fruit-dove

Food energy-dependent epigenetic adaptation

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 http://mobile.the-scientist.com/article/49481/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.
See:

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.” http://dx.doi.org/10.1038/nature13400

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

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

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

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

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.
Cytosis

Energy-dependent epigenetic translation to mRNA stability (6)

See: Energy-dependent epigenetic translation to mRNA stability (5)
Five energy-dependent amino acid substitutions are linked to differences in RNA content and biodiversity in 4 mammalian species.
Excerpt:

Species- and tissue-specific variation in mt-tRNA incorporation into the mt-LSU was analyzed….  Analysis of porcine dermal fibroblasts (C), human osteosarcoma 143B cells (D), bovine cardiac tissue (E), and rat hepatic tissue (F) depicts the relative abundance of each mt-tRNA across fractions (ImageQuant software); represented as a percentage of the total signal.

In my model, the metabolism of food to pheromones controls species specific and tissue specific variation in food energy-dependent mitochondrial transfer RNA (mt-tRNA) and the transgenerational epigenetic inheritance of morphological and behavioral phenotypes. In all models of biologically based cause and effect, the “RNA world” must be linked by metabolism to the pheromone-controlled fixation of RNA-mediated amino acid substitutions in supercoiled DNA. That is how the RNA world is linked from chromosomal rearrangements to energy-dependent RNA-mediated chromosomal inheritance and to protection from virus-driven energy theft, which links mutations to all pathology in species from microbes to humans.
See:  Nutrient-dependent/pheromone-controlled adaptive evolution: a model (published 2013 Jun 14)
My model of “ecological adaptation” was placed into the context of “adaptive evolution” because many theorists do not seem to understand why serious scientists do not believe in “Big Bang” cosmology or neo-Darwinian pseudoscientific nonsense about Mutation-Driven Evolution (also published 2013 Jun 14)
Anyone who tries to tell a theorist that no experimental evidence of biologically-based cause and effect supports their theories about mutation-driven evolution is not likely to see their work get past peer-review. And, when the threat to their ridiculous theories becomes known, theorists are more likely to accept criticisms of a model — even in the absence of a comparable model.
During the past 4 years, there has been no scientific support for neo-Darwinian theories and overwhelming support for the model of food energy-dependent amino acid substitutions and Darwin’s claims about “conditions of life.”
See for instance: Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization (published 2017 May 20)

…initiator-tRNA species proposed to participate in SOS reside in the cell nucleus, are found associated with supraspliceosomes (Table 2c), and appear not to be charged with an amino acid [87].

See also: Human mitochondrial ribosomes can switch their structural RNA composition

Our data demonstrate that only mt-tRNAVal or mt-tRNAPhe are found in the mitoribosomes of five different mammals, each mammal favors the same mt-tRNA in all tissue types, and strikingly, when steady-state levels of mt-tRNAVal are reduced, human mitoribosome biogenesis displays an adaptive response by switching to the incorporation of mt-tRNAPhe to generate translationally competent machinery.

The switches are food energy-dependent and they obviously link ecological variation to ecological adaptation via the Laws of Physics and basic principles of chemistry. In my model, for example, light-induced changes in hydrogen-atom transfer in DNA base pairs in solution cause initiator-transfer RNAs in the nucleus to become charged with an amino acid. Light energy-as-information subsequently appears to biophysically constrain all conditions of life in all living genera by protecting organized genomes from virus-driven energy theft and genomic entropy.
The link from quantum physics via electron resonance to quantum souls is clearer than it has ever been.
See: Electron resonance pervades the brain

Using molecular modeling, the US-Canadian team of Travis Craddock, Stuart Hameroff and Jack Tuszynski had previously shown anesthetic binding in ‘quantum channels’, non-polar arrays of amino acid pi resonance clouds, winding through microtubules.

See also: What is life when it is not protected from virus driven entropy
and
Energy as information and constrained endogenous RNA interference
An endogenous substrate was linked from the biosynthesis of RNA to endogenous RNA interference in this full text .pdf from 1963: PARTICIPATION. OF GLYCOLYSIS. AND THE CITRIC ACID CYCLE. IN NUCLEAR ADENOSINE TRIPHOSPHATE SYNTHESIS

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

I do not know any pseudoscientist who has linked the energy-dependent creation of nucleic acid precursors to the energy-dependent creation of new genes, or to the activation of genes via the endogenous substrate. Indeed, the fact that there is an endogeneous substrate has been ignored, unless it has been replaced by an alternative fact which was somehow linked to all biodiversity via the physiology of reproduction.
See for comparison: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”
Excerpt:

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

See for comparison: A scientist named George Church has a wild idea to upend evolution — here’s what you should know about him

Darwin explained how species evolve. Church wants to turbocharge that process by putting new genes into organisms rather than waiting around for them to evolve those genes on their own.

Darwin did not explain how species evolve. Darwin presciently linked natural selection for food energy-dependent codon optimality to RNA-mediated amino acid substitutions and the physiology of reproduction, which biophysically constrains the hecatombic evolution of all pathology. Nothing known to serious scientists suggests that new genes “evolve.”

In between tRNA and CRISPR, Church coauthored hundreds of scientific papers, from “Predicting regulons and their cis-regulatory motifs by comparative genomics” to “Characterization of Cas9-guide RNA orthologs.”

After he characterized naturally occurring energy-dependent changes in RNA orthologs, George Church refuted neo-Darwinian evolutionary theories when he and others filed this patent application. RNA-Guided Human Genome Engineering

FIG. 3A-1 and FIG. 3A-2 depict a human codon-optimized version of the Cas9 protein and full sequence of the cas9 gene insert.

Human codon-optimized changes in proteins are energy-dependent, RNA-mediated, and the changes are biophysically constrained by the food that organisms eat and the physiology of reproduction in all living genera. That fact was placed into the context of the Structural diversity of supercoiled DNA in the context of this review: Feedback loops link odor and pheromone signaling with reproduction
The review was co-authored by 2004 Nobel Laureate, Linda Buck who helped to link the sun’s anti-entropic virucidal energy to biophysically constrained cause and effect in all species that need to eat to reproduce. Richard Feynman may have been one of many others who also did that.

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

See for comparison: George Church refutes theistic evolution

The future of genetic codes and BRAIN codes (video)

My comment on the video: Biophysically constrained genetic codes are brain codes. They link the epigenetic landscape to the physical landscape of supercoiled DNA via metabolic networks, which link energy as information to all cell type differentiation in all individuals of all living genera.

Virus-driven energy theft is linked from “gene vandalism” to epigenetically effected nutrient energy-as-information dependent RNA-mediated DNA repair.

