Announcing publication of a model that links the creation of quantized energy from changes in subatomic particles to biophysically constrained viral latency and sympatric speciation in all living genera.
This angstroms to ecosystems model of ecological adaptation links nutrient energy-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA/messenger RNA balance and chromosomal rearrangements via the physiology of reproduction in species from microbes to humans.
The invited review of nutritional epigenetics was returned without review and the preprint was posted 4 years ago as:
The only significant change to the manuscript was a change in the title. Atoms to ecosystems became Angstroms to Ecosystems when quantized energy-dependent changes in angstroms were linked to ecological adaptation by what is known to all serious scientists in this 2014 parody. All About that Base (Meghan Trainor Parody) 12/10/14
Repeat after them (and me): “… every angstrom is dynamic from the 5 prime to the three…”
See also the 2015 publication: Structural diversity of supercoiled DNA
DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases.
George Church and others may have been the first to place the naturally occurring biophysically constrained energy-dependent processes of ecological adaptations into the context of a patent. (It is extremely unusual for anyone to attempt to patent a naturally occurring process.) That explains why there is no patent litigation, which still plagues those who claimed to discover the CRISPR-Cas 9 innate immune system of bacteria, which biophysically constrains viral latency and prevents the degradation of messenger RNA that links the energy-dependent creation of bacteria to the virus-driven creation of archaea and L-forms. All biophysically constrained virus-driven pathology has since been placed back into the context of embryogenesis and the dynamics of energy-dependent gene expression at the level of single-cell resolution as if bacteria somehow evolved into humans.
Common Allele Linked to Sugar Consumption Leads to Lower Body Fat, Higher Blood Pressure
One energy-dependent change in a base pair is linked from the FGF21 rs838133 variant to microRNA-mediated changes in morphology and behavior. The quantized energy as information link from microRNAs to morphology and behavior is common to my mouse-to-human model of sympatric speciation.
By linking the common allele to sugar consumption, the authors attest to the fact that sympatric speciation is quantized energy-dependent. Energy as information biophysically constrains viral latency in the context of the game Cytosis for ages 10+.
See also: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
Theorists have been reluctant to comment on this invited review of nutritional epigenetics, which I posted to Figshare.com on 4/10/14. As of today, the model of food energy-dependent pheromone-controlled ecological adaptations / sympatric speciation has been available for 4 years.
In my mouse-to-human model, the variant is rs3827760, aka 1540T/C, 370A or Val370Ala. It is a SNP in the ectodysplasin A receptor EDAR gene on chromosome 2.
Summary: The energy-dependent creation of ATP synthase, ATP, microRNAs, messenger RNA, and supercoiled DNA biophysically constrains viral latency in the context of the “Levels of Biological Organization” I included in this presentation from 2010: Human Pheromones: Linking Neuroendocrinology and Ethology (revisited) See slide # 6.
See also, our award-winning 2001 review: Human pheromones: integrating neuroendocrinology and ethology
…the current models are both consistent with available and new experimental data and offer a number of predictions – notably, through revelation of highly constrained residues (Supplementary Data 9–10) – to guide and visualise structure-function analyses of these unusual sensory receptors.
No experimental evidence of top-down causation links anything except the quantized energy-dependent creation of enzymes, hormones, and receptors to biophysically constrained viral latency and ecological adaptations.
Analyzing the variation of insect OR protein amino acids during evolution revealed a model for transmembrane domain arrangement that is unrelated to GPCRs (Hopf et al., 2015).
Try to refute my model with the latest pseudoscientific nonsense about coevolved amino acids.
…superorganisms may also exhibit such behaviour, suggesting that these laws arise from fundamental mechanisms of information processing and decision-making.
Among the insect olfactory receptors the odorant receptors (ORs) evolved in parallel to the onset of insect flight. A special property of this receptor type is the capability to adjust sensitivity of odor detection according to previous odor contacts. This article presents a current view on regulatory processes affecting the performance of ORs and proposes a model of mechanisms contributing to OR sensitization.
Epithelial-to-Mesenchymal Transition (EMT) and its reverse – Mesenchymal to Epithelial Transition (MET) – are hallmarks of cellular plasticity during embryonic development and cancer metastasis.
Cellular plasticity was linked from the energy-dependent pheromone-controlled physiology of reproduction in bacteria to our visual perception of energy and mass in the context of the space-time continuum.
See: Olfaction Warps Visual Time Perception (2017)
The behavioral gain produced by a congruent relative to an incongruent odor is accompanied by elevated neural oscillatory power around the object’s flicker frequency in the right temporal region ~150-300 ms after object onset, and is not mediated by visual awareness. In parallel, odors bias the subjective duration of visual objects without affecting one’s temporal sensitivity.
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.
Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy. The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection.
This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes. For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.
