…these data suggest that a subset of the identified novel miRNAs may contribute to the pathophysiology of numerous diseases, laying the groundwork for future studies to elucidate the functional connections of miRNAs to the numerous diseases associated with sequence variants within non-coding regions of the MHC.
Dysregulation of miRNAs is commonly observed in cancers and it largely cancer dependent.
The virus-driven theft of quantized energy as information has been linked from changes in the microRNA/messenger RNA balance to all pathology. That fact replaces the circular logic that links cancer-dependent dysregulation of miRNAs to cancer. Simply put, the proliferation of viruses cause cancer. The proliferation of viruses is energy-dependent in the context of established links from atoms to ecosystems in all living genera.
See: Subatomic: An Atom Building Board Game
A deck-building game where particle physics & chemistry collide! Use quarks to build subatomic particles & particles to build Atoms!
This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements.
…these data suggest that a subset of the identified novel miRNAs may contribute to the pathophysiology of numerous diseases, laying the groundwork for future studies to elucidate the functional connections of miRNAs to the numerous diseases associated with sequence variants within non-coding regions of the MHC.
…birds that eat at feeders are more likely to be infected with the disease, which causes red, swollen eyes and often blindness that results in death.
…lower virulence strains could be their own worst enemies, creating a population of hosts that are resistant to them but not the higher virulence strains that remain.
By removing my Disqus comments, the moderators limit discussion of the facts about virus-driven energy theft, which links mutations to all pathology. That allows the biased reporting on preprints that continue to try to support the ridiculous concept of neo-Darwinian evolution.
It also prevents the realization of goals by serious scientists who have linked the biogenic creation of uranium ores to the prevention of radiation sickness via microRNA therapy. See, for examples: miRNA-mediated therapies A miRNA-145/TGF-beta1 Negative Feedback Loop Regulates the Cancer-Associated Fibroblast Phenotype
…miR-145 is a key regulator of the CAF phenotype, acting in a negative feedback loop to dampen acquisition of myofibroblastic traits, a key feature of CAF associated with poor disease outcome.
Gene-edited induced pluripotent stem cells (iPSCs) provide relevant isogenic human disease models in patient-specific or healthy genetic backgrounds. Towards this end, gene targeting using antibiotic selection along with engineered point mutations remains a reliable method to enrich edited cells. Nevertheless, integrated selection markers obstruct scarless transgene-free gene editing. Here, we present a method for scarless selection marker excision using engineered microhomology-mediated end joining (MMEJ). By overlapping the homology arms of standard donor vectors, short tandem microhomologies are generated flanking the selection marker. Unique CRISPR-Cas9 protospacer sequences nested between the selection marker and engineered microhomologies are cleaved after gene targeting, engaging MMEJ and scarless excision. Moreover, when point mutations are positioned unilaterally within engineered microhomologies, both mutant and normal isogenic clones are derived simultaneously. The utility and fidelity of our method is demonstrated in human iPSCs by editing the X-linked HPRT1 locus and biallelic modification of the autosomal APRT locus, eliciting disease-relevant metabolic phenotypes.
To make these very precise edits, an SNP modification is first inserted alongside a fluorescent reporter gene that helps researchers to identify modified cells. The researchers engineered a duplicate DNA sequence known as a microhomology (hence the technique’s name) on each side of the fluorescent gene, targeting sites for CRISPR to go in and cut DNA. The researchers were then able to use a DNA repair system known as microhomology-mediated end joining (MMEJ) to remove the fluorescent gene. That left only the single-base edit, in the form of an SNP, behind.
See also: Inhibition of the Host Translation Shutoff Response by Herpes Simplex Virus 1 Triggers Nuclear Envelope-Derived Autophagy
Nuclear envelope-derived autophagy (NEDA) appears to be a cellular stress response, which is triggered late during HSV-1 infection. An energy-dependent single nucleotide repeat (SNR) might compensate for the viral alteration of the macroautophagic response. At this level of hydrogen-atom energy transfer in DNA base pairs in solution, the link to supercoiled DNA and viral latency becomes increasingly important.
Theorists are angry because they have been left behind. They know very little about what is important. That was expected by all serious scientists, especially those who have accumulated decades of testing experience while working in medical laboratories.
See for example: Applications of ligation-mediated PCR
Using a molecular energy source (which differs depending on the enzyme source organism), DNA ligase reforms the missing covalent bond and the strand is whole again. Two aspects of this are critical:
The nick to be repaired occurs on a single strand but in the context of a double-stranded molecule.
The bases of the nicked strand, and particularly those directly flanking the nick site, must be properly base-paired to the opposite (un-nicked) strand.
It’s not hard to imagine why this is: the base pairing is required to hold the two parts (sugar 3′ -OH and the next phosphate) in place for the ligase enzyme active site to catalyze joining them. If either one of these isn’t base-paired down and is flopping about with thermal motion, the reaction geometry doesn’t occur, and no new bond can be made.
Biologically uninformed theorists cannot even speak the same language. They do not start with a molecular energy source for base pairing and microRNA-mediated amino acid substitutions that differentiate all cell types. Instead, mutations are linked to increasing organismal complexity via the magic of evolution.
Summary: The term innate is used in psychological explanations. The so-called explanations ignore facts about the light energy-dependent activation of endogenous substrates. The anti-entropic virucidal energy of sunlight links the endogenous substrates to biophysically constrained viral latency and healthy longevity via the physiology of reproduction in all living genera.
“Proximate mechanisms” and “evolution” are terms used by biologically uninformed theorists. That fact becomes perfectly clear in the context of The conceptual critique of innateness (paywalled)
One proposal is that innateness can be defined in terms of the biological property of environmental canalization. On this view, a trait is innate to the extent that it is developmentally buffered against a range of different environments. Another proposal is that innateness serves as an explanatory primitive for cognitive science. This view holds that there exist a sharp boundary between psychological and biological explanations and that to identify a trait as innate means that it falls into the latter explanatory domain.
For comparison to the sharp boundary between psychological and biological explanations, we eliminated the concept of innateness and claims about evolution from our 1996 Hormones and Behavior review of experience-dependent epigenetically- effected RNA-mediated cell type differentiation: From Fertilization to Adult Sexual Behavior.
See how our section on molecular epigenetics was linked from effects on hormones to the affects of hormones on behavior via alternative splicings of pre-mRNAs.
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…
Also, in an award-winning 2001 review, other co-authors helped to link energy-dependent top-down causation to biophysically constrained cause and effect via the affects of hormones on behavior. Epigenetic effects on hormones and affects on behavior are studied and integrated in the context of human ethology. See: Human pheromones: integrating neuroendocrinology and ethology
If you ignore the history of all published works on energy-dependent microRNA-mediated (aka pre-mRNA-mediated) top-down causation during the past two decades, you can continue to tout “evolution” as if it had any explanatory power. But it does not have any explanatory power whatsoever in the context of human ethology.
