Wednesday, June 04, 2008

Evolution in action - captured and dissected

A 20 year longitudinal study of bacterial evolution is further constraint on the argument facades creationists use to conceal their faith-based opinions. Emphasis mine, arguably this research evolved a new species of bacteria ...

The Loom : A New Step In Evolution (yes, Carl Zimmer again)

... After 33,127 generations Lenski and his students noticed something strange in one of the colonies. The flask started to turn cloudy. This happens sometimes when contaminating bacteria slip into a flask and start feeding on a compound in the broth known as citrate...

...Many species of bacteria can eat citrate, but in an oxygen-rich environment like Lenski's lab, E. coli can't. The problem is that the bacteria can't pull the molecule in through their membranes. In fact, their failure has long been one of the defining hallmarks of E. coli as a species.

...In nature, there have been a few reports of E. coli that can feed on citrate. But these oddballs all acquired a ring of DNA called a plasmid from some other species of bacteria. Lenski selected a strain of E. coli for his experiments that doesn't have any plasmids, there were no other bacteria in the experiment, and the evolved bacteria remain plasmid-free. So the only explanation was that this one line of E. coli had evolved the ability to eat citrate on its own.

Blount ...went back through the ancestral stocks to see if they included any citrate-eaters.... in generation 31,500, they made up 0.5% of the population. Their population rose to 19% in the next 1000 generations, but then they nearly vanished at generation 33,000. But in the next 120 generations or so, the citrate-eaters went berserk, coming to dominate the population.

This rise and fall and rise suggests that the evolution of citrate-eating was not a one-mutation affair. The first mutation (or mutations) allowed the bacteria to eat citrate, but they were outcompeted by some glucose-eating mutants that still had the upper hand. Only after they mutated further did their citrate-eating become a recipe for success.

... Lenski's research has shown that in many ways, evolution is repeatable. The 12 lines tend to evolve in the same direction... Often these parallel changes are the result of changes to the same genes. And yet when it comes to citrate-eating, evolution seems to have produced a fluke.

To gauge the flukiness of the citrate-eaters, Blount and Lenski replayed evolution. They grew new populations from 12 time points in the 33,000-generations of pre-citrate-eating bacteria. They let the bacteria evolve for thousands of generations, monitoring them for any signs of citrate-eating. They then transferred the bacteria to Petri dishes with nothing but citrate to eat. All told, they tested 40 trillion cells...

... Out of that staggering hoard of bacteria, only a handful of citrate-eating mutants arose. None of the original ancestors or early predecessors gave rise to citrate-eaters; only later stages in the line could--mostly from 27,000 generations or beyond. Still, even among these later E. coli, the odds of evolving into a citrate-eater was staggeringly low, on the order of one-in-a-trillion...

If E. coli is defined as a species that can't eat citrate, does that mean that Lenski's team has witnessed the origin of a new species? The question is actually murkier than it seems, because the traditional concept of species doesn't fit bacteria very comfortably. (For the details, check out my new article on Scientific American, "What is a Species?")...

There's a tangent here Zimmer didn't call out.

The researchers were able to replicate the speciation-vent, but it took trillions of tries from the relatively late stage precursors of the citrate eaters. It might take hundreds or thousands of trillions of "tries" to get the same outcome from wild E. Coli. Of course that's only a few hundred years of bacterial evolution.

If they repeated the same experiments fifty times, they'd probably get other one-in-a-hundred-trillion flukes over a 20 year trial, but they'd likely be different flukes.

Flip a coin a thousand times and there's a 100% probability you'll get a sequence made up of Heads and Tails. The chance that the next thousand flips will get the same sequence is very, very low.

Naive old-style creationists got hung up on the impossibly small probability that evolution, replayed from the start, would produce us.

Well, ummn, no, it wouldn't.

The more interesting question is, if you replayed evolution on earth 1000 times, how many times would you produce something that would do experiments about evolution on earth?

That's a Drake equation question. The "expert" wild guesses are in the 20% to 0.33% range, but we could do with a few data points ...

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