Webinar: Deciphering how bacteria utilize outer membrane vesicles (OMVs) to communicate and infect
Outer Membrane Vesicles (OMVs) are membrane vesicles secreted by bacteria that contain DNA, RNA, proteins and endotoxins. Bacteria respond to many environmental factors by secreting specifically-enriched OMVs, which makes these bacteria more fit for their environment. For example, OMVs may be enriched with invasion proteins at the host-pathogen interface. OMVs have recently gained attention as a novel mechanism for transmission of molecular information within bacteria as well as between bacteria and mammalian cells. Owing to their similarities to well-studied extracellular vesicles (EVs), OMVs are being utilized by researchers to study host-bacterial interactions in pathogenesis, cancer therapy, host immune response modulation, as well as bacterial OMV engineering for use as vaccines. This webinar will give an overview of recent studies on the role of OMVs in host-pathogen interactions and discuss their bioengineering potential as vehicles for cargo delivery. We will also introduce our new & revolutionary ExoBacteria™ OMV Isolation Kit, which will enable you to achieve faster, simpler & better OMV isolation.
Learn how OMVs are being utilized by researchers to study host-bacterial interactions in pathogenesis, cancer therapy, host immune response modulation, as well as bacterial OMV engineering for use as vaccines.
A writer who does not cite the sources in h/h feature article is committing piracy. Piracy is plagiarism… high level quality requires originality and creativity… these inattentions…should be strongly condemned… Accordingly, the originally contributing author may preserve the honor worthily and endeavor to further contribution in scientific study.
…virus-associated cancers show highly increased levels of DNMT expression [75,76,77,85,94,95,96,97,98,99]. In HBV-associated hepatocellular carcinoma (HCC), DNMT expression is inversely correlated with levels of tumor suppressor microRNAs (miRNAs), including miR-152 targeting DNMT1 [97] and miR-101 targeting DNMT3A [99]. Virus-induced DNA hypermethylation is commonly found on several tumor suppressor genes…
RNA-directed DNA methylation links the energy-dependent microRNA-mediated creation of tumor suppressor genes to biophysically constrained viral latency via the proton motive force. The proton motive force links differences in the energy of photons from hydrogen-atom transfer in DNA base pairs in solution to the light-activated endogenous substrates of RNA-mediated DNA repair.
See also: “There is no honor among thieves” is a pithy saying that captures Solomon’s observation concerning the wicked and those who choose their company.
A Twitter search returned several interesting comments related to what is known to serious scientists about the proton motive force and the claim that “There is no honor among thieves.” For instance, writers who modify the claims and questions about the proton motive force are plagiarists and/or thieves. See:
The H+ gradient is called the proton-motive force. This force drives the H+ back across the membrane through H+ channels. ATP synthases aids
The creation of enzymes, such as ATP synthase is energy-dependent. The energy biophysically constrains viral latency via the creation of microRNAs and RNA-mediated amino acid substitutions that differentiate the cell types of all living genera.
This was filmed tonight, so you’ll soon get to see why Nick Lane thinks the key to the origin of life is not amino acids or RNA but proton gradients. (I think he may be right.)
See for comparison: snippet from our June 24, 2017 conversation about the claims of Philip C. Ball.
Dr Frankenstein aimed to create new life from inanimate parts. But how did life first arise on Earth? Join Nick Lane in conversation with Phil Ball as they discuss the latest ideas, from warm ponds to space rocks and hydrothermal vents.
Ask when Nick Lane and/or Philip C. Ball first learned about proton gradients. See how much longer it takes them to link the creation of sunlight from differences in the energy of photons to biophysically constrained viral latency and all biodiversity via the physiology of reproduction and this model: Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013)
Conclusion:
…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.
This angstroms to ecosystems model of ecological adaptation links nutrient energy-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements via the physiology of reproduction in species from microbes to humans. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity. Species-specific pheromones link quorum-sensing in microbes from chemical ecology to the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection for codon optimality links nutritional epigenetics to the behaviors that enable ecological adaptations. All biodiversity is an ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. Simply put, olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of supercoiled DNA in the organized genomes of species from microbes to man during their development.
In my model, microRNAs are the biomolecules that link the creation of sunlight to all energy-dependent biophysically constrained viral latency. Viral latency is required to link the physiology of reproduction to all biologically-based diversity in all species.
Claims about proton gradients that link physics to biology without starting with the creation of sunlight are made by biologically uninformed theorists.
…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.