Non-cell autonomous RNA silencing can spread from cell to cell and over long-distance in animals and plants.
That fact is commonly known among serious scientists. For comparison, pseudoscientists and other theorists also use the term “proximate mechanisms” outside the context of the links from the food energy-dependent non-cell autonomous RNA silencing and pheromone-controlled physiology of reproduction, which were obviously included in Darwin’s “conditions of life.” (Darwin’s “conditions of life” were bastardized by those who invented neo-Darwinian nonsense, and linked the nonsense to explanations of behavior in the context of human ethology.)
See for example: Jay R. Feierman is the antagonistic passive-aggressive moderator of the Human Ethology Yahoo Group.
After brief discussion of my claims in Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013), Jay R. Feierman reported this to the group:
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.
and this:
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.
ETERNAL TAPETUM1 (EAT1) is a basic-helix-loop-helix (bHLH) transcription factor indispensable for induction of programmed cell death (PCD) in postmeiotic anther tapetum, the somatic nursery for pollen production.
It links what organisms “eat” (get it?)to the physiology of pheromone-controlled reproduction in species from microbes to humans via the honeybee model organism and everything known about biophysically constrained viral latency. Theorists and other pseudoscientists, like Jay R. Feierman, must continue to live in fear that their nonsense will be exposed in the context of what might otherwise have become a culture war.
Instead, this group of Japanese researchers appears to have an unparalleled, albeit somewhat biophysically constrained, sense of humor. Sarcasm, for example, is often a humorous way to force pseudoscientists to recognize the facts they have ignored. It is somewhat the same as a rabbinical debate that starts with “You Fool!”
For example, You fool! The link from ETERNAL TAPETUM1 (EAT1) and/or what you eat to a basic biophysically constrained helix-loop-helix (bHLH) transcription factor and/or cell death can be placed into the context of how the death gene is activated by stress in all living genera.
See: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene
The reduced expression is caused by the virus-driven theft of quantized energy, which links nutrient stress and/or social stress from mutations to all pathology via the degradation of messenger RNA in species from archaea to humans. Virus-mediated archaeal hecatomb in the deep seafloor
We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.
…in the case of the primate lentiviruses, amino acid residues that are highly variable in HIV are sometimes conserved in chimpanzee SIV (19), and this may have a significant effect on dating estimates.
The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.
Theorists have been repeatedly told told that there is no such thing as the emergence of the sun’s anti-entropic virucidal energy. They have also been repeatedly told there is no such thing as mutation-driven evolution. They have been warned that serious scientists have linked top-down causation to energy-dependent biophysically constrained viral latency. But, biologically uninformed theorists continue to ignore the facts about virus-driven pathology, and their ignorance will probably continue to cause the unnecessary suffering that leads to premature death, which may lead to the death of nearly everyone and everything on Earth. Sudden emergence of human infections with H7N9 avian influenza A virus in Hubei province, central China (2018)
There have been five waves of H7N9 avian influenza virus (AIV) infection in humans since its initial emergence in China in 2013, posing a significant threat to public health. Hubei province was free local transmission during the first four waves of H7N9 AIV. However, multiple cases of human H7N9 infection were reported in Hubei during January 2017.
Excerpt: What I perceive as apathy can be attributed to the lack of empathy for anyone who suffers from the preventable or controlled virus-driven pathology that, sooner or later, kills us all. In the case of our Vietnam veterans, naturally occurring prevention or effective treatment of glioblastoma might be achieved by dietary intervention with a curcumin supplement. “micrornas”[MeSH Terms] OR “micrornas”[All Fields] OR “microrna”[All Fields] Items: 1 to 20 of 68871
See: The tipping point (revisited): 68,000 publications
69,000 published works on microRNAs will be the next “tipping point.” Predictably, it will be reached during the same 28 day period in which my tweets (@jvkohl) have received more than 70,000 impressions.
On 1/18/18: Tweet impressions 71.2K 602.0% The 602.0% increase has not been accompanied by a significant increase in followers or a significant increase in engagements.
What I perceive as apathy can be attributed to the lack of empathy for anyone who suffers from the preventable or controlled virus-driven pathology that, sooner or later, kills us all.
In the case of our Vietnam veterans, naturally occurring prevention or effective treatment of glioblastoma might be achieved by dietary intervention with a curcumin supplement.
See: A curcumin-loaded polymeric micelle as a carrier of a microRNA-21 antisense-oligonucleotide for enhanced anti-tumor effects in a glioblastoma animal model
DP-Cur is an efficient carrier of miR21ASO and the combined delivery of miR21ASO and curcumin may be useful in the development of combination therapy for glioblastoma.
This is the first study, to our knowledge, to demonstrate the utility of a pharmacological inhibitor of glutamine transport in oncology, representing a new class of targeted therapy and laying a framework for paradigm-shifting therapies targeting cancer cell metabolism.
Glutamine is an essential amino acid for many cell functions including biosynthesis, cell signaling and protection against oxidative damage. Because cancer cells divide more rapidly than do normal cells, they need more glutamine.
A protein called ACST2 is the primary transporter of glutamine into cancer cells. Elevated ASCT2 levels have been linked to poor survival in many human cancers, including those of the lung, breast and colon. Genetic studies that silence the ACST2 gene in cancer cells have produced dramatic anti-tumor effects.
See also: MicroRNA[s] and glutamineItems: 1 to 20 of 65
The facts about food energy-dependent microRNA-mediated RNA-directed DNA methylation and fixation of RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all living genera were removed from this report. Use off the cryo-EM technology links energy-dependent changes in electrons to healthy longevity in all ecosystems. It is apparent that some researchers do not want more people to learn about that fact.
See: Structural basis of RNA polymerase III transcription initiation
The unwound DNA directly contacts both sides of the Pol III cleft. Topologically, the Pol III PIC resembles the Pol II PIC, whereas the Pol I PIC is more divergent. The structures presented unravel the molecular mechanisms underlying the first steps of Pol III transcription and also the general conserved mechanisms of gene transcription initiation.
The information that links the virus-driven theft of quantized energy from the negative supercoiling (unwinding) of supercoiled DNA was removed in this attempt to support the neo-Darwinian pseudoscientific nonsense about the three domains of life. The bastardization of the use of cryo-EM technology occurred in the following context(s).
1) There is no mention of the quantized anti-entropic virucidal energy as information that is required to create ATP and RNA.
2) The energy-dependent creation of ATP and the creation of RNA is not linked to healthy longevity in all living genera via the physiology of pheromone-controlled reproduction.
3) The fixation of RNA-mediated amino acid substitutions that stabilize the differentiated cell types of all living genera are viewed in the context of negative supercoiling that occurs in an ATP-independent manner.
4) A spontaneously formed transcription bubble links the energy-dependent stability of supercoiled DNA to cell type differentiation in species from bacteria to humans.
