Lenski\'s E. Coli mutation rates show two types (Introduction)
by David Turell 
, Sunday, March 20, 2011, 02:08 (4976 days ago)
Fascinating study of Lenski's E. Coli. EW's are winners (more mutations) and EL's, losertfs, (less mutations). -http://www.the-scientist.com/news/display/58057/#ixzz1H33CKeSO-This fellow, who knows the study disagrees with the conclusions, and thinks the EW's are the losers!-"Andrew J. Fabich at Tennessee Temple University, who knows somewhat of bacteria, writes to say that none of the stuff about them is any big surprise, Having read the paper, I'm impressed at the magnitude of the research, but not the conclusions. Wood et al. identified a spoT mutation in E. coli as what made his "Eventually Wins" (EW) strains less fit for competition. That's a no-brainer as spoT mutations studied as much as possible in an isolated background (that of a relA mutant) are always sick. I am not surprised that they identified a gene that made the strain weaker, despite its earlier chances for success. I have passaged an E. coli relA mutant through a mouse intestine and, even though it could colonize on its own, was far inferior to the wild-type in direct competition. Whenever you mess with the translation machinery and, specifically, the stringent response, you're setting yourself up for failure. It would've been more interesting to see a proper control experiment done in which the spoT mutation was introduced at the beginning of the long-term evolution experiment rather than identified at the very end. This has philosophical implications that Lenski thinks evolution has a goal in mind (i.e., spoT) rather than being random and without a goal."-Only Lenski knows what he thinks!
Lenski's E. Coli: citrate eatng type not new species
by David Turell , Tuesday, September 08, 2015, 14:45 (3343 days ago) @ David Turell
A researcher on the E. coli discusses the citrate change, but is not convinced they have created a new species:- http://beacon-center.org/blog/2013/03/25/beacon-researchers-at-work-the-origin-of-a-spe... increases diversity and complexity, and, importantly, it allows organisms to explore new evolutionary paths. There is little in biology that isn't touched by speciation, and it is little wonder that Darwin himself referred to it as “that mystery of mysteries.”-"Despite all the fantastic work done since Darwin's day, speciation is still mysterious. Speciation is complex, multifaceted, tricky to study, and, most importantly, hard to “catch in the act.” It would help if we had a model system in which we could study speciation in fine detail as it occurs, examine and manipulate the processes involved, and to do so over a humanly reasonable time scale.-***-"Is Cit+ a new species? That is a trickier question than you might think. Speciation is a process and not a sudden, instantaneous event, and there is no single, universally accepted species definition. (This reflects how nature really doesn't conform to the human need for sharply-drawn categories.) The most widely accepted, however, is Ernst Mayr's Biological Species Concept (BSC), which equates speciation with the evolution of reproductive isolation. This means that a group of organisms is a new species when its members can mate, mingle genes, and produce fertile offspring with each other, but not with members of its parent species.-"Unfortunately, the BSC is hard to apply to asexual bacteria.-***-"Despite these findings, I am not quite comfortable calling Cit+ a new species just yet. If Cit+ really is evolving to become well-adapted to the citrate niche, it might become better at growing on citrate, and worse at growing on glucose. This pattern could mean that some of the same mutations that are making Cit+ better at eating citrate are also making it worse at eating glucose."-Comment: As he points out, many mutations result in a loss of information.
Lenski's E. Coli: improve fitness without challenge
by David Turell , Thursday, December 17, 2015, 00:47 (3243 days ago) @ David Turell
The very long term E. coli experiment does not change the culture medium environment but the bacteria themselves improve 'fitness'.-http://www.the-scientist.com/?articles.view/articleNo/44787/title/Constant-Evolution/-"In a 2013 Science paper, researchers running the Long-Term Evolution Experiment (LTEE)—a project that has been monitoring 12 flasks of Escherichia coli for almost three decades—predicted that the bacteria would continue to adapt to their never-changing environment forever. Now, two years and 10,000 bacterial generations on, it's clear that their prediction is holding true. The team's latest report, published in Proceedings of the Royal Society B today (December 16), shows that the fitness of the bacterial populations is indeed continuing to improve.-***-"In 1988, evolutionary biologist Richard Lenski of Michigan State University initiated the LTEE. His team divided one starter culture of E. coli into 12 separate flasks and, for the last 27 years, those 12 cultures have been kept in identical conditions, being diluted by a factor of 100—to allow for growth—with the same culture medium each and every day.-"The aim was to investigate “the predictability and repeatability of the evolutionary process,” said study coauthor Michael Wiser, also of Michigan State University. Put simply, “the idea was to look and see whether the different populations were achieving the same results as each other and whether they were doing so at the same time,” he said.-"As the years passed, the team collected and froze sample after sample, performing various analyses on each. Once the bacteria reached 50,000 generations, the researchers compared the fitness of the then-current cultures with that of the microbes' predecessors and their common ancestor. The researchers found that fitness was improving."-Comment: The mechanism to evolve is built-in to living organisms.
