RNA-mediated gene silencing

Can protein folding chemistry be understood by theorists?

Excerpt: The researchers believe their discovery dovetails with their research on how tumor viruses and cancer mutations change a cell’s DNA structure and organization to cause uncontrolled cell growth. Aye group discovers avenue for precision cancer treatment One challenge is that multiple variations, or isoforms, of the same protein can all catalyze the same cellular function, “but the nuances of biology rest in how individual isoforms are regulated,” Aye said. Natural selection for energy-dependent codon optimality regulates the creation of…

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Energy-dependent physical and biophysical constraints (10)

Summary: The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…— Eugene Koonin My comment: Viruses are not life forms. They steal the quantized energy that links sunlight to viral latency in the context of everything known to all serious scientists about the fact that Feedback loops link odor and pheromone signaling with reproduction See for comparison: Olfaction Warps Visual…

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Energy-dependent physical and biophysical constraints (9)

Summary: Energy determines genome compaction because activity in the nucleus is energy-dependent. Chromatin chains link energy-dependent changes in base pairs from single nucleotide polymorphisms to fixation of RNA-mediated amino acid substitutions in organized genomes via the physiology of pheromone-controlled reproduction. It’s all about the base. Energy-dependent physical and biophysical constraints (8) ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells Excerpt 1) The chromatin structure of DNA determines genome compaction and activity in the nucleus. My comment:…

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Energy-dependent physical and biophysical constraints (1)

Summary: The hitchhiking, the epistasis, and the dynamics of adapting populations are energy-dependent and biophysically constrained in the context of RNA-mediated protein folding chemistry. The virus-driven degradation of messenger RNA links mutations to all pathology in all living genera. An upper limit on the functional fraction of the human genome For the human population to maintain a constant size from generation to generation, an increase in fertility must compensate for the reduction in the mean fitness of the population caused,…

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Cell type assembly and the space-time continuum

Summary: The time to adopt energy-dependent cell type assembly as the unit of cognition was in 1944, when Schrodinger published “What is Life.” By the time Roger Penrose made his comment in the reprint edition, everyone else was too late. Penrose wrote: “How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?” (Roger Penrose 8 August 1991) See: Time (and space)…

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Automagical disruption of an eQTL (2)

See: Automagical disruption of an eQTL (1) The automagical disruption of an eQTL, which linked rs34481144 and influenza could also have been reported in the context of this model. Nutrient-dependent/pheromone-controlled adaptive evolution: a model In the model, food energy links the pheromone-controlled physiology of reproduction in all living genera from rs34481144 and other SNPs to species-specific organism-level changes in skin, glands, and hair protection, which link ecological adaptations to protection from the virus-driven degradation of messenger RNA. Mathematical models vs. biological facts…

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Automagical disruption of an eQTL (1)

E Kaitlynn Allen et al, SNP-mediated disruption of CTCF binding at the IFITM3 promoter is associated with risk of severe influenza in humans, Nature Medicine (2017). DOI: 10.1038/nm.4370 We prioritized SNPs in IFITM3 on the basis of putative biological function and identified rs34481144 in the 5′ UTR. We found evidence of a new association of rs34481144 with severe influenza in three influenza-infected cohorts characterized by different levels of influenza illness severity. We determined a role for rs34481144 as an expression…

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Richard P. Feynman refuted theistic evolution

Summary: Among other delightful examples of his expertise in physics, Feynman presciently linked natural selection for energy-dependent codon optimality from food energy-dependent pheromone-controlled biophysically constrained chromosomal rearrangements to healthy longevity. He also linked the radiation-induced theft of quantized energy to mutations in phages via amino acids that increase the virulence of the viruses. Updated information is presented in the context of refutations by many others who might otherwise claim to believe in theistic evolution. The miR-23a~27a~24-2 microRNA cluster buffers transcription…

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Epigenetic effects of stress by Bruce McEwen (1)

A rendering of how changes in an electron’s motion (bottom view) alter the scattering of light (top view), as measured in a new experiment that scattered more than 500 photons of light from a single electron. Previous experiments had managed to scatter no more than a few photons at a time. Credit: Extreme Light Laboratory|University of Nebraska-Lincoln Summary: In the early 1990’s, Bruce McEwen inspired my life’s works, which link the epigenetic effects of nutrient-stress and/or social stress to the fact…

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The emergence of light as energy from a life-giving star (3)

See also: The emergence of light as energy from a life-giving star (2) A rendering of how changes in an electron’s motion (bottom view) alter the scattering of light (top view), as measured in a new experiment that scattered more than 500 photons of light from a single electron. Previous experiments had managed to scatter no more than a few photons at a time. Credit: Extreme Light Laboratory|University of Nebraska-Lincoln One billion suns: World’s brightest laser sparks new behavior in…

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  • What Darwin proved: there’s no such thing as a species
    GENETICS As Animals Mingle, a Baffling Genetic Barrier A short stretch of DNA is challenging what it means to be a species. By: Emily Singer August 5, 2014 Excerpt: “Scientists have dubbed such regions of the genome “islands of speciation.” The persistence of such islands is a phenomenon that has been observed in a variety of […]
  • Randomness and Divine Providence
    A Q&A on randomness and God’s providence …the main goal is to really put together a collection of scholarly studies of these issues: physicists, biologists, mathematicians, statisticians, philosophers and theologians. replaced: Randomness and Divine Providence Supported by the John Templeton...Read more