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Welcome to RNA-Mediated

A Message From J.V.Kohl:

Here you will find information that links physics, chemistry, and molecular epigenetics via RNA-mediated events such as the de novo creation of olfactory receptor genes in order to encourage a public discussion of a paradigm shift.

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Mute points: most are afraid to mention them

In discussion of anthropic theory and the fact that fundamental physical constraints underlie our life-enabling universe, Andrew Jones wrote: “Pathogenicity of E. coli 0157 has nothing to do with its temperature stability.” Like others who are biologically uninformed, Jones defies a common sense approach and he also defies the US president’s call for intelligent researchers to be integrated into areas of medical research: See: Obama Calls for Medical-Research Expansion Excerpt: “President Barack Obama called for a new medical research push…

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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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All of "like kind" in the (bigger) family

All in the (bigger) family Science 16 January 2015: Vol. 347 no. 6219 pp. 220-221 DOI: 10.1126/science.347.6219.220 by Elizabeth Pennisi Abstract: A decade of genetic data and other evidence has persuaded most researchers that insects and crustaceans, long considered widely separated branches of the arthropod family, actually belong together. The new arthropod tree puts hexapods—six-limbed creatures that include insects, springtails, and silverfish—as closer kin to crabs, lobster, shrimp, and crayfish than those “standard” crustaceans are to others such as seed…

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Environment epigenetically shapes the immune system

Environment, more than genetics, shapes immune system 1) –with my emphasis Re: “There’s nothing here that is revolutionary or requires rethinking of our assumptions about how the immune system functions…” My comment: They removed assumptions about cell type differentiation by linking differences in metabolic networks to genetic networks. They indirectly showed that ecological adaptations are nutrient-dependent and the adaptations are controlled by the metabolism of nutrients to species-specific pheromones. The pheromones control the nutrient-dependent physiology of reproduction in species from…

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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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Unconstrained evolutionary innovability

The Strange Inevitability of Evolution by Philip Ball Excerpt 1)  Natural selection supplies an incredibly powerful way of pruning variation into effective solutions to the challenges of the environment. But it can’t explain where all that variation came from. As the biologist Hugo de Vries wrote in 1905, “natural selection may explain the survival of the fittest, but it cannot explain the arrival of the fittest.” Over the past several years, Wagner and a handful of others have been starting…

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RNA-protein interactions reveal biophysical to ecological landscapes

Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes RNA-protein interactions are tethered to DNA via ultra-high-throughput measurement of the RNA-protein interactions that link amino acid substitutions to cell type differentiation. Differences in affinity are often driven by sequence-specific changes in both association and dissociation rates that rapidly link bio-physical constrained RNA-mediated protein folding to models that provide “…generalizable insight into the biophysical basis and evolutionary consequences of sequence-function relationships.” This is the generalizable…

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Mutagenesis: Replacing facts with theories

Never mind the selfish gene – ribosomes are the missing link Excerpt: “All cells share three organelles, or internal structures, besides gene-containing chromosomes: ribosomes which contain the machinery for translating genetic information into the proteins that perform the cell’s work; a cell membrane that selectively permits materials in and out; and acidocalcisomes, which store and regulate the ions that drive the chemical reactions of life.” In his criticisms of my model of cell type differentiation, Andrew Jones (aka anonymous_9001 in…

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  • 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, […]
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