RNA Directed

Correctly modeling life on this planet

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 extant organisms. — Jordan et al., (2005) The increase in the number of…

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Correctly modeling biological energy

The light-activated “origins of life” issue (see: Correctly modeling ecological adaptation) forces others to come out of the woodwork and try to overwhelm the biologically underinformed masses with the complexities of their existence after decades of attributing what is currently known about viruses, viral microRNAs, entropic elasticity, anti-entropic biological energy from the sun, and nutrient-dependent microRNAs, to mutations and evolution. Theorists have denied the obvious facts about light-induced amino acid substitutions and cell type differentiation controlled by the physiology of…

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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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UV-light mutations and gene loss (not gain)

The Neanderthals live on in us March 13, 2015 Excerpt: “He opted instead for a medical degree and then a PhD at the University of Uppsala, where he was supposed to be probing the DNA secrets of a virus.” My comment: If he had done what he was supposed to be doing, he might have learned how viral microRNAs and nutrient-dependent microRNAs contribute to cell type differentiation in all cells of all individuals of all species. If he had done…

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Virus-driven origin of life

On the Origins of Life A new experimental system demonstrates that precursors of ribonucleotides, amino acids, and lipids may have simultaneously arisen from the same prebiotic chemistry. By Jef Akst | March 17, 2015 “This is a very important paper,” Jack Szostak, a molecular biologist and origin-of-life researcher… See also: Luis P. Villarreal: We Need a Nonlinear Language for Life Nobelist Jack Szostak has told me this about autocatalytic sets: the people who came up with the original idea, like…

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Luis P. Villarreal tells it like it is

Luis P. Villarreal has led the way towards discovery of the “origins of life.” He has helped to elucidate what is currently known about how the epigenetic landscape becomes the physical landscape of DNA in the organized genomes of species from microbes to humans. Kudos to Suzan Mazur for admitting that she missed learning about his works. Perhaps a few neo-Darwinian evolutionary theorists will also admit they have missed something very important about the role of viruses in cell type…

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RNA-directed gene choice

March 2015: ChemoSense; see Timothy S. McClintock: “Odorant Receptor Gene Choice” He concludes: “The epigenetic control of OR gene expression through repression and de-repression is a remarkable story, and as a fundamental mechanism intimately associated with the random differentiation of a neural progenitor cell into multiple neuronal subtypes, one wonders whether it might be a framework for understanding other instances of differentiation of neural subtypes (Lyons and Lomvardas, 2014).” My comment: The epigenetic control of OR gene expression is RNA-directed…

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Two types of microRNA are not double agents

Study details microRNA’s role as a double agent during Hep C infection By coopting miRNA-122, the virus appears to alter gene expression in the liver Excerpt: “What if chronic low levels of miRNA-122 prompt changes that, over years, contribute to liver damage and cancer? This could be a molecular link between the viral infection and the pathologies associated with hepatitis C,” Luna says. “More work on miRNA-122 targets in hepatitis C-infected patients may clarify why some go on to develop…

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Epigenetics Skeptism

Thanks to Joost G. Wouters for the alert to this nonsense: 1) Michael White in Pacific Standard magazine flatly states that “Epigenetics Is Not Revolutionizing Biology.” 2) Adrian Bird points out in the journal Cell that many of the field’s assumptions and promises remain unproven and are perhaps excessive. 1) White’s article sketches the field’s promise and hype, from questionable ‪epigenetic‬ diets and wild claims about controlling genes with your thoughts. He follows with a summary of epigenetics, then runs…

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Is DNA-directed transcription RNA-mediated?

Single-cell transcriptogenomics reveals transcriptional exclusion of ENU-mutated alleles. Concluding sentence excerpt: “…rather than a rigid deterministic mechanism, transcription is not hardwired and able to select against potentially adverse changes in the DNA template. Such transcription avoidance may be yet another layer of protection against the detrimental consequences of mutations and provide further clues to understanding its possible consequences, including reduced penetrance and variable expressivity.” Reported as: Rather than being a one-way street, DNA-directed RNA transcription may have profound adaptability Excerpt:…

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  • 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, […]