…and this is a 
Historical contingency in the evolution of E. coli
Category: Evolution • Science
Posted on: June 10, 2008 9:10 PM, by PZ Myers
While I was traveling last week, an important paper came out on evolution in E. coli, describing the work of Blount, Borland, and Lenski on the appearance of novel traits in an experimental population of bacteria. I thought everyone would have covered this story by the time I got back, but there hasn't been a lot of information in the blogosphere yet. Some of the stories get the emphasis wrong, claiming that this is all about the rapid acquisition of complex traits, while the creationists are making a complete hash of the story. Carl Zimmer gets it right, of course, and he has the advantage of having just published a book(amzn/b&n/abe/pwll) on the subject, with some excellent discussion of Lenski's work.
The key phrase is right there at the beginning of the title: historical contingency. This paper is all about how accidents in the genetics of a population can shape its future evolutionary trajectory. It is describing how a new capability that requires some complex novelties can evolve, and it is saying plainly that in this case it is not by the fortuitous simultaneous appearance of a set of mutations, but is conditional on the genetic background of the population. That is, two populations may be roughly equivalent in fitness and phenotype, but the presence of (probably) neutral mutations in one may enable other changes that predispose it to particular patterns of change.
Here, read the abstract for yourself, paying special attention to the parts I've highlighted.
The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations of Escherichia coli were founded in 1988 to investigate this issue. They have since evolved in a glucose-limited medium that also contains citrate, which E. coli cannot use as a carbon source under oxic conditions. No population evolved the capacity to exploit citrate for >30,000 generations, although each population tested billions of mutations. A citrate-using (Cit(+)) variant finally evolved in one population by 31,500 generations, causing an increase in population size and diversity. 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. We tested these hypotheses in experiments that "replayed" evolution from different points in that population's history. We observed no Cit(+) mutants among 8.4 x 1012 ancestral cells, nor among 9 x 1012 cells from 60 clones sampled in the first 15,000 generations. However, we observed a significantly greater tendency for later clones to evolve Cit(+), indicating that some potentiating mutation arose by 20,000 generations. This potentiating change increased the mutation rate to Cit(+) but did not cause generalized hypermutability. Thus, 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.
What Blount et al. are doing is testing SJ Gould's old claim that if we replayed the tape of life, we would not get the same results each time. Each step in evolution is dependent on prior history — it is contingent — and since many of the steps are driven by chance yet unfiltered by selection, we cannot predict the direction of evolution.
We can't rewind the whole planet, but with careful design, we can set up populations that can be rewound. Lenski has done this by setting aside 12 separate populations of E. coli 20 years ago, each one evolving independently and in its own direction. So far, over 44,000 generations have passed in the flasks in Lenski's lab. This is a long time, and at the typical mutation rates present in these creatures, it means that every nucleotide has been mutated singly multiple times in the population — in other words, there has been ample time to thoroughly explore the single substitution search space. In addition, a sample of each population was taken and frozen every 500 generations, so they can go back in time at will and examine their genome or even restart the line. Imagine what we could learn if some ambiguously benevolent space aliens had visited the earth every 5-10,000 years, snatched up a couple of random hominin/primate tribes, and had them tucked away in cryogenic storage — that's what this experiment is like.
These bacteria have been raised in a constant environment, one which is somewhat less than ideal: they've been fed on small quantities of glucose, and nothing but glucose, in a lean regimen that has encouraged selection for somewhat different properties than you'll find in your gut, one of the normal habitats of E. coli. They have evolved, and even have distinctive morphological characters, and many of their properties are consistent from population to population. There is one property that would be useful for the bacteria, but that has evolved in only one of the 12 populations: the ability to use citrate as a carbon source. There's plenty of citrate in the medium, and it would be a bit of a coup for any bacterium to acquire the ability to take up and metabolize it, but it just hasn't happened as often as might be hoped…except in one of the 12 populations, which around the 33,000th generation, suddenly expanded its stable population size by exploiting citrate in its environment.
How did that happen? As the abstract states, they were testing two alternatives. In one, the new ability is purely the product of an extremely rare mutation, some unlikely combination of events that gave a fortunate individual in this population the ability to take up and use citrate. If this were the case, and we rewound the tape of E. coli history back to before the mutation arose, and allowed it to play forward again, we'd expect no enhanced likelihood of a repeat performance — it's just like the other 11 populations. The other alternative is that the population had some prior enabling characteristic, some quirk in its genome that didn't really affect survival in one way or another, but that, in combination with some other ordinary mutation of ordinary probability, could predispose the population to acquire the useful citrate characteristic. In this case, rewinding the tape of life back to before the appearance of the ability, and re-running it forward, would show an increased frequency of reappearance of the ability. Furthermore, by running the tape back further still, they can identify when the enabling change in the population first arose.
