here is an example of what happens when other researchers from Russia included a link from the teleological elements to the purpose of life. Keep in mind that every aspect of neo-Darwinian theory must eventually incorporate “Laws of Biology” that link energy from quantum physics to ecological adaptation via quantum physics and the chemistry of biophysically constrained pheromone-controlled reproduction. For example, in my model of how to link angstroms to ecosystems, Kohl’s “Laws of Biology” are Darwin’s “conditions of life.”
The term “epigenetic adaptation” suggests that others have accepted all the facts about RNA-mediated cell type differentiation. The facts link nutrient energy-dependent changes from angstroms to ecosystems via food energy and the physiology of reproduction, which is controlled by pheromones in species from microbes to humans.

Here’s an example of how the “Laws of Biology’ are linked to energy-dependent ecological adaptation: Genome-wide DNA methylation profiling reveals epigenetic adaptation of stickleback to marine and freshwater conditions

The three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution – adaptation to a freshwater environment. While genetic adaptations to freshwater environments are well-studied, epigenetic adaptations have attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of the marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into a freshwater environment and freshwater sticklebacks placed into seawater. We showed that the DNA methylation profile after placing a marine stickleback into fresh water partially converged to that of a freshwater stickleback. For six genes including ATP4A ion pump and NELL1, believed to be involved in skeletal ossification, we demonstrated similar changes in DNA methylation in both evolutionary and short-term adaptation. This suggested that an immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. For the first time, we demonstrated that genes encoding ion channels KCND3, CACNA1FB, ATP4A were deferentially methylated between the marine and the freshwater populations. Other genes encoding ion channels were previously reported to be under selection in freshwater populations. Nevertheless, the genes that harbor genetic and epigenetic changes were not the same, suggesting that epigenetic adaptation is a complementary mechanism to selection of genetic variants favorable for freshwater environment.

Although they try to separate microevolution and macroevolution, the authors refute every aspect of neo-Darwinian pseudoscientific nonsense. They inadvertently link the quantized energy of sunlight to the creation of ATP, which links food energy-dependent biophysically constrained RNA-directed DNA methylation biosynthesis  from RNA to cell type differentiation in all living genera via my series of blog posts here. See: Search Results for “rna directed DNA methylation”
Anna Di Cosmo’s group linked all invertebrates to all vertebrates via my model in Role of olfaction in Octopus vulgaris reproduction
From the concluding paragraph:
Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).
RNA-directed DNA methylation links the nutrient-dependent pheromone-controlled weekend resurrection of the bacterial flagellum in P. fluorescens to all biodiversity on Earth via conserved molecular mechanisms of controlled cell type differentiation in all living genera. From a teleological perspective, supercoiled DNA protects all organized genomes from the virus-driven degradation of messenger RNA, which links virus-driven energy theft to all pathology in all living genera. See: Structural diversity of supercoiled DNA
See also: Engineering RGB color vision into Escherichia coli, which was reported as Bacterial Photography Goes Technicolor
The requirement for a light-activated endogenous substrate in all cell types has been known to serious scientists who have linked chromosomal inheritance to all biodiversity during the past century. The de novo creation of the endogenous substrate links the de novo creation of G protein-coupled receptors to all energy-dependent cell type differentiation via chemotaxis and phototaxis, which link the ability of microbes to find food to the creation of supercoiled DNA. The supercoiled DNA protects all living genera from the virus-driven degradation of messenger RNA, which is linked from mutations to all pathology.
Indeed, the success of optogenetics is based on the fact that femtosecond blasts of UV light were been linked to RNA-mediated DNA repair. The light activated DNA repair has been linked to the weekend resurrection of the bacterial flagellum in P. fluorescens. That fact refutes all claims about mutation-driven evolution.
Facts that refute mutation-driven evolution are a nightmare for theorists who failed to link sunlight to the life-sustaining energy that Richard Feynman and others placed into the context of food energy. Feynman used that fact as an example of how to “get” physicists who present themselves as know-it-alls. See the video clip, below.
See also: Advances in Non-Viral DNA Vectors for Gene Therapy

