Microbes: living in the past

By: James V. Kohl | Published on: November 15, 2013

Carl Zimmer continues touting his unsupported view on mutation-driven evolution in yet another review, that encapsulates the historical views of others who continue to live in the past (before anything was known about molecular epignetics. See:

A Long Way Left Up Darwin’s Mountain by Carl Zimmer 11/15/13

Excerpt: “–One of Lenski’s lines of bacteria even went off in an unexpected direction, evolving the ability to feed on citrate in the presence of oxygen. This might represent the birth of a new species.”
The lines of lab grown bacteria were placed on a starvation diet, which forced the de novo creation of olfactory receptor genes that would enable them to feed on citrate. The de novo creation of olfactory receptor genes allows nutrients to pass through the cell wall and restore thermodynamically controlled cycles of protein synthesis that are required to meet the constraints of organism-level thermoregulation. The physics of thermodynamically controlled organism-level thermoregulation enable the protein folding that is required for cell survival in all cell types. Thus, differentiation of cell types also is thermodynamically controlled by seemingly futile thermodynamic cycles of intercellular interactions that link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man.
As you can see in my blog posts, I like to use that phrase in its entirety, no matter what organism or species I am focusing on. I continue to hope that others will recognize the pattern, which is one of conserved molecular mechanisms that link olfactory/pheromonal input directly to gene expression and behavior in unicellular and multicellular organisms.
Zimmer, other journalists, and many scientists, like to discuss Darwin’s works (and the bastardization of his theory) in terms of mutations and mutation-initiated natural selection or a revised version of “mutation-driven evolution” sans natural selection.  Thus, this latest article from Zimmer ignores the fact that what the experiments in Lenski’s lab continue to show is that nutrient stress is thermal stress. It forces the molecular mechanisms of the cell to either kick into overdrive and create new receptors and adapt to their ecological niche via the ability that de novo creation of olfactory receptor genes enables, which is the ability to acquire whatever potential nutrients are available. It is the ultimate adapt or die scenario, but the only way adaptations can occur is via de novo creation of receptors in the cell wall.
That is also the theme of his work, published today. “These adaptations arose thanks to the fact that mutations spontaneously occur at random in the bacteria.” NO, THEY DID NOT! The adaptations arose due to the de novo creation of olfactory receptor genes under conditions that would otherswise lead to death by starvation.  The adaptations are unequivocally nutrient-dependent and it is ridiculous for anyone to claim they spontaneously occur at random in bacteria or any other organism on this planet.  I’ll try not to YELL at people from now on. I should be able to make my point simply by exemplifying nutrient-dependent adaptations in model organisms of different species that have not randomly mutated into existence. Species differences depend on nutrient-dependent adaptations that are controlled by the metabolism of nutrients to species-specific pheromones, which control the physiology of reproduction.  There’s a model for that!
Who cares, you might ask?
“Sex-dependent production of a mouse ‘chemosignal’ with incentive salience appears to have arisen de novo via coincident adaptive evolution that involves an obvious two-step synergy between commensal bacteria and a sex-dependent liver enzyme that metabolizes the nutrient chemical choline.
The result of this synergy is (1) a liver enzyme that oxidizes trimethylamine to (2) an odor that causes (3) species-specific behaviors. Thus, the complex systems that biology required to get from nutrient acquisition and nutrient metabolism to species-specific odor-controlled behavior is exemplified by adaptive evolution of an attractive odor to mice that repels rats (see for review Li et al., 2013).”
This extends the model of nutrient-dependent pheromone-controlled adaptive evolution from microbes to man. But obviously, if you believe in mutations theory, like Zimmer, you have no need for any model that incorporates biological facts.

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