Explorers who do not know what is known

By: James V. Kohl | Published on: December 9, 2016

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Can genetic testing determine antimicrobial susceptibility? EUCAST experts say not yet… (link opens pdf)

Reported as: Whole genome sequencing cannot yet be used to determine antimicrobial susceptibility

For most bacterial species there is currently insufficient evidence to support the use of WGS-inferred AST to guide clinical decision making. WGS-AST should be a funding priority if it is to become a rival to phenotypic AST.

My comment:

JVKohl said…: Perhaps the focus should be on what can be done with WGS. It can be used to link energy-dependent bioluminescence from bacteria in the light organ of bobtail squid to the nutrient energy-dependent pheromone controlled weekend resurrection of the bacterial flagellum in Pseudomonas fluorescens via the conserved molecular mechanisms of cell type differentiation in all living genera.
Examining that fact in the context of what is currently known about autophagy (Yoshinori Ohsumi)links everything known about biophysically constrained protein folding chemistry (Ben Feringa) to energy-dependent fixation of RNA-mediated amino acid substitutions in supercoiled DNA, which protect all organized genomes from virus-driven energy theft and genomic entropy (Gunter Witzany). December 9, 2016 at 4:34 PM

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Addendum:
Pleas for funding should be required to include information on what is already known.
Perhaps the focus should be on what can be done with WGS. It can be used to link energy-dependent bioluminescence from bacteria in the light organ of bobtail squid to the nutrient energy-dependent pheromone controlled weekend resurrection of the bacterial flagellum in Pseudomonas fluorescens via the conserved molecular mechanisms of cell type differentiation in all living genera.
Examining that fact in the context of what is currently known about autophagy (Yoshinori Ohsumi)links everything known about biophysically constrained protein folding chemistry (Ben Feringa) to energy-dependent fixation of RNA-mediated amino acid substitutions in supercoiled DNA, which protect all organized genomes from virus-driven energy theft and genomic entropy (Gunter Witzany).
See also: CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling

…improving the resolution of our cryoET data to better than 8Å using the novel lipid-monolayer system described above would allow generation of an atomic homology model of the E. coli chemosensory array, greatly facilitating the use of the wealth of existing biochemical and biophysical data and providing directly transferrable structural and dynamical predictions.

Reported as: Researchers resolve structure of a key component of bacterial decision-making
Excerpt 1)

A new study offers atomic-level details of the molecular machinery that allows swimming bacteria to sense their environment and change direction when needed.

My comment (from last year):

The nutrient-dependent pheromone-controlled links from atoms to ecosystems were established in the context of the report on re-evolution of the bacterial flagellum that occurred in 4 days.

Conclusion: “To know how this mechanical system works, we need to know the structure,” he said. “Once we open the clock, see how the gears fit together, then we can start thinking about how the clock actually works. The gears of the bacterial brain are now in place.”

The “gears” of the “brain” are linked to the “gears” of the bacterial flagellum in 4 days by 2 nutrient-dependent amino acid substitutions in another microbial species. That suggests that the molecular mechanisms may be the same in all individuals of all living genera, unless there is a different model that links ecological variation from atoms to ecosystems and ecological speciation and all morphological and behavioral biodiversity.

The terms they use link the evolution of irreducibly complex structures and functions to life history transitions in morphological and behavioral phenotypes in 4 days.

Serious scientists would probably place this example of atoms to ecosystems adaptations into the context of links from physics and chemistry to the conserved molecular mechanisms that link biophysically constrained nutrient-dependent RNA-mediated cell type differentiation in all living genera via the physiology of reproduction and fixation of the amino acid substitutions in organized genomes that protects all organisms from DNA damage and virus-driven genomic entropy.

Repeated attempts to link conserved molecular mechanisms of energy-dependent protein folding chemistry from species of microbes to humans have failed. Neo-Darwinian theorists are not like molecular biologists because theorists prefer theories to facts.
See also (from last year) Dinosaurs Evolved Rapidly For No Reason

Excerpt: “…apparently that thought falls into a black hole in their evolved brains.”

Again?

Without a thought, another recent report of an evolved microbial “brain” in E.coli linked the “Blind Watchmaker” metaphor to the over-the-weekend re-evolution of the bacterial flagellum in another species.

See: Researchers resolve structure of a key component of bacterial decision-making

Excerpt: “He compares the process of discovery to that of someone encountering a mechanical clock for the first time.

“To know how this mechanical system works, we need to know the structure,” he said. “Once we open the clock, see how the gears fit together, then we can start thinking about how the clock actually works. The gears of the bacterial brain are now in place.”

Explorers who do not know what is known

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