New results from the Lenski E. coli experiment

One of the most beautiful experiments in evolutionary biology is the one by Michigan State University’s Richard Lenski and his team, most recently Zachary Blount, who started out in 1988 with a single strain of E. Coli bacteria, separated it into twelve genetically identical lines, and then did experiments on them to see how each strand evolved. By now 55,000 generations have occurred, a crucial fact since in evolution it is the number of generations that is the appropriate measure of time, not years.

What was interesting was that every 500 generations, they froze a sample of each of the twelve descendants. Thus they had a complete evolutionary record and could, if needed, go back to any point in time and see when any change took place. The experiment was to see whether the bacteria could evolve from the normal ones that live on glucose and not on citrate to ones that could thrive on citrate. (I wrote about this work back in 2008.)

Lenski, Blount, and the rest of the team have published a new paper in which they show that as a result of looking carefully at what happened by examining the samples at various times, they are now better able to understand the stages by which the bacteria evolved from glucose-eaters to citrate eaters. In particular they were able to shed some light on the fascinating question of what might happen if we ran the evolutionary clock again. Would the same or similar things emerge or would evolution go off in a wildly different direction?

Carl Zimmer has been following Lenski’s work and has an update that is well worth reading.

Blount thawed out ancestors from various moments in the history of the bacteria and started putting them through the same evolutionary experiment again. In some trials, the bacteria did indeed evolve into citrate eaters–but only if they came from after generation 20,000. This discovery suggested only after 20,000 generations were the bacteria prepared to evolve into citrate eaters. They must have already acquired other mutations that set the stage.

To test this idea, Blount and his colleagues thawed out some of the “prepared” bacteria: late-generation E. coli that had not yet gained mutations to citT. They created a miniature ring of DNA loaded with many copies of CitT and the oxygen-sensitive switch, and inserted it into the prepared bacteria. As they predicted, the bacteria now could suddenly feast magnificently on citrate.

But if Blount and his colleagues inserted the DNA ring into the original ancestor of the line, it grew poorly on citrate. That failure suggested that the early-generation bacteria were not ready to receive this evolutionary gift.

And thus a history takes shape:

Chapter One (from generation zero to at least generation 20,000): Our hero, E. coli, picks up mutations that don’t seem to have anything to do with feeding on citrate. They might have helped the bacteria grow better on their stingy rations of glucose. At least one of those mutations set the stage for feeding on citrate.

Chapter Two (around generation 31,500): The bacteria accidentally rewire their genome, so that a new copy of citT switches on in the presence of oxygen. Thanks to the mutations of Chapter One, this rewiring yields a modest but important improvement. Now the bacteria can feed a little on citrate, as well as on glucose.

Chapter Three (from about generation 31,500 to 33,000–and beyond): The bacteria make extra copies of the new and improved citT. They can pull in more citrate; new mutations fine-tune their metabolism to grow quickly on the molecule. World domination soon follows.

Zimmer notes that this pattern replicates standard mechanisms postulated for the evolutionary process, such as how snakes develop their venoms. But the beauty of it is that the short life cycle of bacteria enables us to observe these changes in real-time.

The only important difference is that it took millions of years for snakes to evolve their arsenal of venoms, and scientists can only reconstruct their evolution by comparing living species. But in the case of E. coli, the transition unfolded fast enough for someone to track it from start to finish–and restart it when necessary.

Critics of evolution demand that science produce evidence of transitional forms to fill in the ‘gaps’ between a current species and its ancestor. Of course, they are never satisfied by any of the evidence that is provided because when you do show them a transitional fossil, they can now point to two gaps where just one existed before and demand that those be filled too.

They are unlikely to be convinced by these experiments either. We should ignore them. Here we have science at its most beautiful, the result of careful and painstaking work done over a long time.