On Darwin Day (2018) Carl Zimmer suggested use of the twitter hashtag #Istudyevolution to report whatever aspect of biology people were studying. For example, Richard Lenski reported that he studied adaptation in E. coli. When I told others that ecological adaptation is nutrient-dependent and pheromone-controlled in species from microbes to humans, he blocked me from seeing his comments. Evidently he did not want people to know that he had been studying ecological adaptation for more than 2 decades but reporting the adaptations in the context of neo-Darwinian theories about mutations and evolution. For further clarification of that fact see: Cryo-electron tomography reveals that dynactin recruits a team of dyneins for processive motility
…the mechanisms responsible for increased transport activity are not well understood, largely owing to limited structural information. We used cryo-electron tomography (cryo-ET) to visualize the 3D structure of the MT-bound dynein–dynactin complex from Mus musculus and show that the dynactin–cargo adaptor complex binds two dimeric dyneins. This configuration imposes spatial and conformational constraints on both dynein dimers.
This discovery was totally unexpected, and will change how this motor complex is represented in cell biology and biochemistry text books,” says Saikat Chowdhury, PhD, a TSRI research associate and co-first author of the study.
“There had been years of biophysical experiments and biochemical experiments, and it was always assumed that there was just one dynein molecule,” Lander adds.
In conclusion, we have shown for the first time that very low doses of far-UVC light efficiently inactivate airborne viruses carried by aerosols. For example, a very low dose of 2 mJ/cm2 of 222-nm light inactivates >95% of airborne H1N1 virus. Our results indicate that far-UVC light is a powerful and inexpensive approach for prevention and reduction of airborne viral infections without the human health hazards inherent with conventional germicidal UVC lamps. If these results are confirmed in other scenarios, it follows that the use of overhead very low level far-UVC light in public locations may represent a safe and efficient methodology for limiting the transmission and spread of airborne-mediated microbial diseases. Public locations such as hospitals, doctors’ offices, schools, airports and airplanes might be considered here. This approach may help limit seasonal influenza epidemics, transmission of tuberculosis, as well as major pandemics.
In the study, aerosolized H1N1 virus—a common strain of flu virus—was released into a test chamber and exposed to very low doses of 222 nm far-UVC light. A control group of aerosolized virus was not exposed to the UVC light. The far-UVC light efficiently inactivated the flu viruses, with about the same efficiency as conventional germicidal UV light.
Quantum logic gates are fundamental building blocks of quantum computers. Their integration into quantum networks requires strong qubit coupling to network channels, as can be realized with neutral atoms and optical photons in cavity quantum electrodynamics. Here we demonstrate that the long-range interaction mediated by a flying photon performs a gate between two stationary atoms inside an optical cavity from which the photon is reflected. This single step executes the gate in 2μs. We show an entangling operation between the two atoms by generating a Bell state with 76(2)% fidelity. The gate also operates as a cnot. We demonstrate 74.1(1.6)% overlap between the observed and the ideal gate output, limited by the state preparation fidelity of 80.2(0.8)%. As the atoms are efficiently connected to a photonic channel, our gate paves the way towards quantum networking with multiqubit nodes and the distribution of entanglement in repeater-based long-distance quantum networks.
This interaction is the basis for performing characteristic gate operations between the atoms, for example the operation as a CNOT gate or the generation of entanglement. The new method offers a variety of advantages: for example, the gate operations take place within microseconds which is an asset for quantum information processing.
Quantized energy is the information that must be biophysically constrained and transferred from hydrogen-atoms in DNA base pairs in solution. That fact seems to have escaped the attention of biologically uninformed pseudoscientists and most so-called science journalists. The pseudoscientists and other theorists linked the emergence of the energy to the evolution of all biodiversity outside the context of the physiology of reproduction and autophagy, which biophysically constrains viral latency.
See for comparison to what serious scientist have done:Experimental Evidence of Radiation Reaction in the Collision of a High-Intensity Laser Pulse with a Laser-Wakefield Accelerated Electron Beam
The dynamics of energetic particles in strong electromagnetic fields can be heavily influenced by the energy loss arising from the emission of radiation during acceleration, known as radiation reaction. When interacting with a high-energy electron beam, today’s lasers are sufficiently intense to explore the transition between the classical and quantum radiation reaction regimes. We present evidence of radiation reaction in the collision of an ultrarelativistic electron beam generated by laser-wakefield acceleration (ϵ>500MeV) with an intense laser pulse (a0>10). We measure an energy loss in the postcollision electron spectrum that is correlated with the detected signal of hard photons (γ rays), consistent with a quantum description of radiation reaction. The generated γ rays have the highest energies yet reported from an all-optical inverse Compton scattering scheme, with critical energy ϵcrit>30MeV.
“One thing I always find so fascinating about this is that the electrons are stopped as effectively by this sheet of light, a fraction of a hair’s breadth thick, as by something like a millimetre of lead. That is extraordinary.”
The data from the experiment also agrees better with a theoretical model based on the principles of quantum electrodynamics, rather than Maxwell’s equations, potentially providing some of the first evidence of previously untested quantum models.
Effects of quantized energy as information cannot be defined in the context of equations, which is why physicists have traditionally been ridiculed for any attempt to explain energy-dependent top-down causation in the context of biophysically constrained healthy longevity.
