Bacteria see the light and they adapt

By: James V. Kohl | Published on: February 10, 2016

(click to enlarge)

Cyanobacteria use micro-optics to sense light direction

Excerpt:

From the observed dimensions of the spot of 488 nm light focused by Synechocystis cells (Figure 3c) we can estimate that Synechocystis “vision” has an angular resolution (FWHM) of about 21°, essentially limited by light wavelength and the area of the plasma membrane, which is tiny in comparison to an animal retina. However, this resolution is sufficient to incorporate quite complex spatial information into a 360° image of the cell’s surroundings, and our data in Figure 1e indicate that the cell can integrate information from distinct and spatially separated light sources. The directional motile responses of the cells (Figure 1c,d) show a distribution of displacement angles with FWHM ~30°. This is less accurate than the initial imaging of the light source, which suggests an unsurprising degree of spreading and noise during the signal transduction that comes between initial light perception and the response of the motility apparatus.

My comment: The spot of 488 nm light focused by Synechocystis cells links phototaxis and chemotaxis from photosynthesis to all nutrient-dependent RNA-mediated biodiversity. See for instance:

Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution

Introduction:

For over fifty years, the role of interstrand proton or hydrogen-atom transfer in double-helix DNA has been debated as a possible precursor for mutagenesis and carcinogenesis.[1] However, recent theoretical studies postulated that ultrafast interstrand electron-driven proton transfer (EDPT) instead contributes to the prevention of mutagenic photolesions in DNA excited by absorption of solar ultraviolet (UV) radiation. [2]

Excerpt:

At an excitation wavelength of 260 nm, about 80% of the photons are absorbed by G (see the Supporting Information, Figure S5).[5c,8a] Excitation at the red edge of the absorption spectrum at 290 nm promotes the same photochemistry, but the product bands observed in TEAS and TVAS are weaker because of the lower absorption by G at this wavelength. Excitation of C leads to monomer-like deactivation (see Section S12). Therefore, the discussion in this paper focuses on the results after 260 nm excitation.

My comment: The mechanism that emerges is not links UV light to everything currently know to serious scientists about biophotonics. The mechanism is not placed into the context of anything except a biophysically constrained epigenetic trap. The trap links the speed of light on contact with water from different wavelengths to differences in hydrogen-atom transfer in double-helix DNA. Hydrogen-atom transfer in DNA base pairs in solution links phototaxis and chemotaxis.
Chemotaxis links the nutrient-dependent physiology of reproduction to all biomass and all biodiversity. The mechanism that emerges can be compared to claims that evolutionary mechanisms link the emergence of life from mutations to increasing organismal complexity via natural selection in the context of ridiculous neo-Darwinian theories that ignored Darwin’s “conditions of life.”
For examples of that ignorance, see these reports on the article (with my emphasis): Cyanobacteria use micro-optics to sense light direction
Excerpt:

…findings are most likely an example of convergent evolution between bacteria and more complex multi-cellular organisms including animals and humans.

My comment: The findings link the speed of light on contact with water from hydrogen-atom transfer in DNA base pairs in solution to nutrient-dependent cell type differentiation via the biophysically constrained chemistry of RNA-mediated protein folding in all living genera.
Dobzhansky’s “light of evolution” can be placed into the context of the amino acid substitutions that differentiate the cell types of chimpanzees and modern humans from the cell types of gorillas.

Like all other serious scientists, Dobzhansky (1973) linked the anti-entropic energy of sunlight to all biodiversity via nutrient-dependent ecological adaptations and the physiology of reproduction.
Pseudoscientists hate the fact that they didn’t realize Dobzhansky was joking about mutations and evolution. They never learned the difference between mutations and amino acid substitutions, and Dobzhansky knew they would not. The jokes played on pseudoscientists by serious scientists may have started with Dobzhansky (1964).
Excerpt:

Cyanobacteria evolved around 2.7 billion years ago and the fact that they are able to produce oxygen and fix carbon dioxide using energy from the sun – photosynthesis – is thought to have caused mass extinctions and the oldest known ice age.

My comment: Phototaxis and chemotaxis are not linked from the sun’s biological energy to photosynthesis and EVOLUTION or EXTINCTION. Chemotaxis and phototaxis are linked from hydrogen-atom transfer in DNA base pairs in solution to nutrient energy-dependent RNA-mediated DNA repair and supercoiled DNA that protects the organized genomes of all living genera from virus-driven entropy.
For a reality check, see these reports on the article (with my emphasis): Cyanobacteria use micro-optics to sense light direction
Excerpt:

They get energy from photosynthesis, meaning they need plenty of light to perform the same chemical reaction as plants.

