…we show that a genome-encoded transcript harboring a near-perfect and deeply conserved miRNA-binding site for miR-29 controls zebrafish and mouse behavior. This transcript originated in basal vertebrates as a long noncoding RNA (lncRNA) and evolved to the protein-coding gene NREP in mammals… Thus, we demonstrate an endogenous target-RNA-directed miRNA degradation event and its requirement for animal behavior.
Claims that microRNAs regulate animal behavior were expected. The claims about the origination of a transcript and/or evolution of a protein coding gene via an endogenous near-perfect deeply conserved miRNA-binding site has not been supported by any experimental evidence.
Similar claims about evolved differences in amino acids and proteins have not been linked to behavior. In this case, however, the claim about the evolution of a near-perfect miRNA-binding site dismisses everything known to serious scientists about the food energy-dependent pheromone-controlled physiology of reproduction that we detailed in our section on molecular epigenetics from this 1996 review: From Fertilization to Adult Sexual Behavior.
In 1996, microRNAs were called pre-mRNAs and we linked them to alternative splicings of RNA and behavior in species from microbes to humans. The cell biology game “Cytosis” linked the alternative splicings of RNA to food energy-dependent pheromone-controlled biophysically constrained viral latency in the context of the creation of enzymes, hormones, and receptors.
The link from the energy-dependent creation of microRNAs to behavior still must be placed into the context of what is known to all serious scientists. See: RNA: Structure meets function conference and 4th International Congress on Epigenetics & Chromatin, which was announced as if it was a conference on emergence and evolution.
Emergence and evolution are not discussed by serious scientists who read the extant literature such as this: Consequences of RNA oxidation on protein synthesis rate and fidelity: implications for the pathophysiology of neuropsychiatric disorders 10/15/17
…a discovery of oxidized microRNA has been recently reported. The oxidized microRNA causes misrecognizing the target mRNAs and subsequent down-regulation in the protein synthesis. It is noteworthy that oxidative modification to RNA not only interferes with the translational machinery but also with regulatory mechanisms of noncoding RNAs that contribute toward the biological complexity of the mammalian brain.
…our data demonstrate that the Comt+ transcript contains regulatory miRNA signals in its 3′-untranslated region leading to mRNA degradation; these signals, however, are absent in the shorter transcript, resulting in higher mRNA expression and activity levels.
Combination of the COMT functional haplotype model and inverted-U model may shed light on the effect of dopaminergic regulation on the trajectory of affective symptoms over the life course.
…we showed that the Val allele at Val158Met (rs4680) may be associated with the homicidal behavior of schizophrenia patients as well as that the methylation level of Val158Met (rs4680) could be affected by the variation of Val158Met (rs4680) and eventually contribute to the violent behavior of schizophrenia patients.
Synopsis: If you do not understand the experimentally established facts… use caution if you attempt to compare the President of the USA to Hitler. If you tell me I am being disrespectful or condescending, you may be more embarrassed than Nobel Laureate, Jack Szostak, and be subjected to more ridicule than Neil deGrasse Tyson, who was politely called a big ass by the research group that published Structural diversity of supercoiled DNA(2015) Federal Officials and Scientists Respond to Purported CDC Word Ban
…it seems that The Scientist has been highjacked by people that believes that science is fighting Republicans and promoting liberal ideas, right or wrong. For those that were not even born then, most of the advances in medicine and biology occurred during the war of cancer that President Richard Nixon initiated and supported. –dmarciani
Since then, the evolved use of meaningless words, such as evolved, and the use of meaningless phrases by the Center for Disease Control (CDC) has left the citizens of the United States of America (USA) comparatively unprotected from the forthcoming world-wide viral apocalypse. The last one (in 1918) killed ~50 million people. See: Bill Gates warns that a new kind of terrorism could be coming, and the ‘potential damage is very, very huge’ The biologically uninformed masses know nothing about how viruses kill, or how fast they kill. Most people know little or nothing about viruses in vaccines, which may be slow killers. That explains why, on the eve of the 100th anniversary of the year of the 1918 viral terror, the Trump administration is being criticized by non-scientists and pseudoscientists. Researchers who are biologically uniformed science idiots have helped to bankrupt the economy of the USA by submitting proposals for research that include meaningless words and phrases. The biologically uninformed masses (who are not idiots) have not learned the difference between pseudoscience and science, because they have been taught to believe in mutation-driven evolution. The difference between a scientific truth about ecological varaiation and ecological adaptation for comparison to pseudoscientific nonsense can be placed into the context of words, such as: “vulnerable,” “entitlement,” “diversity,” “transgender,” “fetus,” “evidence-based” “science-based” “fetus” and “transgender” With one exception, none of these words or phrases has anything to do with the purpose of the CDC, which is largely to protect the USA from virus-driven pathology. For comparison, the difference between food energy-dependent amino acid substitutions and mutations, which are caused by the virus-driven theft of quantized energy-as-information, clearly shows why USA Patriots for Donald Trump want to change what’s happening at the CDC. See also: Trump administration forbids CDC officials from using 7 words and phrases
The claims of Trump-haters cut to the heart of the disrespect some people show for the President of the USA — and also the disrespect they show for the serious scientists who support him. As a medical laboratory scientist, I can point out the difference that one letter in one word makes to help other USA Patriots for Donald Trump understand what is known about how to protect us all from the next viral apocaplyse.
WORD→WORE→GORE→GONE→GENE. Implicit in this analogy is the idea that epistasis constrains evolution—for example, the original parent sequence does not tolerate three of the four eventual changes, as GORD, WERD and WOND are not words.
Serious scientists know that proteins do not evolve and that viruses do not automagically mutate! Similarly, the serious scientists known that new words, such as GORD, WERD and WOND are not created outside the context of biophysically constrained viral latency. Simply put, new words are not created, and new genes are not created from changes in base pairs outside the context of biophysically constrained viral latency at the level of energy-dependent base editing of food energy-dependent ACTG-linked changes in amino acid substitutions.
Trump knows that the CDC has virtually ignored the facts about food energy-dependent amino acid substitutions via the use of these meaningless words: “vulnerable,” “entitlement,” “diversity,” “transgender,” “fetus,” “evidence-based” “science-based” “fetus” and “transgender.”
In the language of serious scientists, these words cannot be linked to what happens when the virus-driven theft of quantized energy causes a change in one base pair that leads to one amino acid substitution in a virus. Simply put, the change in the virus is linked to constraint breaking mutations. And the change in a virus causes all pathology in all cells of all hosts. Eventually, all human hosts die from the virus-driven degradation of messenger RNA.
Trump knows that. He also knows that viruses cause suicide and glioblastoma in veterans who have served overseas. (SARCASM ALERT: That does not mean he is required to tell John McCain.) But, the facts have been discussed in the context of articles published in the American Legion Magazine.
Whose going to explain how John McCain gets cured — if he is not sacrificed for the sake of the CDC?
If you are easily bored by details but want to learn about what science advisors are telling President Trump, see: Epigenetic modifications poster (Just kidding. If you are bored by the details you won’t look at the details in the poster.) Instead, you are more likely to compare the President of the United States to Hitler, when Trump knows enough about epigenetics to try and help all serious scientists to protect us from the next viral apocalypse, and to protect us from the practice of corporate medicine, which is an assault on our freedom.
Two of Eugene Daev’s subsequent works cited my award-winning publications, yet I have been unfriended on Facebook by many who will continue to not face the facts known to Trump and to all serious scientists in the world.
Humans also have various pheromone-induced physiological effects, especially those associated with reproduction [46, 47]. This suggests that the human olfactory system is still an effective pathway for influencing environmental factors on the human nervous system.