5) The claim that promoters can be opened without ATP hydrolysis is used to suggest that no energy-dependent supercoiling is required to link the three kingdoms of life — assuming that there are three kingdoms of life.
6) The fact that the virus-driven degradation of messenger RNA in humans causes them to become non-human primates and the fact that it also cause bacteria to archaea and L-forms is ignored.
See: Virus-mediated archaeal hecatomb in the deep seafloor
We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.
By deliberately removing virus-archaea interactions from the representations reported as: Scientists zoom in to watch DNA code being read, pseudoscientists have reverted to promotion of their ridiculous gene-centric theories.
See for comparison: “Cytosis”
A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!
…RNA decay machinery plays important roles in antiviral defense. This can involve either direct effects on vRNA stability or indirect regulation of the intracellular milieu. Furthermore, an emerging theme suggests that many RNA binding proteins can be repurposed from their endogenous roles in the nucleus to antiviral roles in the cytoplasm. Future studies are necessary to further elucidate how these RNA binding proteins recognize foreign RNAs and how they interface with the RNA decay machinery to restrict vRNA replication.
Accurate representations of how natural selection for food energy-dependent codon optimality links the physiology of pheromone-controlled reproduction to the transgenerational epigenetic inheritance of healthy longevity will continue to be attacked from all sides.
Biologically uninformed theorists and philosophers can do nothing else but attack after proclaiming the nonsense of mutation-driven evolution during the past decades. They have failed to link their nonsense to the prevention of all pathology or to effective treatments via optimization of autophagy: the innate antiphage defense mechanism of all living genera.
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.
…used mathematical models to reveal that even in a uniform environment, metabolic competition generally leads to the steady coexistence of distinct microbes, collectively called a “consortium”. In a consortium, distinct microbes organize themselves to create a community-level metabolism that best exploits the nutrients present. The models showed that while growing, a consortium depletes the available pool of nutrients to such low levels that only members of the consortium can survive. The findings suggest that the benefit of metabolic diversity stems from the ability of a consortium to automatically deplete nutrients to levels at which no other microbes can invade.
Taillefumier et al. propose that consortia that arise naturally under conditions where there is a steady supply of nutrients produce the maximum mass of microbes. Future experiments that analyze the impact of fluctuating nutrient supply may help us to understand the benefit of metabolic diversity in real-world microbial communities.
Microbes do not organize themselves into consortia via the automatic depletion of nutrients. Natural selection for food energy-dependent codon optimality links quantum physics to the pheromone-controlled physiology of biophysically constrained viral latency. That is how metabolic networks must link ecological variation to ecological adaptation in all living genera.
Pseudoscientists who know nothing about energy-dependent quorum sensing and RNA-mediated cell type differentiation in microbial consoritia have wasted billions of dollars and nearly all the time that humans have existed on Earth. Now they tout automagically evolved consortia in attempts to subvert what is known about the nutrient energy-dependent protection from virus-driven energy theft, which is built into the molecular essence of all cell types. The pseudoscientists have led us to the brink of a viral apocalypse.
…the genomes of two independent gene therapy recipients had sustained more than 1,500 single-nucleotide mutations and more than 100 larger deletions and insertions. None of these DNA mutations were predicted by computer algorithms that are widely used by researchers to look for off-target effects.
…when virus-infected bacterial cells burst, their energy-rich cell contents spill into the water for other bacteria to scavenge. ‘Viruses tend to keep nutrients away from the big stuff and keep them going around in the little stuff,’ says Fuhrman. If so, viruses have shaped the entire structure of the ecosystem.”9
Virus-driven energy theft causes the degradation of messenger RNA that links mutations to all pathology.
We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.
People who believe in mutation-driven evolution are not likely to link virus-driven energy theft in archaea to the morphological and behavioral phenotype of bacteria or from the nutrient-dependent pheromone-controlled physiology of reproduction in bacteria to Alzheimer’s disease. People who believe in mutation-driven evolution may not be capable of understanding how the conserved molecular mechanisms detailed in the published works of serious scientists must be linked from viruses to the the degradation of messenger RNA that links the mutation-driven evolution of pathology to the increase in Alzheimer’s Deaths.
In the video that accompanies this report, the image from a brain scan is paired with the mention of biomarkers. microRNAs are the biomarkers. The changes in energy-dependent microRNA biosynthesis clearly predict the onset and severity of all pathology.
That’s why most people will not seek the most effective and least invasive treatment for Alzheimer’s. They won’t link the loss of olfactory acuity and specificity to the virus-driven degradation of messenger RNA and neurodegenerative diseases, because their physicians don’t understand enough about the creation of G protein-coupled receptors to link chemotaxis and phototaxis to all biodiversity via the physiology of reproduction.
Reports about an article that I have not yet seen published in “Nature Methods” attest to facts about cell type differentiation that have been placed into this context:
“Researchers… may be missing potentially important mutations,” Dr. Tsang remarked. “Even a single nucleotide change can have a huge impact.”
That fact is not just a “Crack in the CRISPR Facade.” It dismisses all claims about mutation-driven evolution. Those ridiculous claims have been replaced by what is known to serious scientists about how viral latency must be biophysically constrained. It must be constrained by a light-activated endogenous substrate in all cell types of all living genera. The light comes from the sun. For example, the anti-entropic energy of ultraviolet light kills viruses.
SARCASM ALERT: Ask your doctor if sunlight could save your life.
Until the publication of “Unexpected mutations after CRISPR-Cas9 editing in vivo” is available to all serious scientists, watch how the prescient claims about food energy that have been made by people like Richard Feynman have forced theorists to do what they have always done. Expect that some of the censorship will end when the news about the unexpected mutations is linked to what all serious scientists have expected since the time that Thomas Hunt Morgan linked energy-dependent chromosomal inheritance to all biodiversity on Earth and virus-driven energy theft was linked to antibiotic resistance.
Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge. — Kalevi Kull
Contrary to expectation, species that have experienced recently accelerated mutation rates have the largest genomes…
Biophysically constrained food energy-dependent pheromone-controlled viral latency protects the organized genomes of all living genera from the degradation of messenger RNA, which links virus-driven energy theft from mutations to all pathology regardless of the size of the organized genome. The measurement of membrane charges in the context of cryo-EM makes it possible to link virus-driven energy theft in bacteria to the degradation of messenger RNA in archaea and the degradation of messenger RNA in archaea to L-forms, which represent the virus-driven destruction of all created cell types. So far as is currently known, only the anti-entropic virucidal energy of sunlight can prevent the virus-driven death of all life on Earth.
Bacterial morphology is determined by the cell wall. Since the L-form has no cell wall, its morphology is different from that of the strain of bacteria from which it is derived.
