RNA-directed DNA methylation and RNA-mediated events

Many colleagues and most of my antagonists seem to be unwilling to accept the fact that RNA-directed DNA methylation links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man. Lack of acceptance appears to be due to the fact that they think mutations and natural selection link evolutionary events to biodiversity. There is no model for that, but they refuse to accept the fact that RNA-mediated events link ecological variation…

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Mathematical model: microRNA and epigenetic regulation

Hypothesis & Theory ARTICLE Front. Genet. | doi: 10.3389/fgene.2014.00345 Interplay of microRNA and epigenetic regulation in the human regulatory network. Excerpt: “…a detailed model of the epigenetic interaction and its relations with the cellular environment would be required, and this is still an open issue (24).” My comment: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. Conclusion:  “Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.” The model starts with…

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Seemingly futile cycles are not thermodynamically futile

Scientists discover an on/off switch for aging cells The switch controls the growth of telomeres, the timekeepers of cells September 19, 2014 Excerpt: Understanding how this “off” switch can be manipulated–thereby slowing down the telomere shortening process–could lead to treatments for diseases of aging (for example, regenerating vital organs later in life).” My comment: Seemingly futile thermodynamic cycles of protein biosynthesis and  degradation appear to be confusing. I’m somewhat certain that the folks at Salk realize that cycles of biophysically-constrained…

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Do bacterial proteins evolve?

Among the phrases most likely to get my attention but least likely to get the attention of an evolutionary theorist is “bacterial proteins evolve.” See for example (with my emphasis): To provide insight into how bacterial proteins evolve to adapt to cold environment…. Most people would assume that evolution led to the ecological adaptation so that these bacteria could survive in a cold environment. In fact, many people must have made that assumption along with all the other assumptions they made…

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Probable changes in connectivity

Table of Contents: Nature Reviews Neuroscience October 2014 Vol 15 No 10 Excerpt from: Research Highlights: Learning and memory: Uncoupling memory traces “The emotional valence of a memory can be changed, and this probably involves a change in the connectivity between hippocampal and amygdalar memory traces.” My comment: 1) The connectivity change is epigenetically-effected by olfactory/pheromonal input. 2) Epigenetically-effected RNA-mediated events link the epigenetic landscape to the physical landscape of DNA in species from microbes to man. 3) Conserved molecular…

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New technique used in report of atomic-level ecological adaptations

Archaerhodopsin variants with enhanced voltage-sensitive fluorescence in mammalian and Caenorhabditis elegans neurons Directed evolution of a far-red fluorescent rhodopsin reported as: New technique uses a genetic tool and light to view and map neuronal circuits Excerpt 1): “This [directed evolution] experiment demonstrates how rapidly these remarkable bacterial proteins can evolve in response to new demands. But even more exciting is what they can do in neurons, as Viviana discovered,” says Arnold. Excerpt 2): After incorporating Archer1 into neurons that were…

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Memory of repression and memory of behavior (2)

“Mutations that become so common that they affect more than 1% of a population are called polymorphisms (for example, the human blood types A, B, AB, and O).“ The claim that human blood types are mutations should be supported with experimental evidence of biologically-based cause and effect. Ask your professor, “What evolutionary event linked the mutation to natural selection and the evolution of human blood types? How did nutrient-dependent cell type differentiation become mutation-initiated cell type differentiation, when it is…

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Memory of repression and memory of behavior

H3K27me and PRC2 transmit a memory of repression across generations and during development Reported as: How epigenetic memory is passed through generations: Sperm and eggs transmit memory of gene repression to embryos Date: September 18, 2014 Excerpt: “There are dozens of potential epigenetic markers. In studies that document parent-to-child epigenetic inheritance, it’s not clear what’s being passed on, and understanding it molecularly is very complicated. We have a specific example of epigenetic memory that is passed on, and we can…

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Quantum physics meets Evolutionary Psychology News

Capturing the motion of a single molecule in real time as it oscillates from one quantum state to another September 18, 2014 Excerpt: “It also moves researchers a step closer to viewing the molecular world in action — being able to see the making and breaking of bonds, which control biological processes such as enzymatic reactions and cellular dynamics.” My comment: The making and breaking of bonds controls all biological processes. Luca Turin tried to do move researchers a step closer…

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RNA-mediated ecological adaptations of teeth

Counting fish teeth reveals DNA changes behind rapid evolution By Robert Sanders, Media Relations | September 17, 2014 Excerpt: “This is one of the first cases where we find that the rules found for traits lost apply as well to traits gained,” said Miller. My comment: Traits are gained and lost in the context of nutrient-dependent, odor-induced, receptor-mediated, RNA-mediated events that lead to amino acid substitutions that differentiate cell types. The cell type differentiation must be manifested in morphological and…

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  • What Darwin proved: there’s no such thing as a species
    GENETICS As Animals Mingle, a Baffling Genetic Barrier A short stretch of DNA is challenging what it means to be a species. By: Emily Singer August 5, 2014 Excerpt: “Scientists have dubbed such regions of the genome “islands of speciation.” The persistence of such islands is a phenomenon that has been observed in a variety of […]
  • 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, […]