The induction of genetic instability leading to a higher genetic heterogeneity in cells of vital tissues and organs may differentially change the fitness of animals and their progeny. Such olfactory effects can affect rates of microevolutionary transformations [5]. With regard to the conservatism and the significant role of the chemical communication in a wide range of mammals, including Homo sapiens [25], we believe extremely promising the study of genetic mechanisms underlying regulation of reproduction and immunity by volatiles that work through the olfactory system.
Activists immediately accused the Administration of censorship, even hysterically comparing the Administration’s move to Orwell’s “1984” and Adolf Hitler’s efforts to control information in Nazi Germany.
Despite the CDC’s own director, Dr. Brenda Fitzgerald, insisting the ban did not extend beyond the scope of a handful of budget documents, it was immediately clear to Democrats that the Trump Administration was moving to throttle all scientific research.
Find out who might benefit from a move to throttle all scientific research. See: Alphagenomix.com and download this sample report. On page 19, the interpretation of results is placed into the context of the food energy-dependent creation of enzymes that are altered by drug therapies. The Trump administration was virtually forced to alter the funding process at CDC by the fact that Jack Szostak’s works with others led to retractions. They thought enzymes could create themselves. Two retractions in 10 years led to the embarrassment of all biologically uninformed theorists. See “Retraction watch”
A Nobel Laureate has retracted a 2016 paper in Nature Chemistry that explored the origins of life on earth, after discovering the main conclusions were not correct.
In retrospect, we were totally blinded by our belief [in our findings]…we were not as careful or rigorous as we should have been (and as Tivoli was) in interpreting these experiments.
The problem with ridiculous complacency-based beliefs has plagued serious scientists for decades. It was recently placed into the context of claims made by the former President of the USA.
Despite the democracy of the Weimar Republic, Adolph Hitler rose to power, he continued.
“Sixty million people died. … So, you’ve got to pay attention. And vote.”
While some could see the remark as a veiled jab at President Trump, Obama did not mention Trump by name during the event, according to the newspaper.
Now, the claims others are making link Obama’s claims to complaints about the fact that Trump took actions against the misinformation coming from the CDC. The complaints are predictably linked to Hitler’s censorship via: Godwin’s Law —
(or Godwin’s rule of Hitler analogies)[1][2] is an Internet adage that asserts that “As an online discussion grows longer, the probability of a comparison involving Hitler approaches 1”;[2][3] that is, if an online discussion (regardless of topic or scope) goes on long enough, sooner or later someone will compare someone or something to Adolf Hitler or his deeds.
The former President of the USA was caught in a thinly veiled attack on President Trump, and that attack was based on Obama’s ignorance — or based on his motives. What motives? Godwin’s Law existe only the context of pseudoscientific nonsense. That nonsense includes nothing known to the serious scientists who are physicists, chemists, biologists, or polymaths ( e.g., some medical laboratory scientists). See for comparison: Caught in the act: Papillomaviruses promote non-melanoma skin cancer November 30, 2017
…papillomaviruses associated with UV light promote the development of non-melanoma skin cancer. The investigators provide an explanation why the viruses can be detected in benign human cancer precursors but not in advanced carcinoma.
Everyone is infected with skin-typical (“cutaneous”) human papillomaviruses (HPV) at some point in their lives, usually in early childhood already. In healthy people, the immune system can fight off the viruses, but this often changes in older age.
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)
The fact that virucidal light links the food energy-dependent biophysically constrained pheromone-controlled physiology of reproduction to epistasis was placed into the context of this 2016 video representation: What is life when it is not protected from virus driven entropy (6:37) Published on 30 Mar 2016
Abstract:
The anti-entropic force of virucidal ultraviolet light links guanine–cytosine (G⋅C) Watson–Crick base pairing from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. For example, protection of DNA from permanent UV damage occurs in the context of photosynthesis and nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to DNA repair. In the context of thermodynamic cycles of protein biosynthesis and degradation, DNA repair enables the de novo creation of G protein coupled receptors (GPCRs). Olfactory receptor genes are GPCRs. The de novo creation of olfactory receptor genes links chemotaxis and phototaxis from foraging behavior to social behavior in species from microbes to humans. Foraging behavior links ecological variation to ecological adaptation in the context of this atoms to ecosystems model of biophysically constrained energy-dependent RNA-mediated protein folding chemistry. Protein folding chemistry links nutrient-dependent microRNAs from microRNA flanking sequences to energy transfer and cell type differentiation in the context of adhesion proteins, and supercoiled DNA that protects all organized genomes from virus-driven entropy.
If you do not understand the experimentally established facts from this presentation, please use caution if you attempt to compare the President of the USA to Hitler. If you tell me I am being disrespectful or condesending, you may be more embarrassed than Nobel Laureate, Jack Szostak, and be subjected to more ridicule than Neil deGrasse Tyson, who was politely called a big ass by the research group that published Structural diversity of supercoiled DNA. All structural diversity is energy-dependent and the pheromone-controlled physiology of reproduction links feedback loops from biophysically constrained viral latency to healthy longevity in all living genera.
See also: Workshop on Quantum Effects in Biological Systems has established itself as an outstanding stage to present the research in the intersection of physics, chemistry and biology. This field has… established excitons in biology as the “must-talk-language” when describing the quantum effects in biological light-harvesting systems. The CDC has failed to link light-harvesting in biological systems from excitons to protection of organized genomes from the virus-driven degradation of messenger RNA in species from bacteria to humans. That is why Trump is again being compared to Hitler. The biologically uninformed masses failed to perceive the CDC’s censorship. The CDC censorship of works published by serious scientists who have linked physics, chemistry and biology to healthy longevity via the anti-entropic energy-dependent creation of RNA and enzymes has nearly bankrupted the USA due to the costs of health care. Who will admit that they were fooled by the use of words? Most people think they are more intelligent than that. But most intelligent people can be fooled by pseudoscientists if the pseudoscientists claim to have reached a consensus. But, what other countries base their healthcare policies on the consensus about theories of neo-Darwinists and “Big Bang” cosmologists? What other agencies can be compared to the CDC and our NIH? See also: Science’s credibility crisis: why it will get worse before it can get better
Several other instances of bad science have gained attention in the media. The problems in “priming research”, relevant to marketing and advertising, prompted Nobel Prize winner Daniel Kahneman to issue a publicised statement of concern about the wave of failed replication.
And a study on “power poses”, which claimed that body posture influences a person’s hormones level and “feelings of power” went first viral on TED when it was published – then again when its replication failed.
We are observing two new phenomena. On the one hand doubt is shed on the quality of entire scientific fields or sub-fields. On the other this doubt is played out in the open, in the media and blogosphere.
I dedicate this effort from the blogosphere to an attempt to reduce the tensions among those who have offered their overwhelming support for the efforts of the American Legion and the American Legion Riders who ride for God and Country. See also The American Legion Magazine. The December 2017 issue contains another article about the stress-linked reactivation of viruses. This time its about the virus that causes shingles. When the issue is available online, see “Reactivation” by Beth W. Orenstein, and link biophysically constrained viral latency to healthy longevity via the food you eat and the pheromone-controlled physiology of reproduction. Ask yourself “What would President Trump do?” And remember, your donations to the American Legion don not support corporate medical practices. They are used to help those who served their country and lived to continue protecting your freedom. Remember them, and everyone who has ever died trying to protect others. –by Wade Youmans (Read 9/09/17 before the 9/11 Memorial Ride of the American Legion Riders–pictured above) Remembrance It is a moral obligation, yea indeed, a most solemn moral and spiritual duty. To remember. To remember is to hold fast to that which is truly important, that which is precious in the wisdom of the heart and mind. By remembering and reflecting, upon things, objects, individual persons, anything material and physical, Which is no more, that which is no more in the mortal sense is yet sustained and can endure. Far better to remember and reflect, even if that is painful for the heart and mind. To forget, to blissfully disregard and discard, is a disservice to that which is gone, and ’tis a disservice to one’s own heart and mind. For remembrance is a needful, essential endeavor for the vitality of the heart and mind, for the whole of the human spirit.