The citrate+ trait was first observed in the population called Ara-3 at roughly generation 33,000. By looking back at the frozen populations, they determined that the initial mutation that enabled growth on citrate actually appeared sometime between generation 31,000 and generation 35,000. These early generations were not as efficient at growing on citrate, so another mutation is thought to have occurred around generation 33,000 that allowed much more rapid growth. E. coli from generations prior to 31,000 had no significant, detectable ability to grow on citrate.
So they pushed it back further, by taking samples from earlier generations and allowing them to replicate again, replaying history. If the citrate mutation was a rare, unique mutation, they wouldn't expect to see the novel trait arise again. What they saw, though, was that the bacteria sampled after the 20,000th generation re-evolved the citrate capability with a greater frequency — there is something that arose around generation 20,000 in the Ara-3 population that did not make them citrate+, but did make it easier for subsequent generations to evolve citrate+, confirming their hypothesis of a historical contingency.
This is the lesson: the likelihood of certain mutations arising is strongly affected by historical contingencies — different populations will have different probabilities of producing a particular trait. There were at least 3 events in the history of this one population of E. coli that enabled growth on citrate. The first was an enabling variation at around generation 20,000; the second was an initial mutation that actually allowed slow citrate uptake at around generation 31,000; and the third was a refinement at generation 33,000 that made the bacteria grow much better on citrate. Note: 3 mutations had to occur to produce the visibly better growing citrate+ population.
The creationists are already leaping all over this result and garbling and twisting it hopelessly. Michael Behe was quick to claim vindication, saying that these results support his interpretation.
I think the results fit a lot more easily into the viewpoint of The Edge of Evolution. One of the major points of the book was that if only one mutation is needed to confer some ability, then Darwinian evolution has little problem finding it. But if more than one is needed, the probability of getting all the right ones grows exponentially worse. "If two mutations have to occur before there is a net beneficial effect — if an intermediate state is harmful, or less fit than the starting state — then there is already a big evolutionary problem." And what if more than two are needed? The task quickly gets out of reach of random mutation.
Wait a minute — has he read the paper? This is an experiment that revealed a trait that required at least three mutations. Yet there it is, produced by natural evolution, with no intelligent design required; and when the experiment is re-run with populations that had the initial enabling variant, they re-evolved the ability multiple times. It seems to me that this work demonstrates that drift, chance, historical contingency, and selection are sufficient to overcome his "big evolutionary problem", and directly refute the premise of his book.
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.
This is simply baffling. Behe claims that he has shown in his book that the result observed by Lenski and colleagues could not occur without intelligent intervention…yet it did. He is trying to argue that an experiment that showed evolution in a test tube did not show evolution in a test tube. Behe's claims are comparable to someone living after the time of Kepler and Newton trying to claim that because Copernican circular orbits don't fit the data cleanly, the earth must be stationary — in response to research that shows the earth is moving. That is how backward Behe's claims are.
Behe is a bad note to end on, so let's look at the paper's conclusion. The answer does not lie in an imaginary designer, but in the reality of historical variation. And this is a lovely discovery.
…our study shows that historical contingency can have a profound and lasting impact under the simplest, and thus most stringent, conditions in which initially identical populations evolve in identical environments. Even from so simple a beginning, small happenstances of history may lead populations along different evolutionary paths. A potentiated cell took the one less traveled by, and that has made all the difference.
(Crossposted to The Panda's Thumb)
Blount ZD, Borland CZ, Lenski RE (2008) Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc Natl Acad Sci U S A 105(23):7899-7906.
Comments
Excellent article. Save those bugs for future sequencing!
Posted by: James F | June 10, 2008 9:23 PM
So when do Behe and friends come out and say that the mutations are the finger of god at work or is that what he is saying?
Posted by: shane | June 10, 2008 9:25 PM
Incredible. The experiment is ingenious for looking at drift, I wonder if there are preserved samples of the parent populations, because a next step could be changing the environment to something more complex (or simply different) than a simple glucose mixture to look at the effects of drift and environment with deep generation depth.
Posted by: Lee Drake | June 10, 2008 9:32 PM
Thanks, PZ. You and Zimmer could help most people understand this imp0ortant and patient work. Of course, "most people" wouldn't include Behe, who seems to retreat further and further into blithering every time he makes an appearance. Hopefully the choir that he is preaching to will get smaller and smaller as he grows in insignificance..