Synthesis of nucleic acids became a “bigger deal” when Sutherland’s group showed that ultraviolet light was linked to the simultaneous de novo creation of nucleic acid precursors, which are the starting materials needed to make natural amino acids and lipids.

See also: Peter Godfrey Smith: “Other Minds: The Octopus, the Sea, and the Deep Origins…”

See for comparison:
Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge.” — Kalevi Kull
In this case, Anna Di Cosmo’s group already linked what is known about the physiology of pheromone-controlled reproduction from the gut bacteria of the octopus to the nutrient energy-dependent pheromone-controlled physiology of reproduction of the octopus. See: 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).

Her group also linked the conserved molecular mechanisms of chemical perception and gene expression in flies to consciousness in octopuses. See: Dose-Dependent Effects of the Clinical Anesthetic Isoflurane on Octopus vulgaris: A Contribution to Cephalopod Welfare via my model, albeit without citation to: Nutrient-dependent/pheromone-controlled adaptive evolution: a model or citation to Electron spin changes during general anesthesia in Drosophila.
Without an energy-dependent change in electron spin, the findings that link virus-driven energy theft to all pathology cannot be linked from cryo-EM to the biophysically constrained changes that link angstroms to ecosystems in all living genera. None of the claims that Richard Feynman made about energy, including his claims about food energy, can be linked from quantum physics to chemistry and biologically-based cause and effect via the physiology of reproduction.
Until recently, I thought that Eugene Koonin was prepared to challenge the nonsense about evolution. No other theorists seem to be willing to address the facts about energy-dependent increasing organismal complexity.
See: Riding the Evolution Paradigm Shift With Eugene Koonin

The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…

Virus-driven energy theft links the degradation of messenger RNA to all pathology, which is biophysically constrained by conserved molecular mechanisms that link food energy from viral latency to all energy-dependent healthy longevity.
Watch for Koonin and other theorists to use experimental evidence of biologically-based cause and effect to eliminate the pseudoscientific nonsense about evolution touted by those who still know nothing about virus-driven pathology manifested in Alzheimer’s and other neurodegenerative diseases. Alternatively, watch for Koonin and other theorists to continue playing their evolution game until everyone who is more than one decade old learns to play this game:

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

Cytosis is a worker placement game that takes place inside a Human Cell! Players utilize the organelles within a cell to collect cellular resources such as mRNA from the Nucleus, Lipids from the Smooth E.R., ATP from the Mitochondria, etc. and score points when they use these resources to complete Hormones, Receptors or Enzymes! 2 to 5 Players, Ages 10 +, Plays in 50 to 75 mins – (Shipping Aug/Sept 2017 – US, EU, CA & AU will ship from WITHIN their country / region) 

See for comparison: How Statistics Weakened mRNA’s Predictive Power

More than 60,000 published works link food from energy-dependent changes in the microRNA/messenger RNA balance to differences in amino acid substitutions in mitochondrial transfer RNA (mt-tRNA).

The amino acid substitutions in different mammals appear to protect the mitochondria from virus-driven energy theft, which links the degradation of messenger RNA from mutations to all pathology.

The link from mt-tRNA to healthy longevity via species- and tissue-specific variation in the structure and function of supercoiled DNA may limit further consideration of neo-Darwinian theories because there is nothing to suggest that supercoiled DNA automagically evolved.

See for example: Figure 1

Species- and tissue-specific variation in mt-tRNA incorporation into the mt-LSU was analyzed….  Analysis of porcine dermal fibroblasts (C), human osteosarcoma 143B cells (D), bovine cardiac tissue (E), and rat hepatic tissue (F) depicts the relative abundance of each mt-tRNA across fractions (ImageQuant software); represented as a percentage of the total signal.

See also: Noncoding RNA Helps Cells Recover from DNA Damage

There is clear evidence that femtosecond blasts of UV light repair DNA in the context of energy-dependent changes in the microRNA/messenger RNA balance and autophagy, which protects all organized genomes from virus-driven energy theft and the degradation of messenger RNA.
The failure to integrate the Nobel Prize winning works of Ben Feringa (Chemisty 2016) and Yoshinori Ohsumi (Physiology or Medicine 2016) prevents theorists from linking what organisms eat to their pheromone-controlled physiology of reproduction in the context of Schrodinger’s claims in “What is Life?”(1944) and this claim by Roger Penrose in the reprint edition:

How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy? (Roger Penrose 8 August 1991)

See also: From Fertilization to Adult Sexual Behavior  In our section on molecular epigenetics, we wrote:

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…

The food energy that is linked from alternative splicing techniques of pre-mRNA to the chemistry of protein folding and the pheromone-controlled physiology of reproduction in all living genera seems to be largely ignored by those who are not Nobel Laureates.

 

Amino acid modification FA_Epigenetics_Table1

Energy-dependent epigenetic translation to mRNA stability (4)

See first: Energy-dependent epigenetic translation to mRNA stability (3)
First-ever direct observation of chiral currents in quantum Hall atomic simulation

The report on the simulation fails to address the facts about what happens at the level of hydrogen-atom transfer in DNA base pairs in solution when you have an MRI. Perhaps the link from chirality to autophagy and all cell type differentiation in all living genera is not obvious.
 

See: Magnetic resonance imaging

MRI is based upon the science of nuclear magnetic resonance (NMR). Certain atomic nuclei can absorb and emit radio frequency energy when placed in an external magnetic field. In clinical and research MRI, hydrogen atoms are most-often used to generate a detectable radio-frequency signal that is received by antennas in close proximity to the anatomy being examined. Hydrogen atoms exist naturally in people and other biological organisms in abundance, particularly in water and fat. For this reason, most MRI scans essentially map the location of water and fat in the body. Pulses of radio waves excite the nuclear spin energy transition, and magnetic field gradients localize the signal in space. By varying the parameters of the pulse sequence, different contrasts can be generated between tissues based on the relaxation properties of the hydrogen atoms therein.

For comparison, see: Affective Neuroscience with Jaak Panksepp (BSP 65)

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My feeling is that the social brain has many levels. If you don’t understand the foundational level, then you can do brain imaging until you’re blue in the face, but you still will not understand the process at a deep causal level.

If you understand the fact that quantized energy must be linked from the anti-entropic virucidal energy of sunlight to diagnostic testing by what is known to serious scientists about the effects of energy on hydrogen-atom transfer in DNA base pairs in solution, you may understand how frustrating it is to see people report pseudoscientific nonsense like this:

The Life of A Thought in the Brain and this: ‘Humanlike’ ways of thinking evolved 1.8 million years ago, suggests new study

See also: MicroRNA GnRH

I urge others who are interested in learning more about energy-dependent endogenous RNA interference and biophysically constrained viral latency to search for the term microRNA and the form of pathology that links the failure of RNA-mediated protein folding chemistry to the disease. You can be as specific or as general as you wish and you will still find that the energy-dependent creation of G protein-coupled receptors, enzymes, hormones et al., must be linked from ecological variation to ecological adaptation by the physiology of reproduction. That fact refutes the pseudoscientific basis for the CRISPR threat to humanity.