Black chicken wire over the bus windows. The odor, the heat, the tropical humidity.
“All the wounded are in the emergency room. They’re sending these sick guys to my unit. They were dehydrated. They were dirty. There was vomit. Wounds weren’t visible, but their suffering was acute and there wouldn’t be any Purple Hearts passed out for their near-death experience.
Nature’s magic” was placed into the context of the evolution of differences in H2. See: https://phys.org/news/2017-11-chemists-reveal-mechanism-dihydrogen-production.html
Excerpt: “This work is a critical step toward a mechanistic understanding of the nitrogenase enzyme. There is still work to be done to understand the mechanism of the other H2 evolution process that leads to N2 binding, activation, and reduction to NH3.”
Please help serious scientists stop those who are still touting the magic of evolution by learning how autophagy helps to protect all organized genomes from the virus-driven degradation of messenger RNA.
Autophagy is the link from the sun’s anti-entropic virucidal energy to the creation of enzymes and the physiology of pheromone-controlled reproduction, which has been linked to all biophysically constrained biodiversity. For example, food energy links error-free DNA repair to all healthy longevity and the virus-driven theft of quantized energy links mutations to all pathology.
Keep in mind that as a member of the American Legion Riders, I ride for God and Country, not for Nature’s magic. Also, with 40 years experience as a medical laboratory scientist, I learned enough about the potential of hydrogen (pH) to realize that the potential did not “evolve.”
See also: https://aeon.co/essays/science-and-metaphysics-must-work-together-to-answer-lifes-deepest-questions Metaphysics of metamorphosis
The swarming, ever-changing character of the living world challenges our deepest assumptions about the nature of reality
Excerpt: …‘physiologists in general never trouble themselves about such things because they suppose themselves to be above “metaphysics” when in fact they are only a very little above it – being up to the neck in it’. Those who have failed to link the metaphysics of energy to biophysically constrained viral latency, have failed to link the virus-driven theft of quantized energy to the death gene by what is known to serious scientists. For example, see: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166303/ When a member of the American Legion suffers and prematurely dies from the same virus-caused pathology that has not yet claimed the life of John McCain, ask yourself what is known about the life and death of all veterans who served overseas. Stop letting politics kill more veterans. Support the Trump administrations efforts to make America great, again. They can do it without your support, but that probably will not end well for you. This is not about Trump’s behavior or about the behavior of anyone else.
An antagonist from Canada complained about Trump’s so-called censorship of the CDC and said his “tactics” didn’t work in Canada. I claim that similar tactics are always effective. The truth hurts but it only hurts those who believed they could keep touting pseudoscientific nonsense. Not only did Canadians get rid of the “transgender” nonsense, they helped to nearly stop James Cantor from promoting pedophilia as another form of sexual orientation.
The misrepresentations of the issues are out of control.
Excerpt: GIC’s “developmental model” was backwards. It blamed symptoms like depression and anxiety on the gender non-conforming behavior itself, rather than on the stigma attached to it or the conflict of not being able to fulfill one’s gender identity. This philosophy allowed the clinic to claim it was treating these negative mental health outcomes without affirming the trans behavior.”
My comment: They never had a developmental model. At best they had a philosophy based on ridiculous theories that never included anything known to serious scientists about the biological basis of cell type differentiation. These clinicians, like most sex researchers, never learned anything about links from nutrient-dependent RNA-mediated events to behavior.
For example, RNA-directed DNA methylation and RNA-mediated amino acid substitutions link sexual orientation in yeasts to sex differences in the morphological and the behavioral phenotypes of humans via conserved molecular mechanisms. We detailed that fact in the context of our 1996 Hormones and Behavior review.
Despite the extension of our molecular epigenetics section and the model of hormone-organized and hormone-activated developmental differences across species from insects to other primates, psychologists and many psychiatrists continued to link their philosophies and theories to damaging practices.
Like the practice of medicine, outcomes are more predictable if they are based on what is known about RNA-mediated cell type differences. Fixation of nutrient-dependent RNA-mediated amino acid substitutions in some patient populations compared to others allows clinicians to predict whether a medication will do more harm than good in the context of what is known about pharmacogenomics and precision medicine. Fixation of RNA-amino acid substitutions in individuals of different species is also linked to their nutrient-dependent pheromone-controlled physiology of reproductive sexual behavior in species from microbes to man.
That fact has been known to serious scientists for several decades. It is the reason that other careers will be ruined until people like Ken Zucker accept the our model of RNA-mediated cell type differentiation instead of continuing to ignore details of the biologically-based development of personal preferences published in From Fertilization to Adult Sexual Behavior (1996).
Summary: Who lets biologically uninformed theorists make presumptions about evolution after all serious scientists have linked light-harvesting from energy-dependent changes in electrons to ecosystems in all living genera via natural selection for food energy-dependent codon optimality. Who lets them pretend not to know that the pheromone-controlled physiology of reproduction links autophagy to the transgenerational epigenetic inheritance of healthy longevity? Who is causing the unnecessary suffering and premature death of your loved ones?
Elsevier publishing supports the pseudoscientific nonsense touted by theorists by who publish articles like this: Neurotransmitter Funneling Optimizes Glutamate Receptor Kinetics (open access) Published Online: December 14, 2017 (with my emphasis)
These studies suggest that neurotransmitter binding is a directed process for which kinetics have been optimized (presumably by evolution)…
Our experiments reveal a strikingly elaborate management of ligand transport by AMPA receptors, whereby flexible positive charges ensure that glutamate binding reactions are fast. The existence of these pathways is surprising, and the fact that they alter the kinetics of receptor activity indicates that the molecular mechanisms that determine the action of neurotransmitters at receptors are more complex than previously thought. R660 is conserved between AMPA and NMDA receptors; in kainate receptors, R660 and R661 are replaced by lysine residues (Figure S8). It is possible that these helix F interactions also coordinate ligand binding in kainate and NMDA receptors. Given that electrostatic interactions are also important for coordination in other neurotransmitter binding sites (McCammon, 2009), these principles of ligand funneling may be general.
They linked the lysine residues (i.e., amino acid substitutions) from electrostatic interactions to RNA-mediated cell type differentiation in all living genera. Their studies do not link any experimental evidence from electrostatic interactions or optimized kinetics to evolution. Evolution cannot optimize any aspect of energy-dependent kinetics. Evolution cannot optimize any aspect of energy-dependent RNA-mediated cell type differentiation, which is biophysically constrained by the physiology of pheromone-controlled reproduction.
The nonsense about evolution was reported as: Scientists chart how brain signals connect to neurons (with my emphasis)
Scientists at Johns Hopkins have used supercomputers to create an atomic scale map that tracks how the signaling chemical glutamate binds to a neuron in the brain. The findings, say the scientists, shed light on the dynamic physics of the chemical’s pathway, as well as the speed of nerve cell communications.
See: Life is physics and chemistry and communication
All experimental evidence of top-down causation links quantized energy from the speed of light on contact with water to energy as information-dependent changes in electrons and all ecosystems via the physiology of pheromone-controlled reproduction, which biophysically constrains viral latency. The use of supercomputers led the researchers to report findings that eliminate everything known to serious scientists about energy-dependent RNA-mediated cell type differentiation. It is common for theorists to eliminate energy as information-dependent changes and replace facts with mathematical models.
