protein-folding

Eliminating correlations from evolutionary ecology

De novo creation of olfactory receptor genes clearly links food odors via amino acid substitutions to cell type differentiation in mosquitoes, and in nematodes, flies, honeybees, etc. It would be surprising if cause and effect did not extend to vertebrates from invertebrates. Indeed, Elekonich and Robinson (2000) linked our 1996 model of RNA-mediated cell type differentiation to hormone-organized and hormone-activated behavior in insects more than a decade ago. Since then, Vosshall’s lab has established the role that amino acid substitutions…

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Biologists puzzled by evolved RNAs and decaying DNA

Horizontal Transfer of Entire Genomes via Mitochondrial Fusion in the Angiosperm Amborella (December, 2013) Excerpt) “The ancestral angiosperm-wide genome duplication apparent in the Amborella genome not only serves as a genetic marker for the origin of extant angiosperms, but it may also have set in motion a series of events as numerous genes evolved novel functions, eventually leading to modern flowering plants.” See also: The Amborella Genome and the Evolution of Flowering Plants Excerpt) “Evolution of Small RNAs More than…

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Nothing new under the sun, except pseudoscientific nonsense

On the Importance of Being a Methodological Naturalist Posted on November 5, 2014 by David Sloan Wilson Excerpt: “…consider the flying spaghetti monster, a deity invented to poke fun at religion. It is ridiculous, but is there any way to prove that it doesn’t exist?” Conclusion: “If religious believers abandon methodological naturalism, then they are forced to deny not only the laws of physics and the facts biological evolution, but the histories of their own religions.” My comments: DS Wilson is…

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Making sense of quotes scattered across disciplines

Speaking of Science November 2014’s selection of notable quotes By The Scientist Staff | November 1, 2014 My comment: The quotes are scattered from across disciplines, but can be linked to what is known about conserved molecular mechanisms of biologically-based cause and effect that, in context, make sense of them. 1) Cell type differentiation occurs via amino acid substitutions in the Ebola viruses. Identification of two amino acid residues on Ebola virus glycoprotein 1 critical for cell entry 2) What…

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Complex behaviors of cell types in cancer

Decoding the emergence of metastatic cancer stem cells Excerpt: “By applying a physics-based approach to understand the dynamics of cancer decision-making, we were able to explain a number of recent experimental observations, including some that seemed contradictory.” My comment: The logic of the physics-based approach links physics, chemistry, biology, and math, etc. to conserved molecular mechanisms at the same time theorists tout their pseudoscientific nonsense about “mutations.” See, for example: Cancer’s deadly mutational tug of war Excerpt: Mutations are either…

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RNA eclipses the importance of DNA to cell type differentiation

Why skin cells are skin cells and not neurons Excerpt: “…we’re using this approach to identify how the epigenome changes when plants are exposed to challenging environmental conditions, such as drought or high temperature, and how these changes might prime the plants for greater tolerance of subsequent exposures.” My comment: The ‘approach’ is DNA methylation at a time when RNA sequencing has since revealed how the epigenetic landscape becomes the physical landscape of DNA in the organized genomes of species…

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Nutrient-dependent gene duplication in plants (but not animals?)

Divergence of Gene Body DNA Methylation and Evolution of Plant Duplicate Genes Excerpt 1) “A recent study demonstrated that the DNA methylation in promoter may play a significant role for functional divergence of duplicated genes in human [48].” Excerpt 1 from the cited work [48]: “For 73% of gene pairs, one copy is always hypomethylated compared with the other. This refutes the idea that [RNA-directed] DNA methylation of genes is strictly determined in a tissue-by-tissue manner and indicates the presence…

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Evolutionary theorists and evolutionary theists live under rocks

CRISPR/Cas: Not Just for DNA Anymore Excerpt 1) “Unless you’ve been living under a rock the past two years, you’ve heard of CRISPR/Cas9, an RNA-guided nuclease that’s redefining synthetic biology and genome engineering.” Excerpt 2) “The authors propose several additional applications as well, including… altering pre-mRNA splicing, and transcript tracking in live cells.” My comment: Are you an evolutionary theorist or evolutionary theist who has continued to ignore everything known about RNA-mediated events that link nutrient-uptake to altered pre-mRNA splicing…

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RNA-mediated genetic engineering (Part 2)

WATCH: Bill Nye the Science Guy predicts end of creationism is nigh Excerpt: “Best known as Bill Nye the Science Guy, the 58-year-old educator, TV personality and author lamented the lingering myth that the universe is a product of divine creation.” My comment: Evolutionary theorists have not described a biologically-based evolutionary event that links one species to the evolution of another. The myth of evolution was exposed via the fact that Richard Lenski’s bacteria and Michael Desai’s yeasts did not…

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RNA-mediated genetic engineering

Epigenetics II: Cellular Memory, Imprinting, and Targeting Genome Configuration With RNA Excerpt: “… germline-specific piRNA-targeted epigenetic control is key to understanding how life history events activate natural genetic engineering.” My comment: Researchers are not reporting the molecular epigenetics of RNA-mediated genetic engineering in the context of natural genetic engineering. Indeed, it sometimes seems that other are avoiding mention of links from RNA-mediated cell type differentiation via amino acid substitutions to nutrient-dependent pheromone-controlled ecological adaptations in species from microbes to man.…

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