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Half truths support theories without facts

How to lie by telling the truth Excerpt: People… trot out half-truths, in full expectation and knowledge that they will create a false impression. And then, when others act on the false impression, the “truth-telling liars” can sit back and pretend that they aren’t liars. They get the benefit of lying, without any damage to their precious self-image. My comment: It is more difficult for others to determine who benefits from half truths when more than one individual or research…

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Hydrogen-Atom Transfer in DNA Base Pairs (4)

Historical perspective: Behold James Vaughn Kohl. Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction. These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people…

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MicroRNA – controlled ecological adaptations

A post-transcriptional mechanism pacing expression of neural genes with precursor cell differentiation status Introduction: Eukaryotic gene expression is an intricate balancing act between transcription and post-transcriptional steps of RNA metabolism. Developmental readjustment of this balance allows large cohorts of genes to be expressed in cell- and tissue-specific manner. Among other regulators, RNA-binding proteins (RBPs) provide an important means for modulating RNA processing and turnover in the context of cellular differentiation1, 2, 3, 4. For example, downregulation of the ubiquitously expressed…

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Is SUMOylation RNA-directed DNA methylation?

System-wide identification of wild-type SUMO-2 conjugation sites Excerpt: SUMOylated proteins were found to be predominantly nuclear, and involved in chromatin remodelling, RNA splicing, transcription and DNA repair. When compared with other SUMOylation studies, a significant overlap with PRISM-identified SUMO sites (48%) and SUMO target proteins (85%) was confirmed. We discovered one-fifth of the PRISM-identified SUMOylated lysines to overlap with ubiquitylation and acetylation. My comment: SUMOylation appears to be a new name for RNA-directed DNA methylation, which links nutrient-dependent RNA-mediated amino…

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How to find a “holy grail” under your nose

Proteomics provides new leads into nerve regeneration Excerpt: “…the “holy grail” of regenerating a nerve enough for it to resume its function has been largely elusive.” My comment:  Theorists who are looking for the “holy grail” of nerve cell regeneration don’t realize that it is literally ‘right under their nose.’ The sense of smell links the anti-entropic epigenetic effects of the sun’s biological energy to nutrient-dependent DNA repair via the light-induced de novo creation of amino acids and the amino…

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Correctly modeling ecological adaptation

Statistics requantitates the central dogma Excerpt: “Mammalian proteins are expressed at ∼103 to 108 molecules per cell (1). Differences between cell types, between normal and disease states, and between individuals are largely defined by changes in the abundance of proteins, which are in turn determined by rates of transcription, messenger RNA (mRNA) degradation, translation, and protein degradation. If the rates for one of these steps differ much more than the rates of the other three, that step would be dominant…

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Imagining that data historically supports evolutionary theory

1) Arguments in the evo-devo debate: say it with flowers! Abstract excerpt: A key question in evolutionary developmental biology is how DNA sequence changes have directed the evolution of morphological diversity. The widely accepted view was that morphological changes resulted from differences in number and/or type of transcription factors, or even from small changes in the amino acid sequence of similar proteins. My comment: This is the first time I have seen anyone claim that the “…small changes in the…

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Single-cell level assay of protein biosynthesis and degradation

High-throughput detection of miRNAs and gene-specific mRNA at the single-cell level by flow cytometry Excerpt: “We use this technique to show modulation of a microRNA critical for T-cell function, miR-155. We adapt this assay for simultaneous detection of mRNA and proteins by ImageStream technology.” Reported as: Technology breakthrough reveals cellular transcription process My comment: Their assay simultaneously detects epigenetically-effected changes in the miRNA/mRNA balance and proteins, which link nutrient-uptake to the physical landscape of DNA in the organized genomes of…

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Thermodynamic constraints and ecological adaptations sans evolution

Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites Excerpt: “…a two-variable model that combines stability and stress signi ficantly improves predictions. Therefore, both the overall stability [symbol] and the stress [symbol] seem to capture distinct thermodynamic constraints on protein evolution.” My comment: Proteins do not evolve. Nutrients are required. Metabolism of nutrients to species-specific pheromones controls the physiology of reproduction in species from microbes to man. The nutrient-dependent pheromone-controlled physiology of reproduction enables epistasis via nutrient-dependent RNA-directed DNA…

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Evolutionary heritage or ecological adaptation? Racism versus reality

Jewish Heritage Written in DNA Fully sequenced genomes of more than 100 Ashkenazi people clarify the group’s history and provide a reference for researchers and physicians trying to pinpoint disease-associated genes. By Kate Yandell | September 9, 2014 Excerpt: These results are compatible with those of prior work on mitochondrial DNA (mtDNA), which is passed on maternally. This prior work suggested that Ashkenazi men from the Middle East intermarried with local European women. The Ashkenazi population “hasn’t been likely as…

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