See for comparison: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition (open access)
The bias between codons or amino acids, and mRNA expression levels has been previously recognized across species and is thought to result from selection for efficient, accurate translation, and folding of highly expressed genes (Ikemura, 1982; Akashi, 1994; Akashi & Gojobori, 2002; Drummond & Wilke, 2008; Kudla et al, 2009; Novoa & Ribas de Pouplana, 2012). The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.
This is not just an alternative perspective. It is a refutation of neo-Darwinian pseudoscientific nonsense that was reported as: Codon optimality at genome transition
Nucleotide triplets, or codons, designate specific amino acids for protein synthesis. However, that is not their only job. In yeast and bacteria, codons contribute to RNA stability, with “optimal” codons stabilizing RNAs and “suboptimal” codons destabilizing RNAs. This is possible because multiple codons can encode the same amino acid.
Nuclear RNAi, regardless of whether it is controlling splicing, transcription, or some other nuclear process, would have distinct advantages as a mechanism for evolution, because it would expand sequence-specific control of gene expression by miRNAs.
No experimental evidence of biologically-based cause and effect suggests that microRNAs evolved to control sequence-specific gene expression. The authors linked TNRC6, MED14, NAT10, and WDR5 to RNA-mediated gene activation. They inadvertently linked the energy-dependent de novo creation of microRNAs to Trinucleotide Repeat Containing (TNRC) 6A expression. See: miR-26a-5p Regulates TNRC6A Expression and Facilitates Theca Cell Proliferation in Chicken Ovarian Follicles
The anti-entropic virucidal energy of sunlight links the creation of microRNAs and multiple codons to the creation of differences and similarities in the same amino acid. That fact has been ignored.
See also: MicroRNAs recruit eIF4E2 to repress translation of target mRNAs
There is increasing evidence indicating that translation initiation is a major target of miRNA repression…
…we provide evidence indicating that TNRC6A, the core component of RISC, can directly recruit eIF4E2 to target mRNA to repress translation.
John Hopkins Kimmel Cancer Center scientists report data from a new study providing evidence that random DNA copying “mistakes” account for nearly two-thirds of the mutations that cause cancer. Their research is grounded on a novel mathematical model based on DNA sequencing and epidemiologic data from around the world.
“The whole idea of bacteria in tumors is fascinating and unexpected,” said Dr. Bert Vogelstein, a colon cancer researcher at Johns Hopkins.
See for comparison: QuEBS: Workshop on Quantum Effects in Biological Systems has established itself as an outstanding stage to present the research in the intersection of physics, chemistry and biology. This field has… established excitons in biology as the “must-talk-language” when describing the quantum effects in biological light-harvesting systems.
All serious scientists have linked the anti-entropic virucidal energy of sunlight from physics and chemistry to biophysically constrained viral latency via the de novo creation of microRNAs and the physiology of pheromone-controlled reproduction, which links autophagy to fixation of amino acid substitutions that stabilize the organized genome of all living genera in the context of autophagy.
Only biologically uniformed researchers, like Bert Vogelstein are surprised to find bacteria in tumors, because all serious scientists have link the viruses in bacteria from the degradation of messenger RNA in bacteria to the degradation of messenger RNA that causes all pathology in all living genera.
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].
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.
…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).
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.
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.
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).
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)
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.
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.
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)
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.
…Optogenetics, a technique that uses genetic modification of neurons so that their electrical activity can be controlled with light pulses – can help us to explore their specific contribution to brain function.
Optogenetics links the speed of light on contact with water to what is known about all energy-dependent cell type differentiation in all individuals of all living genera. Serious scientists, for example, have linked angstroms to ecosystems in all living genera because they know that brain function is experience-dependent and RNA-mediated.
Even in organisms that have no brain, cell type differentiation occurs in the context of biophysically constrained RNA-mediated protein folding chemistry. All chemistry is energy-dependent quantum chemistry and chemistry links quantum physics from the de novo creation of G protein-coupled receptors to the biological basis for all biodiversity on Earth.
For example, food odors link natural selection for energy-dependent codon optimality to the metabolism of food to pheromones. Biophysically constrained RNA-mediated feedback loops link the metabolism of food from the physiology of reproduction to supercoiled DNA, which protects all organized genomes from virus-driven entropy.
Simply put, quantum physics, quantum chemistry, and energy-dependent quantum biology prevent virus-driven entropy, which links everything known to serious scientists about niche construction to consciousness. The Penrose Institute was established to link that fact to human consciousness in the context of everything known about cell type differentiation to everyone since the time that Lewis Thomas began making claims olfaction and smell. A Fear of Pheromones (1971) On Smell (1980)
The act of smelling is remarkably like the act of thinking itself.
See also:
I should think we might fairly gauge the future of biological science, centuries ahead by estimating the time it will take to reach a complete comprehensive understanding of odor. It may not seem a profound enough problem to dominate all the life sciences, but it contains, piece by piece, all the mysteries. — as cited in The Scent of Eros: Mysteries of Odor in Human Sexuality
In 1991, Roger Penrose, summarized what was known about all the mysteries in his forward to the reprint of Schrodinger’s “What is Life?”
For comparison, see this comment by “Sonny” Williams to the International Society for Human Ethology’s yahoo group:
The empirical evidence is overwhelming that the brain is composed of highly specialized regions, whose neuronal members are unique in their cytoarchitecture (down to the molecular level). Moreover, empirical evidence reveals that genes have directed these neural variations during corticogenesis; that is, most specialized neurons are differentiated early during development and directed to their place in the brain by intrinsic cues, and not activity-dependent cues. This fact does not preclude later “rewiring,” or changes that are activity-dependent (plasticity), but this range of plasticity is constrained by the genetically derived regions.
Thus, the metaphor that the brain is “modular” is as accurate as any other metaphor. HOWEVER, “modular” and functionally specialized regions has always included the fact that functional outcomes require a widely distributed network of specialized regions. That is, modules do not exist in isolation, as islands of specialized function, but rather there existence as a specialized region is predicated upon their iterative communication with many other equally specialized regions.
I cannot recall any comment by Clarence “Sonny” Williams that might ever have made sense to a serious scientist. He is, in my opinion, a biologically uninformed science idiot. I once wondered who could have taught anyone to believe what biologically uninformed people believe in, or why they think what they were taught makes sense to serious scientists.
Then, I tried to discuss what I know about the energy-dependent links from angstroms to ecosystems in all living genera with the senior author of Complex Spike Patterns in Olfactory Bulb Neuronal Networks by Alister U Nicol, Anne Segonds-Pinchon, and Magnus S. Magnussen. It was also published as a book chapter in Discovering Hidden Temporal Patterns in Behavior and Interaction: T-Pattern Detection and Analysis with THEME™
Background:
T-pattern analysis is a procedure developed for detecting non-randomly recurring hierarchical and multiordinal real-time sequential patterns (T-patterns).
CONCLUSIONS:
We conclude that such sequences are an important physiological property of the neural system studied, and suggest that they may form a basis for encoding sensory information.
My summary: They link everything known to serious scientists about energy as information to non-randomly recurring patterns of biophysically constrained RNA-mediated protein folding chemistry and “…characterize these patterns in light of their putative role in processing sensory information.”
They ignore the fact that sunlight is the anti-entropic virucidal source of the energy that prevents genomic entropy via the pheromone-controlled physiology of reproduction in all living genera.
Apparently, like other biologically uninformed theorists, they did not realize what Dobzhansky (1973) did when he linked the light of evolution to all biophysically constrained biodiversity via the nutrient energy-dependent pheromone-controlled physiology of reproduction.
Dobzhansky was one of the first self-declared Creationists to level the playing field with his joke about evolution as if it occurred over billions of years.