The cell wall is important for cell division, which, in most bacteria, occurs by binary fission. This process usually requires a cell wall and components of the bacterial cytoskeleton such as FtsZ. The ability of L-form bacteria to grow and divide in the absence of both of these structures is highly unusual, and may represent a form of cell division that was important in early forms of life.[1]
The failure to recognize the fact that virus-driven degradation of the cell wall is an example of how cell type destruction occurs in all cells that contain a light-activated endogenous substrate, is also an example of pervasive ignorance among all theorists and other pseudoscientists.
Project Update #5: Cytosis: A Cell Biology Board Game by John Coveyou (Genius Games)
Many of you have mentioned that you’d like to have an explanation of the biology behind Cytosis available… and I think that is an AWESOME plan. Every time I’ve taught the game to non-science players in the past, they say gameplay made even more sense (and was so much more enjoyable) when I explained the science as well. This way they knew WHY they were doing what they were doing!
If you’ve got a strong background in biology, love explaining complexities in a way that someone unfamiliar with biology could understand, and would be interested in volunteering to help me write a page or two of science explanatory content for the rulebook, please shoot me an email… with the subject line “Cytosis Biology Explanations – [Your Name]” and we can start discussing!
1) Life is nutrient-dependent. See for review [2, 31]. The physiology of reproduction is pheromone-controlled. See for review [30].
In the context of the game “Cytosis,” Kohl’s Laws link the epigenetic effects of food odors and pheromones to changes in the mitochondria of all cell types. The energy-dependent changes in the mitochondria are linked to healthy longevity.
If the epigenetic effects of food odors and pheromones did not clearly link cytosis to healthy longevity, we would be left with only the link from virus-driven energy theft to all pathology. The explanation for all pathology involves more complexity than most people are willing to examine even when it is placed into the context of a book for a general, albeit educated, target audience.
See: The Scent of Eros: Mysteries of Odor in Human Sexuality
This is science at its best, with adventure, ideas, and lots of facts. — Helen Fisher
The feedback loops link Dobzhansky’s claims about amino acid substitutions and RNA-mediated cell type differentiation from natural selection for energy-dependent codon optimality to the pheromone-controlled biodiversity of all living genera.
…transient errors in mRNA synthesis can also cause heritable non-DNA-based phenotypic change. This is observed when low-abundance transcriptional regulators are affected by transcription errors. This disruption can cause a cell to alter its gene expression, resulting in a phenotype that may be heritable (2).
…there is probably no other scientist but Carl Woese who could write about having “no use for natural selection” and have Nature magazine respond with a Nobel endorsement. It is Carl Woese who first identified the Archaea and introduced us to horizontal gene transfer.
Virus-driven energy theft causes the degradation of messenger RNA, which links negative supercoiling of DNA in bacteria to the creation of archaea and links the conserved molecular mechanisms from archaea to the evolution of all pathology. For comparison, horizontal gene transfer links the nutrient energy-dependent de novo creation of genes from the pheromone-controlled fixation of RNA-mediated amino acid substitutions to supercoiled DNA, which prevents virus-driven energy theft from causing more degradation of messenger RNA.
This invited review of nutritional epigenetics includes a model that links nutrient energy-dependent changes from atoms to ecosystems. Most theorists have been caught with their pants down because they are still making claims about mutations and evolution. How can serious scientists compete with pseudoscientists who make claims that link mutations to millions of year of evolution? Most serious scientists know how to link quantized energy from chemistry to biologically-based cause and effect. Most biologically uninformed people accept the claims of pseudoscientists, atheists, and other theorists.
Some Harvard researchers are still trying to hide facts that link research on the synthesis of mRNA to all biophysically constrained biodiversity on Earth via hydrogen-atom transfer in DNA base pairs in solution and RNA-mediated amino acid substitutions in supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy. ATP-dependent cell type differentiation is placed into the context of conserved NAD+ and protein-protein interactions.
It is now widely accepted that cancer is the result of the gradual accumulation of driver gene mutations that successively increase cell proliferation (1–3).
Johns Hopkins researchers framed everything known to serious scientists about cell type differentiation into the contest of cancer as ‘bad luck” as if cytosis was not energy-dependent and healthy longevity arose in the context of mutation-driven evolution — if species were lucky enough to evolve into other species.
No serious scientist has ever accepted that ridiculous claim.
…we characterize two distinct p120-associated complexes with antagonistic functions and we describe a microRNA (miRNA)-mediated mechanism through which the ZA suppresses transformed cell growth.
Backers and players of the game “Cytosis” will learn how the energy-dependent function of mitochondria must be linked to every aspect of healthy longevity or be linked from virus-driven energy theft to all pathology. They will be prepared to learn from the next game: “Photosynthesis,” which will link the sun’s anti-entropic virucidal energy to all biophysically constrained biodiversity via what is known to all serious scientists. They will not need to learn anything more than is required for them to reject the pseudoscientific nonsense of neo-Darwinian theories.
The information has been shared more than 450 times. The number of biologically informed students will force the biologically uninformed professors to stop playing the evolution game until they can begin supporting their ridiculous claims with facts. The facts must link ecological variation to ecological adaptations via what is known to serious scientists about hydrogen-atom transfer in DNA base pairs in solution.
Clearly, the facts tell us that all individuals of all species that live on Earth must eat and reproduce or they become extinct. None mutate and evolve into other species.
I encourage others to support the development of games that teach what pseudoscientists do not want an interested target audience to learn. With enough support for an easy way to learn about energy-dependent cytosis compared to virus-driven pathology, the facts about RNA-mediated cell type differentiation will become clearer.
Every aspect of cytosis is food energy-dependent and RNA-mediated. Virus-driven energy theft cause all pathology. That fact makes sense in the context of all claims made by serious scientists. See for example:
— with forward by Roger Penrose who co-authored with George F.R. Ellis and Stephen Hawking
“How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?”(Roger Penrose 8 August 1991)
See also:
James Vaughn Kohl “New data on how genetic predispositions are epigenetically linked to phenotypically distinct neuroanatomy and behaviors is provided in the honeybee model. Across-species comparisons from insects to vertebrates clearly show that the epigenetic influence of food odors and pheromones continues throughout the life of organisms that collectively survive whereas individuals do not. These comparisons also attest to the relative salience of sensory input from the rearing environment. For example, when viewed from the consistency of animal models and conditioned behaviors, food odors are obviously more important to food selection than is our visual perception of food. Animal models affirm that food odor makes food either appealing or unappealing. Animal models reaffirm that it is the pheromones of other animals that makes them either appealing or unappealing.
Socioaffective neuroscience and psychology may progress more quickly by keeping these apparent facts in mind: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).”
Sunlight exposure induces signalling pathways leading to the activation of melanin synthesis and tanning response. MicroRNAs (miRNAs) can regulate the expression of genes involved in pigmentation pathways by binding to the complementary sequence in their 3′-untrastaled regions (3’UTRs).