See for comparison the never ending nonsense touted by theorists who know nothing about mRNA stability:

Evolution by Gene Duplication

Emergence and evolution of an interaction between intrinsically disordered proteins

ModelFinder: fast model selection for accurate phylogenetic estimates

Other Minds: The Octopus, the Sea, and the Deep Origins...

Novel approach to study the perception of animacy in dogs

We suggest that dogs spontaneously recognized the chasing-like pattern and thus they may have considered the interacting partners as animate agents. This methodological approach may be useful to test perceptual animacy in other non-human species.

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Energy-dependent epigenetic translation to mRNA stability (3)

Energy-dependent epigenetic translation to mRNA stability (2)

Energy-dependent epigenetic translation to mRNA stability (2)


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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The Virus-Driven Suicide March for Science

Genetic analysis of α-synuclein 3′ untranslated region and its corresponding microRNAs in relation to Parkinson’s compared to dementia with Lewy bodies
My summary: Genetic predispositions and energy-dependent microRNA biogenesis link top-down causation to the biophysically constrained transgenerational epigenetic inheritance of neuronal type-specific expression.  Energy-dependent variability in endogenous RNA interference and the SNCA gene contribute to synucleinopathies in the context of two different human pathologies.
Virus-driven energy theft is linked to the regulation of the α-synuclein (SNCA) gene and the etiology of Parkinson’s disease (PD) and to (DLB) dementia with Lewy bodies. RNA-directed DNA methylation is clearly linked from the negative supercoiling of DNA to DLB.
See: DNA methylation changes at SNCA intron 1 in patients with dementia with Lewy bodies
My summary: Lower methylation rates are a biomarker for dementia with Lewy bodies (DLB)
After Robin Williams death was attributed to suicide, he was diagnosed with DLB. The misdiagnosis of Parkinson’s disease contributed to his death.  Virus-driven pathology will continue to contribute to the unnecessary suffering and death of many more victims who have been misdiagnosed by biologically uniformed psychiatrists and other so called “medical professionals.”
See also: Up-regulation of SNCA gene expression: implications to synucleinopathies

…this model system will enable us to compare different neuronal and glial lineages involved in synucleinopathies representing an attractive strategy to elucidate-common and specific-SNCA-genetic variants, regulatory mechanisms, and vulnerable expression levels underlying synucleinopathy spectrum disorders. This forthcoming knowledge will support the development of precision medicine for synucleinopathies.

Synucleinopathies

Because each of the synucleinopathies has a distinct set of symptoms, prognosis and management issues, it has been suggested that the term “has little practical value as a diagnostic term for the clinician.

When did any term used by medical professionals in any model of pathology link nutrient energy-dependent pheromone-controlled ecological adaptations to all healthy longevity and link virus-driven energy theft from synuclinopathologies to all pathology?
See for comparison: 7/25/13 Jay R. Feierman:

Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.

See also: Hypothesis free pseudoscience vs facts (4) 10/3/16

Someone should tell Robin Williams’ widow that these guidelines could apply to the use of antibiotics to treat gut discomfort before virus-driven energy theft causes Lewy Body Disease to be misdiagnosed and leads to death by suicide.

See also: Hypothesis free pseudoscience vs facts (5) (10/4/16)

If others had learned that virus-driven energy theft is the cause of the RNA-mediated changes in gut microbes, the publication of results in 1985 might have prevented the death of Robin Williams from Lewy Body Disease. His first symptom was gut discomfort.

Had the viruses in the bacteria been killed by killing the bacteria with an effective antibiotic, Robin Williams and many others would still be alive — like Barry Marshall. Instead, many researchers are still stuck with the irrelevant theories touted by neo-Darwinists.

See also: Combating evolution: Battlefield medicine vs politicized science (12/4/16)

1) He died from constraint-breaking mutations because his physician’s did not know how to link the National Microbiome Initiative to the Precision Medicine Initiative by what is known to all serious scientists about RNA-mediated biophysically constrained viral latency.

2) Anything more I could say has been said in the context of Nobel Prize-winning works from 1936 to this year’s award to Ohsumi. It is not possible to break it down into language that a layperson will understand, unless the layperson understands why Ohsumi won the award, which was based on all works that have every linked energy-dependent changes in angstroms to ecosystems via autophagy. And yet, Ohsumi has not linked virus-driven energy theft to Lewy Body Disease and all other pathology.

See also: Autophagy: from pre-mRNAs to microRNAs, enhancers, QTLs et al. (1/4/17)

My family members and friends of Robin Williams might be appalled to learn that death from Parkinson’s and death from Lewy Body Disease both include instances of suicide that is caused by untreated virus-driven energy theft. The virus-driven energy theft also is the cause of all pathology in species from archaea to humans. It is manifested as energy-dependent changes in alternative splicings of otherwise identical genes.

The prevention of unnecessary suffering and death could be as simple as restoring the balance of amino acids and sugar to prevent all pathology via RNA-mediated cell type differentiation.

Every aspect of preventative medicine links the National Microbiome Initiative to the Precision Medicine Initiative via energy-dependent changes. The changes link angstroms to ecosystems in all living genera. When do you think you will be told that the obvious link from the changes to healthy longevity is the pheromone-controlled biophysically constrained chemistry of RNA-mediated protein folding. I hope you learn that fact before you die from virus-driven energy theft.

Heading into Today’s March, Here’s When to Doubt a Scientific “Consensus

…the “power of the paradigm” often blinds scientists to alternatives to their view. Question the paradigm, and some respond with anger.

But here’s a checklist to decide when you can, even should, doubt a scientific “consensus,” whatever the subject. One of these signs may be enough to give pause. If they start to pile up, then it’s wise to be leery.

(1) When different claims get bundled together

(2) When ad hominem attacks against dissenters predominate

(3) When scientists are pressured to toe the party line

(4) When publishing and peer review in the discipline is cliquish

(5) When dissenters are excluded from the peer-reviewed journals not because of weak evidence or bad arguments but to marginalize them.

(6) When the actual peer-reviewed literature is misrepresented

(7) When consensus is declared before it even exists

(8) When the subject matter seems, by its nature, to resist consensus

(9) When “scientists say” or “science says” is a common locution

(10) When it is being used to justify dramatic political or economic policies

(11) When the “consensus” is maintained by an army of water-carrying journalists who defend it with partisan zeal, and seem intent on helping certain scientists with their messaging rather than reporting on the field as fairly as possible

(12) When we keep being told that there’s a scientific consensus

Is there any consensus for comparison to one that most people believe in about the fact that they must eat or they will starve to death?