Anyone who followed Dobzhansky’s works probably got the joke. He knew there was experimental evidence of God’s Creation. For example, he linked sensory input from what organisms eat and their physiology of reproduction to amino acid substitutions that differentiate all cell types in all living genera. He also knew that theorists had not found experimental evidence of biologically-based cause and effect that supported their claims about millions to billions of years of evolution.
All serious scientists were made aware of Dobzhansky’s rabbinical form of debate in 1964. He began by referring to theorists as bird-watchers and butterfly collectors. A rather well known form of rabbinical begins with: “Thou fool….”
Dobzhansky was far less damning when he started his address with this:
Dobzhansky probably was referring to himself in the third person when he made the claim about the unidentified Professor of Zoology. Still, to avoid ridicule by biologically uninformed theorists, he tempered the claim.
Clearly, Dobzhansky knew that his claims about amino acid substitutions would be accepted by serious scientists and rejected by pseudoscientists, who have continued to reject the claims of all serious scientists. That’s what pseudoscientists have always done. See for instance:
3/09/17 Jay Feierman: One can’t have Darwinian evolution by natural selection without either “random” mutations or directional selection. They are both necessary, proximate, contributing causes for genes and the proteins they code for changing in frequency over time in a population and by which the population becomes adaptively configured to the current environment.
3/17/17 Jay R. Feierman [NEW]: We are adaptively configured to the current environment because we are the most successful mammal on earth by any measure. There are 7 billion of us and we inhabit every continent on earth. We accomplished this by Darwinian natural selection adaptively influencing the structural design features we call genes and the proteins they make as well as the extra-genetic structural design features developed through our creativity and ingenuity where we pass the instructions on how to make them across generations by social learning. An iPhone is an example today and an obsidian arrow head was an example in the past.
My comment: After attempts to discuss energy-dependent biophysically constrained RNA-mediated cause and effect with Magnus S. Magnusson, I was not surprised to find support for some of Feierman’s claims about human adaptations in:
Indeed, adaptations occur. But, in the same article, they failed to support Feierman’s claims that the adaptations randomly occur.
Abstract excerpt:
BACKGROUND:
T-pattern analysis is a procedure developed for detecting non-randomly recurring hierarchical and multiordinal real-time sequential patterns (T-patterns).
Conclusion: We conclude that such sequences are an important physiological property of the neural system studied, and suggest that they may form a basis for encoding sensory information.
My conclusion:People like Jay R. Feierman should try to support their assertions about adaptations with experimental evidence of biologically-based cause and effect like the evidence that was cited in the article linked above.
Any claims about how a population becomes adaptively configured to the current environment are not true outside the context of what is known about energy as information and biophysically constrained RNA-mediated protein folding chemistry. If those ridiculous claims were true, the experimental evidence of top-down causation that theorists think support the claims could be used to convince serious scientists that something besides natural selection for energy-dependent codon optimality and the physiology of pheromone-controlled reproduction could replace facts to support theories about mutation-driven evolution.
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 for comparison:
7/26/13 Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.
See for comparison:
Resurrected proteins reveal that ancestral uricases have steadily decreased in activity since the last common ancestor of mammals gave rise to descendent primate lineages. We were also able to determine the 3D distribution of amino acid replacements as they accumulated during evolutionary history…
The amino acid substitutions are not accumulated during evolutionary history. The substitutions link nutrient energy-dependent RNA-mediated top down causationk from ecological variation to ecological adaptation via the creation of heat shock proteins. The heat shock proteins “buffer” organized genomes to protect them from virus-driven energy theft and genomic entropy via the physiology of reproduction, which is controlled by pheromones in species from microbes to humans.
See also this discussion attempt: An epigenetics gold rush: new controls for gene expression Sonny:
The other day, I read a new paper from a sociologist who wrote that epigenetics reveals that the environment is “more important than genes” in constructing the phenotype. That is an egregiously misleading statement.
m6A is the link from energy-dependent changes in angstroms to ecosystems via learning and memory, which links ecological variation to ecological adaptation in the context of the physiology of pheromone-controlled reproduction.
Excerpt: “The differential effects of m6A may depend on distinct cis-acting elements that are present on the RNA molecule which may interact with m6A, including micro-RNAs (Alarcón et al., 2015; Chen et al., 2015).” p. 6776
James Kohl: Ultimately, the biggest embarrassment to scientists who have linked energy-dependent changes from angstroms to ecosystems via chirality, autophagy, and supercoiled DNA is that other scientists start with the de novo creation of copy variants.
They conclude that no discussion of nutrient energy-dependent species-specific pheromone-controlled viral latency should allow others to challenge their claims about the energy-dependent RNA-mediated signals that link virus-driven energy theft to dysfunctional relationships among structure, amino acid sequence, and coding sequences.
They prefer that others, like Masatoshi Nei in “Mutation-driven evolution” (2013) place their claims into the context of how discussions about signaling between viruses and the supercoiled DNA of all organized genomes can be placed into the context of possible evolutionary relationships.
The evolutionary relationships do not link energy-dependent changes in chirality from autophagy via the innate immune system to endogenous RNA interference and all biodiversity on Earth.
Without the energy-dependent changes, the virucidal effects of femtosecond blasts of UV light on energy-dependent codon optimality and DNA repair cannot link the de novo creation of the energy in hydrogen atoms to the biophysically constrained coding sequence in all living genera via the physiology of reproduction.
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The “Nature Publications Group” banned me from commenting on their publications several months ago.
Comments on this news are disabled for everyone, which means the Nature Publications Group knows how to hide from any accountability for the lies they have told in the context of gene-centric theories.
See: The RNA code comes into focus Published online
See also:
The presence of an N1 methyl group on adenine bases in DNA and RNA was thought to be a form of damage. Results now show that it also occurs at specific sites in messenger RNAs, where it affects protein expression.
This nutrient energy-dependent methyl mark link RNA methylation from learning and memory to biophysically constrained RNA-directed DNA methylation, which is now represented in the context of endogenous RNA interference (RNAi). The link from the epigenetic landscape to RNAi and to the physical landscape of supercoiled DNA has repeatedly been placed into the context of via RNA-mediated protein folding chemistry and amino acid substitutions that differentiate all cell types in all living genera via the physiology of reproduction.
Typically, the physiology of reproduction prevents the transgenerational epigenetic inheritance of virus-driven pathology in all living genera — until the landscape changes to one in which energy-dependent RNA-mediated DNA repair can no longer keep up with the virus-driven energy theft.
Peter Berean‘s attack on my model of energy as information led him to invent or re-introduce the term “Bio-Functional Information.” The comment from Greg Thurston (below) can be placed into the context of Schrodinger’s claims from “What is Life?”
For instance, Schrodinger challenged de Vries definition of the term mutation with this entry:
“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)”
Watch as Greg launches another personal attack against me because I refuse to allow Peter Berean‘s comments on my representations of energy as information to go unchallenged. In my model, for comparison, the anti-entropic energy of sunlight is linked to all biodiversity,
See:What is life when it is not protected from virus driven entropy?
Greg makes it appear that I am the only person who knows Peter Berean is trying to introduce a term that must be defined before others realize it is synonymous with de Vries 1902 definition of mutation. Peter Berean’s treachery could conceivably delay scientific progress for at least one more generation if students are taught that “Bio-Functional Information” is different that energy as information.
The success of all threats to scientific progress depends on the misrepresentations of theorists, and definitions are one way to eliminate energy as information from biologically-based cause and effect. De Vries definition of mutation did that and his definition has served biologically uninformed theorists very well during the past 114 years.