Top-down causation starts from the creation of the sun’s anti-entropic virucidal energy. Hydrogen atom transfer in DNA base pairs in solution links energy-dependent changes in the microRNA/messenger RNA balance from microRNA flanking sequences to RNA-mediated amino acid substitutions that alter the stability of supercoiled DNA in the context of the physiology of reproduction.
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.
Works, like hers, with the nematode model organism will help others understand how ecological adaptation leads to biodiversity in the morphological phenotypes and behavioral phenotypes of all living genera. For example, P. pacificus is an ecologically adapted C. elegans. It is like a C. elegans with teeth that eats other nematodes.
Anyone who continues to report differences in the two nematodes context of selective inferences based on theories about mutations and evolution should promptly be dismissed from the ranks of serious scientists. People like that are biologically uninformed and they seem to know nothing about biophysically constrained RNA-mediated cell type differentiation. Many of them have built careers on funding from the evolution industry, which supports ridiculous misrepresentations of biologically-based cause and effect by placing them into the context of statistical analyses. The representations omit what is known about biologically-based facts, and report inferences as if the inferences wer based on something besides the definitions and assumptions of others who are biologically uninformed.
…the selective reporting of inferences problem is serious enough a problem in our current industrialized science even when no omission takes place.
Excerpt 2)
What, then, went wrong in the last decade or two? The change in the scale of the scientific work, brought about by high throughput experimentation methodologies, availability of large databases and ease of computation, a change that parallels the industrialization that production processes have already gone through. In Genomics, Proteomics, Brain Imaging and such, the number of potential discoveries scanned is enormous so the selection of the interesting ones for highlighting is a must.
My comment: The selection of interesting discoveries led serious scientists to link everything known about physics, chemistry, and the conserved molecular mechanism of RNA-mediated protein folding from hydrogen-atom transfer in DNA base pairs in solution to biologically-based ecological adaptation in species from microbes to humans. Ecological variation has been linked from nutrient-dependent microRNAs and microRNA flanking sequences to all biodiversity in all invertebrates and vertebrates via supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. See for comparison:
PROF. DR. LAWRENCE M. KRAUSS, is an internationally known theoretical physicist…
DR. STEPHEN C. MEYER …has expanded the scope of the case for intelligent design to the whole sweep of life’s history.
DR. DENIS O. LAMOUREUX… academic specialty focuses on the modern origins controversy.
My comment: The controversy that some people think exists is the focus of this inference: Young Earth Creationists killing Christian credibility? Perry Marshall, like many other biologically uninformed people who are not scientists, failed to grasp the systems complexity that has been detailed in my works, which include citations to the works of those who have established biologically-based cause and effect at every level of examination from angstroms to ecosystems. Perry Marshall’s ignorance led to this attack on Ken Ham’s creationist claims.
When all else fails to detail what theorists know about how mutations lead to evolution, young earth creationists are easy targets. Theorists, like Perry Marshall, attack what they think people like Ken Ham believe. They do not look at experimental evidence that proves how nucleic acids and cells were created in the context of biophysically constrained RNA-mediated protein folding chemistry. The biophysically constrained chemistry of protein folding links supercoiled DNA to protection from virus-driven entropy in all cell types of all individuals of all living genera that have organized genomes. (Note to theorists: All living genera have organized genomes.) Excerpt (from Perry Marshall’s inferences):
When folks like Ham stand up and claim to speak for all Christians, we lose face in the debate.
The good news is, there’s another narrative that allows for God and evolution — religion and science — to coexist. One where all of modern science’s discoveries only support the mystery of God, not debunk it.
My comment: Perry Marshall does not tell us which discoveries he believes support the mystery of God. Does he believe fossil record discoveries that some researchers claim link what is known about dead organisms to genome organization in living genera? Does Perry Marshall have evidence of biologically-based cause and effect that can be placed into the context of his inferences and the simultaneous emergence of hens and eggs? See, for example:Was ribosome the first self-replicator? Excerpt:
…does it make sense to talk about dark variants of cell and cell membrane? Can one tell whether it was pro-cell or bio-molecules that emerged first? It seems that all these structures could have emerged simultaneously. What emerged was dark matter and its emergence involved the emergence of all the others. Hens and eggs emerged simultaneously.
My comment: The claim that ‘Hens and eggs emerged simultaneously’ can be compared to Perry Marshall’s inference that young earth creationists may be killing Christian credibility. See my comments to Perry Marshall’s site, but also see the support for Ken Ham’s scientific/Biblical perspective which begins with atomistic insight, not evolutionary theory: For example:
1) The phylogenetic utility and functional constraint of microRNA flanking sequences
The approach allows rapid resolution of relationships between both closely related and rapidly evolving species, and provides an additional tool for investigation of relationships within the tree of life.
Molecular dynamics simulations independently confirm the conformational heterogeneity and provide atomistic insight into the flexibility of supercoiled DNA. Our integrated approach reveals the three-dimensional structures of DNA that are essential for its function.
…adhesion proteins — the glue that keeps cells together — interact with the microprocessor, a key player in the production of molecules called microRNAs (miRNAs). The miRNAs orchestrate whole cellular programs by simultaneously regulating expression of a group of genes. The investigators found that when normal cells come in contact with each other, a specific subset of miRNAs suppresses genes that promote cell growth. However, when adhesion is disrupted in cancer cells, these miRNAs are misregulated and cells grow out of control. The investigators showed, in laboratory experiments, that restoring the normal miRNA levels in cancer cells can reverse that aberrant cell growth.
My comment: More than 48,000 published works that link atomistic insight to supercoiled DNA are indexed here: “microRNA.” Taken together there is no doubt that nutrient-dependent microRNAs biophysically constrain protein folding in the context of the physiology of reproduction that links supercoiled DNA to protection from virus-driven genomic entropy and all biomass and all biodiversity in all living genera. The published works also are beginning to show that virus-driven energy theft links mutations to all pathology (see below). See for comparison:
…our results provide clear evidence that local adaptation contributed to these allele frequency changes in European populations, as strongly differentiated alleles in Europeans are enriched in likely functional variants: genic, previously constrained and putatively regulatory.
…the team speculates that these variants may be beneficial in populations living at high latitudes with limited exposure to UV light. However, Key is cautious, commenting that: ‘We have to note that our functional understanding of human genetic variants is still limited.’
My comment: Neo-Darwinian theorists consistently fail to grasp any of the experimentally established facts that link ecological variation to nutrient-dependent ecological variations via top-down causation. Key phrases such as “variants may be beneficial” in the context of “local adaptation” manifested in “allele frequency changes”are not linked from top-down causation to biodiversity. Top-down causation links the speed of light on contact with water from UV light to energy-dependent hydrogen-atom transfer in DNA base pairs in solution. See also: Many long intergenic non-coding RNAs distally regulate mRNA gene expression levels Excerpt:
Using Mendelian randomization, we found that there is evidence for lincRNAs having distal effects on the expression levels of protein-coding genes in a dosage-dependent way across the genome in similar proportions to distal effects of mRNA.
