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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

  1. #1 James F
    June 10, 2008

    Excellent article. Save those bugs for future sequencing!

  2. #2 shane
    June 10, 2008

    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?

  3. #3 Lee Drake
    June 10, 2008

    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.

  4. #4 Albarossity
    June 10, 2008

    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..

  5. #5 SC
    June 10, 2008

    Very interesting findings. And I’m amazed by experiments like this that span decades.

    Behe’s a nitwit.

  6. #6 Glen Davidson
    June 10, 2008

    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

  7. #7 dave
    June 10, 2008

    “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.

  8. #8 Jacob Basson
    June 10, 2008

    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…

  9. #9 Ray Mills
    June 10, 2008

    liarbehety really doesn’t talk out of his mouth does he?

  10. #10 Glen Davidson
    June 10, 2008

    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 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

  11. #11 Kel
    June 10, 2008

    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.

  12. #12 ceejayoz
    June 10, 2008

    I hope they win a Nobel for this one. Brilliant experiment.

  13. #13 sprosis
    June 10, 2008

    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.

  14. #14 cicely
    June 10, 2008

    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.

  15. #15 Kel
    June 10, 2008

    @#13

    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.

    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.

  16. #16 SC
    June 10, 2008

    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.

  17. #17 QrazyQat
    June 10, 2008

    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.

  18. #18 Steve LaBonne
    June 10, 2008

    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.

  19. #19 Nathaniel
    June 10, 2008

    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.”

  20. #20 Etha Williams
    June 10, 2008

    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:

    It took trillions of cells and 30,000 generations to develop it, and only one of a dozen lines of cells did so.

    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.

  21. #21 Blake Stacey
    June 10, 2008

    This post has been added to the grand list of demonstrations that Behe is a dunce. Many thanks.

  22. #22 Numerical Thief
    June 10, 2008

    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.

  23. #23 BA
    June 10, 2008

    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.

  24. #24 Tex
    June 10, 2008

    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.

  25. #25 Tristan
    June 10, 2008

    Fascinating and well-written, thanks! I’ll be bookmarking this page, I think.

  26. #26 RamblinDude
    June 10, 2008

    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!

  27. #27 LH
    June 10, 2008

    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!

  28. #28 Chris
    June 10, 2008

    Thanks for the great write-up. What a great experiment!

  29. #29 spudbeach
    June 10, 2008

    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.

  30. #30 Jeff Bell
    June 11, 2008

    What I find amazing is that they went 20 years without a power failure.

  31. #31 Andre
    June 11, 2008

    Beautiful experiment! Scientific elegance at it’s best.

  32. #32 KC
    June 11, 2008

    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. ;)

  33. #33 BlueIndependent
    June 11, 2008

    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!

  34. #34 chainlink
    June 11, 2008

    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?

  35. #35 Blaidd Drwg
    June 11, 2008

    But….But….But…They are STILL E.COLI!!!!11!!!!

    Evilution is WRONG!!!111!!!!!111

    *Sarcastic mode off*

    This is fascinating.

  36. #36 Loc
    June 11, 2008

    chainlink,

    Go home. He’s describing a microevolutionary phenomenon. Not the production of new species.

  37. #37 Nicole
    June 11, 2008

    Wow, that’s fascinating research! And you explain it in a way that is accessible to almost anyone. Bravo.

  38. #38 Tim
    June 11, 2008

    Re-evolved citrate capabilities, could there be an interesting divergence between the first instance and the second?

  39. #39 efrique
    June 11, 2008

    Oh, that New Scientist article makes me stabby.

  40. #40 Josh
    June 11, 2008

    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).

  41. #41 JM Inc.
    June 11, 2008

    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.

  42. #42 Serena
    June 11, 2008

    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.

  43. #43 travc
    June 11, 2008

    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.)

  44. #44 ngong
    June 11, 2008

    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.

  45. #45 travc
    June 11, 2008

    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.

  46. #46 travc
    June 11, 2008

    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).

  47. #47 SC
    June 11, 2008

    The E coli were never “expected” to start metabolizing citrate.

    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.

  48. #48 Nick Gotts
    June 11, 2008

    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!

  49. #49 Stephen Wells
    June 11, 2008

    @RamblinDude, #26: Actually it’s okay to do what you want when you go back into the past, because whatever you did, already happened :)

  50. #50 Rowan
    June 11, 2008

    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

  51. #51 Lilly de Lure
    June 11, 2008

    ngong said:

    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.

    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?

  52. #52 clear as mud
    June 11, 2008

    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:

    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 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)

  53. #53 Steve LaBonne
    June 11, 2008

    Sounds like a story that would be useful in teaching about the process of doing science.

    And also, as noted above, one that should be pounded into the heads of grant reviewers.

  54. #54 chris y
    June 11, 2008

    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…”

  55. #55 DiscoveredJoys
    June 11, 2008

    Yet another, fully documented, counter to the old canard “No one has seen evolution happening”.

  56. #56 tristero
    June 11, 2008

    A gorgeous experiment, beautifully explained. Thanks, again, PZ, for explaining this.

  57. #57 ngong
    June 11, 2008

    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.

  58. #58 DaveH
    June 11, 2008

    Great article, and written so that even a layperson like myself can understand. Thanks PZ.

  59. #59 Torbjörn Larsson, OM
    June 11, 2008

    Wow. I’m used to biologists thinking in terms of generations and deep time by now, but 20 year experiments seems pushing it.

    Hell — I can’t keep plants alive for two weeks — how did they keep bacterial colonies alive and uncontaminated for twenty freaking years???

    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.

  60. #60 Andrés
    June 11, 2008

    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.”

  61. #61 Torbjörn Larsson, OM
    June 11, 2008

    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 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.

    At the end of the day it’s still E. coli, right?

    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?

  62. #62 Torbjörn Larsson, OM
    June 11, 2008

    Oops. My “freezer” should be a cooler, shouldn’t it?

  63. #63 Andrés
    June 11, 2008

    Now let’s have fun quote-mining!

    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. [...] [K]ey innovations [...] are not easily evolved by gradual, cumulative selection.

    Being a cdesign proponentsist sure is easy. Can I have my “science” degree now?

  64. #64 Lorax
    June 11, 2008

    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.

  65. #65 clear as mud
    June 11, 2008

    “At the end of the day it’s still E. coli, right?”

    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…

  66. #66 valor
    June 11, 2008

    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?

  67. #67 katie
    June 11, 2008

    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.

  68. #68 Peter Ashby
    June 11, 2008

    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?

  69. #69 Stephen Wells
    June 11, 2008

    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.

  70. #70 raven
    June 11, 2008

    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.

    movethegoalposts: If you are claiming that research has been proven to show that gene duplication creates new functional genes that have NOT been previously found in an existing organism, please cite your paper. Otherwise, it’s just empty claim.

    Xylitol is also not normally metabolized, but Mortlock and his colleagues were able to develop strains (generally through spontaneous mutations, but sometimes with u.v. ray or chemical induced mutations) that could use it because ribitol dehydrogenase (which is usually present in the cells to convert ribitol to D-ribulose) was able to slightly speed up the conversion of xylitol to D-xylulose, for which metabolic pathways already exist. The ability of the strains to utilize xylitol was increased as much as 20 fold when first production of ribitol dehydrogenase was deregulated (the enzyme was produced all the time, not just when ribitol was present), then duplication of the ribitol dehydrogenase genes occurred, then the structure of the enzyme was changed such that its efficiency at working with xylitol was improved, and finally, in at least one case, a line regained control of the modified ribitol dehydrogenase gene so that the enzyme was only produced in the presence of xylitol. Here we have a complete example of a new metabolic pathway being developed through duplication and modification of an existing pathway.

    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.

  71. #71 raven
    June 11, 2008

    crosspost from PT

    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 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 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.

  72. #72 Josh
    June 11, 2008

    So the species concept is really strained here.

    I think it can be said that the species concept is always really strained. The concept itself is either plastic or a mess depending on what perspective you want to view it from and what taxa you choose as the exemplar du jour. The high school biology species concept works pretty well in high school biology. This paper just does a nice subtle job of reminding us of that.

  73. #73 Nick Gotts
    June 11, 2008

    As Feynman and others have pointed out, many a beautiful theory has been ruined by an ugly fact. – raven

    But in Behe’s case, it’s an ugly pseudo-theory killed by hordes of beautiful facts!

  74. #74 David Marjanovi?, OM
    June 11, 2008

    Now, since I haven’t read the actual Origin of Species (bad bioloist!)

    I haven’t read it either. Very few biologists have. It’s simply not necessary. It’s very interesting from a history of science point of view, but that basically is it.

    (Darwin was great at explaining, though.)

    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.)

    Look at what has died out, and weep.

    – Gigantic terrestrial herbivores that can get bigger than any land mammal can because they combine high metabolism with ovipary.
    – The same animals that can get a longer neck than any mammal because of their bird-style respiratory system.
    – Huge flying animals that can get bigger than any bird because they can launch from the ground on all fours, in other words, employ the wings for jumping.
    – Trees that can grow in a swamp without costly special adaptations because they grow roots like leaves, from the outside of other roots, not from their inside.

    And that was just off the top of my head.

    Who was it who said “everything is the way it is because it got that way“? D’Arcy Thompson?

    So how do you… Speciate (?) asexual bacteria?

    You are thinking of only two of the 25-upwards definitions for “species” out there. Others use wildly different criteria, like similarity, similarity of ecological niche, monophyly etc. etc.. And all of these give different results. Depending on the species concept, there are between 101 and 249 endemic bird species in Mexico.

  75. #75 Sven DiMilo
    June 11, 2008

    because they combine high metabolism with ovipary.

    because of their bird-style respiratory system.
    because they can launch from the ground on all fours

    All three of these paleo-becauses are hypotheses, not consensus. Paleo-types tend to buy them (some with near-religious fervor), physiologists not so much. As one of the latter I’m pretty skeptical. The animals certainly existed, but the proximate explanations for their weirdnesses are largely guesswork (of varying degrees of educatedness).

