amino acid substitutions

Too many targets for theories

Random mutations are the substrates upon which directional natural selection acts.” —  Jay R. Feierman. Others have claimed that random mutations and natural selection somehow lead to the evolution of morphological phenotypes and behavioral phenotypes. They have not placed their claims into the context of what is known about ecological variation and ecological adaptations manifested as RNA-mediated sex differences in cell types of the human brain and all other cell type differences in all genera? Ecological variation is the raw…

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Creating nothing but a theory (3)

Life is physics and chemistry and communication Any model of biologically-based cause and effect must link atoms to ecosystems via the levels of organization in the diagram. That fact has been known to me since the early 1990s, when I was told that my model must start with sensory input linked to gene activation based on articles like this: Understanding the bases of sex differences Excerpt: “The articles in this issue summarize the factors surrounding sex differences with respect to…

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Creating nothing but a theory (2)

Seeing the (UV) light: Previously undetected difference in human mutation rate unique to Europeans Excerpts from the discussion: Q: What’s the threshold at which UV-induced substitutions become UV-induced mutations? A: The balance of viral microRNAs to nutrient-dependent microRNAs is the determinant of controlled vs perturbed cell type differentiation in all cells of all individuals of all genera. Cell type differentiation is biophysically constrained by the nutrient-dependent chemistry of RNA-mediated protein folding, which is perturbed by mutations. That’s why uncontrolled mutations…

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The quantum / classical RNA-mediated ‘tipping point’

Researchers identify ‘tipping point’ between quantum and classical worlds Excerpt: “Any popular explanation of quantum theory usually begins with Schroedinger’s cat – a thought experiment describing a cat inside a closed box, that may be either dead or alive,” Vered says. “Rather than looking at the tipping-point between life and death, our experiment examines the point at which quantum behavior gives way to classical physics. Since quantum behavior kicks in at a very small scale, one could liken our results…

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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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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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RNA directed DNA methylation and cell types

Cell type differentiation is included in all topics in biology, which is why it is important to understand what is currently known about top-down causation in the context of physics and chemistry. Taken together, physics, chemistry, and the conserved molecular mechanisms of biology link Drosophila to Octopuses and all other species on this planet via RNA-directed DNA methylation and RNA-mediated amino acid substitutions that differentiate cell types. See for examples: Let there be anti-entropic light (1) An antagonist led me…

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From 3-D to epigenetically-effected 4-D genome make-up

Discoveries in 3-D Genome Make-Up and Genetic Changes: Clarification of differences amidst chromosome pairs and how gene expression is effected by chromosome folding Excerpt: “…offers a useful guide for future studies of the epigenome’s function in our evolution and diseases that beset us.” My comment: The guide is also useful because it shows how the anti-entropic effects of light-induced amino acid substitutions links the epigenetic landscape to the physical landscape of DNA in species from microbes to man. For example,…

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