…the evidence mentioned above indicates that viruses likely arose from their hosts and not the other way around. As molecular biologist and biochemist Peter Borger notes, “The most parsimonious answer is: the RNA viruses got their genes from their hosts.”6
Regardless of how these sequences originated, our study illuminates how selfish genetic elements have contributed raw material that has been repurposed for cellular innovation.
Re: “The work suggests that these viral fossils probably played a key role in the evolution of our species…”
The work shows that Greg Bear accurately portrayed virus-driven energy theft when he linked it to the creation of new species. In 1999 and 2003, he linked what is now known about the anti-entropic effects of sunlight and hydrogen-energy transfer in DNA base pairs in solution to the creation of a new human subspecies.
What’s currently known outside the context of science fiction also links Einstein’s math and physics to molecular mechanisms of adaptation via Schrodinger’s claims about sunlight when paired with Dobzhansky’s claims about amino acid substitutions in the context of transgenerational epigenetic inheritance.
For example, the Zika virus clearly links primate craniofacial morphology and brain development. DNA damage linked to variations can be compared in the context of the fossil record and what is known about how cell type differentiation occurs. Nutrient energy-dependent RNA-mediated DNA repair and amino acid substitutions are linked to species-wide ecological adaptations.
The energy-dependent adaptations link ecological variation to morphological and behavioral phenotypes in species from microbes to humans. Virus-driven energy theft links a single amino acid substitution to increased virulence when nutrient-stress and/or social stress cause changes in pH that favor viral replication instead of nutrient-dependent immune system-support of controlled cell type differentiation.
Simply put, Dobzhansky’s claims can be placed into the context of what is known about all virus-driven pathology. He wrote: “…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla ( p. 127)” — See: Nothing in Biology Makes Any Sense Except in the Light of Evolution
The “light” is sunlight and it is linked to hydrogen-atom transfer in DNA base pairs in solution to fixation of amino acid substitutions and supercoiled DNA by everything currently known to physicists, chemists, and molecular biologists about biophysically constrained chemistry and the nutrient-dependent biological basis of the physiology of reproduction in all living genera.
Viruses increase their virulence via energy theft linked to a single amino acid substitution. All nutrient-dependent life must ecologically adapt by at least one nutrient-dependent amino acid substitution, which must be linked to supercoiled DNA via the physiology of reproduction in all living genera.
What some people call “viral fossils” are clear indicators of how the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding prevents virus-driven entropy of organized genomes in the context of the physiology of reproduction.
Summary: Claims that include statements like this: “Regardless of how these sequences originated…” invariably lead to claims that link pseudoscientific nonsense to the evolution of what serious scientist understand about the origin of the innate immune system. It is called the innate immune system for a reason. It it did not exist to protect the organized genomes of all living genera from virus-driven entropy, there would be no claims about “…how selfish genetic elements have contributed raw material that has been repurposed for cellular innovation.”
Viruses may be used to frame arguments that include claims about “selfish genetic elements.” But virus-driven energy theft cannot contribute any raw material that can be repurposed for cellular innovation. Cellular innovation is nutrient-dependent, and only the innate immune system can enable repurposing via nutrient energy-dependent feedback loops that link supercoiled DNA to the innate immune system’s protection from virus-driven entropy in the organized genomes of all living genera. See for examples from the past few days.
2016 Mar 15 Downregulation of the stress-induced ligand ULBP1 following SV40 infection confers viral evasion from NK cell cytotoxicity.
2016 Mar 16 Non‑invasive prostate cancer detection by measuring miRNA variants (isomiRs) in urine extracellular vesicles
2016 Mar 16 MicroRNA-1229 overexpression promotes cell proliferation and tumorigenicity and activates Wnt/β-catenin signaling in breast cancer
Our findings suggest that an increase in CSCs, specifically the CD44+ CD166– phenotype in the colon could be a predisposing factor for the increased incidence of CRC among AAs. MicroRNA 1207-5p appears to play a crucial role in regulating stemness in colonic epithelial cells in AAs.
My comment: Each of the articles linked above links stress perturbed changes in pH from virus-driven energy theft to mutations and pathology. Serious scientist have arrived at conclusions that link everything known about RNA-mediated cell type differentiation to the nutrient energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution. Energy-dependent changes in base pairs link atoms to ecosystems in the context of supercoiled DNA and the physiology of reproduction.
Links from atoms to funcitonal ecosystems do not include mutations and evolution except in the context of virus-driven energy theft, genomic instability, and pathology. That fact will lead to the public humiliation of any neo-Darwinian theorist who continues to tout their pseudoscientific nonsense about beneficial mutations. The careers of the pseudoscientists already have begun to end. Do not let them take your career with them or kill anyone else with their theories as they make a hasty exit. At the same time, watch them change the terms they have used to link mutations to evolution.
Learn the difference between a nutrient-dependent RNA-mediated amino acid substitution and a mutation and you won’t get caught making ridiculous claims about weekend evolution of the bacterial flagellum. Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system Excerpt:
Genome resequencing revealed a single-nucleotide point mutation in ntrB in strain AR2S, causing an amino acid substitution within the PAS domain of the histidine kinase sensor NtrB [Thr97→Pro97 (T97P)] (13). The fast-spreading strain AR2F had acquired an additional point mutation in the σ54-dependent EBP gene ntrC, which alters an amino acid (R442C) within the DNA binding domain (Table 1 and table S2).
James, you are one step away from being banned because of your disingenuous comments, your accusations, and your unnecessary combativeness. I am getting tired of it. People accuse you of being a troll for a reason.
