protein-folding

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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Unified nutritional and molecular mechanisms

Endogenous Hydrogen Sulfide Production Is Essential for Dietary Restriction Benefits Article image: Excerpt: “…unifying nutritional and molecular mechanisms remain elusive.” Reported as Molecular mechanism behind health benefits of dietary restriction identified Excerpt 1) “Dietary restriction is a type of intervention that can include reduced overall food intake, decreased consumption of particular macronutrients such as protein, or intermittent bouts of fasting. It is known to have beneficial health effects, including protection from tissue injury and improved metabolism. It has also been…

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Models by evolutionary biologists are not models

How Networks Are Revolutionizing Scientific (and Maybe Human) Thought By John Edward Terrell, Termeh Shafie and Mark Golitko | December 12, 2014 | Excerpt: “…evolutionary biologists are now modeling series of complex networked relationships at multiple levels ranging from individual “letters” in the genome to protein-gene networks to interaction networks between organisms, thereby demonstrating that our genes are only our destinies to the extent that they link to each other and to the surrounding world—both social and natural.” My comment: That’s…

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The future of physics predicts no future for evolutionary theory

The ever-smaller future of physics ‘Theory of everything’ captures Weinberg’s imagination in Lee Historical Lecture Excerpt: “…there are hints that the answers to fundamental questions will reveal themselves at around a million billionths — between 10­-17 and 10-19 — of the radius of the typical atomic nucleus. My comment: Evolutionary theorists may not recognize the problem that this presents. By accepting de Vries definition of “mutation” and rejecting experimental evidence, which links the epigenetic landscape to the physical landscape of…

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Model organisms: the birds and the bees

Bird Genomes Abound Scientists complete the largest-ever comparative genomic study of birds. By Ruth Williams | December 11, 2014 Excerpt: “Birds are model organisms for a number of human behaviors and conditions—For example, Jarvis compares vocal learning in birds and humans—so determining the genetic basis of such traits requires genetic history.” My comment: Honeybees are model organisms for “…human immunity, disease resistance, allergic reaction, circadian rhythms, antibiotic resistance, the development of the brain and behavior, mental health, longevity, diseases of…

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Chemical ecology and RNA-mediated control of DNA loops

DNA Loop-the-Loops A new full-genome map indicates how DNA is folded within the nuclei of human cells.By Kate Yandell | December 11, 2014 Excerpt: “…many loops were conserved among cell types, and even between mice and humans. But others seemed to drive cell type-specific gene expression patterns.” My comment to The Scientist Magazine: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. Excerpt: “A form of GnRH associated with sexual orientation in yeasts links control of the feedback loops and developmental processes required for…

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Jumping back: Science or Pseudoscience?

Daily Comment November 21, 2014 European Science’s Great Leap Backward By Michael Specter Excerpt 1) “When politicians reject verifiable data and reputable research and rely instead on politics or desire, the results can be devastating.” Excerpt 2 with my emphasis) “…scientific organizations from around the world… have strongly endorsed the safety of G.M. foods. (It should be noted that the U.S. can claim no superiority in our approach to evidence-based science, as demonstrated by the fact that nearly half of…

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Glycine and GnRH: Am I being pedantic?

Posted to the FB page on 12/3/14 at Skeptics; Atheists; Realists; Agnostics; Humanists Stephen Hawking and Brian Cox take part in Monty Python sketch – video Excerpt: “I think you are being pedantic.” My comment: Some people may think I am being pedantic. My focus is not on physics; it is on the role of GnRH in cell type differentiation. My focus now extends from what is known about quantum physics, quantum smell, chirality, quantum biology, and quantum consciousness. What is known about chirality…

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Extensive molecular evidence vs ridiculous theories

Mosquito Genomes Galore Whole-genome sequences of 16 different mosquito species reveal rapid evolution and could inform malaria research. By Ruth Williams | November 27, 2014 Excerpt: “…mosquitoes are rapidly evolving, exhibiting high degrees of gene gains, losses, shuffling, and even transmission between closely related species.” It is the reports on rapid evolution of insects that continues to limit the usefulness of any theories about mutations and or natural selection of anything except food. My comments (below) to The Scientist site…

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Dual genomes: exposing the evolution industry

Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes Excerpt: “The CDP showed a significant overrepresentation of certain gene ontology (GO) groups (global tests Po0.001–0.009), using the programme FUNC23 (Methods). These groups included GPCRs, in particular olfactory receptors (ORs), and other membrane and cell-surface proteins, as well as proteins related to the immune system, such as the MHC (Class I and II), and drug metabolism…” My comment: Biodiversity “…converges upon a ‘common diplotypic proteome (CDP)’, a distinctive subset…

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