See for comparison: Could genetics influence what we like to eat?

…little is known about how natural variation in these genes could affect eating behaviors in healthy people. Gene variation is a result of subtle DNA differences among individuals that make each person unique.

What is Life? (reprint edition)

“How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?” — (Roger Penrose 8 August 1991)

See also:  Anesthesia points to deeper level ‘quantum channels’ as origins of consciousness

OR theory is not theory. They linked the anti-entropic virucidal quantised energy of sunlight from ecological variation to ecological adaptation in all living genera via nutrient energy-dependent viral latency as Penrose did in his forward to the reprint of “What is Life?”  Theorists who typically do not understand any aspect of biophysically constrained RNA-mediated protein folding chemistry may continue to tout their pseudoscientific nonsense about mutations and evolution, but all serious scientists know that energy-dependent codon optimality is the key to human consciousness. For example, they know that people who do not eat lose consciousness and die.

Scientist Confirms the Quantum Soul

Scientific Seeker Stuart Kauffman on Free Will, God, ESP and Other Mysteries

He proposed that our scientific understanding of reality is radically incomplete, and that some sort of anti-entropy, order-generating force remains to be discovered.

Quantum Souls

The Quantum Souls blog explores how the sun’s anti-entropic virucidal energy is linked to quantum biology, consciousness and in the soul of humans and animals. Contrary to evolutionary theorists, we are not mutants who evolved after energy emerged from nothing.

Alternative splicing of pre-mRNA

The essence of precision medicine

…Trump’s labeling of the media as the enemy of the state was unfortunate and dangerous.

It was an accurate label that has been supported by Bill Gates and the Allen Institute in the context of the forthcoming viral apocalypse.
See for comparison this enemy of the state-issued media representation:
 

“We are all proud of professor Filipp’s accomplishments,” Vice Chancellor for Research Samuel Traina said. “He exemplifies the attributes of a great UC professor.”

 This biased representation was framed in the context of: The histone demethylase KDM3A regulates the transcriptional program of the androgen receptor in prostate cancer cells

Filipp misrepresented everything known to serious scientists about energy-dependent RNA-mediated cell type differentiation and supercoiled DNA when he made this claim:
 
 

The Precision Medicine Initiative and National Microbiome Initiative link food energy to biophysically constrained RNA-mediated protein folding chemistry and viral latency. Virus-driven energy theft has been linked to all pathology in all living genera via the molecular mechanisms of chromosomal inheritance.

Evidence of chromosomal inheritance led to the 1933 Nobel Prize in Physiology or Medicine, which was awarded to Thomas Hunt Morgan.

The essence of precision medicine involves an understanding of how atomic energy-dependent RNA-mediated fixation of amino acid substitutions differentiates all cell types in all individuals of all living genera in the context of the physiology of reproduction, which has been linked to chromosomal inheritance by all serious scientists since Schrodinger (1944) in What is Life?.
 
For example, Horton et al (2014) put the facts about chromosomal inheritance into the context of epigenetic effects of food and pheromones on estrogen receptors and biodiversity of behavior in a single species.
 
 

…our results illustrate a detailed chain of events linking a chromosomal rearrangement to changes in overt social behavior.

Filipp and others like him probably do not want the details of chromosomal rearrangements to be linked from energy-dependent changes in estrogen receptor polymorphism to virus-driven energy theft and androgen receptor polymorphism in prostate cancer. 
For an example of threat to pseudoscientists posed by facts about sex differences in androgen and/or estrogen receptor polymorphism and healthy longevity compared to virus-drive pathology, see: A third of Americans don’t believe in evolution
My comment to Phys.org:

Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.

These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.

That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.

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

There is no other model or model organism that so clearly integrates what is known to all serious scientists about energy-dependent endogenous RNA interference at a time when Church et al (2015) are waiting to cash in on this patent application. RNA-Guided Human Genome Engineering

Anyone who claims to be proud of professor Filipp’s accomplishments should be asked how he thinks the essence of precision medicine will link drug targets from each person’s unique genetic and epigenetic makeup to what others have claimed is a “billion dollar baby.”

Get Well in the RNAi Way-RNAi, A Billion Dollar Baby in Therapy

RNAi has targeted exogenous genes in models of viral infection…

See also: Obituary: Robert L. Moss

 Most recently, his efforts were directed towards establishing the role of pheromonal signals in activating GnRH neurons.

The nutrient energy-dependent pheromone-controlled activation of GnRH neurons links the androgen and/or estrogen receptor context of different tissues to healthy longevity or to virus-driven pathology in all vertebrates via substitution of achiral glycine in position 6 of the GnRH decapeptide.

Other energy-dependent RNA–mediated amino acid substitutions also link morphological and behavioral phenotypes to all biodiversity via conserved molecular mechanisms in the context of the physiology of reproduction.

See: Nothing in Biology Makes Any Sense Except in the Light of Evolution

E. Margoliash, W. M. Fitch, and others have compared the amino acid sequences in cytochrome C in different branches of the living world. Most significant similarities as well as differences have been brought to light. The cytochrome C of different orders of mammals and birds differ in 2 to 17 amino acids, classes of vertebrates in 7 to 38, and vertebrates and insects in 23 to 41; and animals differ from yeasts and molds in 56 to 72 amino acids. Fitch and Margoliash prefer to express their findings in what are called “minimal mutational distances.” It has been mentioned above that different amino acids are coded by different triplets of nucleotides in DNA of the genes; this code is now known.

Alternative splicing of pre-mRNA

Theistic evolutionists fight back and lose (2)

For a historical perspective on the amount of ignorance theistic evolutionists and atheists have repeatedly displayed as they ignored everything known about the energy-dependent RNA-mediated de novo creation of genes, see:
The heat shock response is self-regulated at both the transcriptional and posttranscriptional levels (1982)
Thirty-five years later, there is another clear indication that theorists and atheists will never consider the fact that there must be an anti-entropic virucidal source of energy.
See for example: HSP90 Shapes the Consequences of Human Genetic Variation (2017)
Reported as: Researchers uncover a role for HSP90 in gene-environment interactions in humans

…uncovered a role for HSP90 in humans, not only as a modifier of the effects of mutations, but as a mediator of the impact of the environment on the function of mutant proteins. And these effects of HSP90 can alter the course of human diseases.