Lenski's E. Coli: another view
by David Turell , Wednesday, February 24, 2016, 19:46 (3174 days ago) @ David Turell
This very long term E. coli experiment does show that the bacteria can change and mutate to find a new food source, but the results are open to debate about the amount of information used:-http://www.the-scientist.com/?articles.view/articleNo/45423/title/Similar-Data--Different-Conclusions/&utm_campaign=NEWSLETTER_TS_The-Scientist-Daily_2016&utm_source=hs_email&utm_medium=email&utm_content=26586249&_hsenc=p2ANqtz-9NFZR6NdJNBHp7kGDXYsI_PxKDOmK4Bu_hd5BV0dBuBSWGC-l--7cED1T2DpTsEFaO2yabbL9TQTCIQf6Jv7pqkEgyxw&_hsmi=26586249/-"By tweaking certain conditions of a long-running experiment on E. coli, scientists found that some bacteria could be prompted to express a mutant phenotype sooner, without the “generation of new genetic information.” The resulting debate—whether the data support evolutionary theory—is more about semantics than science. Since 1988, Richard Lenski has been propagating the same 12 cultures of E. coli at Michigan State University, observing how they change over time. These cultures are grown on a low-glucose medium that includes citrate. Every day, members of the Lenski lab transfer the cultures to new media at a dilution of 1:100.-"The team's 2008 finding that some of the bacteria could use citrate as a carbon source under aerobic conditions was considered a game-changer—a potential example of how a new species could emerge (E. coli's inability to metabolize citrate aerobically is one of its defining phenotypic features). Lenski and colleagues attributed the 15-year delay in the appearance of citrate-eating E. coli to the slow accumulation of “potentiating mutations,” genetic changes that provide no discernible advantage at the time but set the stage for future adaptation. Whether a particular culture has a citrate-friendly genetic background depends on its history, the researchers proposed, an idea called historical contingency.-"Now, the authors of a study published this month (February 1) in the Journal of Bacteriology suggest that the delay in the emergence of citrate-eating E. coli may not have been the result of historical contingency, but of experimental conditions that favored non-citrate-eaters. The University of Idaho's Scott Minnich and colleagues have shown that when certain experimental conditions were altered, citrate-eating E. coli mutants (Cit+) appeared much more quickly and displayed similar genetic changes as those seen in bacteria from Lenski's long-term evolution experiment.-***-"Minnich and colleagues grew the LTEE E. coli strain (REL606) in the same glucose- and citrate-containing medium used in the LTEE, but allowed the bacteria to grow for a week before passaging. Under this condition, the team found, Cit+ mutants appeared much faster: as early as 63 days. In a separate experiment, the researchers grew several E. coli strains (excluding REL606) in a medium in which citrate was the only carbon source, to select for citrate-eating bacteria. Cit+ mutants emerged in fewer than 40 days in all but one strain tested, the researchers reported.-***-"The LTEE researchers applaud the experiments conducted by Minnich's team. “The problem . . . is not with the experiments and data. Rather, the problem is that the results are wrapped in interpretations that are, in our view, unscientific and unbecoming,” Blount and Lenski wrote in their blog post.-"“Cit+ mutants exemplify the adaptation capability of microorganisms but as of yet, the LTEE has not substantiated evolution in the broader sense by generation of new genetic information, i.e. a gene with a new function,” Minnich and colleagues wrote in their paper.-“'When natural selection—that is, differential survival and reproduction—favors bacteria whose genomes have mutations that enable them to grow on citrate, those mutations most certainly provide new and useful information to the bacteria,” Lenski and Blount countered in their blog post. “To say there's no new genetic information when a new function has evolved (or even when an existing function has improved) is a red herring that is promulgated by the opponents of evolutionary science.'”-Comment: Case on Lenski's E. coli proving Darwin's evolution is not closed. Whole article is a complex discussion. The issue of new information is central: rearrangement of info or new info?