All species on Earth exhibit an undefined, incalculable, innate ability to biophysically constrain energy-dependent viral latency. That ability is food energy-dependent and controlled by the physiology of reproduction. Food energy comes from sunlight, either directly or indirectly via plant grown and the creation of microRNAs in plants. Serious scientists know how to light the sun’s anti-entropic virucidal energy to DNA repair.
See: Watson–Crick Base Pairing Controls Excited-State Decay in Natural DNA (2014)
Reported as: Base-pairing protects DNA from UV damage
…the Watson-Crick base-pairing mechanism itself controls the dissipation of the absorbed UV energy. This contradicts the conventional wisdom, which holds that the base sequence within the same strand is responsible for the deactivation of excited states,” says Wolfgang Zinth.
Ultrafast deactivation pathways bestow photostability on nucleobases and hence preserve the structural integrity of DNA following absorption of ultraviolet (UV) radiation. One controversial recovery mechanism proposed to account for this photostability involves electron-driven proton transfer (EDPT) in Watson–Crick base pairs. The first direct observation is reported of the EDPT process after UV excitation of individual guanine–cytosine (G⋅C) Watson–Crick base pairs by ultrafast time-resolved UV/visible and mid-infrared spectroscopy. The formation of an intermediate biradical species (G[−H]⋅C[+H]) with a lifetime of 2.9 ps was tracked. The majority of these biradicals return to the original G⋅C Watson–Crick pairs, but up to 10 % of the initially excited molecules instead form a stable photoproduct G*⋅C* that has undergone double hydrogen-atom transfer. The observation of these sequential EDPT mechanisms across intermolecular hydrogen bonds confirms an important and long debated pathway for the deactivation of photoexcited base pairs, with possible implications for the UV photochemistry of DNA.
There is clear evidence that femtosecond blasts of UV light repair DNA in the context of energy-dependent changes in the microRNA/messenger RNA balance and autophagy, which protects all organized genomes from virus-driven energy theft and the degradation of messenger RNA.
The failure to integrate the Nobel Prize winning works of Ben Feringa (Chemisty 2016) and Yoshinori Ohsumi (Physiology or Medicine 2016) prevents theorists from linking what organisms eat to their pheromone-controlled physiology of reproduction in the context of Schrodinger’s claims in “What is Life?”(1944) and this claim by Roger Penrose in the reprint edition:
“How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?” (Roger Penrose 8 August 1991)
See also: From Fertilization to Adult Sexual Behavior In our section on molecular epigenetics, we wrote:
Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans…
The food energy that is linked from alternative splicing techniques of pre-mRNA to the chemistry of protein folding and the pheromone-controlled physiology of reproduction in all living genera seems to be largely ignored by those who are not Nobel Laureates.
It links the virus-driven theft of quantized energy from the degradation of messenger RNA to mutations and all pathology, and physicists cannot explain that fact with math and definitions. They tried with de Vries 1902 definition of mutations, and they have failed miserably ever since.
To assess whether there are universal rules that govern amino acid–base recognition, we investigate hydrogen bonds, van der Waals contacts and water-mediated bonds in 129 protein–DNA complex structures. DNA–backbone interactions are the most numerous, providing stability rather than specificity. For base interactions, there are significant base–amino acid type correlations, which can be rationalised by considering the stereochemistry of protein side chains and the base edges exposed in the DNA structure.
See also: Systematic prediction of DNA shape changes due to CpG methylation explains [quantized energy-dependent] epigenetic effects… (2018)
The effects of sunlight and quantum chemistry link energy-dependent fixation of RNA-mediated amino acid substitutions to the differentiation of all cell types in all living genera via the physiology of reproduction, which is controlled by pheromones in species from microbes to humans. Pheromones biophysically constrain viral latency in all animals that need to eat for their species to survive.
Cryo-EM technology predicts RNA-mediated DNA shape, which means the technology can be used to link the virus-driven degradation of messenger RNA from mutations to all pathology in the context of the games “Cytosis” and “Subatomic.”
When “Subatomic” is available, players will link what is known to all serious scientists who present during “Schrodinger at 75” to the overwhemling amount of pseudoscientific nonsense touted by theorists during the past 75 years.
Schrodinger linked the anti-entropic virucidal energy of sunlight to all biophysically constrained biodiversity via the physiology of reproduction in all plants and animals. Pseudoscientists decided to use mutations and natural selection instead of Darwin’s “conditions of life.” That is why pseudoscientists can — and soon may be — blamed for all extant pathology.
Theorists failed to link subatomic particles to biophysically constrained viral latency via the “Virus Expansion” from “Cytosis.” That fact led to this admission of ignorance:
Microscopic chariots deliver molecules within our cells https://phys.org/news/2018-02-microscopic-chariots-molecules-cells.html
Excerpt: This discovery was totally unexpected, and will change how this motor complex is represented in cell biology and biochemistry text books,” says Saikat Chowdhury, PhD, a TSRI research associate and co-first author of the study.
