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 to detect initial correlations between system and environment, which, if unaccounted for, can lead to
errors in the characterization of processes [15, 25-29].”

My comment: Non-Markovian evolution is exemplified by links from ecological variation to epigenetically-effected cell type differentiation manifested in ecological adaptations. For example, the light-induced de novo creation of amino acids links quantum physics to metabolic networks and genetic networks via RNA-mediated substitutions of amino acids that stabilize the organized genomes of all genera in the context of their physiology of reproduction.

Top-down causation is the sun’s biological energy (e.g., solar/spectral energy). Epigenetic effects are exemplified by photosynthesis in plants, which links top-down causation via light-induced amino acid substitutions to cell type differentiation in animals. See: Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins

RNA-directed DNA methylation and RNA-mediated cause and effect via amino acid substitutions is also recognized by serious scientists in the context of the nutrient-dependent pheromone-controlled physiology of reproduction in species from microbes to man. See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model.

Excerpt: “…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution.”

See also my comment on: All in the (bigger) family:

Excerpt: Apparently, they’ve learned that the same set of microRNAs controls expression of the genes for rate-limiting enzymes that control the hormone production of different hormones in insects and crustaceans.

For a summary of  what is currently known about nutrient-dependent pheromone-controlled biologically based cause and effect, see senior author Jerome Hui’s The phylogenetic utility and functional constraint of microRNA flanking sequences.

Excerpt: “Despite historic issues regarding their use for phylogenetic inference [8], miRNAs can be employed as both qualitative [9] and quantitative markers, with the latter demonstrated clearly here.”

My comment: What has been clearly demonstrated is the link from viral microRNAs and nutrient-dependent microRNAs. The balance of viral /nutrient-dependent microRNAs links viruses from entropic elasticity and nutrients to anti-entropic epigenesis and epistasis. In species from microbes to man epistasis is nutrient-dependent and pheromone-controlled by the epigenetic effects of food odors and pheromones on reproduction. See:  Feedback loops link odor and pheromone signaling with reproduction, which was co-authored by 2004 Nobel Laureate, Linda Buck.

It links top-down causation from the light-induced de novo creation of amino acid substitutions and takes the biophysically constrained chemistry of protein folding from theoretical physics and correlations to biologically-based cause and effect.

Terms like “causal inference” schemes and “phylogenetic inference” can be viewed in the context of “big bang” cosmology and evolutionary theory. These terms should not be used by serious scientists whose integrity leads them to establish patterns of biologically based cause and effect across species.

Serious scientists do that via experimental evidence. The experimental evidence must link their theories to the sun’s biological energy.

Combating Evolution to Fight Disease has led from nutrigenomics to pharmacogenomics and to clinically actionable genotypes via the conserved molecular mechanisms of biophysically constrained nutrient-dependent RNA-mediated protein folding. Causal inferences, phylogenic inferences and associated ridiculous theories have led from nothing to nowhere.

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