Antithetical conclusions (7)

By: James V. Kohl | Published on: August 21, 2016

Streamlining the E.coli Genetic Code

Once the E. coli genome is pared down to 57 codons, the seven blank codons can be reintegrated and used to introduce nonstandard amino acids, the researchers have proposed; this would open the door to creating a wider range of proteins for industrial applications.
A recoded genome also imparts resistance to viral infection and can be used for biocontainment: the DNA incorporated from wild-type E. coli or viruses can’t be used to build proteins successfully when transfer RNAs (tRNAs) insert a nonstandard amino acid in response to a given codon. One or more of the free codons could also be recoded to an amino acid only available in the lab, making the engineered E. coli metabolically dependent on scientist-supplied media.

RNA-directed DNA methlylation links quantized energy-dependent hydrogen-atom transfer in DNA base pairs in solution from the innate immune system to supercoiled DNA, which protects all organized genomes from virus-driven entropy via the pheromone-controlled physiology of reproduction in species from microbes to humans.  Fixation of energy-dependent RNA-mediated amino acid substitutions links codon usage to biophysically constrained protein folding chemistry.
Virus-driven energy theft forces the organism to adapt to ecological changes by altering its energy-dependent supercoiled DNA.  That is how organized genomes resist viral infection. Organisms will use any available energy source to adapt, which is how the anti-entropic virucidal energy of the sun is linked to the creation of all biodiversity.
Every aspect of cell type differentiation is biophysically constrained by the availability of energy. The antithetical conclusion that biophysical constraints can be replicated in the lab to create a wider range of proteins appears to be based on the neo-Darwinian nonsense that failed to link virus-driven energy theft to all pathology.
See for comparison: Epigenetics and Genetics of Viral Latency

… viral latency is responsible for life-long pathogenesis and mortality risk…

Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system linked two nutrient-dependent RNA-mediated amino acid substitutions to weekend resurrection of what has typically been reported to be an irreducibly complex functional structure. The functional structure links chemotaxis and phototaxis to the genetic nature of Pseudomonas fluorescens, which gets its name because it fluoresces when it is exposed to ultraviolet light.
The amino acid substitutions that linked the metabolic networks to the genetic networks were reported as if they were mutations. No information was provided that linked viruses to the mutations, and nothing was mentioned about ecological adaptation via nutrient energy-dependent codon usage and RNA-mediated protein folding biochemistry. That suggests anyone who thinks biocontainment of virus-driven energy theft can be achieved in the lab may also be prepared for what happens when it is not contained.
For example:

…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements (p. 199).

The underlying theme that pits facts against neo-Darwinian theory is manifested in this patent application. Simply put, genome engineering is RNA-mediated inside or outside the controlled conditions of the laboratory.
RNA-Guided Human Genome Engineering

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).

When a constraint-breaking mutation is released to cause the death of millions, the survivors will be the winners take all — if they can afford the treatment. It is already known as the billion dollar baby. Get Well in the RNAi Way-RNAi, A Billion Dollar Baby in Therapy 

Don’t be surprised if you cannot afford the delivery.

And remember this: Bacteria always find a way to survive when they are under pressure to die.

See: Accessory Gene Regulator-1 Locus Is Essential for Virulence and Pathogenesis of Clostridium difficile

how other strains, such as 630, that do not have the agr2 locus in their genomes sense and transduce the TI signal has yet to be determined. Our investigations to identify all of the key players of the two C. difficile Agr quorum signaling systems and their respective roles are ongoing. We anticipate that identification and characterization of the TI signal sensory and response regulatory elements in all of the strains will likely provide evolutionary insights into this unique toxin regulatory system.

See also: Quorum Sensing Determines the Choice of Antiphage Defense Strategy in Vibrio anguillarum

The nutrient energy-dependent pheromone-controlled antiphage defense strategy did not evolve. It is known to serious scientists as the innate immune system. The energy-dependent de novo creation of the innate immune system links Schrodinger’s claims in “What is Life” to Dobzhansky’s claims about amino acid substitutions that differentiate the cell types of chimpanzees and modern humans from gorillas.

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