“There had been years of biophysical experiments and biochemical experiments, and it was always assumed that there was just one dynein molecule,” Lander adds.
My comment: All the discoveries that have since linked energy-dependent changes from electrons to ecosystems were anticipated by Richard P. Feynman in his claims about “Plenty of Room at the Bottom.” Everything known to serious scientists links cryo-EM technology from ecological niche construction to socio-cognitive niche construction via food energy-dependent amino acid substitutions in the microtubules that link differences in animal behavior to human consciousness.
It will good to see “Subatomic” placed into the context of the admission that there are two dynein molecules. Others may begin to see the levels of complexity that must be represented in game play to prevent further assumptions based on ignorance of particle physics and energy transfer that biophysically constrains viral latency.
The fact that many people can readily learn more than most theoretical physicists have learned about subatomic particles and cell biology by playing games for fun is an exciting development for scientists and laypersons.
Magnus S. Magnusson wrote: James Kohl it [the Neil deGrasse Tyson meme] was not aimed at you, of course, understand that it is about the genera educational situation. BTW Einstein mostly missed biology and Hawking says the 21. century will be that of biology, which I also believe.” The Icelandic atheist and hate monger, blocked me before I could comment further on Neil deGrasse Tyson’s overwhelming display of ignorance. George FR Ellis, who co-authored with Stephen Hawking in the 60’s has already validated my model. See: Understanding and accounting for relational context is critical for social neuroscience
George F R EllisThis is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics.
The Genius Games series from John Coveyou is the way forward. The games successfully link the creation of the sun’s anti-entropic virucidal energy from top-down causation to all biophysically constrained biodiversity via a model that links electrons to ecosystems.
Subatomic is themed around the intersection of particle physics and chemistry! At it’s core, Subatomic is a deck-building game with a light Area Majority mechanic for end game points. Players start with a hand of Up Quarks, Down Quarks and Particle/Wave Duality cards, which they use to form protons, neutrons, and electrons. Players combine these subatomic particles to either build available Elements or buy even more powerful cards for their deck.
We hypothesized that vitamin C mediates these biological processes partially through miRNA regulation.
MiRNA regulation is quantized energy-dependent. The energy comes from the sun. Their hypothesis appears to be based on my claims in my invited review of nutritional epigenetics, which was returned without review by the guest editors of the journal “Nutrients.”
I linked the anti-entropic virucidal energy of sunlight from the claims in Schrodinger (1944) “What is life?” via the quantized energy-dependent creation of microRNAs and vitamin C.
See Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
The likelihood that hemoglobin variants are associated with other beneficial nutrient energy-dependent changes in microbiota populations in the gut can be considered in the context of how balanced nutrition, which includes access to endogenous vitamin C in human populations, supports efficient metabolism and ecological niche construction (McNulty, et al., 2011).
Nutrient-dependent epigenetic effects on histone modifications and DNA methylation play an important role in stabilizing cell type identity and in orchestrating many developmental processes. For example, vitamin C appears to stimulate histone demethylases, which appear to alter the de novo creation of functional G protein-coupled genes such as olfactory receptor genes (Adipietro, Mainland, & Matsunami, 2012; Blaschke et al., 2013; Jazin & Cahill, 2010; Lyons et al., 2013; Tan, Zong, & Xie, 2013).
Researchers recently rediscovered a nutrient-dependent epigenetic variant that links vitamin C to what is probably a glucose and glucose dehydrogenase-dependent base pair change. The base pair change results in addition of a methyl group to a cytosine base, which takes on a hydroxyl group to form different 5-hydroxymethylcytosines (5hmCs). Different 5hmCs are associated with differences in cell types that have the same genetic backgrounds. Nutrient-dependent epigenetically-marked bases help to explain how hundreds of cell types in the human body and in the brain (Kriaucionis & Heintz, 2009) are differentiated and how they maintain their glucose-dependent and other nutrient-dependent receptor-mediated identities (Wu et al., 2014).
Conclusion:
In the context of climate change and changes in diet, the story began with what probably was a nutrient-dependent base pair change and a variant epiallele that arose in a human population in what is now central China. Apparently, the effect of the epiallele was adaptive and it was manifested in the context of an effect on sweat, skin, hair, and teeth. In another mammal, such as the mouse, the effect on sweat, skin, hair, and teeth is probably due to a nutrient-dependent epigenetic effect on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. The pheromones appear to control the nutrient-dependent epigenetically-effected hormone-dependent organization and hormone-activation of reproductive sexual behavior in mammals such as mice and humans, but also in invertebrates and in microbes as previously indicated.The ecological adaptations, which appear to be manifested in the human population are detailed in these two reports (Grossman, et al., 2013; Kamberov, et al., 2013).