Serious scientists placed the effects of HSP90 and all other heat shock proteins into the context of thermodynamic cycles of microRNA-mediated protein biosynthesis and degradation. The fine-tuned cycles link virus-driven energy theft from the degradation of messenger RNA to all pathology via degrees of increasing genomic entropy in species from bacteria to Zika-virus infected humans.
Structural diversity of supercoiled DNA

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

The metabolic processes are energy-dependent. See also: Functional Metabolic Analysis in Live Cells

The role of metabolism in cellular and physiological processes is well established, with many diseases now linked to metabolic dysfunction or reprogramming.

See also: Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity

Our work identifies a mechanism through which adhesion complexes regulate cellular behaviour and reveals their surprising association with the microprocessor.

Reported as Researchers find new code that makes reprogramming of cancer cells possible

with my comments, such as this one:

Oct 14, 2015
“By administering the affected miRNAs in cancer cells to restore their normal levels, we should be able to re-establish the brakes and restore normal cell function,” Dr. Anastasiadis says.
This suggests nutrient-dependent microRNAs can stop the progression of virus-proliferation that links viral microRNAs to cancer pathology.
The suggestion comes from experimental evidence of how biophysically constrained nutrient-dependent RNA-mediated cell type differentiation occurs in the absence of viral proliferation, which young earth creationists have linked to all pathology.
For comparison, evolutionary theorists would probably tell you that the progression of cancer is inevitable via ongoing processes that link accumulated mutations to pathology except when beneficial mutations are linked to the evolution of a new species.
But, I can’t really attest to what theorists might say, and don’t really care what they claim. They are biologically uninformed.

See also:

See for comparison: Dominant evolutionary theme emerges to better predict clinical outcomes for cancer (October 13, 2015)
The only thing that has emerged from any evolutionary theme is the failure to predict outcomes of treatments, which is due to the ignorance of theorists who refuse to consider experimental evidence of energy-dependent biophysically constrained biologically-based cause and effect.
See: Viral and cellular messenger RNA targets of viral microRNAs and Virus-mediated archaeal hecatomb in the deep seafloor

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

Theorists continue to ignore the fact that energy-dependent biophysically constrained protein-folding chemistry, which is manifested in endogenous RNA interference, is the link from sunlight to all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans.
Sunlight, for example, is the source of anti-entropic virucidal ultraviolet (UV) light that clearly links the nutrient-dependent pheromone-controlled physiology of reproduction to the weekend resurrection of the bacterial flagellum in P. fluorescens.
See also: Energy as information and constrained endogenous RNA interference (2/15/2017)

See also: A third of Americans don’t believe in evolution (January 1, 2014)
My comment:

Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.

These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.
That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.
See the claims of PZ Myers and his idiot minions for comparison: One crank dies, another rises to take his place

Amino acid modification FA_Epigenetics_Table1

Francis S. Collins refutes theistic evolution

Criticisms of the nutrient-dependent pheromone-controlled evolutionary model

Based on his writings, both published and unpublished, James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research. — Andrew Jones, BA

Editor’s note

The 2013 review article by James Vaughn Kohl published in Socioaffective Neuroscience & Psychology and criticized in the above Letter to the Editor was subjected to standard peer review and the revised version was accepted by me after it had been accepted by both reviewers.

See for comparison: The Language of God: A Scientist Presents Evidence for Belief, by Francis S. Collins. The current director of the NIH also is a co-author of Genetic regulatory signatures underlying islet gene expression and type 2 diabetes

…T2D risk alleles that overlap with RFX footprints uniformly disrupt the RFX motifs at high-information content positions. Together, these results suggest that common regulatory variations have shaped islet TF footprints and the transcriptome and that a confluent RFX regulatory grammar plays a significant role in the genetic component of T2D predisposition.

No experimental evidence of biologically-based cause and effect suggest that any common regulatory variations has ever evolved. Let me make that fact perfectly clear in the words of the co-authors:

“Individuals who are heterozygous for a frameshift mutation in RFX6 have increased 2-h glucose levels (33). Importantly, rare autosomal recessive mutations that alter DNA-contacting amino acids in the DNA binding domain of RFX6 result in Mitchell–Riley syndrome, which is characterized by neonatal diabetes (29).

The frameshift mutation and rare autosomal recessive mutations occur outside the context of energy-dependent endogenous RNA interference (RNAi). For comparison RNA-directed DNA methylation (aka endogenous RNAi) typically links DNA-contacting amino acids to healthy longevity via the transgenerational epigenetic inheritance of morphological and behavioral phentoypes in species from microbes to humans. It is difficult to describe all the links, but it is clear that RNAi links RNA-directed DNA methylation from energy-dependent changes in chirallity to base pairs, single nucleotide polymorphisms (SNPs) and autophagy via the innate immune system.
Without any mention of how virus-driven energy theft links mutations from SNPs to pathology, Francis S. Collins and his co-authors link the rare autosomal recessive mutations to altered DNA-contacting amino acids. Apparently, they do not want to mention anything about the fact that natural selection for energy-dependent codon optimality is the link from RNA-mediated protein folding chemistry to all biophysically constrained healthy longevity. Instead, they seem willing to ignore the facts about energy-dependent fixation of RNA-mediated amino acid substitutions in cell types.
Indeed, they seem to put everything known to serious scientists into the context of the theistic evolution of pathology. Serious scientists know that nutrient energy-dependent pheromone-controlled cell type differentiation is the link from atoms to ecosystems in models of ecological adaptation.
Clearly, anyone who does not want to expose the pseudoscientific nonsense touted by neo-Darwinian theorists and theistic evolutionists should not mention “amino acid” and “mutation” in the same context. Using only the definitions of both terms in the same sentence (above) alerts all serious scientists to the fact that nutrient energy-dependent amino acid substitutions are not the same as mutations, which are caused by virus-driven energy theft.
Reported as: Diabetes in your DNA? Scientists zero in on the genetic signature of risk

…for now, it’s the first demonstration that many Type 2 diabetes-linked DNA changes have to do with the same DNA-reading molecule. Called Regulatory Factor X, or RFX, it’s a master regulator for a number of genes.

The regulation of genes is energy dependent.

“RFX is probably unable to read the misspelled words, and this disruption of regulatory grammar plays a significant role in the genetic risk of Type 2 diabetes.”

The concept of “misspelled words” is appropriate for use only in the context of pseudoscientific nonsense that fails to address facts about natural selection for energy-dependent codon optimality. Codon optimality links the speed of light on contact with water to biophysically constrained RNA-medidated cell type differentiation in all living genera.

They characterized differences not just in DNA sequences, but also in the way DNA was packaged and modified by epigenetic factors, and the levels of gene expression products that indicated how often the genes had been read and transcribed.