This is your final warning. My comment: Obviously, I can say nothing more about Perry Marshall’s attacks on the credibility of young earth creationists — on his blog site. And there is no reason to reassert my claim that all serious scientists are Combating Evolution to Fight Disease. My comments to the Science Magazine site:
1) “An alternative theory proposes environmentally induced change in an organism’s behavior as the starting point (1), and “phenotypic plasticity” that is inherited across generations through an unspecified process of “genetic assimilation” (2).” http://www.sciencemag.org/content/332/6034/1161.short
This is now more than merely an alternative theory of genetic assimilation. It links transgenerational epigenetic effects from nutrient uptake and RNA-mediated events to amino acid substitutions that differentiate the cell types of all cells in all individuals of all organisms. See, for example: Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans http://www.cell.com/cell/abstract/S0092-8674(14)00806-X The nutrient stress-induced RNA-mediated events, which link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man, also link morphological and behavioral diversity via conserved molecular mechanisms exemplified in the context of biologically plausible ecological speciation in nematodes.See: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes http://linkinghub.elsevier.com/retrieve/pii/S0092867412015000
A difference in their feeding behavior and in the anatomy of their mouth parts is linked from nutrient-dependent pheromone-controlled feedback loops to ecological, social, and neurogenic niche construction. The change in focus from mutations, natural selection, and the evolution of biodiversity via unknown evolutionary events to nutrient-dependent pheromone-controlled RNA-mediated events that differentiate cell types may be required for others to realize the difference between evolutionary theories and biologically-based facts about RNA-mediated events.RNA-mediated events are biophysically constrained, which means they are a biologically plausible way to link the physics and chemistry of protein folding to increasing organismal complexity via molecular biology. RNA-mediated events can also be compared to any unknown evolutionary events that might arise in the context of an alternative theory about constraint-breaking mutations, or other theories that include no mention of RNA-mediated events. Submitted on Sat, 09/13/2014 – 08:58
2) Re: “Molecular biology and evolutionary biology have been separate disciplines and scientific cultures: The former is mechanistic and focused on molecules; the latter is theoretical and focused on populations.”Now see: A mechanistic link between gene regulation and genome architecture in mammalian development http://www.sciencedirect.com/science/article/pii/S0959437X14000495 for the refutation of neo-Darwinian pseudoscientific nonsense.Experimental evidence of biologically-based cause and effect does not support ideas about mutations, natural selection, and the evolution of biodiversity.Experimental evidence of biologically-based cause and effect supports the fact that ecological variation leads to nutrient-dependent pheromone-controlled ecological adaptations in species from microbes to man via conserved molecular mechanisms. Submitted on Tue, 07/15/2014 – 22:13
3) Re:”…the driver of evolution is not mutations or variation but selection, be it natural, artificial, kin or sexual selection. Mutation is but one of the factors that contribute to variation.”I thought Robert Frye knew better than that, because he attended a 1993 symposium I organized and my 2007 Reiss Plenary session of The Mind’s Eyes: Modeling the Development of Diverse Sexual Preferences.Perhaps this is a different Robert Frye or one who thinks that sexual orientation arises via mutations and natural selection in human males but via nutrient-dependent pheromone-controlled cell type differentiation in yeasts as we reported in our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior “Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus…”Robert: What about Anne’s rams. Are they among the selected mutants that you think may have evolved their exclusive homosexual orientation? Submitted on Sun, 09/07/2014 – 20:51
4) Darwin probably anticipated the insemination of population genetics that led to the bastardization of his detailed observations in the “Modern Synthesis.” He politely insisted that ‘conditions of life’ be considered before natural selection. There are two ‘conditions of life.’ It is nutrient-dependent and pheromone-controlled. Rosenberg and Queitsch now note the work with Dobzhansky’s rarely acknowledged claim: “I am a creationist and an evolutionist.” They also declare the need for “Deep understanding of the mechanisms that generate variation at the molecular level…”Deep understanding of the ‘conditions of life’ does not come from theory. Problems with the “modern synthesis” now lead us back to the facts about biologically-based cause and effect that Darwin and Dobzhansky approached with humility, which are the same biological facts that evolutionists approached with ignorance about behavioral affects and the arrogance that accompanies that ignorance. Rosenberg and Queitsch echo the sentiments of those who have been subjected to academic suppression. Clearly, however, “nothing in evolution makes sense except in the light of biology” is not an exaggeration. It is a common sense statement about the biologically plausible genesis of functional cell types. Population genetics and evolutionary theories abandoned the biophysical constraints of ecological variation and the physiology of reproduction, which enable epigenetically-effected nutrient-dependent pheromone-controlled receptor-mediated ecological adaptations and species diversity via the complexities of protein folding and niche construction. It’s time for biophysicists to tell theorists and pathologists how to differentiate between theories about the genesis of different cell types and the biological facts about the nutrient-dependent pheromone-controlled ecological adaptations that enable the genesis of different cell types in individuals of different species. Simply put, it’s time to stop trying to explain ecological adaptations in the context of mutations and evolution. Submitted on Fri, 03/07/2014 – 12:07 Addendum: With his book, and on the FB page and blog site that he controls, Perry Marshall, has joined the ranks of many others who are fighting to keep evolution and disease. The evolution industry has been successfully built from the pseudoscientific nonsense of theory, and Perry Marshall is riding the wave of success with Evolution 2.0.
I apologize, Perry. I thought you were attacking my beliefs. Typically, I am not combative, but I am not defenseless, either.
What aspect of my model are you willing to discuss?
For example, I presented this poster at the Labroots Neuroscience 2016 Virtual event last week:
From hydrogen atom transfer in DNA base pairs to ecosystems https://www.youtube.com/watch?v=5CN2a0Z1fQI
For comparison to my model:
Here is a recent representation of the never-ending focus on visual input, which ignores the fact that chemotaxis must precede phototaxis during the integration of sensory input in the developing brain: Building A Brain: Mysteries of the Brain.
When someone like Perry Marshall, attacks Ken Ham, or anyone else for their beliefs, ask yourself what beliefs they are trying to sell you with their marketing campaign. Perry Marshall, for example, seems to be trying to sell you his belief that hybrids created in the lab are examples of God’s creation of different species. Dobzhansky (1972) Conclusion:
As a category of classification, species was and is being applied to all organisms, and this has led to futile search for universal biological properties of all species. What is actually found is a remarkable variety of different kinds of species. Even confining our attention to sexually reproducing and outbreeding forms, we find more or less monolithic “good” species, superspecies, and semispecies. Finally, it begins to look as if reproductive isolation may sometimes follow and at other times precede the adaptive divergence of gene pools of populations.
My comment: In either case, the physiology of reproduction is nutrient-dependent and must link what is known about the innate immune system from feedback loops to biodiversity via supercoiled DNA, which protects all organized genomes in all living genera from virus-driven entropy.
…it appears essentially certain that the evolution of the code involved some combination of frozen accident with selection for error minimization.
My comment: This claim from 2009 failed to address anything currently known to serious scientists about the Schrodinger’s claim from 1944, in What is Life?
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)
…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla. ( p. 127)
My comment: The claim from 2009 also failed to address anything currently known to serious scientists about supercoiled DNA in the context of the Structural diversity of supercoiled DNA. Conclusion:
Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.
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: How much longer will the serious scientists who have linked nutrient uptake to hydrogen-atom transfer in DNA base pairs allow teleophobic pseudoscientists to claim that:
We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms.
Study shows that controlling neurons with light or drugs may affect the brain in more ways than expected.
Excerpt:
Given that many experiments build on existing knowledge about circuits involved in a behaviour, he cautions, experimental scientists should be particularly careful when using transient techniques to map entirely new circuits in the brain. “This study nicely reminds us that there is no perfect technique,” says Evan Feinberg, a neuroscientist at the University of California, San Francisco.
My Summary of this blog post:
The arguments of serious scientists must include experimental evidence of facts that link physics, chemistry, and the conserved molecular mechanisms of biologically-based cause and effect from atoms to ecosystems.
Epigenetic effects on biophysically constrained nutrient-dependent RNA-mediated protein folding chemistry during thermodynamic cycles of protein biosynthesis and degradation link the epigenetic landscape to the physical landscape of supercoiled DNA in the organized genomes of all living genera.