…synthetic messenger RNAs (mRNAs), which are delivered to the cell and translated in vivo, offer potential for expressing proteins. The nucleotides in these mRNA molecules must be modified to avoid immune detection through pattern recognition receptors…

The fact that synthetic amino acids have been used to create vaccines that may prevent all pathology, links current technology and teleology to pattern recognition across all species that must find food to reproduce.
See: Generation of influenza A viruses as live but replication-incompetent virus vaccines, which was reported as: Engineered virus has artificial amino acid allowing it to serve as a vaccine
See also: A semisynthetic organism engineered for the stable expansion of the genetic alphabet, which was reported as: Scientists create first stable semisynthetic organism

“We can now get the light of life to stay on,” said Romesberg. “That suggests that all of life’s processes can be subject to manipulation.”

If all of life’s processes were not energy-dependent, the processes could not be manipulated by light in the context of Dobzhansky’s claims in 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 (p. 127).”

Similarly, if all of life’s processes were not nutrient energy-dependent and pheromone-controlled, this research could not link pheromones to the control of antibiotic resistance, which is caused by virus-driven energy theft.

Drugs which affect bacteria’s “sense of smell” could potentially be used as substitutes for modern antibiotics. They do not kill bacteria; they simply give them signals that render them harmless to the human body. In theory, in this case it would be impossible for resistance to be developed.

See also:
Bacterial Quorum-Sensing Network Architectures
Social Evolution Selects for Redundancy in Bacterial Quorum Sensing
Killing by Type VI secretion drives genetic phase separation and correlates with increased cooperation
Unfortunately for you and all your dying or deceased loved ones, mathematical model of evolution failed to link nutrient energy-dependent pheromone-controlled ecological adaptations in all genera to healthy longevity. Fortunately, the creation of vaccines via substitutions with artificial amino acids attests to the fact that all of life’s processes are energy-dependent. That may be sufficient proof that RNA-mediated amino acid substitutions protect supercoiled DNA from virus-driven energy theft and the degradation of messenger RNA, which links mutations to all pathology. If not, there will be more proof each day.
See: microRNA
Earlier today, this appeared on my alert. The evolutionary origin of plant and animal microRNAs
The idea that microRNAs automagically evolved appears to be linked to the foolishness of theories that tried to link mutations from natural selection to evolution.  For comparison, see: Genome-wide discovery of viral microRNAs based on phylogenetic analysis and structural evolution of various human papillomavirus subtypes

It is likely that viral miRNAs help viruses enter the latent phase of their life cycle and become undetected by the host’s immune system, while increasing the host’s risk for cancer development.

See also: viral microRNA
For example: Presence of Viral microRNA in Extracellular Environments

Many human viruses of clinical importance including polyomaviruses, hepatitis B virus, hepatitis C virus, human papillomavirus, human immunodeficiency virus produce viral miRNAs (Louten et al., 2015). These specific viral miRNAs have likewise been explored as potential diagnostic platforms (Lagatie et al., 2014, Zhu et al., 2017, Takahashi et al., 2013, Kumar Gupta and Kumar, 2015, Dahiya and Atreya, 2014).

See also: Modified mRNA Vaccines Protect against Zika Virus Infection, which was reported as: More evidence that Zika mRNA vaccines can stop viral replication in mice
The potential for side effects of the vaccines can be evaluated in the same context as the potential for detrimental uncontrolled ecological adaptation of viruses that could be caused by the CRISPR Cas9 gene-editing technology.
See: Obama Advisers Urge Action Against CRISPR Bioterror Threat 

Scientific advisers to President Obama warn that the U.S. urgently needs a new biodefense strategy and should regularly brief President-elect Donald Trump on the dangers posed by new technologies like CRISPR, gene therapy, and synthetic DNA, which they say could be coöpted by terrorists.

