Darwinism for the Genomic Age: Connecting Mutation to Diversification

…the chief cause of our natural unwillingness to admit that one species has given birth to other and distinct species, is that we are always slow in admitting any great change of which we do not see the intermediate steps. (Darwin, 1859)

Darwin put energy-dependent “conditions of life” before what is now known about natural selection for codon optimality. That is the chief cause for ignoring anything that neo-Darwinists claim about mutations and diversification.

Energy-dependent codon optimality links the epigenetic landscape to the physical landscape of supercoiled DNA in all living genera via endogenous RNA interference and fixation of amino acid substitutions. The energy-dependent fixation of amino acid substitutions differentiates all cell types in all living genera in the context of the pheromone-controlled physiology of reproduction and supercoiled DNA

For comparison: Virus-driven energy theft has been linked from mutations to all pathology.

See also: Circulating Plasma and Exosomal microRNAs as Indicators of Drug-Induced Organ Injury in Rodent Models

…circulating plasma and exosomal miRNAs can be used as potential biomarkers specific for drug-induced liver, kidney or muscle injury.

The circulating microRNAs typically link nutrient energy-dependent changes in the microRNA/messenger RNA balance from endogenous RNA interference to supercoiled DNA via RNA-mediated DNA repair.

For comparison, see: DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification

Reported as: Study shows higher than expected sequencing errors in public databases

…the accuracy of public databases has been called into question by work done by the team at NEB, which in turn calls into question the accuracy of the cancer datasets.

The link to specimen processing to the number of errors helps to explain why only serious scientists have refuted theistic evolution. Pseudoscientists incorporated the specimen processing errors into their ridiculous mathematical models. Their mathematical models failed to link energy dependent changes in base pairs to single nucleotide polymorphisms and endogenous RNA interference. That fact destroyed any chance that natural selection for energy-dependent codon optimality would be linked from supercoiled DNA to protection from virus-driven energy theft and genomic entropy in all living genera.

See for example: 2007 Using genomic data to unravel the root of the placental mammal phylogeny

A revised molecular timescale based on these phylogenetic inferences suggests Afrotheria and Xenarthra diverged from other placental mammals ∼103 (95–114) million years ago.

Then this: 2013  Making the impossible possible: rooting the tree of placental mammals

…two groups of researchers have scrutinized the largest available genomic data sets bearing on the question and have come to opposite conclusions, as reported in this issue of Molecular Biology and Evolution.

Then this: 2016  Rooting the family tree of placental mammals

“The molecular clock analysis uses a combination of fossils and genomic data to estimate when these lineages diverged from each other,” said author Dr Mario Dos-Reis of Queen Mary London, UK. “The results show that the afrotherians and xenarthrens diverged from one another around 90 million years ago.”

“You don’t always need to overturn the status quo to make a big impact,” said Dr Tarver. “All of the competing hypotheses had some evidence to support them — that’s precisely why it was the source of such controversy. Proving the roots of the placental family tree with hard empirical evidence is a massive accomplishment.”

Nothing about the roots of any family tree has ever been proved in the context of the fossil record and genomic data. The organization of genomes is nutrient-dependent and pheromone-controlled in the context of energy-dependent links from chirality to autophagy and supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy, which is clearly the only link to pathology that consistently shows up in the pathology of dead things.

It’s time to admit that many researchers do not know how RNA-mediated cell type differentiation is biophysically constrained in the context of energy-dependent endogenous RNA interference. The magnitude of the problem increases every day for students in the USA who are taught to believe in mutation-driven evolution.

See for comparison: Endogenous RNAi Pathways Are Required in Neurons for Dauer Formation in Caenorhabditis elegans

Conclusion:

Our data presented here suggest the intriguing possibility that RNAi pathways may mediate distinct effects on gene expression in postdauer animals that experienced different environmental stresses. Since other animals, such as pea aphids, form polyphenisms due to crowding or starvation as well, we predict that this work may have broader implications for the RNAi-mediated regulation phenotypic plasticity.

My goodness, what an “intriguing possiblity.” It might be possible to link energy-dependent RNAi from chirality to autophagy and all biodiversity on Earth by starting from the anti-entropic virucidal energy of sunlight and linking it to the differences between bacteria and virus-infected archaea in the ocean via the physiology of their pheromone-controlled reproduction.

See also: Dobzhansky 1973 and precision medicine (5)

See also: RNA-Guided Human Genome Engineering

5. Repetitive elements or endogenous viral elements can be targeted with engineered Cas+gRNA systems in microbes, plants, animals, or human cells to reduce deleterious transposition or to aid in sequencing or other analytic genomic/transcriptomic/proteomic/diagnostic tools (in which nearly identical copies can be problematic).

Targeting viral elements with energy-dependent Cas+gRNA systems in microbes, plants, animals, or human cells links energy-dependent RNA-mediated amino acid substitutions to viral latency in all living genera. That fact links these three refutations of theist evolution to the examples of the refutations in this model. Nutrient-dependent/pheromone-controlled adaptive evolution: a model

One George Church refutes theistic evolution (3-part series)

Two Francis S. Collins refutes theistic evolution

Three Stuart Kauffman refutes theistic evolution

See also: Scientific Seeker Stuart Kauffman on Free Will, God, ESP and Other Mysteries

He proposed that our scientific understanding of reality is radically incomplete, and that some sort of anti-entropy, order-generating force remains to be discovered.

Let me make this perfectly clear:

The anti-entropic order-generating force is sunlight.

 

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