Biologically-based cause and effect cannot be established in the context of metaphors.
The following presents several ecological metaphors for ritual adaptation: sexual selection, the isolated island, and the clearcut forest. Once these metaphors are established, I will explain how they apply to ritual, and suggest some policy recommendations based on this speculation.
…this echoes a tension at the heart of philosophy between two modes of philosophizing: a speculative-revisionary mode that is metaphorical and an analytic-explanatory mode that is conditional. The tasks are generally complementary so that the difference can be ignored with impunity. However, if we do not respect that difference, we may find ourselves analyzing metaphors and seeing logical analyses as metaphorical, and thus missing the point on both fronts.
My comment: Logical analyses of biologically-based cause and effect are not metaphorical. Any theorist or philosopher whose arguments are based on ecological metaphors that attempt to link ecological variation to ecological adaptations via selection in the context of speculation can be compared to any serious scientist. The difference between theorists, philosophers and serious scientists is clear.
The arguments of serious scientists must include experimental evidence of facts that link physics, chemistry, and the conserved molecular mechanisms of biologically-based cause and effect from atoms to ecosystems.
Serious scientists do not use metaphors linked to speculation in the context of their models of top-down causation or bottom-up effects on cell type differentiation. Top-down causation is the sun’s biological / virucidal energy and bottom-up effects always must include epigenetic effects.
Epigenetic effects on biophysically constrained nutrient-dependent RNA-mediated protein folding chemistry during thermodynamic cycles of protein biosynthesis and degradation link the epigenetic landscape to the physical landscape of supercoiled DNA in the organized genomes of all living genera.
For an example of why all serious scientists are Combating Evolution to Fight Disease by accurately representing biologically-based cause and effect, see: Structural diversity of supercoiled DNA Excerpt:
Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.
My comment: Their ABILITY to present data that links atoms to ecosystems via RNA-mediated events in an entertaining way is exemplified in less than 4 minutes. See: All About that Base (Meghan Trainor Parody) 10 Dec 2014
The INABILITY of theorists and philosophers to address any aspect of that data is represented in less than 2 minutes. See: Bacteria evolve over a weekend.
The ability of bacteria to recognize all proteins, nucleic acids, and small molecules that modulate DNA metabolic processes is miraculous. The miraculous ability can be viewed outside the context of the magic of evolution. For example, if all organisms did not have the innate ability to recognize all proteins, nucleic acids, and small molecules that modulate DNA metabolic processes, there would be no examples of what is obviously required to link the epigenetic landscape to nutrient-dependent RNA-mediated protein folding chemistry, which is biophysically constrained by the physiology of reproduction. Without fixation of RNA-mediated amino acid substitutions in different species, there is no link from the epigenetic landscape to the physical landscape of differences in the supercoiled DNA of organized genomes. Without fixation of amino acid substitutions, only ridiculous theories are left to consider. Serious scientists don’t consider ridiculous theories.
Instead, for example, serious scientists have linked the sequencing of the octopus genome to the nutrient-dependent pheromone-controlled physiology of all invertebrates and vertebrates via nutrient-dependent microRNAs and cell adhesion proteins that link supercoiled DNA to the protection from virus-driven entropy in the organized genomes of all living genera.
See: Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity Excerpt 1
In the present study, we sought to reconcile the apparently contradictory observations and clarify the roles of p120 and E-cadherin in epithelial cell behaviour. Recently, the p120 binding partner PLEKHA7 was shown to specifically localize at the apical zonula adherens (ZA) but not along lateral surfaces of epithelial cells, as for p120 or E-cadherin21,22. By using PLEKHA7 as a marker of the apical ZA in mature epithelial cells,we characterize two distinct p120-associated complexes with antagonistic functions and we describe a microRNA (miRNA)-mediated mechanism through which the ZA suppresses transformed cell growth.
Conclusion:
Taken together, our data untangle the complicated roles of E-cadherin and p120 in the context of distinct junctional complexes, spatially separating their functions and providing an explanation for their conflicting behaviour in cell growth. In addition, they identify PLEKHA7 as a specific marker of ZA that mediates suppression of growth-related signalling. Finally, they reveal an interaction of the ZA with the microprocessor complex, and uncover a mechanism whereby the ZA regulates a set of miRNAs to suppress cellular transformation and maintain the epithelial phenotype.
Serious scientists have describes a microRNA (miRNA)-mediated mechanism of transformed cell growth that links viral microRNAs to pathology and nutrient-dependent microRNAs to healthy longevity. However, I may need to keep reminding others of this fact:
More than 45,000 published journal articles indexed on PubMed already contained the term microRNA before evolutionary theorists declared the microRNAs were linked from their emergence to all biodiversity via mutations and evolution in: MicroRNA mechanisms of action: what have we learned from mice?
I do not mind repeatedly reminding others of the fact that these theorists are biologically uninformed science idiots because they may be responsible for teaching yet another generation of unsuspecting students to become biologically uninformed science idiots.
Please remind any biologically uniformed student that you encounter that RNA-mediated theory killers will kill their chance of a successful career in any scientific discipline unless someone shows that the speed of light on contact with water cannot be linked from quantum physics to biologically-based cause and effect via RNA-mediated events in all living genera. The number of published works that help to establish that fact in the context of what is known about RNA-mediated amino acids substitutions has reached the tipping point where theorists must fight to their death against the paradigm shift that comes from their death in the context of Max Planck’s oft-echoed claim. Guide to Thomas Kuhn’s The Structure of Scientific Revolutions Excerpt:
19. How Communication is Restored by Conversion to the New Paradigm: What I want to highlight here is the further thesis that (p.150) “before they can hope to communicate fully, one group or the other must experience the conversion that we have been calling a paradigm shift.” For example, (p.151) “Max Planck … sadly remarked that ‘a new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.’” Or, (p.152) “Conversions will occur a few at a time until, after the last hold-outs have died, the whole profession will again be practicing under a single, but now different, paradigm.” Partly by way of explication, and partly by way of argument, Kuhn tells us how conversion is induced and how resisted.
My comment: Pseudoscientists resist converison, serious scientists usher in the paradigm shift despite that resistance. A phone call from a contractor whose efforts I agreed to help promote without the conflict of interest that financial considerations would create reminded me to first restate the fact that all experimental evidence of biologically-based cause and links the Precision Medicine Initiative to preventative medicine in the context of this brief video representation.
If the contractor begins to pay me, pseudoscientists and all theorists may continue to claim that my commercial interests invalidate my representations, which is what they have done since 1995. I would like to wrap up my attempts to refute them and enjoy my retirement, even more than I already have. My wrap-up will include examples of RNA-mediated theory killers in a series of blog posts and on my FB group until someone makes me an offer to purchase the domain and continue to use it for dissemination of accurate information about biologically-based cause and effect.
