microbes to man

All of “like kind” (Part 2)

See: All of “like kind” in the (bigger) family I’ve since tried, but failed, to succinctly express my thoughts about representations in the article All in the (bigger) family. I exceeded the allowable word count. Here they are, in the first of two comments about the article that I submitted to Science. Received: Mon, 19 Jan 2015 11:51:50 -0500 Your Comment: The 2015 Society for Integrative and Comparative Biology (SICB) presenters may not recognize how much progress has been made…

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Beneficial microbes kill beneficial mutations

Microbiology: Here’s looking at you, squid Margaret McFall-Ngai has dissected the relationship between a beautiful squid and its live-in bacteria — and found lessons for microbiome research on the way. Ed Yong 14 January 2015 Excerpt: “We now know that microbes make up the vast diversity of the biosphere, and that animal biology was shaped by interacting with microbes,” she says. “In my mind, this is the most significant revolution in biology since Darwin.” My comment: I agree. Darwin’s works…

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Constrained evolution is ecological adaptation

See also: Unconstrained evolutionary innovability Ideas that evolution is not constrained can be compared to experimental evidence of biophysically constrained ecological adaptations. The most recent relevant open access published work from the Jakobsson lab is: TRIM28 Represses Transcription of Endogenous Retroviruses in Neural Progenitor Cells. This is a link to a prior publication (also open access): microRNA-125 distinguishes developmentally generated and adult-born olfactory bulb interneurons Taken together these two published works extend our 1996 model of RNA-mediated cell type differentiation…

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A single amino acid substitution differentiates cell types of E. coli

Rare amino acid influences E. coli infection Excerpt: “They found that E. coli O157 is unable to attach itself to host tissue in high concentrations of D-Serine. Other strains, such as those that cause meningitis, thrive in the presence of the amino-acid.” My comment: Three steps are required to link the amino acid substitution in E. coli to RNA-mediated stability of the DNA in the organized genome of a nutrient-dependent strain. 1) nutrient-dependent potentiation makes a trait possible; 2) receptor-mediated…

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Models by evolutionary biologists are not models

How Networks Are Revolutionizing Scientific (and Maybe Human) Thought By John Edward Terrell, Termeh Shafie and Mark Golitko | December 12, 2014 | Excerpt: “…evolutionary biologists are now modeling series of complex networked relationships at multiple levels ranging from individual “letters” in the genome to protein-gene networks to interaction networks between organisms, thereby demonstrating that our genes are only our destinies to the extent that they link to each other and to the surrounding world—both social and natural.” My comment: That’s…

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Chemical ecology and RNA-mediated control of DNA loops

DNA Loop-the-Loops A new full-genome map indicates how DNA is folded within the nuclei of human cells.By Kate Yandell | December 11, 2014 Excerpt: “…many loops were conserved among cell types, and even between mice and humans. But others seemed to drive cell type-specific gene expression patterns.” My comment to The Scientist Magazine: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. Excerpt: “A form of GnRH associated with sexual orientation in yeasts links control of the feedback loops and developmental processes required for…

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Jumping back: Science or Pseudoscience? (2)

See: Jumping back: Science or Pseudoscience? European Science’s Great Leap Backward inferred that evolutionary theory is evidence-based science: Excerpt: “… the U.S. can claim no superiority in our approach to evidence-based science, as demonstrated by the fact that nearly half of the country rejects the “theory” of evolution…” This article attests to the need to substitute evidence-based science: Leading Activist Apologizes For Starting Anti-GMO Movement Excerpt: “But what about mixing genes between unrelated species? The fish and the tomato? Turns…

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Jumping back: Science or Pseudoscience?

Daily Comment November 21, 2014 European Science’s Great Leap Backward By Michael Specter Excerpt 1) “When politicians reject verifiable data and reputable research and rely instead on politics or desire, the results can be devastating.” Excerpt 2 with my emphasis) “…scientific organizations from around the world… have strongly endorsed the safety of G.M. foods. (It should be noted that the U.S. can claim no superiority in our approach to evidence-based science, as demonstrated by the fact that nearly half of…

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Glycine and GnRH: Am I being pedantic?

Posted to the FB page on 12/3/14 at Skeptics; Atheists; Realists; Agnostics; Humanists Stephen Hawking and Brian Cox take part in Monty Python sketch – video Excerpt: “I think you are being pedantic.” My comment: Some people may think I am being pedantic. My focus is not on physics; it is on the role of GnRH in cell type differentiation. My focus now extends from what is known about quantum physics, quantum smell, chirality, quantum biology, and quantum consciousness. What is known about chirality…

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Dual genomes: exposing the evolution industry

Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes Excerpt: “The CDP showed a significant overrepresentation of certain gene ontology (GO) groups (global tests Po0.001–0.009), using the programme FUNC23 (Methods). These groups included GPCRs, in particular olfactory receptors (ORs), and other membrane and cell-surface proteins, as well as proteins related to the immune system, such as the MHC (Class I and II), and drug metabolism…” My comment: Biodiversity “…converges upon a ‘common diplotypic proteome (CDP)’, a distinctive subset…

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