DNA

From 3-D to epigenetically-effected 4-D genome make-up

Discoveries in 3-D Genome Make-Up and Genetic Changes: Clarification of differences amidst chromosome pairs and how gene expression is effected by chromosome folding Excerpt: “…offers a useful guide for future studies of the epigenome’s function in our evolution and diseases that beset us.” My comment: The guide is also useful because it shows how the anti-entropic effects of light-induced amino acid substitutions links the epigenetic landscape to the physical landscape of DNA in species from microbes to man. For example,…

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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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An epigenetic trap (the prequel)

See also: An epigenetic trap (the sequel) Excerpt: “Support for the link from one epigenetic trap to cell type differentiation was included in the molecular epigenetics section of our 1996 review, which detailed how RNA-mediated chromatin remodeling occurs.” My comment: One epigenetic trap leads to the de novo creation of olfactory receptor genes and cell type differentiation. See also: Heterochromatin-mediated gene silencing facilitates the diversification of olfactory neurons. The first epigenetic trap links the sun’s biological energy to cell type…

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The anti-entropic force of "Nature"

Exploring the Epigenome A National Institutes of Health-funded consortium publishes 111 reference maps of DNA and histone marks. By Jenny Rood | February 18, 2015 Excerpt:  “All our cells have a copy of the same book, but they’re all reading different chapters, bookmarking different pages, and highlighting different paragraphs and words.” These chemical bookmarks, such as methylation and acetylation, help control which genes are transcribed into RNA and expressed in a given cell type, thus aiding the maintenance of a…

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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…

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Physicists: Desperate Acts

Participation on the FB group Thinking Allowed Original led to an invite by Ulla Mattfolk to participate on her secret group  Quantum Biology, coherence and decoherence. On January 22 at 11:45pm, discussion led me to ask whether biophotonic energy differences could be recognized by the photons at the quantum level of their interactions/energies. I thought the answer might explain biodiversity via a link from quantum level self – other recognition to immune system recognition and to macromolecular self – other recognition. My focus has been on well-established…

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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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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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