Epigenetically-effected reading and transcription is energy dependent and biophysically constrained via the speed of light and hydrogen-atom transfer in DNA base pairs in solution such as seawater and blood. Serious scientists noticed that pattern and linked virus-driven energy theft from pathology in bacteria to archaea and from the transgenerational epigenetic inheritance of Zika-virus damaged DNA in human infants. The craniofacial morphology and brain development of infected human infants clearly links energy-dependent fixation of amino acids to the morphological and behavioral phenotypes of all living genera.
See: Nothing in Biology Makes Any Sense Except in the Light of Evolution

E. Margoliash, W. M. Fitch, and others have compared the amino acid sequences in cytochrome C in different branches of the living world. Most significant similarities as well as differences have been brought to light. The cytochrome C of different orders of mammals and birds differ in 2 to 17 amino acids, classes of vertebrates in 7 to 38, and vertebrates and insects in 23 to 41; and animals differ from yeasts and molds in 56 to 72 amino acids. Fitch and Margoliash prefer to express their findings in what are called “minimal mutational distances.” It has been mentioned above that different amino acids are coded by different triplets of nucleotides in DNA of the genes; this code is now known.

Facts about nutrient energy-dependent codon optimality also are known to be refutations of neo-Darwinian pseudoscientific nonsense because codon optimality links Darwin’s “conditions of life” to the physiology of reproduction in all living genera.
See: Codon optimality controls differential mRNA translation during amino acid starvation and Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
See for comparison: Epigenetic Editing of Ascl1 Gene in Neural Stem Cells by Optogenetics

Each DNA change might alter this binding in a different way, leading to a slightly different effect on Type 2 diabetes risk or blood sugar regulation. But the common factor for many of these changes was its effect on the area where RFX is predicted to bind, in the cells of pancreatic islets.

So, says Parker, this shows how the genome – the actual sequence of DNA—can influence the epigenome, or the factors that influence gene expression.

The sequence of DNA cannot influence the epigenome before the energy-dependent sequence has been created via natural selection for codon optimality. That is why epigenetically-effected nutrient-dependent pheromone-controlled energy-dependent changes in supercoiled DNA were linked from the weekend resurrection of the bacterial flagellum in Pseudomonas fluorescens to all biodiversity in all living genera via the conserved molecular mechanisms that link light energy-induced changes in microRNAs to all biodiversity.
See also: Optokinetically encoded nanoprobe-based multiplexing strategy for microRNA profiling
Programmable artificial phototactic microswimmer

For active drug delivery, the nanomotor should be able to orient towards specific chemical signals, such as those demonstrated in chemotaxis21–25 and pH taxis26.

See also: pH-Taxis of Biohybrid Microsystems

…assuming that it is possible to tune the preferred pH of bioactuators by genetic engineering, these biohybrid microsystems could potentially be applied to sense the pH gradient induced by cancerous cells in stagnant fluids inside human body and realize targeted drug delivery.

If naturally occurring chemotaxis could not readily be linked from pH-taxis and phototaxis to natural selection for codon optimaility and supercoiled DNA, light energy as information could not be linked to communication between the microscopic and the macroscopic world.
Light Could Propel Nanorobots on a “Fantastic Voyage” Through the Human Body

“Light is a more effective option to communicate between the microscopic world and the macroscopic world,” said Tang.

The fact that the energy-dependent virucidal effects of sunlight have been linked to the weekend resurrection of the bacterial flagellum in an organism that fluoresces on exposure to UV light was placed into the context of claims about two amino acid substitutions that were reported as if they were mutations.
Summary: Francis S. Collins, current NIH director, is a theistic evolutionist. He should not use his position to tout the pseudoscientific nonsense of evolution. He is supposed to link experimental evidence of biologically-based facts to healthy longevity or to pathology.
See also: United states health care reform: Progress to date and next steps

All of the individuals who assisted with the preparation of the manuscript are employed by the Executive Office of the President.

Former President Barrack Obama should not have used his position or his employees to mislead the voters in the United States of America. He correctly stated that “…partisanship and special interest opposition remain…,” which ensured that “…experience with the Affordable Care Act…” would demonstrate “…that positive change is achievable on some of the nation’s most complex challenges.” That claim was placed into the context of misrepresentations made by ~50% of people who are biologically uninformed theorists and/or those who are atheists. Clearly there is overlap among those groups of people. Hopefully, others will see why. They’ve been taught to believe in theistic evolution or nothing.
Experimental evidence of biologically-based cause and effect refutes theistic evolution by linking virus-driven energy theft to all pathology in all living genera. In the context of  Genetic regulatory signatures underlying islet gene expression and type 2 diabetes, Francis S. Collins revealed either his ignorance or his treachery.
The article links the nutrient energy-dependent pheromone-controlled physiology of reproduction to the weekend resurrection of the bacterial flagellum in P. fluorescens via RNA synthesis, not mutations.
Virus-driven energy theft influences energy-dependent RNA-mediated gene expression, and the energy theft is clearly linked to mutations. See for example: DEPENDENCE OF RNA SYNTHESIS IN ISOLATED THYMUS NUCLEI ON GLYCOLYSIS, OXIDATIVE CARBOHYDRATE CATABOLISM AND A TYPE OF “OXIDATIVE PHOSPHORYLATION”

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

See also: microRNA “Regulatory Factor X” 
 

terrarium-eco-system

George Church refutes theistic evolution (3)

Fifty years of illumination about the natural levels of adaptation

… George C. Williams developed in his 1966 book Adaptation and Natural Selection the essentials of a unifying theory of adaptation that remains robust today and has inspired immense progress in understanding how natural selection works.

Light Could Propel Nanorobots on a “Fantastic Voyage” Through the Human Body

“Light is a more effective option to communicate between the microscopic world and the macroscopic world,” said Tang.

See also: George Church refutes theistic evolution and George Church refutes theistic evolution (2)
Why did so many pseudoscientists fail to link ecological variation to ecological adaptation via natural selection for energy-dependent changes in supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy? Why have they continued to tout ridiculous theories for comparison to what is being reported about adaptation by serious scientists. Almost every day there is something old reported as if it was new information to be considered before it is again ignored by theorists.
See for examples from this past week:
Optokinetically encoded nanoprobe-based multiplexing strategy for microRNA profiling
Interplay between miRNAs and Human Diseases: A Review
400 pilot whales stranded on New Zealand’s ‘whale trap’ beach

Other factors include whales’ incredibly tight social bonding, which is especially strong within groups of pilot whales.
 
Social bonding is nutrient energy-dependent and controlled by the physiology of reproduction. In species from microbes to humans, the physiology of reproduction is controlled by the metabolism of nutrients to species-specific pheromones.
 

Rather than tout theories about solar storms and geographical traps, serious scientists investigate the facts that link the sun’s anti-entropic virucidal energy to endogenous RNA interference via olfaction and the innate immune system. Serious scientists link food odors and pheromones to behavior in all living genera.

