Behe on Darwin: E coli Lenski study: loss of genes (Introduction)

by David Turell , Wednesday, June 24, 2020, 23:58 (1401 days ago) @ David Turell

The citrate eating e.Coli devolves its genome after a mutation allowws citrate as food source:

https://evolutionnews.org/2020/06/citrate-death-spiral/

"Richard Lenski and collaborators have just published a terrific new paper in the journal eLife.1 Anyone who wants to see a crystal-clear example of the inherent, unavoidable, fatal difficulties that the Darwinian mechanism itself poses for unguided evolution should read it closely.

"The paper concerns the further evolution of a widely discussed mutant strain of the bacterium E. coli discovered during the course of Lenski’s Long Term Evolution Experiment (LTEE). The LTEE is his more-than-three-decades-long project in which E. coli was allowed to grow continuously in laboratory flasks simply to observe how it would evolve. As I’ve written before, almost all of the beneficial mutations that were discovered to have spread through the populations of bacteria in the LTEE were ones that either blunted pre-existing genes (decreasing their previous biochemical activity) or outright broke them.

***

"The duplication mutation placed the control region of a different gene next to that of the citrate transporter.

"Here’s why that helped. The citrate-transporter gene’s natural regulator causes the gene to be turned off whenever oxygen is around, as it was under the normal laboratory growth conditions at MSU. The second regulator, however, allows the gene it controls to be turned on in the presence of oxygen. The mutation that placed a copy of the regulator of the second gene next to the citrate gene then allowed the citrate gene to be turned on in the presence of oxygen, too. Since for technical purposes there was a lot of dissolved citrate in the nutrient broth, the mutant E. coli could import and metabolize (“eat”) the citrate, which was unavailable to nonmutants. With all that extra food, the mutant grew like crazy, quickly surpassing nonmutants.

***

"...the citrate mutant had accumulated many of the same beneficial-but-degradative mutations that had previously spread through the population — the new mutation did not, could not, restore them. And later work showed that several more broken genes had been selected in the mutant, apparently to help it metabolize citrate more efficiently.

***

"As always with the Lenski lab, the research is well and thoroughly done. But the resulting E. coli is one sick puppy. Inside the paper they report that “The spectrum of mutations identified in evolved clones was dominated by structural variation, including insertions, deletions, and mobile element transpositions.” All of those are exceedingly likely to break or degrade genes. Dozens more genes were lost. The citrate mutant tossed genetic information with mindless abandon for short term advantage.

***

"In other words, those initial random “beneficial” citrate mutations that had been seized on by natural selection tens of thousands of generations earlier had led to a death spiral. The death rate of the ancestor of the LTEE was ~10 percent; after 33,000 generations it was ~30 percent; after 50,000, ~40 percent. For the newer set of experiments, the death rate varied for different strains of cells in different media, but exceeded 50 percent for some cell lines in a citrate-only environment. Indeed, the authors identified a number of mutations — again, almost certainly degradative ones — in genes for fatty acid metabolism that, they write with admirable detachment, “suggest adaptation to scavenging on dead and dying cells.”
The degraded E. coli was eating its dead.

***

"So, thanks to the Lenski group, we know that devolution is relentless — it never rests. In good times and bad, if a change in a species could help it adapt more closely to its environment, degradative mutations will arrive most quickly by far to offer their assistance. And, of course, under selective pressure a species has no choice but to accept helpful ones, even if that eventually leads to the species languishing. Thanks in very large part to the fine work done over decades at Michigan State we can now be certain that, like the citrate-eating E. coli, as an explanation for the great features of life Darwin’s theory itself is in a death spiral."

Comment: very clear evidence that in evolution a bad mutation that transiently gives a survival advantage is really bad news and 'Darwin Devolving' is the correct view of evolution. This implies all the information in the DNA code may likely been here in the beginning.