June 12, 2008

20 Years of Evolution in a Flask

ResearchBlogging.orgUpdate: This experiment has picked up a lot of attention. Unfortunately some are claiming this experiment is evidence of creationism. Many of them haven't even read the paper because its behind a subscription wall, but the researchers have posted it on their website to be seen by everyone, very cool.

Ok guys, we're gonna try something for the first time here. I've reported on some pretty serious science stuff but I finally got my new toy today (thanks researchblogging.org) and I'm anxious to use it. When you see the "blogging on peer-reviewed research" icon you know I'm going to be writing about some recent professional science happenings. But don't let it scare you, the goal is to present the article in a way that is accessible to the general public (so let me know what you think). Alright, enough with my rambling, let's get to it.

In 1988, Richard Lenski filled 12 flasks full of identical E. coli colonies and put them on a gentle shaker. Inside that Michigan State University lab the bacteria have continued to swirl undisturbed except when Richard would stop to refill spent nutrients and take a small sample from each flask. Those samples now fill a freezer with a genetic snapshot of 12 isolated strains of evolution. Just like the birds of Galapagos that Darwin studied over 170 years ago, each flask had separated the colonies into islands, each sent on its own evolutionary trajectory. And since Lenski paid such close attention to those 12 flasks they have offered up some very unique and compelling insights into the mechanics of evolution.

What Lenski knew was that in each generation, some of the bugs would have a mutation. Most of these would be harmful and kill the bacteria, cause them to grow slow, or keep them from creating progeny. But others would offer benefits like faster growth or the ability to breed faster. These microbes, that were the fortunate recipients of beneficial mutations, eventually would grow to dominate the population, at least until the next more suitable mutant arose. And this is how the experiment went, with the microbes now breeding at a rate 75% faster than the original colonies. This is good enough experiment in itself, but Lenski threw in a few details that makes this one of the more elegant genetic experiments conducted.

The E. coli colonies were grown in a glucose limited environment which also contained citrate. Glucose is a sugar that E. coli shuttles into its cell membrane and uses to extract energy. Citrate, on the other hand, cannot be taken in by E. coli in the presence of oxygen, this failure is a distinguishing characteristic of E. coli. In Richard's well oxygenated lab the citrate went unused, but the glucose had to be replenished daily. For over 33,000 generations this trend continued; a sample was collected, a limited amount of glucose was added, and the cells continued to shake. But one day a flask was cloudy, meaning a huge explosion of growth had taken place. As a microbiologist I know that as soon as this happens you assume contamination, a microbe that got in your flask that could use a previously unused nutrient (in this case citrate), takes hold and with the abundance of an unused resource breeds fast. The huge increase in population turns the flask cloudy.

But this flask hadn't been contaminated, the E. coli was the organism using the citrate. After being placed in pure citrate the microbes continued to grow with no other source of carbon. The researchers then traced the history of the citrate eaters and found that they appeared first in generation 31,500, making up a whole 0.5% of the population. For the next 2,500 generations the citrate eaters battled with the glucose eaters for dominance, almost being eliminated at generation 33,000. But eventually they came to dominate the population, suggesting that only after further mutations was the citrate absorption mechanism efficient enough to overtake the other populations.

The advantage Lenski had over nature was that he could replay evolution with the frozen samples he had collected. And he did just that, growing new populations from 12 time points in the 33,000 generations of bacteria that didn't eat citrate. And out of those new colonies only a small amount of bacteria had the ability to use citrate. And only individuals who had come from after the 20,000th generation were able to develop the ability. This meant that something happened around generation 20,000, specifically in a population dubbed "Ara-3", that allowed for a later mutation to becoming a citrate user.

That is the biggest implication of this paper. Lenski explains it eloquently:
The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population...The evolution of this phenotype was contingent on the particular history of that population. More generally, we suggest that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.

If the citrate-eating was the result of a very rare mutation you would expect that at any point you could restart the colony and each would have an equal likelihood of producing the citrate-eating mutation. But this isn't what Lenski saw, only those progeny from generation 20,000 or later (and population Ara-3) evolved the ability to use citrate as a carbon source. Stephen Jay Gould once claimed that if we replayed life we wouldn't get the same result. In fact, if we replayed it 100's of times we would get 100's of different results. This experiment is demonstrating just that, that each step in the ladder of evolution is dependent on the history that preceded it. As Lenski states in his title, historical contingency is the true meaning behind the data he collected. Some quirk that happened around generation 20,000, which didn't alter fitness or affect survival, allowed for a combination of mutations (all equally likely) which resulted in an advantageous citrate characteristic.

This is evolution as we should understand it, the combined effects of many mutations which eliminates those who struggle and rewards those who develop the most efficient means at conveying DNA to the next generation. This is probably the first definitive experiment showing historical contingency through natural evolution, but even science as clear and illuminating as this can be misconstrued.

To tell you the truth I really wanted to cover this paper but knew it was big enough that everyone in the blogosphere would write about it. I have restrained so far, but today I happened upon Michael Behe's blog at Amazon and now I can't hold back. His last sentence probably sums up best what he wrote:
"If the development of many of the features of the cell required multiple mutations during the course of evolution, then the cell is beyond Darwinian explanation. I show in The Edge of Evolution that it is very reasonable to conclude they did."
Behe would like you to believe in his "irreducibly complex" belief, which conveniently disguises for 'someone had to make it so because it's too complex'. Here's the problem with his argument that multiple mutations are "beyond Darwinian" evolution. Richard Lenski's experiment was just that, the course of Darwinian evolution which showed multiple mutations developed to allow E. coli to use citrate. Behe uses a rather weak argument here to try and push his intelligent design agenda, especially in the face of overwhelming praise from the science community. It is irresponsible for those in science to place an agenda behind their research, especially one that clashes so fundamentally with all legitimate science. But it is stupid to continue to throw out tired lines on public forums that even the most untrained of scientists can debunk. This isn't even an attempt at true science as much as it is a commercial for a book, one that claims to "extensively" speak about Lenski's experiements. So save up from those book sales Michael, cause your credibility isn't going to get you into the afterlife.

Lenski, R.E. (2008). Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proceedings of the National Academy of Sciences, 105(23), 7899-7906.

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Drewsky said...

Straight up gangster post bro!