Sudden energy jumps were used to link the assumptions of theorists to claims about mutation-driven evolution, which supposedly occurred via natural selection. All serious scientists have since realized that natural selection for energy as information must be linked from codon usage to energy-dependent changes, which link the physiology of reproduction to supercoiled DNA in all living genera.
Theorists are not likely to ever accept that fact. The levels of complexity are too difficult for pseudoscientists to integrate, which helps to explain why many of them are also atheists or agnostics. When creationists tout the same pseudoscientific nonsense, it shows why we have come so close to the virus-driven apocalypse.
———————————–
Greg Thurston wrote:
December 17 at 10:59am
James Kohl – it was nice to see your name in the comments on this thread when it first appeared. Then it was quite a surprise to see the nature of your comments. It’s been a while since we connected. I believe you are onto something, but somehow you are unable to convey it in a way that anyone (or at least most) can assimilate. As you may recall, I even thought for a while that I could help unpack it enough to make it clear (to me and then others), but the more I waded into it, the denser the thicket seemed to get, and I was overwhelmed. I don’t have the time. I am so disappointed to see the tone of your comment [to] Peter Berean. I thought you were above ad hominem et al. I hope you can take this as not an insult, but a caution from one who would like to be considered a friend, that it seems perhaps ego has clouded your ability to be gracious and have courteous discourse with others who see things differently. It is amazing to me how much ego commandeers intellect in so many instances. It is a threat to us all, of which we must be exceedingly diligent to resist.
———————–
See also: What is Life?
“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)
I get the impression that Greg Thurston might think Roger Penrose is an ego-maniacal threat to Peter Berean‘s intellect.
Perhaps, someone like Greg Thurston will first ask Peter Berean to tell others the difference between a “mutation” and “bio-functional information.” For contrast, in the context of my model, the fixation of energy-dependent RNA-mediated amino acid substitutions links biophysically constrained cell type differentiation to the physiology of reproduction in all living genera.
Theorists do not have a model for how that occurs in the context of biophysical constraints. They have theories, which helps to explain why Peter Berean is tweaking the theories via his usage of words. He knows nothing about natural selection for energy-dependent codon optimality. That requires the invention and/or reuse of the term “bio-functional information.” It is a great way for pseudoscientists to dismiss everything known to serious scientists via a vague term.
This is a multi-part series. See also: Energy-dependent purifying selection / autophagy (2-6) Pain from Cells that Are Not Neurons Introduction: Recent research on pain shows a very surprising result. A new type of neuroplasticity has been discovered… My comment: It’s discovery does not make it a new type of neuroplasticity. Discoveries like this attest only to the ignorance of theorists who have never considered the role that virus-driven energy theft plays in all pathology.
Excerpt 1)
Injuries produce ATP energy molecules which stimulate astrocytes and microglia to send signals that travel widely—spreading the pain information.
Excerpt 2)
Virus infections cause pain such as sore throat and shingles.
Jon Lieff once again attests to the overwhelming ignorance expressed by theorists. They know nothing about biophysically constrained energy-dependent RNA-mediated protein folding chemistry and cell type differentiation in the context of the physiology of reproduction or pain as a signal of virus-caused cell type distress. They fail to link link ATP-dependent / energy-dependent changes from angstroms to ecosystems in all living genera.
If ATP-dependent / energy-dependent viral latency had not already been achieved in the context of ecological adaptations, we would not see these reports from last week. All of them attest to the fact that nutrient energy-dependent viral latency has been achieved. All of them attest to the fact the viral latency must be maintained across the life-span of all individuals to protect them from all pathology
Ultimately, 3′ UTR-directed translational fine-tuning differentially modulates MECP2 protein in the two cell types to levels appropriate for normal neurodevelopment.
My comment: Once again we see that the fine tuning of cell type differentiation is transgenerationally epigenetically inherited via energy-dependent control of virus-driven energy theft (i.e., autophagy) during every aspect of normal neurodevelopment. That fact links the physiology of energy-dependent reproduction in marine microbes and soil bacteria from the bull sperm microRNAome to brain development in human infants, which is altered by virus-driven energy theft.
…mutation is crucial in speciation because reproductive barriers cannot be generated without mutations.
My comment: Chromosomal rearrangements link autophagy from energy-dependent changes in RNA-mediated amino acid substitutions and supercoiled DNA to all biodiversity via speciation.
…high frequency radiation and particles of high velocity are very important components of the environment, causing heritable changes by a process called mutation. Even if we could conduct our experiments behind 30 metres of lead the fact that mutation has a temperature coefficient is enough to show that it depends in part on energy fluctuations which are uncontrollable.
My comment: In 1902, De Vries defined the uncontrollable energy fluctuations in the context of his definition of “mutation.” Others have since linked Darwin’s “conditions of life” from energy fluctuations to natural selection for energy-dependent codon optimality and healthy longevity via biophysically constrained polycombic ecological adaptation. See for example:miR-125a-5p regulates differential activation of macrophages and inflammation
My comment: Nutrient energy-dependent changes in the microRNA/messenger RNA balance link autophagy to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.
…the same five amino acid sequence that binds cGAS also binds cellular proteins (such as Rb), disrupting their function and leading to uncontrolled cell growth!
Re: Could both functions have been simultaneously selected for? My comment: No. Both functions could not have been simultaneously selected for!
Nothing known to serious scientists about top-down causation suggests that the RNA-mediated amino acid sequences in proteins can be simultaneously selected to link natural selection for energy-dependent codon optimality to healthy longevity and to simultaneously link virus-driven energy theft to all pathology. In the context of everything known to serious scientists about all living genera, cell type differentiation is energy-dependent and it must be biophysically constrained. For a review of the biophysical constraints that link all invertebrates to all vertebrates, see:From Fertilization to Adult Sexual Behavior
Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.
My comment: In 1996, we reviewed the established facts about energy-dependent biophysically constrained polycombic ecological adaptation based on what was known about the small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. The facts about energy-dependent polycombic ecological adaptation have not changed. Only the pseudoscientific nonsense of neo-Darwinian theories has been forced to include the changes portrayed in the context of virus-driven hecatombic evolution. See for comparison: Virus-mediated archaeal hecatomb in the deep seafloor
We estimated that viral infections were responsible for the abatement of 1.0 to 2.2% day−1 (on average 1.6% day−1) of the bacterial abundance and 2.3 to 4.3% day−1 (on average 3.2% day−1) of the archaeal abundance in deep-sea sediments (Fig. 6).
My comment: The claim that viruses kill ~1.6% of bacteria each day and ~3.2 % of archaea in deep-sea sediments is buried in technical jargon. It was previously resurrected in the report of the weekend resurrection of the bacterial flagellum. See:Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
The nutrient energy-dependent pheromone-controlled weekend resurrection of the bacterial flagellum eliminates the confusing rhetoric that theorists use to explain how differences in cell death from archaea to bacteria might be attributed to evolution. The differences are obviously linked from ecological variation to nutrient-dependent pheromone-controlled ecological adaptation in all living genera. For comparison to hecatombic evolution, healthy longevity exemplifies polycombic ecological adaptation.
The cause of death in all cell types is linked to virus-driven energy theft and nutrient energy-dependent healthy longevity is linked from cell type differentiation to all biodiversity. Simply put, virus-driven energy theft is linked from hecatombic evolution to all pathology.
The claim that mutation-driven hecatombic pathology and polycombic ecological adaptation could be simultaneously selected is a claim that only a biologically uninformed theorist would make, or accept. See for comparison: Neurons adjust their proteins during homeostatic scaling Excerpt:
Changes in the synthesis of cellular proteins lie at the heart of all adaptations that cells undergo.