    But back on-thread, Lenski’s techniques are a goldmine for actually studying (micro)evolution in real time. Among many other extremely cool experiments has been a long-running collaboration with Al Bennett at UC Irvine looking at adaptation of coli to different temperatures and, more recently, pHs. They call it “natural selection in the laboratory” because the environments are imposed, but the evolutionary responses of the bugs are not. The interested can pull down pdfs here.

  76. #76 mothra
    June 11, 2008

    It is gratifying to see evolutionary concepts backed up by experimental data, instead of mere mountains of observational evidence. It strikes me that historical contingency is almost a polysyllabic homonym of co-option. The latter involves a switch in function while the former can also (but is not required) to work from neutral mutations.
    __

    When I read PZ’s summary of the work of Lenski et al, my first thoughts concerned House finches and House sparrows. In suburban areas, the native House finches appeared to be out competing House sparrows.(Backstory: House finches were originally a birds found in the U.S. west of the Rockies and later introduced into the northeastern U.S. and have subsequently spread westward to meet with their parent populations. House sparrows were an 19th century import from Eurasia.) With the importation of West Nile Virus, House finch populations have been decimate- House sparrows are still ‘bird mice.’

  77. #77 windy
    June 11, 2008

    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.”

    Randy Olson is right: who would you rather play poker with? I would really, really like to play some poker with Behe. With high cash stakes.

  78. #78 Jud
    June 11, 2008

    #68 – And not only Robert Frost, but Darwin: “…from so simple a beginning….”

    #60 – Yes, this is exactly how and why Behe and IDers always get the probabilities wrong. Hell, what are the chances 20 generations of Behe’s ancestors would meet each other and have kids? By his own calculations, Behe can’t exist!

    QrazyQat wrote: So if you assume an omnipotent god, as Behe does, you’ve got an out for any possible experiment….

    Actually, if you want to parse the logic, Behe can’t assume an omnipotent God, and this is the unexamined contradiction at the heart of ID. The concept of irreducible complexity, insofar as it pretends to have meaning, says there are features in living things that could not have evolved. But if God is omnipotent, he plainly could have set in motion an evolutionary chain that resulted in those features, right? And if He couldn’t (in other words, if ID is true), then there is no omnipotent God.

    Fundamentalists should be turning out in hordes to prevent the teaching of ID in schools.

  79. #79 Jason
    June 11, 2008

    “We can’t rewind the whole planet, but with careful design, we can set up populations that can be rewound.”

    See? This disproves evolution and proves ID!! ;-)

  80. #80 demallien
    June 11, 2008

    Hmmm, I once again note a complete absence of our favourite creationist trolls on a science thread. Funny that – they whinge that this blog is all about bashing religion, not science, and yet when there is science, especially science that blows their POV away, not a peep!

    I suppose I shouldn’t be surprised…

  81. #81 Leland
    June 11, 2008

    #48 – That metaphor betrays some anthropocentric and teleological leanings which I don’t think are at all appropriate when discussing evolution. What makes humans the “bottom of the hill”?

  82. #82 Jordan
    June 11, 2008

    I’ve long been interested in bacteria, archaea and their evolutionary biochemical oddities (especially “extremophiles”). Can anyone recommend a good book? Nothing too technical, I’m not a biologist but AM a practicing organic chemist.

  83. #83 David Marjanovi?, OM
    June 11, 2008

    All three of these paleo-becauses are hypotheses, not consensus. Paleo-types tend to buy them (some with near-religious fervor), physiologists not so much. As one of the latter I’m pretty skeptical. The animals certainly existed, but the proximate explanations for their weirdnesses are largely guesswork (of varying degrees of educatedness).

    You come across as not having read much of the relevant physiological, histological, and biomechanical literature. Not even PZ’s own post about the skeletal pneumatization of Majungasaurus.

    Where do you want me to start to explain?

  84. #84 Longtime Lurker
    June 11, 2008

    Hmm… in other words, Behe is saying that the E. coli able to grow on citrate are THE CHOSEN ONES.

    I for one, welcome our new bacterial overlords.

  85. #85 Paul Lundgren
    June 11, 2008

    Beautifully done, my compliments to the researchers. I have no background in scientific research at all, so this type of insight into even the basics is fascinating to me.

    I’ve been trying to determine the best means of disposing of my copy of Darwin’s Black Box. I’m torn between using it as confetti, a fireplace starter, or practice on the target range. Any creative suggestions?

  86. #86 Longtime Lurker
    June 11, 2008

    “I’ve been trying to determine the best means of disposing of my copy of Darwin’s Black Box. I’m torn between using it as confetti, a fireplace starter, or practice on the target range. Any creative suggestions?”

    Use the paper as a substrate on which to grow your own E. coli cultures.

    How’d you end up with your copy… fundy uncle? Office grab-bag?

  87. #87 astroande
    June 11, 2008

    Just got a chance to read this, and my, what a beautiful experiment.

    I’m reading Carl Zimmer’s book now and thoroughly enjoying it. Many elegant experiments like this have been done with E. coli — it’s proven to be a very useful little microbe.

  88. #88 Andrés
    June 11, 2008

    “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.”

    Whoops. I forgot the division part. The number is closer to 2.6 million.

    “Still not enough, Mr. Behe! That royal flush is irreducibly complex, so you must be cheating!”

  89. #89 Sven DiMilo
    June 11, 2008

    Apologies for the length of this one, replying to DM.
    Well, I try to keep up, but paleophysiology is pretty tangential to what I have to spend the vast majority my productive-reading time on. And unlike some people I have to teach for a living :)

    I think we have discussed, or started discussing, some of these issues before, perhaps at Tet Zoo? But here are my arguments, have at ‘em:
    a) “high metabolism” and “high growth rates” are not synonymous (I think this is what you implied with your first example). Paleopeople seem to think that metabolic rate is some kind of potentiating engine; that an animal “requires” a high metabolic rate to “fuel” a high growth rate. It doesn’t work that way. The fastest-growing animals today are (AFAIK) altricial birds, which are ectothermic while growing really rapidly. There is a metabolic cost to growth–it requires ATP to form peptide bonds, run mitosis, etc.–so that high growth rates necessarily cause a relatively high metabolic rate. To summarize, I would argue that the high growth rates of large dinosaurs required a physiological capacity for the resultant relatively high metabolic rate, but this is a different concept than endothermy or tachymetabolism (at rest). [Now, I would entertain an argument that the capacity to support high metabolic rates resulting from high growth rates requires larger digestive and perhaps cardiovascular organs, and that such larger organs would result in a higher resting metabolic rate, but I have not seen the paleo-argument couched that way.]
    Nor do I see how ovipary enters into it–maybe you can start your explanations there?

    b.) I do not doubt that (some?) dinosaurs had pneumaticized bones, and I will even accept that as strong evidence for some type of air-sac system. That does not, contrary to you, PZ, and the authors of the Majungasaurus paper, necessarily imply bird-style flow-through lungs. Bird lungs evolved from tidal ancestors; bird lungs cannot possibly work without airsacs; therefore there had to have been animals with both airsacs and tidal lungs.
    And I do not follow the logic, in any case, from flow-through lungs to long necks. Deadspace is deadspace either way, no? Another place to start ‘splaining?

    c.) The ability-to-jump thing makes no sense at all to me. The many apparent physiological problems inherent in powered flight at 250 kg are in no way alleviated by a jump. Either those gigantic pterosaurs (and the larger extinct birds) i.) did little in the way of powered flying and were nearly entirely reliant on soaring in thermals (presumably therefore taking off from and needing to land on high cliffs); ii.) they had a functionally different kind of skeletal muscle than modern birds (which seems doubtful, especially for the extinct birds), or iii.) there is something seriously missing from our understanding of powered flight in modern birds; yet this is a very well-studied area. These are serious conundra, and using the wings to jump does not even begin to answer them.

    Over to you, DM, OM!

  90. #90 Josh
    June 11, 2008

    Not even PZ’s own post about the skeletal pneumatization of Majungasaurus.

    Abelisaurid relevancy. Nice.

    *claps*

  91. #91 astroande
    June 11, 2008

    Forgot to add: Behe is a moron. He came to speak to my grad school class once and answer our questions and we soundly beat him (though I doubt he would see it that way, since he’s clearly deluded).

  92. #92 website design
    June 11, 2008

    I submitted this instead of a news story because it does a far better job of explaining the experiment and what it means to our understanding of evolution. A more in depth look can be found by visiting Carl Zimmer’s blog: http://scienceblogs.com/loom/2008/06/02/a_new_step_in_evolution.php

  93. #93 web design company
    June 11, 2008

    I submitted this instead of a news story because it does a far better job of explaining the experiment and what it means to our understanding of evolution. A more in depth look can be found by visiting Carl Zimmer’s blog: http://scienceblogs.com/loom/2008/06/02/a_new_step_in_evolution.php

  94. #94 Nick Gotts
    June 11, 2008

    Leland@81. True – the leanings are SCM’s, not mine.

  95. #95 Owlmirror
    June 11, 2008

    I’ve long been interested in bacteria, archaea and their evolutionary biochemical oddities (especially “extremophiles”). Can anyone recommend a good book?

    Did you miss the first paragraph of this post where PZ does exactly that?

    (Microcosm, by Carl Zimmer)

  96. #96 BAllanJ
    June 11, 2008

    I didn’t follow the links to Behe’s stuff, but it doesn’t sound as though he’s thought this through (doh!)

    What happened was….around the 20,000 generation in just one of the samples, a tiny e-coli ….let’s call him abraham… was born. He did what god wanted him to do, got all the other ecoli to give over a small share of their glucose etc…then around generation 31,000 along came another ecoli…lets call him jebus… and straightened out some of the worshipping stuff the ecoli had got up to… then at generation 33,000 or so, yet another ecoli came along …let’s call him paul… and reinvented all the citrate stuff, hijacked the teachings of the previous dudes so everyone could eat of the new fruit and the lab techs ^H^H^H^H^H^H gods were happy .

  97. #97 Numerical Thief
    June 11, 2008

    the lab techs ^H^H^H^H^H^H gods were happy .

