protein-folding

Misunderstanding cancer

Tumor-Only Genetic Sequencing May Misguide Cancer Treatment in Nearly Half of All Patients, Study Shows Excerpt 1) “…they counted 382 possible tumor-related changes. But after comparing a patient’s full germline genome to his or her tumor genomes, they determined that, on average, 249 of these changes were part of the patient’s normal, inherited genetic variation and were not tumor-specific.” Excerpt 2) “In addition to selecting personalized therapies for patients with cancer, sequencing the normal tissue genome can also increase the…

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Mutisensory integration: watching the paradigm shift

Multisensory integration and causal inference in the brain Excerpt (with my emphasis):  It is largely unknown how the brain implements prior knowledge and expectations. Various mechanisms have been proposed such as spontaneous activity (Berkes et al., 2011), the fraction of neurons encoding a particular feature (Girshick et al., 2011), their response gain and tuning curves or connectivity and top-down projections from higher order areas (Rao and Ballard, 1999).” My comment: The brain implements prior knowledge and expectations through nutrient-dependent pheromone-controlled…

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Origin of life and cancer (1,2,3)

1) On the Origins of Life The physics of the light-induced de novo creation of the amino acids was placed into the context of  ‘cyanosulfidic’ protometabolic systems chemistry. The systems chemistry links substitution of achiral glycine in the gonadotropin releasing hormone (GnRH) decapeptide to the biophysically constrained nutrient dependent RNA-mediated chemistry of protein folding in all vertebrates. The role of food odors and hormone-controlled cell type differentiation in all vertebrates also links changes in the balance of viral microRNAs and…

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A genetic variant refutes neo-Darwinism

Summary: They link a single nucleotide polymorphism (SNP) to a genetic variant that decreases viability of an embryo, without linking a nutrient-dependent RNA-mediated amino acid substitution to pheromone-controlled cell type differentiation that begins in the embryo and continues throughout the life history transitions of invertebrates and vertebrates. A Benefit of Failed Pregnancy? This genome-wide association study revealed “…a striking link between mitotic aneuploidy and a single nucleotide variant (SNP rs2305957) on chromosome 4 of maternal genomes.” Excerpt: “There’s this genetic…

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The miRNA/mRNA balance: a suboptimal strategy?

Cells exercise suboptimal strategy to survive Excerpt: “Learning the secrets of alternate molecular pathways could provide clues about how to use them to patients’ advantage, she said.” My comment: The same molecular pathways control the nutrient-dependent physiology of reproduction in all genera. They link RNA-directed DNA methylation to RNA-mediated cell type differentiation via fixation of amino acid substitutions that determine cell types. See also: Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin “Mechanisms of epistasis are often best revealed through…

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Deeply ingrained thoughts

A universal trend of amino acid gain and loss in protein evolution Excerpt: “We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all…

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Graphic misrepresentations of ecological adaptation

This infographic breaks down the top five misconceptions about evolution Excerpt: “Share with all your creationist friends”. Excerpt: “This definition is the best description to date that captures the ever-changing living world.” “[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. Evolution was defined as “changes in gene frequencies in natural populations.” The accumulation of genetic mutations was touted to be enough to change one species to another…. Assumptions, made but not verified, were taught as fact.”…

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Creating nothing but a theory (2)

Seeing the (UV) light: Previously undetected difference in human mutation rate unique to Europeans Excerpts from the discussion: Q: What’s the threshold at which UV-induced substitutions become UV-induced mutations? A: The balance of viral microRNAs to nutrient-dependent microRNAs is the determinant of controlled vs perturbed cell type differentiation in all cells of all individuals of all genera. Cell type differentiation is biophysically constrained by the nutrient-dependent chemistry of RNA-mediated protein folding, which is perturbed by mutations. That’s why uncontrolled mutations…

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The quantum / classical RNA-mediated ‘tipping point’

Researchers identify ‘tipping point’ between quantum and classical worlds Excerpt: “Any popular explanation of quantum theory usually begins with Schroedinger’s cat – a thought experiment describing a cat inside a closed box, that may be either dead or alive,” Vered says. “Rather than looking at the tipping-point between life and death, our experiment examines the point at which quantum behavior gives way to classical physics. Since quantum behavior kicks in at a very small scale, one could liken our results…

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