S. cerevisiae smell great (well, they’re bread/brewing yeast) in early, aerobic growth but let an overgrown culture sit around a few days and… whew.

Not that you’d necessarily want to try this sort of sniff-the-culture thing with V. cholerae…

Depends on their media. Aerated, glucose-minimal media cultures don’t smell unpleasant, even in late-log phase. I wonder how fast-growers smell on citrate media.

Depends on their media. Aerated, glucose-minimal media cultures don’t smell unpleasant, even in late-log phase. I wonder how fast-growers smell on citrate media.

GROAN. Carl. And the rest of you being so interested in your discussions as to ignore this awful pun, for shame

[E. coli] don’t come when called,

I suppose you could put a streak of glucose in the direction that you want them to go…

They might not come themselves, but they’ll send their kids.

I almost forgot about the pet thing: 1. keep in mind that you and your son, and your wife all have E. coli already in you, and thus you can be said to already be keeping them as pets. 2. Be forewarned that E. coli cultures are not the most pleasant-smelling of things. 3. They aren’t that snuggly, and they don’t come when called, though they don’t have to be housebroken. Still, it is an interesting idea!

Zachary

When at low frequency (such as when they first occur) or in a population sufficiently small, even beneficial mutations may be lost at random due to genetic drift. (Wikipedia has a good entry on drift if you are interested in more details on it, and its role in experimental evolution experiments is dealt with in publication #145 on Dr. Lenski’s webpage. You might also want to consult any decent college evolution or genetics text for more.) Drift, the change in allele frequencies due to chance (one major component of this in the LTEE is the random manner in which a few million cells of each population are transferred each day to new medium), is not a confounding factor in the long term evolution experiment, as it is a part of the core evolutionary process, and has been recognized as such since Sewell Wright first wrote about it in the 1920′s. As such, loss of mutations, even beneficial ones, has been as much a part of the evolution of the twelve long term E. coli populations as has natural selection. Each population thus has an evolutionary history within the experiment in which mutations of a variety of effects arose at random, and were then either lost at random by drift or non-randomly by natural selection against detrimental mutations, or even non-randomly rose to high frequencies if beneficial and at a selective advantage, provided they became frequent enough to escape drift. Add to this that, because the bacteria are asexual, there is a phenomenon called “clonal interference”, and it involves instances in which two different beneficial mutations arise in the population, but in different clones. Because there is no sex, there is no way for the two mutations to come to be in the same chromosome by recombination. As a consequence, competition between the two mutations can result in the loss of the weaker one. Again, all of these factors, the occurrence of mutations, and their subsequent fates due to drift, natural selection, and clonal interference are a part of evolution.

It just happened that Ara-3′s history saw the occurrence, rise, and persistence of the potentiating mutation, whatever it might be. Could the potentiating mutation have occurred in the other eleven populations? It is possible. Could it have arisen and been lost in those populations? It is possible. Could it be present in any of those populations now? It is possible. For that matter, what was its fitness effect? Aside from it being clear that the potentiating mutation was not detrimental (if it were detrimental it would not have persisted in the population for the 11,000+ generations that it did), we won’t know that until we can identify it and construct strains of E. coli that vary only in that one mutation and compete them. Indeed, once we identify it, we will then be able to answer those above questions. Unfortunately we can’t right now.

I hope that answers you question about lost mutations. I will see about including a bit about drift in the upcoming post (which should be better than these “on the fly” comments).

As to your question about what has been selected for, I recommend that you read publication #147, as it goes in that in detail, and there are a number of other papers on Dr. Lenski’s webpage that go into aspects of that question. I will say in regard to the environment, that the experiment is really a matter of us providing the bacteria with an environment. The environment then selects among the variation that arises by random mutation in the populations, with the added complications I discussed above. This is just like what happens in nature. Publication #145 is a fairly easy to read that reviews experimental evolution using microbial model systems, and I think you would find much there of interest.

Thank you, and I hope that helps!
Zachary

I assume that the answer is that the vast majority of each new generation are the ones that out compete the others. After all, those are the ones who reproduce faster.

Clearly, this is a selection for fast breeders. That isn’t what you’d always get in the wild. This is a new environment. Does the artificialness of the new environment mean much?

I assume that the answer is no. Any new environment is one that evolution should be able to adapt to.

My son wants a pet. Mom is allergic to dogs and cats. I want it to be something easy to take care of, and if it dies, no one will be too sad. E. Coli is just the thing.

But there will be trillions of them. And he’ll want to name them individually.

Just knowing that Larry is worried about “lost” mutations because “(1) only one percent of old populations were used to start new populations and (2) there were very few generations per population,” makes me believe he has never taken a genetics course in his life let alone ever done any research. Poor guy should go back to school.

You stupid fathead, even Zachary Blount, a co-author of the paper, expressed concern about “lost” mutations. He wrote in a comment in another thread,

. . . one cannot ignore the possibility of the loss of even weakly beneficial mutations during transfer (especially of a new mutation that had occurred during the last generation of the previous day) . . .

Sheeeesh

tyrone slothrop said,

commenting about articles you have not read is to take the arrogance of ignorance to a new level.

Presumably most people who have commented on this paper have not read it.