    ^H^H^H Nice touch =)

  98. #98 hje
    June 11, 2008

    Nothing ever surprises the remarkable M. Behe. He’s always: “See I was right all along.” You got to wonder whether Behe even believes in microevolution, let alone macro.

    All that aside, there is one huge difference between Behe and Lenski. The former thinks experiments are a waste of time–because he already knows the answer. The latter actually does the experiment to find an answer.

    Of course if you are Behe, and have “[published] over 35 articles in refereed biochemical journals, … ,” you can opt out of actually doing science. Smugness or laziness?

  99. #99 Steve LaBonne
    June 11, 2008

    I’ve been trying to determine the best means of disposing of my copy of Darwin’s Black Box. I’m torn between using it as confetti, a fireplace starter, or practice on the target range. Any creative suggestions?

    Please, back away from the book before anybody gets hurt, and call a reputable toxic-waste hauling company to get it disposed of safely.

  100. #100 Steve LaBonne
    June 11, 2008

    All that aside, there is one huge difference between Behe and Lenski. The former thinks experiments are a waste of time–because he already knows the answer.

    See, I actually haven’t been able to believe that for quite a while now. I simply don’t think it’s possible that Behe is really this stupid and ignorant. I think he’s just lying for the dollars and the “celebrity” status.

  101. #101 David Marjanovi?, OM
    June 11, 2008

    The fastest-growing animals today are (AFAIK) altricial birds, which are ectothermic while growing really rapidly.

    Ectothermic, yes — but homeothermic, tachymetabolic and tachyaerobic. If they had insulation and were big enough to hold their body temperatures on their own (as opposed to their parents having to do that for them), they couldn’t help being endothermic. Endothermy ( = deriving most of one’s body temperature from one’s own metabolism, as opposed to behavior) is beside the point. :-)

    Now, I would entertain an argument that the capacity to support high metabolic rates resulting from high growth rates requires larger digestive and perhaps cardiovascular organs, and that such larger organs would result in a higher resting metabolic rate, but I have not seen the paleo-argument couched that way.

    I have (G. S. Paul, 1994, 1998 — refs later). He has argued that for this reason bradymetabolic terrestrial animals over about 1 t are impossible. The fossil record fits nicely so far: turtles, pareiasaurs and so on all max out at that mass, and the wide range of mass estimates for Megalania (or rather Varanus priscus) also ends there.

    And then there’s the phenomenon that the cell membranes of extant tachymetabolic animals are more permeable to sodium ions than those of bradymetabolic ones. Therefore, tachymetabolic animals have to keep pumping at high energy expense — that’s a good part of where our body temperature comes from.

    Nor do I see how ovipary enters into it

    More strictly, it’s r-strategy. One of the limits on how big a land animal can get is that the size of the adult population shrinks when body size grows, because larger animals need a bigger area to sustain them. Elephants and rhinos are K-strategists and depend on their parents for a long time. Sauropods (and nonavian dinosaurs in general) laid lots and lots of fairly small eggs (always smaller than the biggest known bird eggs). Evidently, they were r-strategists — and that means it doesn’t matter if occasionally all adults die: you only have to wait till the next generation has grown up.

    (some?) dinosaurs

    Almost all saurischians. Also, all pterosaurs, and the neural arches of Silesaurus are also suggestive.

    there had to have been animals with both airsacs and tidal lungs.

    Sure, but why should the complete system — cervical, thoracic, and abdominal air sacs, as evidence by the bones that are pneumatized — have appeared before the air sacs started to work? There are dinosaurs (basal theropods and basal sauropods) that show evidence for pneumatization only in the caudal cervical and cranial dorsal vertebrae, but Majungasaurus as well as all of the reasonably huge sauropods have much more widespread postcranial pneumaticity. There are lots of papers on this; I recommend Matt Wedel‘s.

    And I do not follow the logic, in any case, from flow-through lungs to long necks. Deadspace is deadspace either way, no?

    The ratio of deadspace to tidal space is what matters here, together with lung efficiency. The tidal space is moved away from the lungs, mostly into the abdomen, which is spacious enough to make the tidal space much larger than the deadspace (indeed, birds breathe much less often and much deeper than mammals); the lungs shrink drastically, leaving more room for tidal space — and so does their histology: bird lungs consist of tiny tubes that have extremely thin walls (thus much better diffusion), work by countercurrent exchange* because the air moves through the lungs in a single direction, and would collapse and stick together if the lungs moved.

    Various skeletal features, like the length of the rearmost ribs (those that most mammals lack altogether) more or less throughout saurischians and the architecture of the gastralia in theropods, confirm that the abdomen was used as tidal space.

    * BTW, crocodiles have crosscurrent exchange. Even that’s better than what all other tetrapods have mustered so far.

    The many apparent physiological problems inherent in powered flight at 250 kg are in no way alleviated by a jump.

    I was only talking about the launching. That’s something that hasn’t been published yet, but a discussion of it is ongoing right now in the Dinosaur Mailing List.

    And yes, the largest ones clearly must have soared a lot, but they were also capable of motor-gliding (anaerobic flapping followed by gliding). Spend a few hours in the DML archives. :-)

  102. #102 Owlmirror
    June 11, 2008

    Speaking of Darwin’s Black Box, Icons of Evolution, and other IDiotic books, the local libraries have copies of many of these.

    It would be very wrong to steal or mutilate books that belong to the public, but I think it might be acceptable to print out a well-written refutation (such as by PZ, and others) and place it between the covers.

    Makes sense?

  103. #103 Owlmirror
    June 11, 2008

    Sauropods (and nonavian dinosaurs in general) laid lots and lots of fairly small eggs (always smaller than the biggest known bird eggs).

    Quibble: IIRC, the eggs of the elephant bird (Aepyornis) were comparable in size to sauropod eggs. And of course, there were dwarf sauropods. And the giant sauropods didn’t start out that size, after all.

  104. #104 Rich Blinne
    June 11, 2008

    Behe said:

    “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.”

    Lenski et al said:

    After depleting the glucose in DM25, the
    earliest Cit+ clones grow almost imperceptibly, if at all, for many
    hours before they begin ef ficiently using the citrate (dat a not
    shown), whereas later Cit+ clones switch to growth on citrate
    almost immediately (Fig. 2). Thus, the population expansion
    bet ween generations 33,000 and 33,500 (Fig. 1) was triggered by
    one or more mutations that improved citrate utilization, rather
    than by the growth of the original Cit+ mutant.

    and

    The origin of the Cit+ function also had profound consequences for the ecology and subsequent evolution of that population. This new capacity was refined over the next 2,000 generations, leading to a massive population expansion as the Cit+ cells evolved to exploit more efficiently the abundant citrate in their environment. Although the Cit+ cells continued to use glucose, they did not drive the Cit- subpopulation extinct because the Cit- cells were superior competitors for glucose. Thus, the overall diversity increased as one population gave rise evolutionarily to an ecological community with two members, one a resource specialist and the other a generalist.

    The weak Cit+ variant was a less fit intermediate state. The second quote shows that the misconception of “survival of the fittest” does not imply the non-survival of the less fit, Another thing that should be noted is no plasmids were involved so the usual creationist argument is void. This is straight up natural selection.

    I say:

    Na na na na. Na na na na. Hey hey hey. Good bye

  105. #105 David Marjanovi?, OM
    June 11, 2008

    Hey! And what about Lepidodendron and its fellow tree-shaped clubmosses? :-)

    over 35 articles in refereed [...] journals

    Only? My thesis supervisor has about 70, and he’s only 42 years old. And people who get suspected of things like Aetogate have several hundred (Lucas has 1400 publications in total — if we count his own journal as peer-reviewed, then I guess that easily makes 1300 peer-reviewed publications).

  106. #106 midwifetoad
    June 11, 2008

    ” …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.”

    Isn’t the point that evolution has no “bottom”? That is to say, no pre-specified goal. You can’t have a Manhattan Project to evolve a flagellum because evolution doesn’t produce complex structures to order. Complexity is something seen in hindsight.

  107. #107 David Marjanovi?, OM
    June 11, 2008

    IIRC, the eggs of the elephant bird (Aepyornis) were comparable in size to sauropod eggs.

    Bigger.

    That’s why I wrote “always smaller than the biggest known bird eggs” (emphasis added).

    The second quote shows that the misconception of “survival of the fittest” does not imply the non-survival of the less fit

    Niche partitioning. Yet another prediction of the theory of evolution confirmed by experiment.

  108. #108 travc
    June 11, 2008

    I thought PNAS made articles available online for free, but apparently not. Does anyone know if/when this goes into the public domain? You’d think as a country we could shell out enough cash to at least support a few journals.

  109. #109 Owlmirror
    June 11, 2008

    That’s why I wrote “always smaller than the biggest known bird eggs”

    *looks embarrassed*

    We violently agree!

    I thought PNAS made articles available online for free, but apparently not. Does anyone know if/when this goes into the public domain?

    I think after 12 months or so

    I just clicked on articles from May 2007 and June 2007 and it lets me view the full text.

    However, articles from Dec 2007 still throw up the demand for payment.

  110. #110 Chad
    June 11, 2008

    #30 – Power failures happen at least once every summer in one part or another on MSU’s campus (or at least they did when I was there). I’m more amazed his lab got generators in time to save the colonies.

  111. #111 Sven DiMilo
    June 11, 2008

    DM (#101): Thanks for your response. Probably not the place or time for a long and drawn-out discussion on this off-Topic, but a few (yet way too long anyway) quick responses:

    re nestilings of altricial birds;

    homeothermic, tachymetabolic and tachyaerobic

    Yes, I unnecessarily conflated endothermy and metabolic rate; apologies. Homeothermic? nah, except while being brooded by a parent. Tachymetabolic? My point, which you ignored, is that they have high metabolic rates becasue of their high growth rates, not the other way around. If you know offhand of measurements showing that post-absorptive altricial nestlings have higher resting metabolic rates than same-sized lizards at the same temperature, I’d like to know about it. Tachyaerobic? Not sure what this means, but it sounds like a Paulism for high aerobic capacity (i.e. the physiological ability to maintain high aerobic metabolic rates). Again, show me the measurements…they certainly have the aerobic capacity necessary to support their empirical growth rates, but my educated guess is not much more. Aerobic capacity develops ontogenetically.
    But regardless, shooting down my example does not address my real point, which is that I am skeptical of any ineluctable, causal relationship between growth rate and resting metabolic rate or aerobic capacity. (The evidence for a link between aerobic capacity and resting metabolic rate is itself highly equivocal, by the way.)

