Bacteria see the light and they adapt (2)

By: James V. Kohl | Published on: February 22, 2016

Differential Odour Coding of Isotopomers in the Honeybee Brain


In summary, we provided the first neurophysiological evidence of differential neural coding of isotopomers. Also, in light of the recent literature on ODEs, and considering that odour transduction in insects occurs in ≈2 ms24, it seems unlikely that perireceptor events could be responsible for the reported isotope sensitivity. Finally, we performed direct measurements of the vibrational spectra of each odorant, and reported that spectral differences among isotopomers well reflect differences in the elicited neural representation. In conclusion, common and deuterated odorants elicit different physiological responses within the honeybee antennal lobe. Nevertheless, the mechanism behind isotopomer recognition remains elusive, and may rely on different biophysical properties such as molecular weight, enzyme susceptibility, vibrational spectra, or, possibly, on a combination of them.

Reported as: New evidence for the vibration theory of smell
Excerpt 1)

The predictive power and galvanizing influence that theoretical models routinely enjoy in physics is only rarely replicated in biology.
Excerpt 2)
This predictable progression in the complexity of enzymes precisely mirrored that of their granddaddy, the ribosome. By accreting its own product, the ribosome gradually proteinized the least RNA snippets possessing the kernel of catalytic function it needed, culminating in the most massive synthesis conglomeration we find in all phylogeny—the human ribosome. Perhaps surprisingly, the now sophisticated receptor ion channel culture in our cells similarly accrued around another fundamental nugget—the leakiness of bare membranes. The Hodgkin and Huxley models mentioned above, which work well for the describing the electrical dynamics of spikes, unfortunately have little to say about other critical aspects of pulsating membranes (like heat capacity, enthalpy, and compressibility), and nothing of the thermodynamics of the spontaneous self-assembly of their proteins and lipids.
Some clues to a way forward from our current position were recently suggested by Shamit Shrivastava. Reaching back to re-examine some critical ideas from the mind of none other than the man first intuited the existence of gravity waves, Shamit recalls Einstein’s conception of a ‘complete molecular mechanical theory’.
My comment: Schrodinger (1944) linked the anti-entropic force of the sun’s biological energy from what serious scientists now know is the virucidal effect of UV light via what is now known about hydrogen-atom transfer in DNA base pairs in solution and RNA-mediated DNA repair. Nutrient-dependent amino acid substitutions that stabilize the organized genomes of all living genera link atoms to ecosystems via the physiology of reproduction and supercoiled DNA in all living genera.
See also: Bacteria see the light and they adapt
Stress alters pH via virus-driven energy theft. Altered pH promoted viral replication/proliferation. The proliferation of viruses and viral microRNAs prevents RNA-mediated DNA repair. For example, viruses prevent repair of damage due to excess infrared light exposure.

Chemists used ultra short blasts of UV light to stimulate hydrogen-atom transfer in the base pairs guanine (G) and cytosine (C), which were in a solution. Thus the title: Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution. 

In a process that happened within a few quadrillionths of second, they revealed a protective molecular mechanism that links UV light from hydrogen-atom transfer in base pairs to RNA-mediated cell type differentiation in species from microbes to humans.

See also: Watson–Crick Base Pairing Controls Excited-State Decay in Natural DNA, which was reported as: Base-pairing protects DNA from UV damage 

I have not seen a news report on this: UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair.  Science journalists tend to report stories about mutations and evolution as if UV light-induced RNA-mediated DNA repair was of no consequence.