Posted by: Albarossity | June 10, 2008 9:33 PM
Very interesting findings. And I'm amazed by experiments like this that span decades.
Behe's a nitwit.
Posted by: SC | June 10, 2008 9:38 PM
More recently the blogosphere, and even New Scientist have been covering the story to a considerable extent.
I didn't really bother reading Behe's junk, just scanned it. It looks like he's doing all that he can do, denying what's plainly occurring, evolution passing the reasonable form of the test that he proposed (yes, I know that his actual proposal is the recapitulation of the evolution of the flagellum or something absurd like that--which contingency alone makes improbable).
This is one of the best tests of what evolution can do. Behe stupidly forgot about the fact that Plasmodium reproduces sexually (at least he does in most of his "discussion" of the matter), which indeed appears not to be how most of the basic chemical pathways evolved. OTOH, it is how most of the morphological variation appeared, so there's nothing wrong with demonstrating how much evolution resulting from sexual reproduction can do. Nevertheless, finding out what asexual organisms can do without inter-specific conjugations is important for understanding evolution.
Well, it's just another nail in the ID coffin. Sad little rear-guard shots are about all that they can muster any more, as actual science continues while ID's whine gets thinner, and thinner, and thinner...
Glen D
http://tinyurl.com/2kxyc7
Posted by: Glen Davidson | June 10, 2008 9:43 PM
"If two mutations have to occur before there is a net beneficial effect -- if an intermediate state is harmful, or less fit than the starting state -- then there is already a big evolutionary problem. And what if more than two are needed? The task quickly gets out of reach of random mutation."
The beauty of science is that no matter how arcane the subject under comsideration, the truth of a hypothesis can be plainly demonstrated by a clever experiment. Unless you're Michael Behe, apparently.
Posted by: dave | June 10, 2008 9:43 PM
Wow, that is f***ing fascinating. The results of the described experiments are so pithy in their negation of Behe/irreducible complexity/ID, but even besides that satisfaction they give concrete proof of a phenomenon that was previously suspected to be of fundamental importance but was not as well conceptualized as it will be now, likely enabling a deeper and clearer grasp of genetics, evolution, and biology as a whole. Sounds like 20 years worth of work to me...
Posted by: Jacob Basson | June 10, 2008 9:44 PM
liarbehety really doesn't talk out of his mouth does he?
Posted by: Ray Mills | June 10, 2008 9:45 PM
The obvious retort is, what if the intermediate state is not less fit, or extremely close to neutral? Happens all the time, you mindless twerp.
Glen D
http://tinyurl.com/2kxyc7
Posted by: Glen Davidson | June 10, 2008 9:47 PM
That was really poor form on account of Behe. You'd think if he wanted to be respected as a scientist he'd at least try and make his conclusion fit the evidence.
Posted by: Kel | June 10, 2008 9:49 PM
I hope they win a Nobel for this one. Brilliant experiment.
Posted by: ceejayoz | June 10, 2008 9:57 PM
Great post. I hope you realize that not all creationists are dogmatic morons. Many of them believe what they do because of indoctrination from their parents or community. Contrasting the logic and evidence for evolution against the idiocy of creationism really does make a difference.
Posted by: sprosis | June 10, 2008 9:57 PM
Am I completely off-base in seeing a similarity to lactase persistence in some populations of humans? I don't have the enough background to know, but that's what popped to mind.
Posted by: cicely | June 10, 2008 10:13 PM
@#13
Not to be picky, but wouldn't the process of indoctrination make them dogmatic morons? Yes, a lot of them can blame in on the teachings of their parents and the community in which they live but that still doesn't take away from the fact that they behave like dogmatic morons.
Posted by: Kel | June 10, 2008 10:20 PM
The fascinating thing about Behe's piece is that it doesn't appear (to my untrained eye, at least) to distort or misrepresent Lenski's findings, reporting them pretty accurately. Then he proceeds to interpret them in the most nonsensical way possible. He's a very special man.
Posted by: SC | June 10, 2008 10:22 PM
There's a problem with rejecting Behe's premise, and it's the reason ID isn't science too. How do you devise an experiment that excludes the possibility of action by an omnipotent god? You don't. Such a being could make any experiment come out however it wanted, and disguise its actions/effects while doing it. So if you assume an omnipotent god, as Behe does, you've got an out for any possible experiment; you have a hypothesis incapable of being disproved.
Posted by: QrazyQat | June 10, 2008 10:29 PM
I love all the fascinating stuff Lenski has done with this brilliantly designed long-running experimental plan over the years- he's one of my scientific heroes. With the fierce competition for funds and short time horizons nowadays, the patience and vision to sustain this kind of decades-spanning project are commodities in very short supply.
