Epigenetic

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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Theorists have not seen the light

2015 Physiologists uncover a new code at the heart of biology Excerpt: It was long known that almost every amino acid can be encoded by multiple synonymous codons and that every organism, from humans to fungi, has a preference for certain codons. My comment: That fact underlies our representation of RNA-mediated cell type differentiation from our 1996 review From Fertilization to Adult Sexual BehaviorSee our section on molecular epigenetics. Our representation was subsequently linked to organization of genomes in insects…

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“New” quantum biology. Pirating the old

Jim Al-Khalili is a nuclear physicist. Luca Turin is a biologist. Both presenters link Schrödinger’s claims in What is Life? Which one knows most about it? Jim Al-Khalili  frames his presentation in the context of evolutionary theory. See the text or the 20-minute Video presentation: Jim Al-Khalili: How quantum biology might explain life’s biggest questions Luca Turin frames his presentation in the context of what is known to serious scientists about the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding. See also: …

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Thermotolerance and Longevity

Heterotypic Signals from Neural HSF-1 Separate Thermotolerance from Longevity Excerpt: …it was hypothesized that hsf-1 regulates the aging process by modulating chaperone network components to directly influence the folding state of the proteome ( Morimoto, 2008). Our data suggest an alternate method by which hsf-1 can regulate the aging process. In this model, hsf-1 activates the FOXO transcription factor, which initiates a pro-longevity stress response that is distinct from the heat shock response. My comment: The separation of the nutrient…

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The “great filter” is an epigenetic trap

The great filter The silence of universe seems ominous. Was Earth lucky? Thanks to George Ellis​ for alerting others to this. Excerpt: Nick Lane in his magnificent new book The Vital Question thinks that a peculiar feature of all earthly life — that it traps energy in the form of protons pumped across membranes… Excerpt 2) Next, after a couple of billion years, creatures bigger than microbes emerged, once (Nick Lane argues) an energy-per-gene limit was breached by the invention…

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Information and communication (2)

Leaving an Imprint Among the first to discover epigenetic reprogramming during mammalian development, Wolf Reik has been studying the dynamics of the epigenome for 30 years. By Anna Azvolinsky | August 1, 2015 Excerpt: In the mammalian field, the imprinting field, together with the X-inactivation field, was the birthplace of epigenetics. My comment: Researchers like Wolf Reik never mentioned the role viruses play in preventing cell type differentiation. The birthplace of epigenetics became associated with a “still-birth.” The still-birth continued to…

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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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Becoming biologically informed (3)

See also: Becoming biologically informed and Becoming biologically informed (2) Now available for free: New Perspectives on microRNA in Disease and Therapy (July 22, 2015) My comments: Perhaps someone will correct me if I am wrong. The microRNAs do not appear to participate in a direct response to viruses. But, over long periods of time they may fine-tune the microRNA/messenger RNA balance in the organized genomes of all living genera.  If so, the changes are manifested in morphology and in…

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Riding the wrong direction

Riding the Evolution Paradigm Shift With Eugene Koonin Excerpt: The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis… Excerpt: [T]he entire ideology of personalized medicine should be taken with many grains of salt. My comment: Personalized medicine links the conserved molecular mechanisms of biologically-based cause and effect from nutrient-dependent RNA-mediated gene duplication to RNA-mediated amino acid substitutions, which differentiate…

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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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