The ecological adaptations are likely to be nutrient-dependent and pheromone-controlled. If so, ecological variation probably leads to ecological, social, neurogenic, and socio-cognitive niche construction, which is manifested in increasing organismal complexity and species diversity. If not, there may be something as yet unknown about mutations and evolution that makes sense in the light of what is known about nutritional epigenetics and the molecular biology of species from microbes to man.
…our study demonstrates that NONO post-transcriptionally coordinates circadian mRNA expression of metabolic genes with the feeding/fasting cycle, thereby playing a critical role in energy homeostasis.
Wednesday, February 7, 2018 12PM EST (available on demand with registration)
Everything I claimed about the need to link microRNAs to RNA-mediated amino acid substitution ins proteins was included in the context of this Webinar
Within the first 10 minutes, the speaker describes the ability to link specific amino acids to the structure of the protein strand, which allows for the differentiation of pathology from healthy longevity.
Within the first 17 minutes, he links energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution from microtubules to neurodegenerative diseases, such as Alzheimer’s, Parkinson’s, Lewy Body Disease, and ALS.
He adds that others who are interested in his approach may contact him and he many help them to refine their approach.
Simply put, he does not seem to be among a group of competitors with interests that might prevent the dissemination of accurate information or to prevent rapid scientific advances linked from preventative medicine to Precision Medicine via cryo-EM technology.
…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.
Splicing is the process by which the coding regions of genes are joined to generate genetic messages that specify the production of proteins, the key structural and functional constituents of cells. Splicing can occur in alternative ways in the same genetic message to generate more than one type of protein. The new findings reveal that the alternative splicing process differs significantly between humans and chimpanzees.
See also: Tissue-Specific Alternative Splicing Remodels Protein-Protein Interaction Networks (2012)
Stop touting ridiculous theories before everyone who understands the fact that cryo-EM links everything known to serious scientists about the creation of the sun’s anti-entropic virucidal energy from the physiology of reproduction to healthy longevity. Only then will you begin to understand how the virus-driven theft of quantized energy links the degradation of messenger RNA from mutations to all pathology.
Teach your children well. If you teach them to believe in ridiculous theories, your hell will become theirs. Alzheimer’s is a form of hell on Earth, for example.
Make no mistake, pseudoscientists have stolen the soul of science for more than 20 years, with their ridiculous claims about mutations and evolution.
For comparison, see:
“…considering that we have just 3 such round Nos ‘100’ ‘1000’ ‘10000’, its just three out of all realistic possibilities, no? Admit its looks cool just bec. we calc in Dec system. History books claims was invented by ancient societies; but I think its evolution: We have 10 fingers!”
My reply (SARCASM ALERT):
Thanks. The correlations are intriguing. Templeton funding might help you prove that the numbers game of evolution is true in the context of Cosmopsychism. With enough correlations, facts that link physics and chemistry to viral latency can be dismissed.
Thanks to the Ralser lab for bringing this to my attention with a claim about:
A reductive TCA cycle in a thermophile, which uses the same citrate synthase [enzyme] both for the oxidative and the reductive directionality.
“Every day it looks more likely that primoridial and modern metabolism look similar”
…raises the possibility of a facultatively chemolithomixotrophic origin of life.
Has anyone else considered that possibility?
I tried to look at it from the perspective of chemoorganoheterotrophic metabolism and electron-eating microbes that enzymatically (not automagically) create uranium isotopes, but I got side-tracked by the claims about mutations and evolution. I could not link those claims from the physiology of reproduction in microbes to claims that link the metabolism of food energy to pheromones that biophysically constrain viral latency in species from microbes to humans.
Now, the physiology of pheromone-controlled reproduction in electron-eating microbes that create uranium isotopes suggests the same thing that the Ralser lab suggested: SARCASM ALERT: “It’s turtles all the way down” (the infinite regress problem in cosmology).Unless, like the folks at the Ralser Lab, you are a serious scientist.
The problem for pseudoscientists, theorists, and many so-called science journalists may be familiar to those at the Ralser lab. McEwen et al., (1964) reported “The synthesis of RNA in isolated thymus nuclei is ATP dependent.” All serious scientists know “ATP controls the crowd.”
These findings suggest an additional way for cells to use ATP to maintain proteostasis in the crowded cytoplasm and also fine-tune the material properties of nonmembrane-bound organelles and the cell interior in general.
Obviously, there are now several groups of serious scientists that can make fun of all the pseudoscientists and so-called science journalists who have failed to link physics and chemistry to biophysically constrained viral latency via energy-dependent changes in base pairs in species from thermophiles to those that create uranium isotopes. But Kudos to the first group, or one of the first, to do that:
Sarcasm Alert: I hope that claims about the emergence of energy and mutation-driven evolution did not confuse others as much as they confused so-called science journalists such as John Hewitt, Philip C. Ball, Carl Zimmer, and many others.