Posted by: Steve LaBonne | June 10, 2008 10:31 PM
Off-topic but always makes me giggle.
Overheard once:
"You know, we can put a man on the moon... you think we'd be able to wipe out E. Coli once and for all."
Posted by: Nathaniel | June 10, 2008 10:39 PM
Behe's ability to more or less correctly apprehend the details while completely missing their meaning is incredible. For a biochem PhD, he has astonishingly poor grasp of evolution. Does he actually believe this crap, or is he just willing to sell his scientific integrity to the highest bidder?
To pick out just one bit of stupidity/lying, Behe wrote:
Yeah, only one in a dozen lines evolved the mutation. So what? 1/12th (8.3%) of a population is not trivial, and in nature, once that 1/12th of the population did evolve the citrate+ mutation, it would likely be selected for (due to environmental pressures of limited glucose & presence of citrate), with the citrate-using organisms out-competing the others.
Posted by: Etha Williams | June 10, 2008 10:48 PM
This post has been added to the grand list of demonstrations that Behe is a dunce. Many thanks.
Posted by: Blake Stacey | June 10, 2008 11:02 PM
Brilliant work by Lenski and his team. It must be wonderful after 20 years of work for this experiment to have paid off so well. Great breakdown too PZ; I always find Bio papers a bit difficult to get through (of course, my background is Mathematics.)
@Etha,
Do you really expect Behe to even make sense? I mean, the comment you quoted from him solidly demonstrates evolution at work (controlled for Behe's spin, of course). I honestly only skimmed Behe's comments, but he didn't make a lot of sense in any case (thusly why I only skimmed his comments).
In any case, I look forward to future papers on the subtleties of this data by Lenski et al.
Posted by: Numerical Thief | June 10, 2008 11:07 PM
Fascinating peek at the interplay between genes and environment. Spinning this any way other than showing evolutionary process can lead to unexpected but well explained ends is completely out of line with the work.
Posted by: BA | June 10, 2008 11:09 PM
I beleive that this also gives lie to Simon Conway-Morris's claim that evolution is inevitable, and that replaying history would still result in humans or someting very nearly like us.
Posted by: Tex | June 10, 2008 11:17 PM
Fascinating and well-written, thanks! I'll be bookmarking this page, I think.
Posted by: Tristan | June 10, 2008 11:22 PM
Boy, this is bad news for physicists. If they ever figure out how to go back in time, it's going to be even more important to not touch anything!
Posted by: RamblinDude | June 10, 2008 11:32 PM
Superb post, PZ!
As this study eloquently demonstrates, new mutations are the rate limiting step in the development of certain evolutionary novelties. Here, natural selection only plays a secondary role.
Hurray for new mutation theory!
Posted by: LH | June 10, 2008 11:36 PM
Thanks for the great write-up. What a great experiment!
Posted by: Chris | June 10, 2008 11:37 PM
Wow -- what a great experiment, and thanks for the writeup PZ. I love that it's not just an example, a hard example, of evolution really occurring, but that it lets us look at the _way_ evolution occurs.
The thing that jumps right out at me isn't the beauty of the experiment ("Hey, let's set up an environment and see what we see!"), but the amount of labor put into it. TWENTY YEARS OF TENDING THE DAMN BACTERIAL COLONIES!!! That's a solid chunk of one's life, and just as well, a lot of undergrads / grad students / post-docs. The next time somebody tells me that scientists just don't work, or don't have courage, I'll tell them about this experiment. Hell -- I can't keep plants alive for two weeks -- how did they keep bacterial colonies alive and uncontaminated for twenty freaking years???
There's gotta be some sort of prize for this paper.
Posted by: spudbeach | June 10, 2008 11:51 PM
What I find amazing is that they went 20 years without a power failure.
Posted by: Jeff Bell | June 11, 2008 12:09 AM
Beautiful experiment! Scientific elegance at it's best.
Posted by: Andre | June 11, 2008 12:28 AM
This is why side-projects are sometimes more important than what we write grants for. Sure, a large number of them go absolutely nowhere, but for the portion like the one represented by this publication, their value is unequivocal. I only wish granting agencies would realize this.
Lovely write up; I think you did a superb job putting this topic in its proper context. My only regret is that that ugly Behe nonsense dripped into it. ;)
Posted by: KC | June 11, 2008 12:28 AM
Could Behe's "review" sound any more like wanton whoring of his book?
I love how casually he references the National Review as rating his crap worthy of the 100 best of the last century. The National Review. PAH!
Posted by: BlueIndependent | June 11, 2008 12:36 AM
Can somebody explain this to me?