In addition, although it has not been explicitly addressed here, it is obvious that the regulated degradation of proteins must also play a role in sculpting the proteome during homeostatic scaling. Indeed, we observed many proteins in the ubiquitin proteasome pathway that were regulated by scaling (Figure 3C; Table S3).
My comment: Nascent proteome remodeling links nutrient energy-dependent autophagy from natural selection for codon optimality to changes in protein biosynthesis and degradation. The changers link RNA-mediated amino acid substitutions to the differentiation of all cell types in all living genera in the context of the physiology of reproduction. Pseudoscientists, atheists, and most science journalists do not seem to understand that fact.
For comparison, serious scientists do not need more proof that autophagy did not simply emerge to link energy as information to all biodiversity via the conserved molecular mechanisms of cell type differentiation that link angstroms to ecosystems in species from microbes to humans. Serious scientists do not need more proof that all neo-Darwinian pseudoscientific nonsense is nothing more than one theory added to another after de Vries defined “mutation” in 1902.
Do you know any serious scientists who has used any definition in the context of reporting their results of testing in the medical laboratory? For example, have you ever used a definition to link the results of a blood gas analysis from hydrogen-atom transfer in DNA base pairs in solution to the patient’s outcome?
See also (video): Feynman explains the difference between science and the pseudoscientific nonsense of neo-Darwinian theory with added feedback on the claims of expert theoretical physicists who have failed to link energy-dependent changes from angstroms to ecosystems in all living genera. http://dai.ly/x24hxji My comment: Experimental evidence of biologically based cause and effect links physics and chemistry to the conserved molecular mechanisms of cell type differentiation that we detailed in our 1996 Hormones and Behavior review. See for comparison: Different rates of mRNA degradation can be explained by the existence of different regulatory mechanisms.
My comment: Researchers like him should stop ignoring the facts. Energy-dependent autophagy mediates the mRNA turnover rate and links nutrient energy-dependent RNA-mediated amino acid substitutions to healthy longevity via the physiology of reproduction and transgenerational epigenetic inheritance of morphological and behavioral phenotypes. Virus-driven energy theft links mRNA degradation to all pathology. See also: This virus may have stolen deadly DNA from black widow spiders (10/12, Feltman) reports researchers have discovered that the WO virus, which infects bacteria, contains “snippets” of DNA from several animals including black widow spiders, according to a study published in Nature Communications. The virus infects the Wolbachia bacteria, which primarily affects arthropods including insects and spiders. Researchers found that the WO virus “contains part of the gene for latrotoxin, the chemical that gives the black widow spider venom its punch.”
The Virus With Spider DNA (10/12, Yong) reports the researchers suspect that the virus obtained the genetic material directly from the spiders infected by Wolbachia, or the bacteria may have obtained it from the spiders before passing it on to the virus.
Additional coverage is provided by: How the Heck Did Black Widow Spider DNA Get Inside a Virus? (10/11, Choi) and Virus stole poison genes from black widow spider (10/12, Rincon). My comment: Virus-driven energy theft occurs in only one direction. It links cell type death from archaea to Zika virus damage in human infants via transgenerational epigenetic inheritance of pathology. The idea that a virus that infects bacteria could have come from the DNA of animals is one that misrepresents everything currently known to serious scientists about autophagy.
Ideas like that are the source of pathology that alters the behavior of family members who believe that any idea is as good as a model of biologically-based cause and effect.
Biologically uniformed family members have unfriended me on Facebook because they do not want anyone to become informed.
Jeanette C SeemanWow, I’m sorry to hear that. The subject seems complex and a little grace could go a long way. They could have unfollowed you instead of unfriending you. Hope they will see you in person. Wishing you the best.
James Kohl Thanks for putting their actions into perspective, Jeanette C Seeman.
I’ve learned that expertise on any given topic may cause embarrassment in non-experts who think experts are insulting their intelligence or criticizing their beliefs. This is true at all levels. 2004 Templeton Prize winner, George FR Ellis, who is or was an active Quaker, unfriended me when I commented on the book he published in June. He left out the information on my model, even after he claimed I was correct.
He has had an ongoing disagreement with Roger Penrose about the fact that the source of all information links the creation of the sun to energy-dependent healthy longevity. Ellis and Penrose have co-authored with Stephen Hawking. I linked energy as information to the Resurrection of Christ via everything currently known to all serious scientists about biologically-based cause and effect. George FR Ellis refuses to address that fact in any context.
This is what he is avoiding. In 1991, Roger Penrose wrote: “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?”
Last month, this assault on the beliefs of all who tout nonsense about the emergence of everything from nothing and neo-Darwinian theories about millions of years of evolution should have cinched the election of Donald Trump for President. http://dx.doi.org/10.1038/nnano.2016.164
Trump, for example, is supported by young earth creationists such as Mike Pence and Dr. Ben Carson. Now, we have examples of ignorance from a well-respected cosmologist/astrophysicist (Ellis), for comparison to a mathematical physicist, mathematician and philosopher of science (Penrose), and Mike Pence and Dr. Ben Carson.
If Hillary wins, we will have another example of what the term “reprobate mind” actually means. It means people would rather believe anything they are told as long as it cannot be placed into the context of physics, chemistry, biology and Biblical Genesis via what is known about molecular epigenetics, which is that “…we eat food in order to gain energy?” The energy biophysically constrains the viral apocalypse that the liberals predictably will cause.
This is science, not religion: https://www.ncbi.nlm.nih.gov/pubmed/24693353 Why do you think it was published in Socioaffective Neuroscience & Psychology? What has any pseudoscientist/atheist written for comparison?
I simply do not see the evidence for the claim that Viruses cause ALL pathology.
– Bacteria can cause pathology.
– Toxins can cause pathology.
– Heavy metals can cause pathology.
– Fungi can cause pathology.
– Parasites can cause pathology.
I do not see the warrant to state that NONE of the above can cause pathology and so ONLY viruses can cause pathology.
What is known about energy-dependent autophagy is the evidence for the claim that viruses cause all pathology. The 2016 Nobel Laureate in Physiology or Medicine won the prize for experimental evidence that autophagy was the link to chromosomal rearrangements and all biodiversity, which was addressed by the 1933 Prize winner, and 2004 Prize Winners. You are claiming to not see the evidence that I put into this context:
“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.”
Read more at: http://phys.org/news/2014-01-americans-dont-evolution.html#jCp
See also:
Conclusion: Everything known to serious scientists about physics, chemistry, molecular epigenetics, chemical ecology, and adaptation is included in Biblical Genesis. Only biologically uninformed atheists and Demoncrats continue to challenge the only accurate representation of biologically-based cause and effect that starts with ‘you are what you eat’ and claims that ‘if you eat this you will surely die.’
Epigenetic mechanisms, particularly DNA methylation and miRNA expression, attract increasing attention as potential links between the genetic and environmental determinants of health and disease. Unlike genetics, epigenetic mechanisms could be reversible and an understanding of their role may lead to better protection of susceptible populations and improved public health.
I have asked that you offer experimental evidence of biologically-based cause and effect. You provide nothing but rhetoric and fail to address any of the evidence I have provided. I have asked you which part of the Holy Bible you believe in, and your only answer seems to be that you are a Christian.
Peter BereanJames Kohl,
You asked be for scientific evidence for OEC (a old universe and/or an old-earth) and so I did so (see my comments above).
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In Addition:
1) I subscribe to the view that Some Pathology can be caused by Bacteria. You do not appear to subscribe to that view?
2) I subscribe to the view that Some Pathology can be caused by some Biological Toxins that are Not Viruses. You do not appear to subscribe to that view?
3) I subscribe to the view that Some Pathology can be caused by some Inorganic Toxins such as some heavy metals. You do not appear to subscribe to that view?
