Post-transcriptional regulation, mRNA translation, Splicing, mRNA localization, Development, Epigenetic, Biophysics, Ecology, Variant, Constraint, Adaptation, Vitamin, Nutrient, Species, Diversity, RNA structure, RNA folding, High-throughput biophysics, RNA tertiary structure, nucleic acid thermodynamics
Summary: I am an American who does not think that most Americans are as gullible as all neo-Darwinian theorists. The issue may come down to a claim from Robert Karl Stonjek about who he thinks created the anti-entropic virucidal energy of sunlight.
As others prepare to try and sneak up from behind and link ecological variation to quantized energy-dependent biophysically constrained ecological adaptions, they should also prepare to answer questions about biophysically constrained viral latency.
My comment to BioRXiv
Isoform-expression in all cell types of all individuals of all species is quantized energy-dependent and RNA-mediated. See: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964) https://www.sciencedirect.com/science/article/pii/0926655064901665 Excerpt: “The synthesis of RNA in isolated thymus nuclei is ATP dependent.” Without the ATP-dependent synthesis of RNA, you cannot get from isoform expression to cell type differentiation.
Past attempts have failed miserably. See: Co-evolved genetically integrated mitonuclear communication?
Mitonuclear communication is quantized energy-dependent and biophysically constrained. The details of the microRNA-mediated biophysical constraints across the time-space continuum have been discussed in four recent publications.
Olfaction Warps Visual Time Perception (Wen Zhou’s group)
High-Throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding (William James Greenleaf’s group)
A Light-Releasable Potentially Prebiotic Nucleotide Activating Agent (Sutherland’s group)
A Fluorescent G-Quadruplex Sensor for Chemical RNA Copying (Szostak’s group)
It is no longer possible for most serious scientists to look back on Szostak’s past claims and his retractions without laughing. Sutherland’s group and several other groups have consistently linked the epigenetic effects of food odors and pheromones from light-activated endogenous substrates to the creation of all biodiversity on Earth.
The end to the pseudoscientific nonsense touted by theorists may be in sight. See also: Schrödinger at 75 – The Future of Biology – September 2018
See also: Structure of the mitochondrial ATP synthase from Pichia angusta determined by electron cryo-microscopy (John E. Walker’s group)
Living cells need fuel in the form of adenosine triphosphate, or ATP, to stay alive. This fuel is generated by a molecular machine made of two motors joined by a rotor. One generates rotation by using energy provided by oxidative metabolism or photosynthesis; the other uses energy transmitted by the rotor to make ATP molecules from its building blocks, adenosine diphosphate, or ADP, and inorganic phosphate. The structure has been determined of a fungal machine, isolated from its cellular power stations, the mitochondria, where the machine operates. It provides unsuspected details of the blueprint of the machine and how it works. The working principles of the fungal machine apply to similar machines in all species.
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model Published on 14 Jun 2013
See: Amazing Atheist Archive Published on 24 Aug 2013
For a historical perspective, see:
Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism (2015)
Reported as: Researchers may have solved origin-of-life conundrum
…the conditions that produce nucleic acid precursors also create the starting materials needed to make natural amino acids and lipids. That suggests a single set of [light activated] reactions could have given rise to most of life’s building blocks simultaneously.
See also: Wnt proteins as modulators of synaptic plasticity on the Neuroscience FB group
See also: Mitochondria on the move: BMSCs fuel AML energy
The treatment of AML, the most common type of leukemia in adults, has not improved over the past several decades, with outcomes remaining poor and most patients dying of relapse.
Suicide prevention outcomes suffer from the same problem: human idiocy. Suicide has been linked to the virus-driven degradation of messenger RNA, which links mutations to all pathology.
Food energy biophysically constrains the pheromone-controlled physiology of reproduction in species from microbes to humans.
I reiterate: Evolution of compensatory substitutions through G.U intermediate state in Drosophila rRNA (1991)
The rate of evolution of compensatory substitution is close to that predicted by a simple model of compensatory substitution through slightly deleterious or slightly advantageous G.U pairs, although some exceptions are presented.
Compensatory substitutions in all advantageous G.U pairs are quantized energy-dependent and they are biophysically constrained by the physiology of reproduction in species from microbes to humans. The compensatory substitutions do not evolve and neither did humans or any other species.
Pheromones biophysically constrain viral latency. See also: Pheromonal Regulation of Genetic Processes: Research on the House Mouse (Mus musculus L.) (1994)
Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes (13 April 2014)
We observe that evolutionary landscapes of RNA-protein interactions are highly constrained…
Any constrained evolutionary landscape exemplifies biophysically constrained ecological adaptations. Therefore, anyone who still refers to “evolutionary landscapes” as if they did not link the epigenetic landscape to the energy-dependent physical landscape of supercoiled DNA is qualified to be an example of human idiocy.
They must first learn to ask the right question.
If the base pairs in the RNA structure do not evolve with a random mutation model, then what is the mechanism of this evolution? — RR Gutell (2015)
See for comparison: Kimura & Crow: Infinite alleles
The 1964 paper began by describing a basic model under the assumption that each mutation has no net effect on the bearer’s survival and reproduction, that is, each mutation is “neutral”. The rest of the paper built on this foundation by introducing the effects of natural selection and random drift, but it was the first, introductory section that was to become most influential. The infinite alleles model was ready and waiting for the arrival of molecular data to population genetics two years later…
Before then, McEwen et al., (1964) had linked the energy-dependent creation of ATP to the creation of RNA and every aspect of RNA-mediated cell type differentiation in all living genera.
Co-author, Rebecca Vega Thurber is one of the plenary speakers at the 2018 ACM International Conference on Interactive Surfaces and Spaces! Her lab investigates the role and dynamics of bacteria and viruses in marine hosts and habitats in order to better understand the proximate causes of disease, habitat degradation, and ecosystem alterations.
See also: Virus-mediated archaeal hecatomb in the deep seafloor It seems likely that her presentation will embarrass all biologically uninformed theorists who still tout evolution instead of sympatric speciation.
Added embarrassment comes from the fact that the Virus-mediated archaeal hecatomb in the deep seafloor has since been linked to the virus-driven pathology of Alzheimer’s disease.
James V. Kohl detailedl how quantized energy-dependent microRNA biogenesis links the pheromone-controlled physiology of reproduction to biophysically constrained viral latency and healthy longevity. Links from what organisms eat to the enzyme-dependent metabolism of food also link metabolic networks to microRNA-mediated genetic networks in the context of RNA interference. Drug therapies alter RNA interference by altering cell type differentiation in all cells of all individuals of all species. For comparison, during the past 26 years, Kohl has detailed how the chemistry of protein folding is biophysically constrained at every level of biological organization by conserved molecular mechanisms.