From Carl Zimmer's page:
"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."
At the end of the day it's still E. coli, right?
Posted by: chainlink | June 11, 2008 12:38 AM
But....But....But...They are STILL E.COLI!!!!11!!!!
Evilution is WRONG!!!111!!!!!111
*Sarcastic mode off*
This is fascinating.
Posted by: Blaidd Drwg | June 11, 2008 12:47 AM
chainlink,
Go home. He's describing a microevolutionary phenomenon. Not the production of new species.
Posted by: Loc | June 11, 2008 12:55 AM
Wow, that's fascinating research! And you explain it in a way that is accessible to almost anyone. Bravo.
Posted by: Nicole | June 11, 2008 1:00 AM
Re-evolved citrate capabilities, could there be an interesting divergence between the first instance and the second?
Posted by: Tim | June 11, 2008 1:01 AM
Oh, that New Scientist article makes me stabby.
Posted by: efrique | June 11, 2008 1:11 AM
Don't creationists have a concept of 'historical contingency', whereby genetic diversity recovers after every kind is reduced to a pair of individuals from the Flood? Sure, it's divinely created contingency, but still they should be jumping on this story to explain how all the species of canines re-evolved just after the flood (it's always canines).
Posted by: Josh | June 11, 2008 1:24 AM
I've always been interested in the question of evolutionary contingency (although not couched in the appropriate terminology, obviously). It just struck me as something worth looking into. Thanks PZ, I'll be sure to check into this in further detail.
Obligatory Behe/ID abuse here.
Posted by: JM Inc. | June 11, 2008 2:24 AM
This is a great post. Thanks to PZ for explaining it for all us lay people.
And I just bought Zimmer's book over the weekend. So I am now looking forward to getting immersed in the world of E.coli.
Posted by: Serena | June 11, 2008 2:28 AM
There was a short 1995 paper by Lenski et al which is relevant here.
http://www.sciencemag.org/cgi/content/abstract/267/5194/87
Experimental tests of the roles of adaptation, chance, and history in evolution
The method is extremely clever, measuring the relative importance of adapation vs chance vs history using nested ANOVA statistics. Almost as elegant as the Luria & Delbruck Fluctuation Test (if you don't know that one, google it... it is beautiful.)
Posted by: travc | June 11, 2008 2:47 AM
How do you devise an experiment that excludes the possibility of action by an omnipotent god?
Behe has said that if you could evolve a flagella from scratch, he'd concede that ID has been disproven. That's his stock response to the accusation that ID is not falsifiable. Intuitively, the time and lab space required would prohibit this sort of experiment. But the spirit of Lenski's work is not qualitatively different...it's incredibly disengenous for Behe to claim a victory for ID here.
It seems that Behe has given up any hope of swaying the minds of folks who actually have a clue about the science.
Posted by: ngong | June 11, 2008 3:11 AM
I've mentioned this elsewhere, but it is a fun (true) story.
The E coli were never "expected" to start metabolizing citrate. In fact, the citrate only media was used as a 'no growth' control. I happened to be visiting Lenski shortly after that uppity new strain evolved, and one of the lab meeting topics was 'what can we use for a control now'.
If you want to see some more really cool experiments, google "lenski myxococcus". Social bacteria... ooh the experimental possibilities.
Oh, and "The Evolutionary Origin of Complex Features" is always good if you haven't read it yet. It was pretty much an explicit reply to the Irreducible Complexity nonsense.
http://myxo.css.msu.edu/papers/nature2003/
Figure 2 provides some insight into drift and historical contingency IMO, but I'm partial to that particular fig.
Posted by: travc | June 11, 2008 3:25 AM
I think several people are over-interpreting the 'historical contingency' aspect. Adaptation (selection) is still very powerful too. Which dominates really depends on the timescale and the mutational distance being covered. It is also critical to remember that adaptation is all about function and not form (many forms may have similar functionality).
What is quite clear, neutral drift leads to much more efficient exploration of genotype space than one might expect.
The 1995 paper I linked in #43 really does lay the groundwork for this discussion.
PS: This is not really the culmination of a 20 year experiment. Lenski's group has been doing all sorts of clever and important experiments using their long term E coli lines as a tool. Oh, and to #1, those bugs are saved safe in a freezer hooked up to a backup generator ;)
PPS: Not exactly Nobel work, but the NSF or NIH should give his lab a 'center' establishing grant so he has guaranteed funding to keep the experiment going (and expand it).
Posted by: travc | June 11, 2008 3:51 AM
I was wondering about this. That makes it even more impressive. Because the study was well-designed to begin with, they were able to improvise further research and ultimately produce important findings. Sounds like a story that would be useful in teaching about the process of doing science.