    G. S. Paul, 1994, 1998 — refs later

    yes, please

    for this reason bradymetabolic terrestrial animals over about 1 t are impossible

    Sorry, for what reason, exactly? Is it large size itself or growth rate that is hypothesized to require large support organs (and therefore cause “tachymetabolism”)?

    cell membranes of extant tachymetabolic animals are more permeable to sodium ions

    I am well aware of the cellular correlates of metabolic rates, but what’s your point? I have never seen a convincing explanation for the leakiness of bird and mammal membranes that does not invoke heat production per se–i.e. it seems to be you who are now conflating endothermy and “tachymetabolism” (a term, by the way, that I have never known a neontophysiologist to employ).

    More strictly, it’s r-strategy.

    I see no reason to link ovipary and r- vs. K-strategy (itself, as you surely know, a highly simplistic view of life-history evolution). Lots of small offspring can be produced oviparously or viviparously, and there isn’t even any necessary relationship between -parity and parental care. So I still don’t get your original point, which seems (now) to be that small offspring plus fast growth rates permits gigantic adult size (“can get bigger than any land mammal can because they combine high metabolism with ovipary”).

    Sure, but why should the complete system [of air sacs] have appeared before the air sacs started to work?

    Huh? Air sacs “worked”–had some function (I don’t know what: weight reduction? buoyancy?)–before they were exapted into the modern bird respiratory system. Further, what is the function of pneumatic bones (as opposed to air sacs) in modern bird respiratory systems? I suspect your argument is to be found in Wedel 2003 (the pdf of which I just tracked down and printed for later reading [no thanks to you :)--what was the point of linking to the guy's blog instead of the article?]), which indeed I had missed.

    The ratio of deadspace to tidal space is what matters here…

    Here follows a longish but elementary discussion of the respiratory anatomy of birds without ever addressing the long-neck question. No matter, I see that it is discussed in Wedel’s article.

    crocodiles have crosscurrent exchange

    ???? Impossible, I think, with a tidal lung. It is birds that use crosscurrent (not countercurent) exchange.

    they were also capable of motor-gliding (anaerobic flapping followed by gliding)

    I do not doubt that they could flap their wings, but this is a long way from true powered flight. May I remind you of your original claim: “can get bigger than any bird because they can launch from the ground on all fours”? Are you defending that?

    Spend a few hours in the DML archives

    What, and miss out on valuable procrastinating-at-Pharyngula time?:)

    So thanks for the tip on the Wedel paper, which looks very interesting. (By the way, should this discussion continue, you can skip the basic-level explanations and definitions, at least for my sake. I teach comparative physiology for a living and have measured several orders of magnitude more metabolic rates than anybody else around here, I imagine. If I am not completely current with the paleophysiology literature, it’s because I study reptiles, living ones, and yes I know you hate that term, and that’s why I used it :P)

  112. #112 Rich Blinne
    June 11, 2008

    travc said:

    I thought PNAS made articles available online for free, but apparently not. Does anyone know if/when this goes into the public domain? You’d think as a country we could shell out enough cash to at least support a few journals.

    As Owlmirror stated articles six months old are free and some papers are free from the get go. I purchased my copy as a $10 pay per view.

    Speaking of tax money at work note this:

    This research has been supported in part by grants from the National Science Foundation (currently DEB-0515729) and the Defense Advanced Research Projects Agency ”Fun Bio” Program (HR0011-05-1-0057).

    DARPA has a “Fun Bio” program???!?? Now here’s some defense spending that PZ would enjoy!

  113. #113 Rich Blinne
    June 11, 2008

    One other thing. This is part of the long-term evolution experiment (LTEE). Not only does Michael Behe need to explain this particular finding but some other findings summarized in the paper as follows:

    Previous analyses of this experiment have shown numerous
    examples of parallel phenotypic and genetic evolution. All twelve
    populations underwent rapid improvement in fitness that decelerated
    over time (2, 3, 22, 23). All evolved higher maximum
    growth rates on glucose, shorter lag phases upon transfer into
    fresh medium, reduced peak population densities, and larger
    average cell sizes relative to their ancestor (22-26). Ten populations
    evolved increased DNA supercoiling (27), and those
    populations examined to date show parallel changes in global
    gene-expression profiles (4, 28, 29). At least three genes have
    substitutions in all 12 populations (30, 31), and several others
    have substitutions in many populations (27-30), even though
    most loci harbor no substitutions in any of them (32). At the same
    time, there has also been some divergence between populations.
    Four have evolved defects in DNA repair, causing mutator
    phenotypes (3, 33). There is subtle, but significant, between population
    variation in mean fitness in the glucose-limited
    medium in which they evolved (2, 23). In media containing other
    carbon sources, such as maltose or lactose, the variation in
    performance is much greater (34). And while the same genes
    often harbor substitutions, the precise location and details of the
    mutations almost always differ between the populations (27-31).

  114. #114 travc
    June 11, 2008

    #104

    Behe is actually nominally correct (stopped watch) in that quote:
    “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.”

    The trick is that the environment actually had more than one niche to fill. The Cit- strains were superior at glucose uptake and/or metabolism, but the glucose concentration dropped to very low levels before the populations were transferred each day. This time spent at low glucose (but still plenty of citrate) gave the Cit+ an opportunity to reproduce up to a respectable fraction of the population (while the number of Cit- individuals was constrained by a lack of glucose.)

    The actual experimental setup is a ‘serial dilution’. Every day a small (random) fraction of the previous day’s culture is transferred into a new tube of growth media. If there is only a single resource, the situation is pretty simple… faster replicating strains will increase in frequency and slower strains decrease. However, with more than one resource (and specialization), multiple strains can stably exist. In many ways, this is a much more interesting result than the historical contingency aspect… it isn’t anything ‘new’ per se, but I don’t remember it ever being demonstrated so clearly before.

  115. #115 Rich Blinne
    June 11, 2008

    References from above:
    2. Lenski RE, Rose MR, Simpson SC, Tadler SC (1991) Long-term experimental evolution in
    Escherichia coli. I. Adaptation and divergence during 2,000 generations. Am Nat 138:1315-1341.

    3. Cooper VS, Lenski RE (2000) The population genetics of ecological specialization in
    evolving E. coli populations. Nature 407:736-739.

    4. Cooper TF, Remold SK, Lenski RE, Schneider D (2008) Expression profiles reveal parallel
    evolution of epistatic interactions involving the CRP regulon in Escherichia coli. PLoS
    Genet 4:e35.

    22. Lenski RE (2004) Phenotypic and genomic evolution during a 20,000-generation experiment
    with the bacterium Escherichia coli. Plant Breed Rev 24:225-265.

    23. Lenski RE, Travisano M (1994) Dynamics of adaptation and diversification: A 10,000-
    generation experiment with bacterial populations. Proc Natl Acad Sci USA 91:6808-
    6814.

    24. Vasi F, Travisano M, Lenski RE (1994) Long-term experimental evolution in Escherichia
    coli. II. Changes in life-history traits during adaptation to a seasonal environment. Am
    Nat 144:432-456.

    25. Lenski RE, Mongold JA (2000) in Scaling in Biology, eds Brown J, West G (Oxford Univ
    Press, Oxford, UK), pp 221-235.

    26. Novak M, Pfeiffer T, Lenski RE, Sauer U, Bonhoeffer S (2006) Experimental tests for an
    evolutionary trade-off between growth rate and yield in E. coli. Am Nat 168:242-251.

    27. Crozat E, Philippe N, Lenski RE, Geiselmann J, Schneider D (2005) Long-term experimental
    evolution in Escherichia coli. XII. DNA topology as a key target of selection.
    Genetics 169:523-532.

    28. Cooper TF, Rozen DE, Lenski RE (2003) Parallel changes in gene expression after 20,000
    generations of evolution in Escherichia coli. Proc Natl Acad Sci USA 100:1072-1077.

    29. Pelosi L, et al. (2006) Parallel changes in global protein profiles during long-term
    experimental evolution in Escherichia coli. Genetics 173:1851-1869.

    30. Woods R, Schneider D, Winkworth CL, Riley MA, Lenski RE (2006) Tests of parallel
    molecular evolution in a long-term experiment with Escherichia coli. Proc Natl Acad Sci
    USA 103:9107-9122.

    31. Cooper VS, Schneider S, Blot M, Lenski RE (2001) Mechanisms causing rapid and parallel
    losses of ribose catabolism in evolving populations of E. coli B. J Bacteriol 183:2834-
    2841.

    32. Lenski RE, Winkworth CL, Riley MA (2003) Rates of DNA sequence evolution in
    experimental populations of Escherichia coli during 20,000 generations. J Mol Evol
    56:498-508.

    33. Sniegowski PD, Gerrish PJ, Lenski RE (1997) Evolution of high mutation rates in
    experimental populations of Escherichia coli. Nature 387:703-705.

    34. Travisano M, Vasi F, Lenski RE (1995) Long-term experimental evolution in Escherichia
    coli. III. Variation among replicate populations in correlated responses to novel environments.
    Evolution 49:189-200.

  116. #116 travc
    June 11, 2008

    Rich Blinne, thanks for the PNAS info. I normally have site-based access, so I don’t notice such things.

    BTW: DARPA “Fun Bio” is the Fundamental Laws of Biology program.

  117. #117 Rich Blinne
    June 11, 2008

    I just thought it was fun biology. I know I have a twisted idea of fun. :-) Oh, well.

  118. #118 Drew
    June 11, 2008

    Rich @ 112

    The FUN Bio program is set up to try and recognize fundamental biological “laws” if they exist. I just today sat through a presentation regarding modularity of evolution or evolution of modularity and how it seems to be inevitable by a professor funded by FUNBIO.