Previous studies have shown Synechocysti contain photosensors and that they are able to perceive the position of a light source and move towards it – a phenomenon called phototaxis. This study showed how this process works. Bacteria moving towards a light is pictured
Excerpt:

The ability of optical objects to distinguish fine detail is determined by “angular resolution”. In the human eye this is an impressive 0.02 degrees. The team estimate that in Synechocystis it is about 21 degrees.

My comment: Is anyone willing to place the change in the degrees of resolution into the context of beneficial mutations and evolution of human visual acuity and specificity?
Excerpt:

Within minutes, the bacteria grow tiny tentacle-like structures called pili that reach out towards the light source.

My comment: The light source is the energy source for growth of the pili, which occurs within minutes. The light source links metabolic networks from their energy source to genetic networks that control colony growth. Colony growth is biophysically constrained in bacteria via the systems complexity of nutrient-dependent quorum sensing, a function of pheromone-controlled morphological and behavioral phenotypes. The structure and function of the phenotypes extends to humans via biophysically constrained RNA-mediated amino acid substitutions in the context of protein folding chemistry.
Conclusion: The laws of physics and the chemistry of protein folding link the sun’s biological energy to RNA-mediated cell type differentiation via the physiology of nutrient-dependent reproduction, which is controlled by pheromones in species from microbes to humans.
See also: Researchers illuminate ‘dark side’ of the transcriptome

A new method to detect, quantify and visualize RNA splicing helps to shed light on the “dark side” of the transcriptome: complex splicing variations that have been known to exist but have not been well studied.

Credit: Illustration conceived by Matthew Gazzara in the Barash lab, Perelman School of Medicine, University of Pennsylvania

My comment: Credit for linking RNA splicing to cell type differentiation in species from microbes to humans should be given to Teresa Binstock, who co-authored our 1996 Hormones and Behavior review and was solely responsible for the section on molecular epigenetics.

See: From Fertilization to Adult Sexual Behavior
Excerpt:

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.
A potential ramification of epigenetic imprinting and alternative splicing may be occurring in Xq28, a chromosomal region implicated in homosexual orientation (Brook, 1993; Hu, Pattatucci, Patterson, Li, Fulker, Cherny, Kruglyak, and Hamer, 1995; Turner, 1995). Xq28 contains one of the X chromosome’s two pseudoautosomal regions (PARs), adjoins the telomere, and has various means of gene expression control (D’Esposito, Ciccodicola, Gianfrancesco, Esposito, Flagiello, Mazzarella, Schiessinger, and D’Urso (1996). Xq28, therefore, is a chromosomal region that has many of the heterochromatic and telomeric characteristics that participate in sexual determination and behavior in other species.

See also: The Light and Darkness of “Evolution 2.0”
Excerpt: The sun’s biological energy links its anti-entropic virucidal epigenetic effects to RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all living genera.”
See also: Sighted Microbes
Excerpt:

…the study offered an “elegant demonstration” of the mechanism for phototaxis in these bacteria. “Cyanobacteria are 2.7 billion years old…

My comment to “The Scientist”
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.

Conclusion:

Based on his writings, both published and unpublished, James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research. It was a mistake to let such a sloppy review through to be published.

My comment: So far as I know, the criticisms of this biologically uninformed undergraduate have not been placed into the context of a model that links hydrogen-atom transfer in DNA base pairs in solution to RNA-mediated amino acid substitutions and cell type differentiation in all individuals of all living genera via the conserved molecular mechanisms I detailed.
The molecular mechanisms link information transfer in microbes to information transfer in the human brain via two epigenetic traps. Others have detailed aspects of the epigenetic trap that traps the anti-entropic virucidal energy of UV light. But, so far as I know, no one else has linked the first epigenetic trap to the de novo creation of odor receptor genes. The de novo creation of olfactory receptor genes in all vertebrates and invertebrates links the second epigenetic trap to supercoiled DNA during thermodynamic cycles of nutrient-dependent protein folding biosythesis and degradation. The supercoiled DNA protects organized genomes from virus-driven entropy.

That fact has now been placed into the context of RNA-mediated DNA repair, which typically occurs in the absence of nutrient stress and or social stress.
Stress alters pH via virus-driven energy theft. The proliferation of viruses prevents RNA-mediated DNA repair. For example, viruses would prevent repair of damage due to excess infrared light.