Posted by: SC | June 11, 2008 4:44 AM
I beleive that this also gives lie to Simon Conway-Morris's claim that evolution is inevitable, and that replaying history would still result in humans or someting very nearly like us.
I'm not sure about that - not that I think SCM is right, but he could surely argue that if you set a ball rolling down a hill, the path it takes and the place it reaches the bottom depend sensitively on the exact weight, shape, etc. of the ball - but you can be sure it will reach the bottom. (Hm, no, actually you can't in general, it might get stuck in a small dip or a patch of mud - but in many cases it would reach the bottom with very high probability.)
Anyway, truly fascinating stuff - thanks!
Posted by: Nick Gotts | June 11, 2008 5:13 AM
@RamblinDude, #26: Actually it's okay to do what you want when you go back into the past, because whatever you did, already happened :)
Posted by: Stephen Wells | June 11, 2008 5:49 AM
Behe is a true IDiot:
"Now here we have Richard Lenski affirming that the evolution of some pretty simple cellular features likely requires multiple mutations.
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."
Does he think the Intelligent Designer stepped in and zapped the bugs with his magic wand? I guess so...
Its a pity Lenski forgot to put an Intelligent Designer Intervention section in the Materials and Methods. They'll have publish an erratum now....! Shoddy work!
http://www.youtube.com/watch?v=MO2n3GHGK7c
Posted by: Rowan | June 11, 2008 6:00 AM
ngong said:
Michael Behe being disingenuous and borderline dishonest? No! Say it ain't so!
Am I a bad person for enjoying watching him wriggle on the hook of actual experimental evidence though?
Posted by: Lilly de Lure | June 11, 2008 6:01 AM
You know, since my old life focused so much on micro- and molecular biology, I always assumed I was mildly dense when it came to discussing evolution.
But then I read the Behe comment:
I really have a hard time thinking he's a biologist of any stripe!
Am I wrong, or is his statement the opposite of true? Or to be blunt, is he lying, intentionally or not?
Is he playing a word game? Is he meaning "Darwinian" as in "going strictly by only what Darwin wrote and not considering a single development in biology since the 1800's"?
Now, since I haven't read the actual Origin of Species (bad bioloist!), I don't know if Darwin considered changes that were essentially unnoticed or not. But that only matters if you're an anti-Evolutionist, since they seem to bone up on every work of Darwin and nothing else, as if science stopped. (I wonder if they do the same with Newton and ignore Einstein, etc.)
I mean, has he cracked open a current textbook (or 20 year old one, even)?
Anyway, this kind of accumulation concept is - I had thought - a basic component of current evolutionary thought. Maybe it's because I played with bacteria enough in the past that it's easier to see the obviousness of it - I don't know.
(great overview, by the way... I need to call in favors to get a copy of the paper, but I'm looking forward to reading the details)
Posted by: clear as mud | June 11, 2008 6:24 AM
Posted by: Steve LaBonne | June 11, 2008 6:48 AM
Actually it's okay to do what you want when you go back into the past, because whatever you did, already happened
You going to be the one who tests that hypothesis? - "Oh shit, now my tentacles have changed colour..."
Posted by: chris y | June 11, 2008 6:50 AM
Yet another, fully documented, counter to the old canard "No one has seen evolution happening".
Posted by: DiscoveredJoys | June 11, 2008 6:51 AM
A gorgeous experiment, beautifully explained. Thanks, again, PZ, for explaining this.
Posted by: tristero | June 11, 2008 7:32 AM
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."
Brilliant. If multiple mutations are required, we have proof of intelligent design. If, on the other hand, multiple mutations aren't required, we have proof of intelligent design (since all organisms were obviously plopped down as is).
Generally speaking, if you wanted to make a case for ID, you'd find a series of simple mutations that lead to a new function, and then point out that nature has never trod down that path. Behe hasn't been able to do that. Instead, in his twisted way, he calculates the odds for known simple mutations, and asks us to gawk at the improbability of more complex transitions.
As I recall, he saw the two mutation chloroquinine resistance transition as right on the border of possibility. Presumably, a three mutation sequence is then impossible.
Posted by: ngong | June 11, 2008 7:36 AM
Great article, and written so that even a layperson like myself can understand. Thanks PZ.
Posted by: DaveH | June 11, 2008 8:06 AM
Wow. I'm used to biologists thinking in terms of generations and deep time by now, but 20 year experiments seems pushing it.
I don't think they kept them uncontaminated as much as screened them thoroughly.