    Also I have seen several people talking about it and I don’t know if anyone has mentioned this but, IIRC from my microbiology, for the most part, bacterial species are usually defined by metabolic processes, and other characteristics and not by genetics…Gram positive/negative, obligate aerobe/obligate anaerobe/facultative anaerobe, indole, hemolysis, ability to utilize certain carbon sources, etc. The article above mentions that one of the definitions for E. coli is an inability to take up and metabolize citrate.

  119. #119 David Marjanovi?, OM
    June 11, 2008

    I’ll reply at length tomorrow. Just so much:

    * The crosscurrent exchange in crocodile lungs is possible because these lungs have a respiratory part (front) and a tidal part (back). This partitioning is shared with loads of lepidosaurs. The only real innovation in the evolution of the air-sac system was the outlet from that system directly into the trachea, bypassing the lung. Everything else is a matter of degree.

    * Weight-saving cannot have been the original selection pressure, because most of the bone tissue is just moved, not removed. The weight saving is only 4 % in… I think in a derived sauropod skeleton… that’s described in one of Wedel’s several papers.

    * G. S. Paul and Guy D. Leahy 1994: Terramegathermy in the Time of the Titans: Restoring the Metabolics of Colossal Dinosaurs, 177 — 198 in G. D. Rosenberg & D. L. Wolberg (eds): Dinofest [1992] (Paleontological Society Special Publication 7), University of Tennessee, Knoxville.
    G. S. Paul 1998: Terramegathermy and Cope’s Rule in
    the land of titans
    , Modern Geology 23: 179 — 217.
    I also recommend this here, among several months’ worth of DML discussions on both publications.

    * Paul’s size argument IIRC boils down to: if bradyaerobic animals can get as big as tachyaerobic ones and still carry their weight, why don’t they? Why does that one-tonne limit exist? He thinks it’s because carrying one’s weight requires high endurance, which requires a tachyaerobic metabolism.

    * Also keep in mind the exceedingly slow size at which Deinosuchus grew: it kept juvenile growth rates for a very long time, yet still needed 50 years to reach the length of 10 to 12 m. Dinosaurs of that adult size grew much, much faster. What prevented the great and mighty Deinosuchus from growing just as fast?

  120. #120 Sven DiMilo
    June 11, 2008

    crosscurrent exchange in crocodile lungs is possible because these lungs have a respiratory part (front) and a tidal part (back).

    Still doesn’t make sense; sorry. If air is passing across perfused respiratory epithelium in two directions it can’t be crosscurrent exchange.

    I suggested weight-reduction as an original function of airsacs (I do not have a rigorous scenario to argue), not pneumaticized vertebrae. They are not synonymous (for example, one I just learned skimming the Wedel paper, diving birds like loons lack pneumaticized bones but have perfectly functional airsac/flowthrough lung systems). Which is, sort of, my point: pneumatic bone is not a sure sign of a flow-through lung. But I haven’t read Wedel carefully yet.

    Thanks for the Paul citations; I have heard of those and may even have one of them…in a box…somewhere around here…

    Of course, the “one-tonne limit” only exists if you buy “tachyaerobic” dinosaurs in the first place.

    That said, “why don’t they?”-type arguments are tricky. My usual answer is “I don’t know, but neither do you!” Hell, rhinos are a lot smaller than (some of them) used to be…why? Do extant rhinos have lower aerobic capacities?

    So I remain unconvinced of the high aerobic capacity (let alone resting MR) of sauropods. But I hope you do post a more thorough treatment tomorrow; I’d like to learn more about these issues.

  121. #121 John Bay
    June 11, 2008

    Dr. Behe quickly dispelled the significance of this experiment. Basically, the E. coli already had the machinery to digest citrate, but just lacked a gateway to get the nutrient inside, which was not that improbable a hurdle for a couple of mutations to permit. This accomplishment is orders of magnitude simpler than the kind of luck required to build the machinery in the first place. It’s like blindly pushing and finding a weakness in a fence. This is all the longest-running lab experiment in evolution was able to accomplish in 20 years of trying, with almost 40,000 generations. Are you impressed? If you can tell a lawyer is lying when his lips are moving, you can tell an evolutionist is lying when the reporters go wild about how Darwin has been vindicated.

  122. #122 John Bay
    June 11, 2008

    Dispelling the overhyped experiment, meant that Behe drove away the smoke and mirrors. He boiled it down to show how nothing extraordinary happened within an evolutionary framework.

    according to Behe:

    Other workers (cited by Lenski) in the past several decades have also identified mutant E. coli that could use citrate as a food source. In one instance the mutation wasn’t tracked down. (2) In another instance a protein coded by a gene called citT, which normally transports citrate in the absence of oxygen, was overexpressed. (3) The overexpressed protein allowed E. coli to grow on citrate in the presence of oxygen. It seems likely that Lenski’s mutant will turn out to be either this gene or another of the bacterium’s citrate-using genes, tweaked a bit to allow it to transport citrate in the presence of oxygen. (He hasn’t yet tracked down the mutation.)

    So, there was no transporter mutating from nothing. There was already a transporter present, it just didn’t normally transport citrate.

    This is so typical. After 40,000 generations this is the best you can do?!!! Activating an already present transporter. This is not even close to evolution of bacterium becoming something else.

    The fact this is the best evidence really shows why evolution theory is on its way out. Eventually, students will realize how stupid it is and laugh out loud at their teachers.

  123. #123 Brownian, OM
    June 11, 2008

    The fact this is the best evidence really shows why evolution theory is on its way out. Eventually, students will realize how stupid it is and laugh out loud at their teachers.

    That’s great. You guys have been saying that for the last 50 years at least.

    When will you learn that a theory needs to make accurate predictions before it counts as science?

  124. #124 Brownian, OM
    June 11, 2008

    Oh, and psst: your hatred for teachers is showing.

    That’s not gonna be real positive for your creationist campaign of lies.

  125. #125 Sven DiMilo
    June 11, 2008

    Mr. Bay (and I can be pretty confident in avoiding the honorific “Dr.” in this case), your use of the word “machinery” to describe the biochemical pathways for metabolizing citrate brands you as somebody who has no idea what he’s talking about right at the outset.

  126. #126 Sven DiMilo
    June 11, 2008

    p.s. perhaps you missed the fact that PZ linked directly to Behe’s se;lf-serving, book-shilling “blog” at Amazon in the original post? And explained clearly why Behe is a nut?

  127. #127 raven
    June 11, 2008

    Bay the troll:

    Activating an already present transporter. This is not even close to evolution of bacterium becoming something else.

    That isn’t clear from the article yet. You are making an assumption based on no data. That isn’t science.

    Even if a transporter was mutated, that is how evolution works. It always builds on what is already present. If you understood the first thing about evolution, you would know that.

    Bacterium is singular. If you knew any science, you would know that. As to what the bacteria would become, a different kind of bacteria. Which is what was seen. If you knew any science, you would know that.

    Is that the best the creos can do, an ignorant troll with psychological problems? Yes, of course, reality denial is the domain of crackpots.

  128. #128 Glen Davidson
    June 11, 2008

    So, there was no transporter mutating from nothing. There was already a transporter present, it just didn’t normally transport citrate.

    OMG, it wasn’t creation ex nihilo.

    If you’re really stupid you think this is a problem for evolution, instead of for the intelligent design which actually does posit creation ex nihilo, with absolutely no evidence for it.

    And what, pinhead, do you think “mutation” means? It means the change of one thing into another one. That’s evolution, dependent upon mutating what already exists.

    Like all creationists, Bray, you’re very stupid, very ignorant, or some combination of the two.

    Glen Davidson
    http://tinyurl.com/2kxyc7

  129. #129 Owlmirror
    June 11, 2008

    So, there was no transporter mutating from nothing. There was already a transporter present, it just didn’t normally transport citrate.

    And because most transporters don’t normally transport citrate, this rare and unusual mutant is new and interesting.

    I infer that you only have a problem with this because you have an idealogical bias against thinking rationally.

  130. #130 Jud
    June 11, 2008

    Owlmirror wrote: I infer that you only have a problem with this because you have an idealogical bias against thinking rationally.

    Fixed that for you.

  131. #131 travc
    June 11, 2008

    I assume John Bay is a drive-by poster, but he does serve some use in pointing out what is really interesting about Lenski’s long term lines… by completely missing it.

    The precise nature of the mutations aren’t known yet, but are probably pretty mundane. The gross probability of those mutations occurring isn’t very interesting either.

    What is cool about Lenski’s setup is that we can very directly answer those routine questions and trace exactly what happened. They have done this in previous work for other, less dramatic mutations.

    What is really important about this paper is that it provides hard data testing otherwise (mostly) theoretical hypotheses. Does neutral drift play an important role exploring genotype space and ‘paving the way’ for adaptations… apparently yes. Are environments with with multiple (substitutable) limiting resources enough to lead to stable coexistence of different strains/species… again, apparently yes.

    We’ve done mathematical models and ‘in silico’ (computer) experiments exploring these questions, but this is some of the clearest real-world results yet.

    BTW: I’m surprised we there hasn’t been more ‘it was just breeding in a lab, not real evolution’ sorts of complaints. Then again, I guess the ‘it is only micro-evolution’ stuff is basically the same complaint. How hard is it to grasp that ‘macro-evolution’ is just lots of micro-evolution piled up over time.

    Caveat: The term macro-evolution has some use when looking at complex adaptive systems aspects of evolutionary dynamics. Basically emergent large scale properties produced by the underlying ‘micro-evolution’ system. If you don’t know what I’m talking about, don’t use the term… it doesn’t mean what you think it means.

  132. #132 raven
    June 12, 2008

    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 salient point is that it took 3 mutations to produce citrate eating E. coli. Behe says the limit of evolution is two mutations. So he is wrong for the nth time.

  133. #133 Stephen Wells
    June 12, 2008

    Re. the reading Darwin point: I’m a physicist and I wouldn’t even consider trying to read Newton. I mean, why? We;ve moved on, and my Latin is a tad rusty.

