More complicated than 1-2-3

By: James V. Kohl | Published on: September 20, 2012

Genomic analysis of a key innovation in an experimental Escherichia coli population
Nature (2012)
Abstract excerpt: “Our findings illustrate the importance of promoter capture and altered gene regulation in mediating the exaptation events that often underlie evolutionary innovations.”

How Organisms Evolve New Functions: Evolution Is as Complicated as 1-2-3

Excerpt: “The actual mutation involved is quite complex. It re-arranged part of the bacteria’s DNA, making a new regulatory module that had not existed before. This new module causes the production of a protein that allows the bacteria to bring citrate into the cell when oxygen is present. ”
Excerpt: “It wasn’t a typical mutation at all, where just one base-pair, one letter, in the genome is changed,” he said. “Instead, part of the genome was copied so that two chunks of DNA were stitched together in a new way. One chunk encoded a protein to get citrate into the cell, and the other chunk caused that protein to be expressed.”
My comment: The evolution of the ability to use citrate occurs over generations of change, which means that nutrient chemical-dependent pheromone-controlled reproduction also occurs. This adds an important factor to their details of promoter capture and altered gene regulation in mediating the exaptation events.
The complexity of altered gene regulation must somehow be controlled across generations, which involves the transgenerational epigenetic effects of nutrient chemicals like the citrate. The use of a new nutrient chemical, for example, promotes an individual survival. For use of a new nutrient to promote species survival, the nutrient chemical must be metabolized to a species-specific pheromone that helps to controls the reproduction of  organisms as they evolve to better use the citrate molecule.
The problem here is that their concept of evolution via exaptation events and innovations is incompletely detailed. The level of complexity increases when the re-arranged DNA that makes a de novo regulatory module must somehow also lead to production of two different proteins.
One protein is a receptor protein that allows the nutrient chemical to enter the cell. The metabolism of that nutrient must then lead to production of another protein that controls reproduction by epigenetically enabling the production of another receptor for a species-specific chemical (i.e., a pheromone that controls reproduction). This complicates what has already been described as a complicated 1-2-3 process. A second-phase 1-2-3 process is required to control the reproduction of organisms that can evolve only if they do not starve to death.
If too many of them use too much of the available nutrient supply, the species becomes extinct. Extinction is an important factor to consider in the context of evolution. Isn’t it? Nutrient chemical use is altered by pheromones that control reproduction via quorum sensing, which is an important factor to consider in the context of mutations. It means you must have concurrent mutations that result from the epigenetic effect of a nutrient chemical that metabolizes to a pheromone that causes epigenetically controlled reproduction. Has anyone calculated the odds that two 1-2-3 stage dependent exaptation events would concurrently occur? That’s complicated

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