RNA Directed

Quantum correlations/pseudoscience

A quantum advantage for inferring causal structure Preprint excerpt: “The causal inference schemes described here promise extensive applications in experiments exhibiting quantum eff ects. For instance, they can provide a test of whether the dynamics of a given open quantum system is Markovian or not [17{24]. This is because in a non-Markovian evolution, the environment acts as a common cause between the dynamical system at one time and the same system at a later time. Our inference schemes may also help…

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Anti-entropic solar energy

“We have a group trying to model the mitochondrion” — Ulla Mattfolk Trash pickup problem Excerpt: “The PGAM5 protein would be regulated by an allosteric mechanism, in which its biological function would switch from activation of the PINK1/PARKIN pathway for removal of damaged mitochondria to the FUNDC1 pathway for removal of damaged mitochondria,” according to Hannink. “Peptides behave like drug molecules; any time you can identify a biological process that is regulated by a peptide, that peptide becomes a leading…

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Mimicking claims and ignoring facts

Summary: Last week, researchers reported they had caught up to “Nature” despite their inability to link viral microRNAs and nutrient-dependent microRNAs from the nature of non-living viruses to the nature of cellular life and to cell type differentiation via RNA-mediated amino acid substitutions, metabolic networks, and genetic networks. Today, we see the “billions of years” claim, with no mention of the over-the-weekend re-evolution of the bacterial flagellum or 1.8 billion years of epistasis in bacteria at the bottom of the…

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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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