    Darwin was, though, a fantastic English prose stylist; worth reading the Voyage of the Beagle for that alone, and of course the final chapter of Origin is a tour de force.

  134. #134 amphiox
    June 12, 2008

    Just to add my two cents to the creo stomping.

    20 years and 12 culture lines and already we have interesting results. That’s peanuts. In nature how many billions of years have E.coli and its ancestors been around? How many different microenvironments have they lived in in all that time? Just the number of warm-blooded animal intestinal tracts alone in the hundred or so million years that such intestinal tracts have existed must number in the trillions.

  135. #135 ngong
    June 12, 2008

    How many different microenvironments have they lived in in all that time?

    Let’s say Lenski’s bacteria occupy 10 liters of water at a time. There are about 1.3 * 10^20 times that figure on the earth. And there has been roughly 2*10^8 more time on earth. So nature has run Lenski’s experiments roughly 2*10^28 times more than Lenski. And that’s without getting exotic and invoking panspermia or the anthropic principle.

    If there is a god, it’s funny how the creos underestimate her grandeur.

    (OK, OK, not every liter of water on earth has such an abundance of energy-packed substrates)

  136. #136 Peter Ashby
    June 12, 2008

    Darwin was, though, a fantastic English prose stylist; worth reading the Voyage of the Beagle for that alone, and of course the final chapter of Origin is a tour de force.

    It is indeed which is why in Almost Like A Whale Steve Jones left the last chapter as was. No updating was required and no improvement necessary.

  137. #137 Tulse
    June 12, 2008

    20 years and 12 culture lines and already we have interesting results. That’s peanuts. In nature how many billions of years have E.coli and its ancestors been around?

    “Billions of years”?!? It’s only about 6,000 years, silly!

  138. #138 ndt
    June 12, 2008

    So, there was no transporter mutating from nothing.
    Posted by: John Bay | June 11, 2008 7:49 PM

    Of course not. That would completely disprove our understanding of evolution.

    There was already a transporter present, it just didn’t normally transport citrate.
    Posted by: John Bay | June 11, 2008 7:49 PM

    Exactly. It required at least three mutations for that transporter to be able to transport citrate, which Behe has claimed is impossible.

  139. #139 Helioprogenus
    June 12, 2008

    Finally, vindication for Dawkins’ view over Gould’s. He assumed that every mutational event is independent from another, and that if you run the clock backwards, you’re going to develop a whole different array of mutations. Fortunately, as this experiment shows, the neutral mutations acquired help pave the way for the critical mutations in species development.

    We can extrapolate this to our own species, when considering the evolution of our larger brains. How many steps were involved, as far as neutral mutations, before our brains reached a critical point and hypertrophied? And as for the explosion of art and culture dating to about 50,000 years ago, what mutations arose, both neutral and influential in our ability to suddenly expand our thinking?

  140. #140 Tulse
    June 12, 2008

    Finally, vindication for Dawkins’ view over Gould’s.

    If you actually read the original posting, the authors of the study are very clear that their work supports Gould’s notion of historical contingency, as in: “our study shows that historical contingency can have a profound and lasting impact [...] small happenstances of history may lead populations along different evolutionary paths.”

  141. #141 Helioprogenus
    June 12, 2008

    Oops, screwed the pooch on that one. Still, it’s not cut-and-dry that gradualism cannot play a role. Not every mutation is going to be phenotypically adaptive, and nobody’s arguing that neutral mutations do not exist. The environment at the genomic level can still tweak even neutral mutations towards some form of influence. Whether it’s a slight change in expression rate or other regulatory function.

  142. #142 Tulse
    June 12, 2008

    it’s not cut-and-dry that gradualism cannot play a role.

    I’m not sure that gradualism is necessarily the enemy of contingency — identical populations can gradually drift and/or acquire different beneficial mutations. Although Gould argued for the importance of both historical contingency and punctuated equilibrium, the two notions are not identical (punctuated equilibrium may imply historical contingency, but not vice-versa).

  143. #143 Chris Crawford
    June 12, 2008

    Forgive me if this question has already been asked (I scanned through the previous comments and didn’t find it, but I may have missed it):

    How did Lenski know that he’d get the mutation arising within his lifetime? When he started this grand project, did he think he’d get results in one year? Five years? Twenty years? Can you imagine the conversations with the dean:

    “Lenski, you’re using up a lot of electricity on those refrigerators. Are you SURE that they’ll eventually figure out how to metabolize citrate?”

    “Sure thing, boss, I just know in my gut (ahem!) that those little buggers will get it figured out Real Soon Now.”

    “Lenski, you’ve been promising that for the last fifteen years now. You’re starting to sound like a programmer!”

    “Don’t worry! I just know they can do it!”

    Right.

  144. #144 windy
    June 12, 2008

    And this is an example of both historical contingency and convergence – there were those previous rare mutants in E. coli and all those “contaminants” that could already eat citrate. Actually I’m a bit curious about why they chose to emphasize “historical contingency” – this is perfectly OK, but there has been a lot of modeling work recently on crossing “fitness valleys” by neutral or nearly neutral mutations, so it would have been useful to put it in that context as well. And Gould’s “contingency” tended to emphasize how certain phenotypes might not in other circumstances have appeared at all in any species during the entire history of life, which is not the case here.

  145. #145 Sven DiMilo
    June 12, 2008

    This particular result was not the point of the project–this 20-y study has been mined for all kinds of cool stuff over the years. This one was serendipitous. Of course, then they capitalized on their luck (plus preparation and just-in-case-type foresight) to test some hypotheses that would have been damn hard to study any other way.

  146. #146 Sven DiMilo
    June 12, 2008

    (my previous post was in response to Chris Crawford #143)

  147. #147 PZ Myers
    June 12, 2008

    Um, we know the approximate mutation rate per nucleotide per replication, typically about 10-8. We know the E coli genome contains 4-5 million nucleotides. Simple math tells us that a large population reproducing for 10s of thousand of generations is going to produce lots of mutants.

    They actually used citrate as a control, not expecting that they would get that specific set of variants at all. Lenski’s lab has published multiple examples of other interesting phenomena in their colonies.

  148. #148 Helioprogenus
    June 12, 2008

    Thanks for clearing that up Tulse. I hadn’t really sat down and differentiated the two based on Gould’s thinking. His ultimate purpose however, was incorporating spandrals and whatever else to almost dictate how things would evolve to fit a certain almost deterministic agenda. And there’s something to be said about overstating punctuated equilibrium to make it seem independent of gradualism. The only difference between then two is the perspective on the passage of time, and the scarcity of the fossil record.

  149. #149 David Marjanovi?, OM
    June 12, 2008

    May I remind you of your original claim: “can get bigger than any bird because they can launch from the ground on all fours”? Are you defending that?

    Of course. Yesterday’s discussion is now online in the DML archives; read it. 90 % of the power needed to make a bird (or vampire bat) launch from the ground comes from the legs (they jump into the air, they don’t just stand there and start flapping — that wouldn’t work!). In the case of birds, that means the hindlimbs — which are payload in flight. In the case of bats and pterosaurs, that means mostly the wings.

    Still doesn’t make sense; sorry. If air is passing across perfused respiratory epithelium in two directions it can’t be crosscurrent exchange.

    Of course it can. The air moves craniocaudally, and the blood moves mediolaterally. As opposed to mammal lungs where the air also moves largely craniocaudally (with the foamy architecture of the lungs adding a random element) but the blood vessels are non-arranged at random. (Even in bats AFAIK.)

    And birds really do have countercurrent exchange: the air moves from cranial to caudal, and the blood moves in the opposite direction. That’s the trick about the unidirectional lung.

    I suggested weight-reduction as an original function of airsacs (I do not have a rigorous scenario to argue), not pneumaticized vertebrae.

    This doesn’t make sense :-) because air sacs don’t replace anything other than bone. They are additions to the volume of the body. They lie between the muscles and between the organs, not in their places.

    the Wedel paper

    There are several. That’s why I lazily referred you to his blog; it ought to have some link to his academic homepage and publications list somewhere.

    Of course, the “one-tonne limit” only exists if you buy “tachyaerobic” dinosaurs in the first place.

    If they weren’t tachyaerobic, why did only they ever manage to break that limit? Why didn’t any turtles, let alone pareiasaurs, get bigger?

    That said, “why don’t they?”-type arguments are tricky. My usual answer is “I don’t know, but neither do you!” Hell, rhinos are a lot smaller than (some of them) used to be…why? Do extant rhinos have lower aerobic capacities?

    The extra-large rhinos were high-browsers and AFAIK disappeared during some climatic hiccup or other. (May well bolster the argument that K-strategic giants are much more prone to extinction than r-strategic ones.) Also, they lived before any proboscideans had got out of Africa.

    Just because we don’t know doesn’t mean we can’t figure out which hypothesis is most parsimonious!

    But I hope you do post a more thorough treatment tomorrow; I’d like to learn more about these issues.

    Unfortunately you’ll have to wait at least a day longer, perhaps till Sunday. I’m way to tired to write anything of substance tonight.

    BTW, at least the Paul & Leahy 1994 paper includes calculations of the minimal possible resting MR required to keep Brachiosaurus standing upright. Though that might be exaggerated by the fact that a vertical neck was assumed; the base of the neck of that particular animal is poorly known, and people are fighting vigorously…

    Incidentally, do you have any idea on why there are no freshwater cephalopods and never have been?

    ——————-

    This accomplishment is orders of magnitude simpler than the kind of luck required to build the machinery in the first place.

    You and Behe are shifting the goalposts.

    This is so typical. After 40,000 generations this is the best you can do?!!! Activating an already present transporter. This is not even close to evolution of bacterium becoming something else.

    Don’t you understand that 40,000 generations is absolutely nothing?

    Look what happened in the last 40,000 generations of humans (100,000 years): three mutations for lactase persistence, one for blue eyes, a couple defects in melanin production, and that’s about it. But that was just a bit after the beginning of last week ice age.