2005 Feedback loops link odor and pheromone signaling with reproduction

2015 Role of olfaction in Octopus vulgaris reproduction

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).

Ecological variation that is not manifested in ecological adaptation links virus-driven energy theft to the stranded whales. The energy theft prevents nutrient energy-dependent ecological adaptation. Unfortunately, theorists do not understand any aspect of natural selection for energy-dependent codon optimality.The prefer to use definitions and assumptions for comparison to the experimental evidence of biologically-based cause and effect that serious scientists must use in the context of their religion.

Pseudoscientists claim that atheism is not a religion. Atheism is a religion by definition.

See: atheism

  1. 1a :  a lack of belief or a strong disbelief in the existence of a god or any godsb :  a philosophical or religious position characterized by disbelief in the existence of a god or any gods

See for comparison:  How an obscure oriental cult in a corner of Roman Palestine grew to become the dominant religion of the Western world
Even historians know that the history of a religion can influence the faith of believers today. For example, atheism today arose in the context of de Vries 1902 definition of “mutation” and acceptance of assumptions that accumulated mutations could lead from natural selection to the evolution of one species from another species.

Christianity can clearly be linked from events that start from the creation of energy as information in Biblical Genesis to the weekend resurrection of the bacterial flagellum in P. fluorescens, which fluoresces with exposure to UV light.

Atheism as a religion cannot stand up to the overwhelming amount of experimental evidence that supports claims in the Old Testament, which were linked to claims in the New Testament. There is nothing that appears to link the emergence of everything from nothing or the evolution of one species from another. That fact links three more definitions to all biodiversity on Earth.

The emergence of atheism as a world religion can now be placed into the context of definitions that recently were added to the Merriam-Webster dictionary.

Phytoremediation

the treatment of pollutants or waste (as in contaminated soil or groundwater) by the use of green plants that remove, degrade, or stabilize the undesirable substances (such as toxic metals)

CRISPR

The CRISPR segment encodes, via transcription, short RNA sequences that pair with complementary sequences of viral DNA. The pairing is used to guide an enzyme to cleave the viral DNA and prevent further infection.

 Microbiome

  1. 1 :  a community of microorganisms (such as bacteria, fungi, and viruses) that inhabit a particular environment and especially the collection of microorganisms living in or on the human body <Your body is home to about 100 trillion bacteria and other microbes, collectively known as your microbiome. — Carl Zimmer> < … what’s arguably become the hottest area of medicine: microbiome research, an emerging field that’s investigating how the bacteria that live in and on our bodies affect our health. — Sunny Sea Gold>
    1. 2 :  the collective genomes of microorganisms inhabiting a particular environment and especially the human body <They form one community among the many that make up the human microbiome: the full genetic complement of bacteria and other organisms at home on your skin, gums, and teeth, in your genital tract, and especially in your gut. — Nathan Wolfe>

The definitions that were recently added to the Merriam-Webster dictionary link the energy-dependent pheromone-controlled physiology of reproduction in bacteria from the National Microbiome Initiative to the Precision Medicine Initiative via endogenous RNA interference, which prevents the virus-driven energy theft that links mutations to all pathology.

For comparison, see: How algorithms (secretly) run the world

“Algorithms are not inherently fair, because the person who builds the model defines success,” she said.
See also: Digital Star Chamber

Following the advice of Jeff Jarvis’s What Would Google Do, they are collecting data from both workers and customers, using algorithmic tools to make decisions, to sort the desirable from the disposable.

What would Jesus do about the use of algorithms to predict outcomes?

Algorithms can be made more accountable, respecting rights of fairness and dignity for which generations have fought. The challenge is not technical, but political, and the first step is law that empowers people to see and challenge what the algorithms are saying about us.

Did Jesus know the creation of energy and virus-driven energy theft are predictable links to outcomes that pseudoscientists think can be linked via algorithms? Did He ever mention the fact that pseudoscientists might be called theorists by serious scientists who have linked energy-dependent changes from angstroms to ecosystems in all living genera via what is known about the physiology of reproduction and the functional structure of supercoiled DNA.

See for example: Structural diversity of supercoiled DNA
The functional structure of supercoiled DNA links what organisms eat to endogenous RNA interference and the physiology of reproduction, which links chromosomal inheritance from chirality to autophagy and all biodiversity on Earth. That cannot be done with definitions and/or algorithms.

See also: microRNA
How will you continue to avoid discussing the energy-dependent link from nutrient-dependent changes in the microRNA/messenger RNA balance to all healthy longevity, as everything known about virus-driven energy theft continues to be linked to all pathology?

Amino acid modification FA_Epigenetics_Table1

Physicists: Desperate Acts (revisited)

Physicists: Desperate Acts
Light-induced endogenous RNA interference in bioluminescent microbes links Schrodinger’s claims in “What is LIfe?” (1944) from a light-to-chemical pathway of information exchange in all living genera via amino acid substitutions in supercoiled DNA.
All subsequent works on the evolutionary synthesis failed to link  the anti-entropic virucidal energy of sunlight to Darwin’s “conditions of life” from the claims of Schrodinger (1944) or the claims of any other serious scientist.

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.) (pp. 73 and 74)

See also: A theoretical physicist approaches the complexity — and mystery — of quantum gravity head-on

We thought that matter was continuous, and it took quite some time to realize that matter is not continuous,” he explains. “It’s atomic, it’s made by atoms and molecules, by particles. This was only understood about the beginning of the 20th century, not before that. It’s one of those ideas that is very old. It was suggested in ancient times. But it was realized recently.”

“So matter is discrete, and light is discrete, it’s made by photons. A wave of light is actually a cloud of photons. And it’s not surprising, after all, that space itself is sort of a cloud of little teeny small things.
Serious scientists used what is known about subatomic particles to show that all the assumptions of pseudoscientists have always been wrong. The pseudoscientists now must deal with serious scientists who have linked the creation of energy as information to all biodiversity and others who linked virus-driven energy theft to all pathology.
Some of the best among the serious scientists scientists who did that are young earth creationists who have always been right. They somehow knew that gravity did not create itself and most of them began to realize that hydrogen-atom transfer in DNA base pairs in solution must be linked from energy-dependent changes in chirality to autophagy.
When pseudoscientist failed to link chirality from autophagy to endogenous RNA interference and supercoiled DNA, which prevents virus-driven energy theft and genomic entropy in all organized genomes of all living genera, the serious scientists started to ridicule the theorists in parodies.
For a historical perspective on the ridicule, see Was ribosome the first self-replicator?

Two years ago, I asked Matti Pitkanen if differences between biophotons were recognized by the photons at the quantum level of their interactions. His response was a classic example of evading the question with claims that theoretical physicists tout in their pseudoscientific nonsense.

