Archaerhodopsin variants with enhanced voltage-sensitive fluorescence in mammalian and Caenorhabditis elegans neurons

Directed evolution of a far-red fluorescent rhodopsin

reported as:

New technique uses a genetic tool and light to view and map neuronal circuits

Excerpt 1): “This [directed evolution] experiment demonstrates how rapidly these remarkable bacterial proteins can evolve in response to new demands. But even more exciting is what they can do in neurons, as Viviana discovered,” says Arnold.
Excerpt 2): After incorporating Archer1 into neurons that were a part of the worm’s olfactory system—a [THE] primary source of sensory information for C. elegans —[and every other species on this planet] the researchers exposed the worm to an odorant. When the odorant was present, a baseline fluorescent signal was seen, and when the odorant was removed, the researchers could see the circuit of neurons light up, meaning that these particular neurons are repressed in the presence of the stimulus and active in the absence of the stimulus. The experiment was the first time that an Arch variant had been used to observe an active circuit in a living organism.
Excerpt 3): “As neuroscientists we often encounter experimental barriers, which open the potential for new methods. We then collaborate to generate tools through chemistry or instrumentation, then we validate them and suggest optimizations, and it just keeps going,” she says. “There are a few things that we’d like to be better, and through these many iterations and hard work it can happen.”
My comment: The experimental barriers are insignificant compared to the barriers of ignorance represented in this news article. The collaboration appears not to include efforts made by biophysicists to convince theorists that the chemistry of protein folding required for increasing organismal complexity is biophysically constrained by the second LAW of thermodynamics, which is linked from chemistry to perturbed protein folding via nutrient stress and social stress manifested in “heat shock” that alters protein folding. Neurons “…repressed in the presence of the stimulus and active in the absence of the stimulus…” respond to the presence or absence of chemical cues associated with food odors an social odors called pheromones. If enough food is present and not too many pheromone-producing conspecifics, no response is required. But when ecological variation leads to an absence of food or too many conspecifics, an ecological adaptation is required, which is why circuits of neurons light up. If the neuronal circuitry did not light up, there could be no link from ecological variation to any potential ecological adaptation. The population of organisms would die of starvation; they would not evolve.
The researchers link light-induced amino acid substitutions across species that they may think have evolved via conserved molecular mechanisms. But the report on light-induced cell type differentiation and ecological adaptations manifested in the behavior of cells in the nematodes organisms suggests the proteins somehow evolved. Proteins do not ‘evolve.’ Behaviors do not ‘evolve.’
Proteins are produced in the context of of nutrient-dependent thermodynamic cycles of biosynthesis and degradation. Amino acid substitutions that stabilize DNA in the organized genomes of species from microbes to man must lead to cell type differentiation accompanied by changes in behavior or the amino acid substitutions will not be fixed in the DNA at any stage of morphological or behavioral development.
The behavioral changes in C. elegans are clearly nutrient-dependent and pheromone-controlled. They arise during nutrient-dependent ecological niche construction and pheromone-controlled social niche construction, which lead to the construction of neurogenic niches in nematodes.
For example, the nematode P. pacificus has teeth and exhibits predatory behavior because its diet varies from that of the nematode C. elegans. A nutrient-dependent amino acid substitution links the differences in these species protein production to their pheromone-controlled physiology of reproduction, which is how the epigenetic landscape is linked to the physical landscape of DNA in the organized genomes of species from microbes to man. Proteins don’t evolve; behaviors don’t evolve and species don’t evolve. See: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes and Signaling Crosstalk: Integrating Nutrient Availability and Sex and Feedback loops link odor and pheromone signaling with reproduction.
This news report included too much of the magic of evolutionary theory in what could otherwise have been a report used to link ecological variation to ecological adaptation via conserved molecular mechanisms in species from microbes to man. It is either a report on cause and effect for dummies who believe in evolutionary theories, or a report from dummies who thinks that proteins evolve. For example, if bacterial proteins evolve, bacteria can evolve to become nematodes and nematodes can evolve to become mammals.
What these reports actually show is how rapidly light-induced amino acid substitutions lead from nutrient-dependent amino acid substitutions to ecological adaptations in bacterial proteins that link their nutrient-dependent pheromone-controlled physiology of reproduction to ecological adaptations manifested in the morphological and behavioral phenotypes of species from microbes to man via conserved molecular mechanisms in an atoms to ecosystems model of biophysically-constrained cause and effect. Simply put, they start with quantum physics and end with evolution without an evolutionary event that links nutrient-dependent RNA-mediated events from ecological variation to ecological adaptations via conserved molecular mechanisms of species from microbes to man.