    —————–

    Finally, vindication for Dawkins’ view over Gould’s. He assumed that every mutational event is independent from another, and that if you run the clock backwards, you’re going to develop a whole different array of mutations. Fortunately, as this experiment shows, the neutral mutations acquired help pave the way for the critical mutations in species development.

    If you run the tape backwards to before the neutral mutations had happened, you get a Gould scenario…

    Still, it’s not cut-and-dry that gradualism cannot play a role.

    That’s a completely different question, and hardly one that can be decided over just 40,000 generations. Try ten times that at the very least.

    How did Lenski know that he’d get the mutation arising within his lifetime?

    He didn’t. When the third mutation happened, he thought he had a contamination. He didn’t think they’d ever evolve citrate-eating and was looking for completely different features (efficiency of glucose metabolism, cell division speed and the like).

    Let alone the observed niche partitioning. This is big, big news. It’s not a surprise, but… under the Ecological Species Concept it equals witnessing speciation in the lab (eat that, Mr Bay).

  150. #150 David Marjanovi?, OM
    June 12, 2008

    The only difference between then two is the perspective on the passage of time, and the scarcity of the fossil record.

    Not quite.

    (This is more food for Mr Bay, BTW. It’s the pdf of a paper called “Speciation in the fossil record”.)

  151. #151 David Marjanovi?, OM
    June 12, 2008

    under the Ecological Species Concept it equals witnessing speciation in the lab

    Better yet: sympatric speciation!

  152. #152 windy
    June 12, 2008

    Look what happened in the last 40,000 generations of humans (100,000 years): three mutations for lactase persistence, one for blue eyes, a couple defects in melanin production, and that’s about it.

    There are a lot more than just those in all those “maps of recent positive selection in the human genome”. We don’t even know what most of that stuff does. And there are the differences in amylase copy number related to the amount of starch in diet – I wouldn’t bet on that being the only adaptive CNV in humans.

  153. #153 negentropyeater
    June 12, 2008

    and it’s more like 4,000 generations… not much really.

  154. #154 Torbjörn Larsson, OM
    June 12, 2008

    The problem with ecological modeling is that horizontal gene transfer is so rampant that looking at growth properties isn’t necessarily definitive.

    I’m not a biologist obviously, but AFAIU those scientists found the complementary approach better than the isolated modeling. I understand that the isolated traits concept is weaker.

    I also see what you mean on species.

    And that was just off the top of my head.

    Ah, you are just begging for a “big head” accolade, aren’t you?

    But yes, how the resources are exploited (and how well) is certainly changing.

  155. #155 Helioprogenus
    June 12, 2008

    I never stated that the fossil record is devoid of giving us an understanding of speciation. All I was stating was the difference between Gould and Dawkins view as to the importance of punctuated equilibrium. As the fossil record becomes more detailed, the less speciation appears as punctuated equilibrium. Punctuated Equilibrium exists within the grounds of gradualism. If we look at a hypothetical speciation event spanning every millenia, we don’t see leaps as Gould suggest. We do see perhaps increased rates of morphological change, but overstating such events as a seperate phenomenon from gradualism is a bit too much. It’s like calling a large landslide a punctuated geological event. We know that erosion occurs at a given rate, and yes, there are instances that lead to increased erosion rates, but we all know erosion generally works gradually. A monster earthquake may cause significant changes in the landscape, but you can’t state it as a distinct erosion related phenomenon.

  156. #156 Hap
    June 12, 2008

    #149: Wouldn’t that be 1 000 000 y rather than 100 000 y for the last 40 000 generations – 100 000/40 000 = 2.5 (not 25, as probably intended)? I thought that some significant things have happened in the past million years in our genome anyway, though it doesn’t really change the point.

    Unfortunately, I think ID proponents are immune to reason and logic. Their target audience is hoping that if they ignore all the things they dislike, those things will go away, which is not exactly a logical position. Why should the ID proponents even bother with logical presumptions if they do them no good? They don’t want to convince scientists, they just want to sustain their adherents’ trust long enough to get into power. I don’t have much hope that there is any fact (or set thereof) too large for them to ignore. (Example A: the 2004 U.S. Presidential election)

    Oh, and Mr. Bay – maybe you should go to work for a biotech – the “Insta-Magical Mutation Analyzer” you appear to have developed could be a real moneymaker. How you managed to identify the mutation of the E. coli (and its gene product) that rapidly would be worth something – well, if it were based on something other than the contents of your lower colon, it would.

  157. #157 David Marjanovi?, OM
    June 12, 2008

    And there are the differences in amylase copy number related to the amount of starch in diet

    Oho!

    And yes, 40,000 generations are indeed a million years, not 0.1 Ma. Did I mention I hate math? :-)

    (Example A: the 2004 U.S. Presidential election)

    I have yet to see evidence that anyone won that election. But I digress.

  158. #158 Peter Ashby
    June 13, 2008

    Um I thought the air in bird lungs moves caudio-cranially? It first goes into the air sacks in the bones, gas exchange happens on the exhail as the air is moved through the lungs and out.

  159. #159 Hap
    June 13, 2008

    (/rant on)

    I think almost everyone lost the 2004 US Presidential election, but there seem to be quite a few people here in Flyover Land that flaunt their vote for Bush/Cheney in 2004. I guess I figured after their dishonesty about Iraq, the Republicans’ lack of fiscal responsibility, and their lack of respect for the Constitution or the personal rights they claimed to desire to preserve, that voting for them in 2004 required either a desire to commit evil or a willingness to ignore a lot of large and inconvenient facts. I would prefer to believe the latter.

    (/rant off)

  160. #160 Sven DiMilo
    June 13, 2008

    In my experience it’s very seldom one catches David Marjanovi?, OM being WOTI, but David, your understanding of comparative respiratory physiology is incorrect. If you’re getting all your physiology from paleontologists, you might want to reconsider that strategy. (By the way, I sometimes find your ‘but of course!’ borderline-condescending tone really offputting; of course I mostly feel this way when I think you’re both wrong and condescending to me! I gather it’s unusual, but some people really do know more about some subjects than you…you should at least remain open to that possibility).

    birds really do have countercurrent exchange

    No, they really do not. Really. Birds are the classic example of crosscurrent exchange, which does not mean what you think it means. (This all goes back at least as far as the work of Piiper and Scheid in the 1970s)
    As I’m sure you know (but perhaps for the benefit of others), true countercurrent exchange is what occurs in fish gills; the blood and respiratory medium move in opposite directions (each, importantly, unidirectionally) across the respiratory epithelium, and this permits the blood leaving the respiratory organ to reach near-equilibrium (in terms, here, of the partial pressure of oxygen, PO2) with the incurrent–i.e. fresh and fully oxygenated–respiratory medium (here, water, but it would work in theory with air as well). Tidal alveolar lungs as in mammals can only bring blood to equilibrium with the excurrent (O2-depleted) air. Best illustrations I can find on the Web are the bottom and top models, respectively, here.

    The crosscurrent situation in birds is different and more complex. The flow of air through the lungs is indeed unidirectional (but, as Peter Ashby correctly points out, caudo-cranial, from the posterior abdominal airsacs to the anterior sacs). The flow of blood through the lung is indeed in the opposite direction at the gross level. However, the capillaries that actually contact the respiratory epithelium of the parabronchi cross the airflow orthogonally (hence, cross-current). The classic Piiper/Scheid model is illustrated adequately in Fig. 6 here. In this situation, different capillaries encounter air of different oxygen content, and then the blood of the respiratory capillaries is mixed in the pulmonary veins to reach an intermediate oxygen content. The point is that blood exiting the bird lung can achieve a higher PO2 than the excurrent air (but not nearly as high as the incurrent air, which true countercurrent exchange could achieve). [Just to complicate things further, the just-linked reference points out that exchange may be of the countercurrent type within individual blood-capillary/air-capillary pairs, but this is at a microlevel that is not the point of the current discussion. current, get it?]

    OK, crocodilians. Crocs have septate lungs (as opposed to mammalian alveolar lungs) and the blood capillaries are suspended in the airflow instead of surrounding dead-end alveoli as in mammals. And I think you are correct that blood flow is generally orthogonal to airflow. BUT this is not–and cannot be–“crosscurrent exchange” in the classical Piiper/Scheid sense, because airflow is bidirectional (not, as you state, craniocaudal). You just can’t set up the necessary geometric relationships between blood capillaries and respiratory exchange surfaces to achieve crosscurrent exchange in a bidirectional lung. In fact, in a tidal, bidirectional lung it doesn’t matter at all what direction the blood is flowing. The entire lung functions essentially as a single giant alveolus because–here’s the crucial point at last–PO2 of the blood cannot ever exceed the excurrent air. Crocodile lungs are not–can not be–more effective in oxygen extraction than mammalian lungs.
    If you are going to argue with this, it will have to be by reference instead of simple assertion; if it turns out to be me who’s wrong I’ll be properly chastened and embarassed. And really, really surprised. (phew–comparative physiology arguments really get my SIWOTI going!)

    So, I really really don’t have time for this right now but let me get a few thoughts out before I have to go check my traps.
    Wedel’s 2003 Paleobiology paper (I have skimmed his more recent stuff, which I did indeed find–eventually–via his blog, so thanks, and apologies for the earlier snark, but this is the only one that focuses on functional questions) establishes to my satisfaction that many dinosaurs had cervical airsacs and at least some probably (not certainly) had abdominal airsacs. But–and this was my original point–the conclusions that they therefore had unidirectional bird-type lungs and therefore were tachyaerobic are both nothing but arm-waving. There are four different characters here (pneumatized bone, airsacs, flow-through lungs, and aerobic capacity) and in my opinion Wedel repeatedly conflates the last three when convenient for his argument. Sure, they are linked in extant birds, but although birds are dinosaurs dinosaurs were not birds, the sauropods most especially!
    a) Again, to get from tidal crocodile-type respiration to flow-through bird-type respiration, there had to exist animals with both airsacs and tidal lungs. Therefore the presence of airsacs can not be regarded as solid evidence for lung type. It just can’t. Wedel does not seem to realize this (though he cites some models of “intermediate” pulmonary systems–by Perry–that I have not yet tracked down).
    b) Even if saurischians had flow-through bird-type lungs, that does not mean they were tachyaerobic. Increased oxygen extraction could have been selected for another reason; for example, Ward has suggested that efficient lung function may simply reflect the constraints of large body size in the lower oxygen content of air–about half of today–in the Mesozoic.

