Alternative Splicings

Viruses and ecologically adapted animals

“I should think we might fairly gauge the future of biological science, centuries ahead by estimating the time it will take to reach a complete comprehensive understanding of odor. It may not seem a profound enough problem to dominate all the life sciences, but it contains, piece by piece, all the mysteries” (p. 732). — Lewis Thomas (1980) Olfaction and odor receptors link what you can read about here or at Perfuming the and at Searching for the…

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UV-light mutations and gene loss (not gain)

The Neanderthals live on in us March 13, 2015 Excerpt: “He opted instead for a medical degree and then a PhD at the University of Uppsala, where he was supposed to be probing the DNA secrets of a virus.” My comment: If he had done what he was supposed to be doing, he might have learned how viral microRNAs and nutrient-dependent microRNAs contribute to cell type differentiation in all cells of all individuals of all species. If he had done…

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RNA directed DNA methylation and cell types

Cell type differentiation is included in all topics in biology, which is why it is important to understand what is currently known about top-down causation in the context of physics and chemistry. Taken together, physics, chemistry, and the conserved molecular mechanisms of biology link Drosophila to Octopuses and all other species on this planet via RNA-directed DNA methylation and RNA-mediated amino acid substitutions that differentiate cell types. See for examples: Let there be anti-entropic light (1) An antagonist led me…

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RNA-mediated repurposing in microbes and adaptations in primate brains

Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion Excerpt: “…the C-terminal 47 amino-acids of ARHGAP11B (after lysine-220) constitute not only a unique sequence, resulting from a frameshifting deletion (fig. S10), but also are functionally distinct from their counterpart in ARHGAP11A.” My comment: Co-author Svante Paabo is the senior author of this 2003 publication: Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees The 2015 publication was reported as: A gene for brain size only found…

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RNA-mediated “repurposing” is nutrient-dependent and pheromone-controlled

 Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system Excerpt: 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). Reported as: Evolutionary Rewiring Strong selective pressure can lead to rapid and reproducible evolution in bacteria. By Ruth Williams | February 26, 2015 Excerpt: NtrC shares 30 percent amino acid identity with FleQ, suggesting the…

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Let there be anti-entropic light (1)

Summary: Light-induced amino acid substitutions link cell type differentiation in plants to nutrient-dependent pheromone-controlled reproduction in animals via the biophysically constrained chemistry of protein folding. Protein folding is perturbed by mutations that limit the ability of organisms to adapt to ecological variation. Viruses contribute to mutations. The sun’s biological energy appears to supply the anti-entropic force that links entropic elasticity to the development of successful morphological and behavioral phenotypes that are exemplified in extant versus extinct biodiversity. The importance of…

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Are mutations beneficial?

Researchers develop non-invasive method to detect tumor-causing mutations in saliva Excerpt: “…a multiplexible electrochemical sensor uses electrode chips to enable vesicular entities in saliva called exosomes to rapidly release molecular constituents (DNA, RNA and proteins) while simultaneously detecting any mutations in tumor-causing DNA sequences. The total detection time is less than 10 minutes and required a small saliva sample.” My comment: This news about multiplexing attests to the complexity of systems biology, which links amino acid substitutions to mutated DNA…

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Intelligent viruses and cancers?

The Very Intelligent Ebola Virus Takes Front and Center Excerpt 1) “Ebola doesn’t enter the nucleus. It uses the cell’s machinery of ribosomes and transfer RNA to make proteins from the viral messengerRNA.” Excerpt 2) “Normally, mechanisms inside the nucleus have complex relations with messenger RNA and the alternative RNA editing process (see RNA alternative editing post). Specific protein complexes help splice the messengerRNA before it is sent from the nucleus to the ribosomes in the cytoplasm to make proteins.”…

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Biophysically constrained beginnings of RNA and DNA

Any anonymous participant in the discussion of: DNA may have had humble beginnings as nutrient carrier (Sep 01, 2014 by Adam Hadhazy) asks: “when are you going to keep quiet?” In a series of responses, I have explained the problem I have with honoring his request. The following excerpts from Wikipedia and other sources are loosely strung together because there is no point to providing more extensive details of biologically-based cause and effect until others accept the fact that mutations…

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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