When you see the facts reported by an intelligent science journalist, please tell others about the claims that link the creation of energy from the game “Subatomic” to biophysically constrained viral latency in “Cytosis.” Comparisons will be made. It will become clearer that pseudoscientists, theorists and many others have lost their games.
See for example: Attacked from All Sides: RNA Decay in Antiviral Defense
…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.”
Alternatively, everyone can simply accept the fact that food energy typically restricts the virus-driven degradation of messenger RNA, and tell all the pseudoscientists and so-called science journalists where to put their pseudoscientific nonsense (e.g., where the sun don’t shine).
For example: Is the Universe a conscious mind?
Cosmopsychism might seem crazy, but it provides a robust explanatory model for how the Universe became fine-tuned for life
Mitochondria, a subcellular organelle with its own genome, produce the energy required for life and generate signals that enable stress adaptation. An emerging concept proposes that mitochondria sense, integrate, and transduce psychosocial and behavioral factors into cellular and molecular modifications. Mitochondrial signaling might in turn contribute to the biological embedding of psychological states.
Evidence from metabolomic, proteomic, and transcriptomic studies also suggest additional layers of regulation by which stressful experiences may alter mitochondrial components among rodents. Although these metabolites, protein composition, and gene expression outcomes do not reflect the functionality of mitochondria, when assessed in parallel with functional outcomes, they will help explain and refine our understanding of the mechanisms by which stress influences mitochondrial function and health. In addition, whereas functional changes should be regarded as primary indicators of MAL (21), stress-induced molecular changes within mitochondria may also reflect compensatory mechanisms or recalibrations that contribute to long-term changes in mitochondrial function and to the accumulation of MAL. [mitochondrial allostatic load (MAL)]
The multitudinous self mediates scientific explanations of the complexity of real people with and without mental disorders. It also provides resources for enhancing the moral agency that permits people to flourish. For me, flourishing is simply the development of a person’s psychological and social skills in engagement with herself and with others, in the face of the challenges triggered by her physical, social and psychological environment. If we know the characteristics of the self, we might be able to improve the lives of those whose self-experiences are not conducive to flourishing. The self is not an idle concept, either scientifically or ethically; it organises human experience and proliferates moral possibilities. So, yes, know thyself. Every single part.
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 (Runge and Zakian, 1996; Wu and Haber, 1995).
Make no more mistakes, pseudoscientists have stolen the soul of science for more than 20 years, with their ridiculous claims about mutations and evolution.
Excerpt: Summaries of mutation categories: The summaries attest to the fact that human interethnic biodiversity can be linked to all biodiversity via the food energy-dependent creation of enzymes and the pheromone-controlled physiology of reproduction, which link autophagy to biophysically constrained viral latency. Immune Issue
…the findings are “not a show stopper, but the field needs to know about this…
RNAi based drugs have now advanced steps closer towards clinical trials. The powerful in-vivo RNAi machinery and its delicate factors apprehend that RNAi-dependent therapies might create a billion dollar business against the pathogenic organisms and disease for which treatment options are currently restricted conventionally.
The “…miRNA-mediated regulation of enzymes and transporters affecting drug metabolism…” links the National Microbiome Initiative to the Precision Medicine Initiative and to all healthy longevity or to all virus-driven pathology in all living genera via differences in energy as information.
Now that the cause of the symptoms is known [i.e., the loss of the conserved amino acid substitution], it is possible to think about an enzyme replacement therapy for the patients [whose symptoms are obviously caused by the virus-driven degradation of messenger RNA, which links the missense variation and all other mutations to all pathology via the loss of fixed amino acid substitutions in all living genera].
The enzyme replacement therapy would not be required in the context of what is known to all serious scientists about energy-dependent RNA-mediated cell type differentiation in all living genera. See for examples of what is known about the conserved amino acid substitution on page 19 of this sample report. The creation of CYP enzymes clearly links the food that people eat to healthy longevity. Alternatively, the virus-driven theft of quantized energy can be linked to the virus-driven degradation of messenger RNA and all pathology, which traditional medicine has attempted to treat with pharmaceuticals and/or surgery. Alpha Genomix download a Sample report
See for details of how biophysically constrained viral latency is linked from the energy-dependent creation of microRNAs to all biodiversity in the context of a model that links atoms to ecosystems and refutes all theoretical pseudoscientific nonsense.
…the explanatory power of a model of ecological variation and biophysically constrained nutrient-dependent pheromone-controlled ecological adaptations became clear with companion papers published in 2013. See for review [30].
The companion papers [162-163] told a new short story of ecological adaptations. In the context of climate change and changes in diet, the story began with what probably was a nutrient-dependent base pair change and a variant epiallele that arose in a human population in what is now central China.