    I therefore reiterate my position that we do not know what kind of lungs dinosaurs had, nor their functional significance–only that some of them had airsacs.

    Random bits:
    After some thought and reading, I see now that the long-neck argument makes sense, but note that this is permitted by airsacs (and consequent larger tidal volume), NOT by the efficiency of a flow-through crosscurrent lung.
    The postcranial pneumaticity of bird bones serves no respiratory function at all. Many birds have perfectly functional airsac/flowthrough lung systems with much reduced or even absent pneumaticity of bones (as per Wedel). And (also per Wedel) although skeletal weight reduction was probably not the initial function of pneumaticity, it certainly served that function in sauropods [Wedel 2007:

    The one obvious advantage that 'prosauropods' did not share with sauropods is the very lightweight skeletal construction afforded by pneumaticity. In life, the average pneumatic sauropod vertebra was approximately 60 per
    cent air by volume. All else being equal, a sauropod could have a neck two-thirds longer than that of a prosauropod for the same skeletal mass

    ], and it is certainly the primary function in extant birds.
    I concur completely that weight reduction could not have been a function of airsacs themselves (threw that out off the top of my head and regretted it later), but I must insist that they had some intial function other than driving air through a unidirectional lung. Increase of tidal volume to ameliorate deadspace in a long trachea? Buoyancy control in a semiaquatic animal? Just guesses of course.

    [me:] Of course, the “one-tonne limit” only exists if you buy “tachyaerobic” dinosaurs in the first place.
    [DM:]If they weren’t tachyaerobic, why did only they ever manage to break that limit?

    Do you really not see the circularity of your argument here? No undoubted bradyaerobic animals have ever exceeded one tonne. Dinosaurs exceeded one tonne. Therefore they were tachyarobic. But how do we know that bradyaerobic animals can never exceed one tonne? Because we assume that dinosaurs were not bradyaerobic.

    Your ad-hoc explanation of the rhino example I threw out just makes my point for me: there are many, many physiological and ecological factors that determine body size, and it cannot be regarded as necessarily indicative of metabolic physiology.

    Why didn’t any turtles, let alone pareiasaurs, get bigger?

    I know nothing of pareiasaurs, but I know a little bit about turtles :) They are dragging around a huge skeletal mass, and the energy costs of supporting and transporting that mass just outweigh (heh heh) the ecological and physiological benefits. The largest turtles, both extinct and extant, are marine because they do not have to pay to support that mass.

    By the way, I have already asked for a copy of the Dinofest volume through interlibrary loan, and I managed to get a pdf of the other–very long–Paul paper, and I am looking forward to (someday) dealing with his functional arguments. So thanks again for those tips.

    As for the bird/pterosaur size thing, I’ll peruse the DML archives when I have time but I remain extremely skeptical that a slightly more powerful jump is going to solve the problems of powered flight at huge body size. After the jump, then what? it’s flapping from there on unless taking off from a height, as from a cliff-face.

    OK, REALLY gotta go. Thanks for the fun discussion.

  161. #161 Josh
    June 13, 2008

    If we look at a hypothetical speciation event spanning every millenia, we don’t see leaps as Gould suggest.

    Maybe, but then again, perhaps not. I would check out the Benton & Pearson (2001) article that David provided a link to. It should be illustrative…or at the very least interesting.

    It’s like calling a large landslide a punctuated geological event. We know that erosion occurs at a given rate, and yes, there are instances that lead to increased erosion rates, but we all know erosion generally works gradually. A monster earthquake may cause significant changes in the landscape, but you can’t state it as a distinct erosion related phenomenon.

    If, as Benton & Pearson wrote, “the plurality of evolutionary modes” is an accurate description of what’s really going on, then your analogy with erosion actually might work, but only if properly characterized. As written, it’s not. Erosion does not occur at a given rate. It is a highly variable process involving a bunch of interconnected factors, including, to name a few, geography (as it relates to overall climate), substrate character (and all that it is tied into that), vegetation, precipitation, and tectonics. Just like with sedimentation, to say that erosion works gradually is to oversimplify the process as to being broadly inaccurate. I know that’s nitpicking, but it’s Friday here…

  162. #162 Sven DiMilo
    June 15, 2008

    Well so I am partially embarrassed as it seems my knowledge of crocodilian lungs was outdated. (I stand by everything I said about birds.) The idea of bidirectional crosscurrent exchange has been haunting me since my last post, and it began to seem more and more to me that it made sense, i.e. that even in a tidal lung with bidirectional airflow, higher PO2 might be achieved in arterial blood than excurrent air in such a system. I have spent this morning trying to learn more, and I am now prepared to admit that I was wrong. According to some recent publications of Steve Perry, the bidirectional crosscurrent system of crocs is indeed more efficient at oxygen extraction than the “single giant alveolus” model I had learned and accepted. Indeed, according to Perry and Sander (Respiratory Physiology & Neurobiology 144 (2004) 125-139):

    for sauropods, which at sexual maturity were already gigantic but continued to increase in size…the greater efficiency of crosscurrent gas exchange compared with the uniform ventilated pool model could have…allow[ed] gigantic adults to continue reproductive activity without reaching the anatomical limits of respiratory function.
    Cross-current gas exchange can also be postulated for theropod dinosaurs (to which group the ancestors of birds belong), since it is not dependent on unidirectional flow, but only on the presence of tubular exchange units…. Although airsacs cannot be demonstrated with certainty in dinosaurs, the postulated dynamic gastralia of theropods…are consistent with the presence of abdominal
    airsacs, which are crucial for unidirectional flow in the paleopulmo of birds. [my emphasis to highlight where I was wrong]

    Fascinating stuff. Unfortunately I do not have easy access to any of Perry’s papers that explicitly treat possible intermediate systems between extant crocs and birds, but it still seems to me that both tidal/bidirectional lungs and airsacs had to both be present at some stage (my original point). I believe that the bird system is still more effective than the bidirectional croc system because fresh, oxygenated air ventilates the one-way bird lung both on inspiration and expiration.
    And that’s my mea culpa for the day; I doubt it will be the last time I am WOTI!

  163. #163 Torbjörn Larsson, OM
    June 21, 2008

    “WOTI”? Ah, SIWOTI:

    SIWOTI Someone Is Wrong on the Internet (PZ Myers)
    [TheFreeDictionary]

    Pharyngula acronyms – COOL! (Case Of Obscene Laughter).

  164. #164 Sillywabbit
    October 27, 2008

    My thoughts:
    E. coli are facultative anaerobic organisms, meaning that in the presence of oxygen, pyruvate (from glycolysis) will enter the Krebs (citric acid) cycle to produce energy and in the absence of oxygen, pyruvate will ferment to form lactate and/or ethanol (depending on the organism). Thus, E. coli can metabolize intracellular citrate just fine. All the machinery necessary to metabolize citrate is present in E. coli and the biochemical processes/reactions are highly coordinated and complex. Therefore, the evolutionary “leap/jump” cited is not an example of a suddenly acquired ability to metabolize citrate as E. coli posses the necessary intracellular machinery to metabolize citrate. What did evolve then?

    First look at the experimental conditions.
    The E. coli (subtype B) bacteria where grown in DM25, a minimal salts medium that has 139microM glucose and 1,700microM citrate for about 20 years. Meaning a lot of extracellular citrate and little extracellular glucose. This specific strain does not have a citrate symporter to import the extracellular citrate. Other strains of E. coli posses such membrane proteins (e.g. citT), however some of them are situated on plasmids and the researchers made sure that horizontal transfer of plasmids was not possible in this experiment. Basically, the bacteria were swimming in an ocean of food but could only use a fraction of it because they could not get their “hands” on the goods. At around the 31000-31500th generation the first citrate “importers” arose. It will be fascinating to see the actual mutations that gave rise to this function and it is probably more than one (article speculates on possibly three genetic events over many generations). E. coli has many other symporter membrane proteins for dicarboxylic acids and other molecules with similar properties to citrate (e.g. Tartrate or alpha-ketoglutarate). Citrate is a tricarboxylic acid and it is possible that a few key mutations from an existing symporter protein allowed citrate to be imported by an existing protein. If so, it would be interesting how the mutations affected the properties of the original symporter system. The researchers however have not tracked down the exact mutations.

    30 000 generations is the equivalent of +-600 000 years of evolution in a species with an average generation of 20 years (like primates). Is this an example of a “leap/jump”? If you are lactose intolerant, it might very well take 600 000 years before a mutation makes your descendants lactose tolerant (lactase gene beneficial mutation if all your descendants are also lactose intolerant). So in the end it is more like an evolutionary stutter (without us knowing the full extent of the other mutations during the 30 000 generations), much like nylonase “evolution”, which was a a pre-existing esterase with B-lactam folds that had minimal nylon hydrolysis activity from the start.

  165. #165 ?????????
    November 21, 2008

    There are human cells that contain round, compact, electron-dense granules filled with ghrelin found in the submucosal layer of the stomach they are the evolution of highly specialized multinucleated cells the pancreatic which preceded islets of Langerhans by 500 million years adapted to the calcium channel particles as well are capable of passing cascade information throught the signal transduction molecules but are as yet uncloned as to the mid-line which have both humoral and cellular immune responses as still operable. mRNA-binding cold shock protein uses the same sites, the lateral and apical membrane entry matched basal to the basolateral exit or in the basal ancini deficiency that can form normal ancini if identified, that can be novel seroconverted HLA thats haploidentical with bioavability to the preferred pattern, could be defined and reported.

  166. #166 Doug
    May 7, 2009

    I have read the background material on the e. coli experiment.
    I am looking at Table 1.
    What happened at the 20,000th generation in Replay Experiment Three?
    What does the 2 represent? Does it mean there were 2 occurrences of cit+? Does this mean that the 3 mutations were there and working at that time?

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