IIRC they were initially thinking the citrate+ population clouding the meager media was a bacterial contamination, since other bacteria can metabolize citrate. In such cases I believe they took a deep breath, popped out a freezer backup from some generations back, and replayed that segment of the experiment.
Perhaps it is plausible that some bacteria (or virus, since ERV explained about Morons in Microbiology) could have transfered one or more of the required mutations in the form of a new gene by HGT? But it seems very unlikely.
Posted by: Torbjörn Larsson, OM | June 11, 2008 8:13 AM
Alright, if I understand correctly, what Behe is saying is akin to:
"The likelihood of getting the poker hand I just was dealt is less than 1 in 300 million. Therefore, I was never dealt this hand."
Posted by: Andrés | June 11, 2008 8:20 AM
I was immediately drawn to thinking on this subject too; but couldn't such a biologist instead claim he got support for his views? Despite contingency a new resource was exploited, and observing the biosphere, it seems to me no obvious resource have been left unexploited. (Chemical energy from weathering or radioactivity, thermal energy, solar energy, et cetera.)
I guess in terms of Nick Gott's analogy one could say there seems to be support for that such now probable balls will find their way down to the bottom of a hill.
Is it?
The biologists will set me right here, but species is a human description of different populations, and as for bacteria it seems to me an ecological description makes much sense. (As for example the recent paper where sea water bacteria populations were most easily separated by sequencing and evolutionary ecological modeling in combination.)
I'm reasonably sure that you now could set up an environment where a population of the citrate+ strain will be able to survive in but not the native one that prefers your gut. That would be speciation by the ecological criteria, wouldn't it?
Posted by: Torbjörn Larsson, OM | June 11, 2008 8:26 AM
Oops. My "freezer" should be a cooler, shouldn't it?
Posted by: Torbjörn Larsson, OM | June 11, 2008 8:30 AM
Now let's have fun quote-mining!
Being a cdesign proponentsist sure is easy. Can I have my "science" degree now?
Posted by: Andrés | June 11, 2008 8:30 AM
but species is a human description of different populations, and as for bacteria it seems to me an ecological description makes much sense. (As for example the recent paper where sea water bacteria populations were most easily separated by sequencing and evolutionary ecological modeling in combination.)
Asexual microbes make the whole "species" issue a huge pain in the ass. I believe the primary way microbes are definitively classified is by DNA sequence, and if I recall correctly the cut-off is generally excepted at 70% identity. The problem with ecological modeling is that horizontal gene transfer is so rampant that looking at growth properties isn't necessarily definitive.
Posted by: Lorax | June 11, 2008 8:45 AM
I say, if it helps anti-evolutionists stop saying "It's still E. coli NOTHING HAPPENED AT ALL LALALALALALALALA!" then someone should just make it official at call it Escherichia lenski or something. I mean, if there is a technical validity to that claim, that is.
I mean, normally this would be a totally valid long-term discussion about "what is a species?", but screw it - anti-evolution folks don't give a crap for informed discussion, so...
Posted by: clear as mud | June 11, 2008 8:47 AM
I just want to express my joy at the elegance of this experiment. And such dedication! Those bacterial samples are older than me.
And thank you, PZ, for writing about it in such a manner that I can grasp all of it.
I also wonder whether or not it's still the same species. E. Coli are asexual, aren't they? Because I seem to recall that the ability to procreate was the speciating line. So how do you... Speciate (?) asexual bacteria?
Posted by: valor | June 11, 2008 8:55 AM
I have a big soft spot for this type of research: the very long-term things that really don't cost more than a few plates and some time and that you would never get funding for. My supervisor has a few of these on the go, and while we all grumble when he asks us to do something for them, it really doesn't take more than a few hours every few months. And who knows? Maybe we'll see something nifty in 10 years time. Not all biologically relevant things happen in 2-3 years.
Posted by: katie | June 11, 2008 8:58 AM
Thankyou for drawing attention to this PZ. I am in awe at the beauty of this experiment it is truly beautiful. Can you just imagine what it must have been like in that lab as they realised the coli were eating citrate? Since 1988, the year I started my PhD. Wonderful stuff.
Love the riff on Robert Frost at the end too. Who says us boffins ain't literate, huh?
Posted by: Peter Ashby | June 11, 2008 9:08 AM
Thinking of the species issue, I was just reading the Science paper on massive horizontal gene transfer in bdelloid rotifers. They have really good DNA repair mechanisms which let them survive dessication, and it turns out the ends of their chromosomes are packed with genes from bacteria, fungi, all sorts, just bits of DNA that got picked up and incorporated. Also they're completely asexual. So the species concept is really strained here.