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30) Kohl, J. V., Nutrient–dependent / pheromone–controlled adaptive evolution: a model. Socioaffective Neuroscience & Psychology 2013,3. doi: 10.3402/snp.v3i0.20553
162) Kamberov, Yana G.; Wang, S.; Tan, J.; Gerbault, P.; Wark, A.; Tan, L.; Yang, Y.; Li, S.; Tang, K.; Chen, H., et al., Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant. Cell 2013,152 (4), 691-702. doi: 10.1016/j.cell.2013.01.016
163 Grossman, Sharon R.; Andersen, Kristian G.; Shlyakhter, I.; Tabrizi, S.; Winnicki, S.; Yen, A.; Park, Daniel J.; Griesemer, D.; Karlsson, Elinor K.; Wong, Sunny H., et al., Identifying Recent Adaptations in Large-Scale Genomic Data. Cell 2013,152 (4), 703-713. doi: 10.1016/j.cell.2013.01.035
The naturally selected food energy-dependent EDAR variant and two amino acid substitutions have since been linked to human interethnic biodiversity in the context of other energy-dependent RNA-mediated fixation of all amino acids in all cell types of all individuals of all living genera.
See: Brief report: Geographic variation in EGFR mutation frequency in lung adenocarcinoma may be explained by interethnic genetic variation The full article can be downloaded from here:
G180A (aka ABCC11, Gly180Ala) and V370A (aka 1540T/C, 370A or Val370Ala) are established biomarkers of East Asian ancestry. Taken together, the two amino acid substitutions clearly linked rs17822931 and rs3827760 respectively to other food energy-dependent changes in base pairs via the physiology of pheromone-controlled reproduction and biophysically constrained interethnic biodiversity in a human population.
Val370Ala is a single nucleotide polynmorphism (SNP) in the ectodysplasin A receptor (EDAR) gene on chromosome 2. The adaptive variant links food energy-dependent changes in immunity from the mouse model to human biodiversity via autophagy, the innate antiphage defense mechanism.
Eighteen years ago, Gly180Ala was linked from the creation of ATP to the creation of RNA and all food energy-dependent hemoglobin variants via the publication of Rotation of F(1)-ATPase and the hinge residues of the beta subunit
The mean work done by a 120 degrees step was approximately 80 pN nm, a value close to the free energy liberated by hydrolysis of one ATP molecule, implying nearly 100% efficiency of energy conversion. The torque is probably generated by the beta subunit, which undergoes large opening-closing domain motion upon binding of AT(D)P. We identified three hinge residues, betaHis179, betaGly180 and betaGly181, whose peptide bond dihedral angles are drastically changed during domain motion. Simultaneous substitution of these residues with alanine resulted in nearly complete loss (99%) of ATPase activity.
Simply put, the Val370Ala and Gly180Ala substitutions exemplify how the anti-entropic virucidal energy of sunlight is biophysically constrained by the substitution of achiral glycine in position 6 of the gonadotropin releasing hormone (GnRH) decapeptide and the food energy-dependent pheromone-controlled fixation of other amino acid substitution that differentiate all cell types in all living genera. In humans.
For example, more than 1700 hemoglobin variants have bee linked to interethnic bidiversity and to primate species biodiversity via the nutrient energy-dependent pheromone-controlled fixation of one or more amino acid substitutions in the organized genomes of humans, chimpanzees, and gorillas.
See: Nothing in Biology Makes Any Sense Except in the Light of Evolution (1973)
For example, 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.
Single nucleotide substitutions or indels [INsertions/DELetionS] can lead to several hemoglobin variants owing to amino acid replacements, while molecular defects in either regulatory or coding regions of the human HBA2, HBA1, HBB or HBD genes can minimally or drastically reduce their expression, leading to α-, β- or δ-thalassemia, respectively.
The nucleotide substitutions are food energy-dependent. The virus-driven theft of quantized energy causes the deletions. Ecological variation links the ability to find food to ecological adaptations only in the context of the pheromone-controlled physiology of reproduction, which biophysically constrains viral latency during the transgenerational epigenetic inheritance of healthy morphological and behavioral phenotypes.
See also: HbVar: A Database of Human Hemoglobin Variants and Thalassemias: Summaries of mutation categories
The summaries attest to the fact that food energy-dependent human interethnic biodiversity can be linked to all biodiversity via the creation of enzymes and the pheromone-controlled physiology of reproduction, which link autophagy to biophysically constrained viral latency.
Re: Monetization of these facts: First, consider short-selling the stocks of companies that have built their capitalization on ridiculous claims that link mutations to evolution. Those claims disappeared with release of the cell biology game “Cytosis.”
Next, buy or lease one — or all three — of the following domains from the owner / founder of the only domains that have continued to disseminate the facts about pheromone constrained viral latency, since 1995 (which is when I founded Pheromones.com). Then RNA-mediated.com. Then Autophagy.pro.
If you have any doubts about what your future holds, see:
