microbes to man

Quantum initiation of cold chemistry vs Hypeology (3)

See: Quantum initiation of cold chemistry vs Hypeology (2) Facts about the quantized energy-dependent creation of reverse transcriptase, an enzyme that converts a sequence in an RNA molecule into a sequence in a DNA molecule, have been placed into the context of social organization. Social organization: The thermodynamic basis The objective of this work is to establish the connection between energy engineering and social organization and to bring social organization under the big tent of physics. Reported as: How physics…

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Is mainstream science in “Science” pseudoscience?

See: Single neuron may carry over 1,000 mutations (with my comments),  A natural history of neurons: Diverse mutations reveal lineage of brain cells (with my comments), and Study examines scale of gene mutations in human neurons, All three of the links above are to reports on the study results published as: Somatic mutation in single human neurons tracks developmental and transcriptional history Excerpt 1) We also observed a signature of methylated cytosine (meC) to thymine (T) transitions (fig. S8), which…

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Viruses, amino acids, and somatic cell types (2)

Quantitative and functional interrogation of parent-of-origin allelic expression biases in the brain Excerpt: The RNA-seq data enabled us to detect a positive correlation between developmental changes in the magnitude of parental biases and overall gene expression for most imprinted genes. Conclusion: At the level of the organism, our data uncover how paternal and maternal alleles of Bcl-x make vastly different contributions to brain development, a result that has profound implications for the analysis of parentally-inherited polymorphisms in human health. Reported…

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“New” epigenetic mechanism for lifelong learning?

Critical Role of Histone Turnover in Neuronal Transcription and Plasticity Reported as: Lifelong learning is made possible by recycling of histones, study says Also reported as: New epigenetic mechanism revealed in brain cells Excerpt: In humans, researchers used a technique called 14C/12C bomb pulse dating to measure turnover. The technique is based on the fact that high levels of radioactive carbon (14C) were released into the atmosphere during the 1950s and 1960s, when open-air nuclear bomb testing occurred following the…

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Epigenetic regulation of aging by glycine and GnRH

Summary:  “…the regulation of two genes involved with the production of glycine, the smallest and simplest amino acid, is partly responsible for some of the characteristics of aging. This indicates that the aging process in the mitochondrion is controlled by epigenetic regulation, not by mutations.” My comment: The broad-based extension of the fact that aging is epigenetically controlled, extends everything known about RNA-mediated cell type differentiation across the life history transitions of all genera. The focus here is on vertebrates,…

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Creating nothing but a theory (3)

Life is physics and chemistry and communication Any model of biologically-based cause and effect must link atoms to ecosystems via the levels of organization in the diagram. That fact has been known to me since the early 1990s, when I was told that my model must start with sensory input linked to gene activation based on articles like this: Understanding the bases of sex differences Excerpt: “The articles in this issue summarize the factors surrounding sex differences with respect to…

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Questions about life’s diversity

Questions about life can be answered in the context of what sustains it. 1) Answers must explain the diversity of life. 2) The diversity of life may help to explain the purpose of life. 3) Explaining the purpose of life may assist anyone who does not think they will live forever. 4) Answers to questions about life that explain life’s diversity must include what is known about the conserved molecular mechanisms that link differences in morphological and behavioral phenotypes in…

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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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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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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…

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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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