Posted by: Stephen Wells | June 11, 2008 9:17 AM
A related finding from a recent hosing of a creo on pharyngula. By selecting bacteria to utilize a novel sugar, scientists have been able to observe gene duplication followed by mutation/divergence. Which is what everyone has been saying for decades.
Doesn't matter, the creos just move the goal posts again. Already we are hearing that if scientists can't product a Big Bang in the laboratory to create a new universe, that it must not have happened. This the ultimate in unfalsifiability. If they did, there would be no one left alive to write up the paper or read it.
Actually we have seen duplication followed by mutation in at least one model system. So much for whereismysanity. So it isn't an empty claim. Time to move the goal posts once again. Or maybe realize that evolution is a fact and theory. No doubt which way he will go.
You guys have been doing this for thousands of years now. First it was Zeus and Apollo Helios. Then it was the flat earth followed shortly by geocentrism. Then it was creationism. Some people never gave up any of those.
Posted by: raven | June 11, 2008 9:24 AM
crosspost from PT
.There is a lot of data that contradicts Behe's fallacies of more than 2 mutations are impossible. Here is one such paper.
Another is below. This model system starts with a deletion of the beta gal. gene, which hydrolyzes lactose. These E. coli strains are then selected which evolve a new beta gal., ebg=evolved beta gal. This requires 2 mutations since a repressor regulates the ancestral operon. In one case, by sequencing they found a triple mutation.
The theory for this is that organisms under stress due to selection may show a higher mutation frequency as bursts of mutagenic polymerases are produced or DNA repair mechanisms become overwhelmed or dysfunctional. Not sure if the mechanisms are known too well.
Behe's theories are equivalent to proving that bumble bees can't fly with mathematical aerodynamic modeling. The problem with that theory is that bumble bees do fly. As Feynman and others have pointed out, many a beautiful theory has been ruined by an ugly fact.
Proc Natl Acad Sci U S A. 1991 Jul 1;88(13):5882-6. Links Adaptive evolution that requires multiple spontaneous mutations: mutations involving base substitutions.Hall BG. Biology Department, University of Rochester, NY 14627.
A previous study has demonstrated that adaptive missense mutations occur in the trp operon of Escherichia coli. In this study it is shown that, under conditions of intense selection, a strain carrying missense mutations in both trpA and trpB reverts to Trp+ 10(8) times more frequently than would be expected if the two mutations were the result of independent events. Comparison of the single mutation rates with the double mutation rate and information obtained by sequencing DNA from double revertants show that neither our classical understanding of spontaneous mutation processes nor extant models for adaptive mutations can account for all of the observations. Despite a current lack of mechanistic understanding, it is clear that adaptive mutations can permit advantageous phenotypes that require multiple mutations to arise and that they appear enormously more frequently than would be expected.
There is a lot of data that contradicts Behe's fallacies of more than 2 mutations are impossible. Here is one such paper.
Another is below. This model system starts with a deletion of the beta gal. gene, which hydrolyzes lactose. These E. coli strains are then selected which evolve a new beta gal., ebg=evolved beta gal. This requires 2 mutations since a repressor regulates the ancestral operon. In one case, by sequencing they found a triple mutation.
1: Genetics. 1989 Dec;123(4):635-48. Links
Erratum in: Genetics 1990 Mar;124(3):791. DNA sequence analysis of artificially evolved ebg enzyme and ebg repressor genes.Hall BG, Betts PW, Wootton JC. Molecular and Cell Biology, University of Connecticut, Storrs 06268.
The ebg system has been used as a model to study the artificial selection of new catalytic functions of enzymes and of inducer specificities of repressors. A series of mutant enzymes with altered catalytic specificities were previously characterized biochemically as were the changes in inducer specificities of mutant, but fully functional, repressors. The wild type ebg operon has been sequenced, and the sequence differences of the mutant enzymes and repressors have been determined. We now report that, contrary to our previous understanding, ebg enzyme contains 180-kD alpha-subunits and 20-kD beta-subunits, both of which are required for full activity. Mutations that dramatically affect substrate specificity and catalytic efficiency lie in two distinct regions, both well outside of the active site region. Mutations that affect inducer specificity of the ebg repressor lie within predicted sugar binding domains. Comparisons of the ebg beta-galactosidase and repressor with homologous proteins of the Escherichia coli and Klebsiella pneumoniae lac operons, and with the galactose operon repressor, suggest that the ebg and lac operons diverged prior to the divergence of E. coli from Klebsiella. One case of a triple substitution as the consequence of a single event is reported, and the implications of that observation for mechanisms of spontaneous mutagenesis are discussed.
The theory for this is that organisms under stress due to selection may