protein-folding

RNA-mediated epigenetic modification via DNA-methylation

I have repeatedly used the phrase “RNA-directed DNA methylation and RNA-mediated amino acid substitutions” in the context of links from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man. See for example: RNA-mediated, with links to ~200 blog posts. In the introduction to my 2012 review I attested to the importance of the pathway that links the epigenetic landscape to pharmacogenomics. Excerpt: “The gene, cell, tissue, organ, organ-system pathway is…

Read More

How fast can evolutionary theory be changed?

Boston, land of…creationists? Excerpt: “For example, right now a creationist with a Harvard science degree is lecturing in Boston on Evolution: Bankrupt Science; Creationism: Science You Can Bank On. Obviously, Dr Nathaniel Jeanson is one of the fruit loops who plodded through a graduate program.” My comment: Dr Nathaniel Jeanson continues to politely lead the way to understanding the science of creation. See: Purpose, Progress, and Promise, Part 5 Excerpt: “The intense focus the secular community has placed on human…

Read More

Biological energy and a microbiome model of a light-driven time machine

I am not quite finished with this blog post, but will update it after posting to protect against piracy of the concept. Experimental simulation of closed timelike curves Abstract excerpt: The study of these systems therefore provides valuable insight into nonlinearities and the emergence of causal structures in quantum mechanics—essential for any formulation of a quantum theory of gravity. Here we experimentally simulate the nonlinear behaviour of a qubit interacting unitarily with an older version of itself, addressing some of…

Read More

Quantum Superpositions: let there be light

Ideal Negative Measurements in Quantum Walks Disprove Theories Based on Classical Trajectories Reported as: Atoms can be in two places at the same time Excerpt: “This is not yet a proof that quantum mechanics hold for large objects,” cautions Alberti. My comment: I framed my comments and a question in the context of this article on physics. Their claim of a possible size limit on quantum superpositions seemed to divorce top-down causation from cell–cell communication in mammals. That suggested there…

Read More

Are viruses microRNAs? (2)

The role of microRNAs in cell type differentiation can be compared in the context of the role of viruses and mutations that cause cancer. Facts provide a basis for explaining the biological basis of epigenetically-effected cell type differentiation in species from microbes to man. But first, those who are biologically uninformed must answer the question: Are viruses microRNAs? Andrew Jones aka anonymous_9001 is correct. Viruses are not microRNAs. anonymous_9001 5 / 5 (6) 11 hours ago Stupid question of the…

Read More

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…

Read More

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…

Read More

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…

Read More

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…

Read More

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…

Read More