protein-folding

Physics, Chemistry, and Molecular biology (PCMb)

Physics, Chemistry, and Molecular biology (PCMb) link ecological variation to ecological adaptations via a model of gene-cell-tissue-organ-organ system complexity that I first presented in 1992. After adding gene activation by pheromones, I co-authored a book that linked the pheromone-controlled physiology of reproduction across species from microbes to man: The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002) Since then, others have written books that claimed that pheromones evolved: Pheromones and Animal Behaviour (2003/2014) and one claimed that mammals…

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Epigenetically-effected metabolic shifts and ecological adaptations

Epigenetics of Trained Innate Immunity: Documenting the epigenetic landscape of human innate immune cells reveals pathways essential for training macrophages. By Ruth Williams | September 25, 2014 [open access] Excerpt: “…they then analyzed genome-wide distributions of four epigenetic indicators of gene activity: DNAse hypersensitivity and three different histone modifications—trimethylation of histone H3 at lysine 4, monomethylation of histone H3 at lysine 4, and acetylation of histone H3 at lysine 27. They also analyzed genome-wide transcription and transcription factor binding. Together…

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Mathematical model: microRNA and epigenetic regulation

Hypothesis & Theory ARTICLE Front. Genet. | doi: 10.3389/fgene.2014.00345 Interplay of microRNA and epigenetic regulation in the human regulatory network. Excerpt: “…a detailed model of the epigenetic interaction and its relations with the cellular environment would be required, and this is still an open issue (24).” My comment: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. Conclusion:  “Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.” The model starts with…

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Seemingly futile cycles are not thermodynamically futile

Scientists discover an on/off switch for aging cells The switch controls the growth of telomeres, the timekeepers of cells September 19, 2014 Excerpt: Understanding how this “off” switch can be manipulated–thereby slowing down the telomere shortening process–could lead to treatments for diseases of aging (for example, regenerating vital organs later in life).” My comment: Seemingly futile thermodynamic cycles of protein biosynthesis and  degradation appear to be confusing. I’m somewhat certain that the folks at Salk realize that cycles of biophysically-constrained…

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New technique used in report of atomic-level ecological adaptations

Archaerhodopsin variants with enhanced voltage-sensitive fluorescence in mammalian and Caenorhabditis elegans neurons Directed evolution of a far-red fluorescent rhodopsin reported as: New technique uses a genetic tool and light to view and map neuronal circuits Excerpt 1): “This [directed evolution] experiment demonstrates how rapidly these remarkable bacterial proteins can evolve in response to new demands. But even more exciting is what they can do in neurons, as Viviana discovered,” says Arnold. Excerpt 2): After incorporating Archer1 into neurons that were…

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Can epigenetic inheritance occur without concurrent changes in morphology AND behavior?

Heritable Histones Scientists show how roundworm daughter cells remember the histone modification patterns of their parents. By Ruth Williams | September 18, 2014 My comment: Strike three, your theories are out. Re: Strike 1) Combating Evolution to Fight Disease Strike 2) RNA and dynamic nuclear organization Strike 3) Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans Does anyone think this latest addition of experimental evidence on heritable histones is not just another thinly-veiled attempt to continue the fight against disease?…

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Behavior: The first response is RNA-mediated not genetically-determined

Diana Maria Petrosanu asked a question in an Evolutionary Psychology News discussion about Evolution’s Random Paths Lead to One Place. I’ve been very vocal in other discussions that tout ridiculous theories that have been repeatedly refuted by biological facts. My answer to her question might help others to understand the language of RNA-mediated events. That’s why I added details to my representation at Combating Evolution to Fight Disease.  Whether or not the addition to my comments is published or understood…

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A microRNA-mediated mechanism that is epigenetically inherited

Pregnancy Stress Spans Generations The stressors a female rat experiences during pregnancy can have repercussions for her granddaughters, a study shows. By Anna Azvolinsky | August 7, 2014 Excerpt: “These changes could be the result of a microRNA (miRNA)-mediated mechanism, which may be epigenetically inherited across generations.” My comment:  There is currently no alternative explanation for these changes. However, a model of how nutrient-dependent pheromone-controlled amino acid substitutions link cell type differentiation (e.g., from the epigenetic landscape to the physical landscape of DNA in…

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The quantum biology of consciousness

Everything known about quantum biology “…suggests conscious experience is intrinsically connected to the fine-scale structure of space–time geometry, and that consciousness could be deeply related to the operation of the laws of the universe.” See for review: Consciousness in the universe: A review of the ‘Orch OR’ theory. These laws of the universe might lead others to think in terms of “laws of biology” (biological laws). Indeed, many informed scientists could expect that ecological, social, and neurogenic niche construction would result…

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MiRNAs methylation and ecological adaptation sans mutations

MiRNAs methylation and ecological adaptation sans mutations  “Our 2003 Molecular and Cellular Biology paper …opened the mechanistic ‘black box’ of the developmental origins of adult disease susceptibility, and firmly placed the word, epigenetics, in the vernacular of this research field.”  — Randy Jirtle (2009) Our 1996 Hormones and Behavior paper included a section on molecular epigenetics with evidence that attested to the involvement of epigenetics in the context of olfactory/pheromonal input and the developmental origins of hormone-organized and hormone-activated adult sexual behavior.…

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