The CRISPR Bioterror Threat links all current technology to refutations of every aspect of neo-Darwinian pseudoscientific nonsense and the pseudoscientific nonsense touted by “Big Bang” cosmologists. That fact has forced those who once led the scientific advances in technology to place them into a teleological perspective.
For example, I suspect that is what George Church and others are trying to do.
See: Human Genome Project 2: Synth meeting takes place in Boston16 May 16

Yes, the meeting was behind closed doors, but it’s not quite what you’d call a ‘secret meeting’. Word has it, that the organisers have a high impact publication in the works that they can’t talk about openly yet.

See: “This is not a secret meeting” – George Church 29 Jun 2016
See: George Church refutes theistic evolution 9 Feb 2017
See also: A scientist named George Church has a wild idea to upend evolution — here’s what you should know about him

Harvard biologist George Church burst into the headlines (yet again) last week when he helped organize a closed-door meeting of scores of top scientists to discuss accelerating efforts to create synthetic DNA — including a complete human genome.

Begley reports that a meeting held last year was held last week. I think I can explain why placing her report into the context of George Church’s business practices is good business for people like her. For example, George Church already refuted every aspect of neo-Darwinian pseudoscientific nonsense when he and others filed the patent for ‘RNA-guided human genome engineering,’ which is an energy-dependent naturally occurring RNA-mediated process. It links natural selection for energy-dependent codon optimality to supercoiled DNA and every aspect of biodiversity.
That fact forces many of the world’s top experts to acknowledge that Darwin’s ‘conditions of life’ are nutrient energy-dependent and pheromone-controlled. That fact links quantum physics to quantum consciousness via claims made by Richard Feynman. For example, he claimed that theoretical physicists exemplify idiocy by using too many different terms for the measurement of “energy.”

The “…proof that physicists are human…” he claims, “… is the idiocy of all the different units which they use in measuring energy.”

The apparent corruption among evolutionists may simply be another example of what Richard Feynman placed into the context of idiocy. In any case, we will continue to see attempts to make it appear that neo-Darwinian theorists have not displayed that same level of idiocy.
They have failed to link ecological variation to energy-dependent ecological adaptation via the physiology of pheromone-controlled reproduction in all living genera. The report by Begley could be “spin-doctoring” at its finest, or it could simply be her mistake.
In either case, those who have been caught touting alternative facts about evolution must now try to make it appear that they have not done that during the past year. During the past year many academics and liberals have been fighting against the claims of corruption made by the Trump administration when the corruption obviously extends to academia.
The fact that reports from researchers in Russia and researchers in China consistently have linked what is known about energy-dependent changes in the microRNA/messenger RNA balance from ecological variation to ecological adaptation or to pathology is not well known to all researchers in the United States. That problem led to accusations that the Russians had hacked the election of our President.
Those accusations can now be placed into the context of Combating Evolution to Fight Disease and support for the State of Israel.
See:  Israeli Middle Schools School to Include Theory of Evolution

 …learning about evolution is not the primary function of the decision, but rather to use it as a building block for students to learn more about their ecology.

For review see: Virus-driven energy theft Archives and RNA directed DNA methylation Archives
Finally see: The phylogenetic utility and functional constraint of microRNA flanking sequences (2015) reported as: All in the (bigger) family
My comment: 

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

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

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

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

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

I will add that the number of terms that could be reduced to link claims about energy to claims about cell type differentiation increasing. Attempts to avoid making claims that link energy-dependent changes in microRNAs from RNA-directed DNA methylation to amino acid substitutions and healthy longevity are prevented by researchers use these different terms for the same thing.
MicroRNAs are contextualized as enhancers, promotors, quantitative trait loci, RNA-based switches. mobile elements, extra-coding RNAs, CRISPR effectors, Oncocers, oncomiRNA, regeneration enhancer elements, isomiRs, regulatory polymorphisms, c-fos enhancers, potential signatures of environmental exposure or effect, key triggers of neuronal cell fate, and many other terms for the same thing.

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