To how high level can one continue this parallelism. For instance, does it make sense to talk about dark variants of cell and cell membrane? Can one tell whether it was pro-cell or bio-molecules that emerged first? It seems that all these structures could have emerged simultaneously. What emerged was dark matter and its emergence involved the emergence of all the others. Hens and eggs emerged simultaneously.

See for comparison: “How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?” — Roger Penrose (8 August 1991)

See also: Why metabolism and what happens in bio-catalysis? Matti Pitkanen (2 February 2017)

  1. The simplest and at the same time most difficult question that innocent student can make about biology class is simple: “Why we must eat?”
  2. …the energies of the hydrogen atom depend on hbareff=n× h in as hbareffm, m=-2<0. Hydrogen atoms in dimension D have Coulomb potential behaving as 1/rD-2 from Gauss law and the Schrödinger equation predicts for D≠ 4 that the energies satisfy En∝ (heff/h)m, m=2+4/(D-4). For D=4 the formula breaks since in this case the dependence on hbar is not given by power law. m is negative only for D=3 and one has m=-2. There D=3 would be unique dimension in allowing the hydrino-like states making possible bio-catalysis and life in the proposed scenario.
  3. The condition that the dark binding energy is above the thermal energy gives a condition on the value of heff/h=n as n≤ 32. The size scale of the dark largest allowed dark atom would be about 100 nm, 10 times the thickness of the cell membrane.

Pitkanen is unable to grasp the fact that the speed of light on contact with water is the source of all binding energy, which links hydrogen-atom transfer in DNA base pairs in solution from endogenous RNA interference to healthy longevity in all living genera via chromosomal inheritance. His attempts to place dark binding energy above the anti-entropic virucidal energy of sunlight is still one of the most foolish attempts I have seen anyone make to deny that the energy in a hydrogen atom has been there from the time God created the heavens and the earth — as detailed in Biblical Genesis.
Matti Pitkänen What new physics do you want to introduce to support your claims about dark energy and dark matter for comparison to the claims of Schrodinger about the anti-entropic energy of sunlight?

I call it adelic physics or number theoretic physics.

Does everyone who knows you except Ulla Mattfolk laugh at your pseudoscientific nonsense?

Matti Pitkänen …one must assume that space-time is what topologist calle n-fold covering space. n sheets of covering effectively multiply Planck constant by n to give h_eff. The quantum of action is n-fold since there are n sheets.

I told him that all the assumptions made by others have been wrong.

Matti Pitkänen  It took more than 10 years to deduce this from adelic physics which is fusion of real physics for matter and various p-adic physics for cognition, p = prime.

Matti Pitkänen I think very few laugh to my theory now. If they do so I can safely conclude that they are idiots.

Matti Pitkänen …your understanding of physics could be better. One must distinguish between continuity at space-time level and continuity of matter.

Matti Pitkänen  The cognitive representations defined by the intersections of real and p-adic space-time surfaces as intersection of reality and imagination/cognition are discrete: points have coordinates in extension of rationals. In this sense discreteness makes sense but is has nothing to do with the quantum mechanical discretization of quantum numbers.

Matti Pitkänen …the odor of nutrients is determined by pheromones. Is this true. This would be nice since pheromones could provide information about distribution of h_eff=n*h and thus about the number theoretic evolutionary level of food or potential mating partner. Good odors would correspond to large average n. Bad odors to low value of n and low negentropy.

Matti Pitkänen  TGD predicts both dark matter and energy naturally and this explanation leads to vision about quantum biology and cognition unlike other proposals.

The pre-publication reviews of this book came from people who I think George FR Ellis and others probably believe are serious scientists. I do not believe those people are anything more than theorists. When they include claims about viruses, serious scientists may discuss the reality of pattern recognition with them. But not until then. Energy vs virus-driven energy theft must be considered in the context of adaptive changes in the brain, June 12, 2016

See for comparison: Thomas Hunt Morgan

Morgan contributed to the neo-Darwinian synthesis, despite his criticism of Darwin at the beginning of his career. Much work on the Evolutionary Synthesis remained to be done.

See also: Gamma oscillations organize top-down signalling to hypothalamus and enable food seeking
Reported as: Gamma oscillations coordinate food seeking

 “Preferential and selective control of feeding-related cells by rhythmic inputs to hypothalamus demonstrates a beautiful interaction of structure and function in the brain” says Alexey Ponomarenko. “Here we see how fast synchronization, combined with a precise information transfer between brain regions and cells types, drives behaviors crucial for survival.”

Coevolutionary dynamics of phenotypic diversity and contingent cooperation
Reported as: Study finds mutual reinforcement of phenotypic diversity and cooperation

A new model exploring how evolutionary dynamics work in natural selection has found that phenotypic diversity, or an organism’s observable traits, co-evolves with contingent cooperation when organisms with like traits work together to protect themselves from outsiders, according to a Dartmouth-led study published in PLOS Computational Biology. The study also finds that diversity helps prevent the collapse of cooperation.

Achieving Reversible H2/H+ Interconversion at Room Temperature with Enzyme-Inspired Molecular Complexes: A Mechanistic Study
Reported as: Catalyst mediates energy-efficient proton transport for reversibility

Scientists at Pacific Northwest National Laboratory built a catalyst that mimics nature’s hydrogen-splitting enzymes—working reversibly at room temperature and pressure without added energy. This was achieved by stabilizing the catalyst’s structure by attaching an amino acid…

Increasing Type 1 Poliovirus Capsid Stability by Thermal Selection

Our data show that some capsid mutations stabilize the ECs and could be applied as candidates to synthesize stable VLPs as future genome-free poliovirus vaccines.

‘Virus-Like Particle’ Method to Make new Polio Vaccines Proven Effective

The investigators have demonstrated that stabilized VLPs can be utilized effectively under controlled conditions. Additional research with model organisms like mice and rats will be necessary and is planned as an important part of crucial procedure of ensuring the safety and efficacy of these new VLPs for use in people.

All experimental evidence of biologically-based cause and effect has shown that controlled conditions are not exemplified in the context of how ecological variation must be linked from natural selection for energy-dependent codon optimality to the physiology of reproduction. Energy-dependent changes must be linked from chirality to autophagy by natural information processing. The control of information processing links energy-dependent endogenous RNA interference from amino acid substitutions in supercoiled DNA to all healthy longevity in all living genera. Negative supercoiling links virus-driven energy theft from mutations to all pathology.

If you would like to learn more about how virus-driven energy theft is linked to messenger RNA degradation and all pathology in species from microbes to humans, see: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
The resurrection clearly links energy-dependent RNA-mediated amino acid substitutions to the functional structure that enables the search for nutrients, which are metabolized to pheromones that control the physiology of reproduction in species from microbes to humans.