4) I subscribe to the view that SOME Pathology can be caused by Viruses. You do not appear to subscribe to that view because of the word SOME?
5) All of the evidence you have provided shows that Viruses cause SOME pathology. However, NONE of the evidence you provided shows that Viruses cause ALL pathology.
6) I am arguing that the evidence is consistent with the view that there are MULTIPLE Causes for Pathology.
7) You appear to be arguing that there is ONLY ONE cause for Pathology (viruses).
Please correct me if I am wrong in understanding your positions regarding the numbered questions/points I bring up above.
Cordially.
James KohlI asked for experimental evidence of biologically-based cause and effect and you twisted that request into one for scientific evidence. You may think you are devilishly clever, but no serious scientist would agree.
I do not care what you subscribe to and will not answer any more questions about my views. They have been detailed in a series of published works during the past 20 years and no one has refuted the model we presented in the molecular epigenetics section of this review. From Fertilization to Adult Sexual Behavior
for the design and synthesis of molecular machines
Excerpt:
They have developed molecules with controllable movements, which can perform a task when energy is added.
My comment:When energy is added is the key to understanding healthy longevity in the context of popular information Popular information (link opens pdf) Excerpt:
All chemical systems strive for equilibrium – a lower energy state – but this is somewhat of a stalemate. We can take life as an example. When we eat, the body’s molecules extract the energy from the food and push our molecular systems away from equilibrium, to higher energy levels. The biomolecules then use the energy to drive the chemical reactions necessary for the body to work. If the body was in chemical equilibrium, we’d be dead.
Just like the molecules of life, Sauvage’s, Stoddart’s and Feringa’s artificial molecular sytems perform a controlled task. Chemistry has thus taken the first steps into a new world.
My comment: All steps that were designed to link energy as information to the physiology of reproduction and healthy longevity existed at the dawn of creation. Chemistry finally links the differences between Old Earth Creationists (OEC) and Young Earth Creationists (YEC). The OEC appear to have assumed that the reaction times Schrodinger (1944) placed into the context of his claims in “What is Life?” occur across billions of years. Excerpt:
Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.)
In that context the emergence of energy automagically linked the “Big Bang” to theories about all reaction times. The reaction times linked what organisms eat to natural selection for mutations. Theorists may still think that de Vries 1902 definition of ‘mutation’ links their assumptions to the evolution of all biodiversity.
In 1991, Roger Penrose succinctly addressed that problem with the theorists claims in the forward to the reprint edition of “What is Life?”
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?
My comment: The answer to that question was placed into the context of “…his discoveries of mechanisms for autophagy,” when Yoshinori Ohsumi won the 2016 Nobel Prize in Physiology or Medicine.
Virus-driven energy theft is the link to all negative outcomes in the context of autophagy. The nutrient-dependent pheromone-controlled physiology of reproduction in species from microbes to mammals is the link from RNA-mediated protein folding chemistry to all biophysically constrained limits on life.
Life exemplifies natural selection for codon optimality, which links RNA-mediated amino acid substitutions to supercoiled DNA, which protects all organized genomes from virus-driven entropy. The virus-driven theft of quantised energy links changes in base pairs to amino acid substitutions in viruses that facilitate their energy dependent replication. Differences in their rate of replication can be compared to differences in rates of energy-dependent cell type differentiation and proliferation in all cell types of all individuals of all living genera.
That has already been done in the context of the Precision Medicine Initiative and National Microbiome Initiative, which link energy-dependent differences in metabolic networks to genetic networks via the pheromone-controlled physiology of reproduction in species from microbes to humans. If the fine-tuned balance of life in all its diversity is not maintained by the proper use of available energy, nutrient-stress and/or social stress link energy-dependent viral latency to all pathology.
See: Epigenetics and Genetics of Viral Latency
… viral latency is responsible for life-long pathogenesis and mortality risk…
My comment: When the 2017 Nobel Prizes in the hard sciences are again awarded to those who are Combating Evolution to Fight Disease, which is what happened in 2015, how many more times will neo-Darwinian theorists and “Big Bang” cosmologists try to dumb-down the findings on how energy as information biophysically constrains cellular differentiation and proliferation in the context of ecological variation and energy-dependent ecological adaptations?
Autophagy is the link from the sun’s anti-entropic virucidal energy to the creation of enzymes and the physiology of pheromone-controlled reproduction, which has been linked to all biophysically constrained biodiversity. For example, food energy links error-free DNA repair to all healthy longevity and the virus-driven theft of quantized energy links mutations to all pathology.
Keep in mind that as a member of the American Legion Riders, I ride for God and Country, not for Nature’s magic. Also, with 40 years experience as a medical laboratory scientist, I learned enough about the potential of hydrogen (pH) to realize that the potential did not “evolve.”
See also: https://aeon.co/essays/science-and-metaphysics-must-work-together-to-answer-lifes-deepest-questions
Metaphysics of metamorphosis
The swarming, ever-changing character of the living world challenges our deepest assumptions about the nature of reality
Excerpt: …‘physiologists in general never trouble themselves about such things because they suppose themselves to be above “metaphysics” when in fact they are only a very little above it – being up to the neck in it’.
Those who have failed to link the metaphysics of energy to biophysically constrained viral latency, have failed to link the virus-driven theft of quantized energy to the death gene by what is known to serious scientists.
For example, see: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166303/
When a member of the American Legion suffers and prematurely dies from the same virus-caused pathology that has not yet claimed the life of John McCain, ask yourself what is known about the life and death of all veterans who served overseas. Stop letting politics kill more veterans.
Support the Trump administrations efforts to make America great, again. They can do it without your support, but that probably will not end well for you. This is not about Trump’s behavior or about the behavior of anyone else.
See also: Latest on scientist who mainstreamed pedophilia
See: Infamous Reparative Therapy Clinic For Transgender Youth Set To Close
Two years ago, I wrote:
The misrepresentations of the issues are out of control.
Excerpt: GIC’s “developmental model” was backwards. It blamed symptoms like depression and anxiety on the gender non-conforming behavior itself, rather than on the stigma attached to it or the conflict of not being able to fulfill one’s gender identity. This philosophy allowed the clinic to claim it was treating these negative mental health outcomes without affirming the trans behavior.”
My comment: They never had a developmental model. At best they had a philosophy based on ridiculous theories that never included anything known to serious scientists about the biological basis of cell type differentiation. These clinicians, like most sex researchers, never learned anything about links from nutrient-dependent RNA-mediated events to behavior.
For example, RNA-directed DNA methylation and RNA-mediated amino acid substitutions link sexual orientation in yeasts to sex differences in the morphological and the behavioral phenotypes of humans via conserved molecular mechanisms. We detailed that fact in the context of our 1996 Hormones and Behavior review.
Despite the extension of our molecular epigenetics section and the model of hormone-organized and hormone-activated developmental differences across species from insects to other primates, psychologists and many psychiatrists continued to link their philosophies and theories to damaging practices.
Like the practice of medicine, outcomes are more predictable if they are based on what is known about RNA-mediated cell type differences. Fixation of nutrient-dependent RNA-mediated amino acid substitutions in some patient populations compared to others allows clinicians to predict whether a medication will do more harm than good in the context of what is known about pharmacogenomics and precision medicine. Fixation of RNA-amino acid substitutions in individuals of different species is also linked to their nutrient-dependent pheromone-controlled physiology of reproductive sexual behavior in species from microbes to man.
That fact has been known to serious scientists for several decades. It is the reason that other careers will be ruined until people like Ken Zucker accept the our model of RNA-mediated cell type differentiation instead of continuing to ignore details of the biologically-based development of personal preferences published in From Fertilization to Adult Sexual Behavior (1996).