See also:  Novel Method for Neuronal Nanosurgical Connection
My comment: They directed ultra short blasts of infrared light to the meeting point of two nerve cells. After the outside protective layer of the two cells was partially damaged the intact inside of the protective layer enabled the two cells to established solid bonds, which formed a common membrane at the targeted area. This appears to link UV absorption to hydrogen-atom transfer in DNA base pairs in solution to RNA-mediated repair of a common membrane in nerve cells of the brain. That has broad-based implications in the context of what is currently known to serious scientists about biophysically constrained nutrient-dependent RNA-mediated protein folding chemistry in species from microbes to man. For example, it places chemotaxis before phototaxis and links foraging behavior from sensory input to behavior via nutrient-dependent RNA-mediated amino acid substitutions in all living genera.
See for example:

Cyanobacteria use micro-optics to sense light direction

See also: Sighted Microbes

…the study offered an “elegant demonstration” of the mechanism for phototaxis in these bacteria. “Cyanobacteria are 2.7 billion years old…Their results link phototaxis to chemotaxis. They also link microbial foraging behavior to human metabolic networks and genetic networks via hydrogen-atom transfer in DNA base pair in solutions like sea water and circulating blood.Facts about light intensity and energy-dependent changes in base pairs link everything known to serious scientists about physics, chemistry, and the conserved molecular mechanisms of biologically-based RNA-mediated cause and effect. The insertion of the spurious claim that the “Cyanobacteria are 2.7 billion years old” should not be placed into the context of what is known to serious scientists about nutrient-dependent biophysically constrained cell type differentiation.Theorists invite more ridicule when they make such claims and ignore facts like these:…a family of microbes has persisted essentially unchanged for the past 2.3 billion years—half the age of Earth.

Bacteria that lack a vital protein for growing flagella—tail-like structures that enable the microbes to swim—can attain flagella in as little as four days given enough pressure to evolve…The facts link energy-dependent base pair substitutions and RNA-mediated amino acid substitutions via the nutrient-dependent pheromone-controlled physiology of reproduction in species from microbes to humans. Only neo-Darwinists and others who are equally biologically uninformed will continue to place what is known about hydrogen-atom transfer in DNA base pairs in solution into the context of evolution without explaining how “evolution” occurs in 4 days or does not occur in 2.3 billion years.

For the most recent example of neo-Darwinian nonsense see:

Dynamics of Dark-Fly Genome Under Environmental Selections…we considered several hypotheses about possible roles of candidate genes. Among the candidates (Table 2), Or22a, Or22b, and CheA87a encode olfactory and chemosensory receptors. Although the chemical entities binding to these receptors have not been identified yet, it is possible that these receptors might perceive pheromonal signals. We speculate that the mutations of pheromone receptors might enhance sexual activity in Dark-fly.

The experience-dependent de novo creation of olfactory receptor genes in insects links energy-dependent hydrogen-atom transfer in DNA base pairs in solution to the pheromone-controlled physiology of reprodution in bacteria via metabolic networks and genetic networks.

Virus-driven energy theft is linked to perturbed protein folding chemistry, which links mutations to pathology in all living genera. The claim that  “…mutations of pheromone receptors might enhance sexual activity in Dark-fly” fails to integrate anything known to serious scientists.

Serious scientists know that the nutrient-dependent biophysically constrained chemistry of RNA-mediated protein folding links amino acid substitutions to the stability of supercoiled DNA in the organized genomes of all living genera.

See also: 

MicroRNAs Form Triplexes with Double Stranded DNA at Sequence-Specific Binding Sites; a Eukaryotic Mechanism via which microRNAs Could Directly Alter Gene Expression

My comment: Keep in mind that nothing can be made from anything without an energy source and that stolen energy by viruses is the most likely cause of mutations, which cannot link energy-dependent cell type differentiation to supercoiled DNA in any organism on Earth.

Making an Artificial Leaf: Creating Hydrogen Fuels through Water, Sunlight and Carbon Dioxide


The molecular action of these heterotriplexes may include the inducement of conformational changes in the immediately surrounding DNA, including a slight unwinding [28], a potential mechanism for promoting transcription.

My comment: Unwinding supercoiled DNA is the most likely route from stress-induced changes in pH to virus-perturbed protein folding chemistry and pathology in my model, which links the de novo creation of receptors from hydrogen-atom transfer in DNA base pairs in solution to the de novo creation of different cell types in and artificial leaf for comparison to cell types in a real leaf, and all living genera.

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