The Birth of the New, The Rewiring of the Old

By Carl Zimmer | September 19, 2012 1:00 pm

In 1988, Richard Lenski, an evolutionary biologist now at Michigan State University, launched the longest running experiment on natural selection. It started with a single microbe–E. coli–which Lenski used to seed twelve genetically identical lines of bacteria. He placed each line in a separate flask, which he provisioned with a scant supply of glucose. The bacteria ate up the sugar in a few hours. The next day, he took a droplet of microbial broth from each flask and let it tumble into a new one, complete with a fresh supply of food. The bacteria boomed again, then starved again, and then were transferred again to a new home. Lenski and his colleagues have repeated this procedure every day for the past 24 years, rearing over 55,000 generations of bacteria.

I first reported on Lenski’s experiment 12 years ago, and since then I’ve revisited it every few years. The bacteria have been evolving in all sorts of interesting ways, and Lenski has been able to reconstruct the history of that evolution in great detail, thanks to a frozen fossil record. Every 500 generations Lenski and his students sock away some bacteria from each flask in a freezer. They can thaw out these ancestors whenever they wish and compare them to their youngest descendants. Biotechnology has improved drastically since 1988, giving Lenski an increasingly powerful evolutionary microscope. When he started out, it could take months to identify just one of the many mutations that arose in each lineage. These days, he and his colleagues can sequence an entire E. coli genome for a few hundred dollars and find every single new mutation in its DNA.

Four years ago, I wrote here about one particularly fascinating episode in the evolution going on in Lenski’s lab. It started in 2003, when the scientists there noticed something odd in one of the 12 flasks. It had become much more cloudy than the others. In a microbiology lab, that’s a sure-fire sign that the bacteria in a flask have experienced a population explosion.

At first the team suspected that some other species of bacteria had slipped into the flask and was breeding quickly. But they found that the flask was packed with E. coli—descendants of the original ancestor that Lenski had used to start the entire experiment. Somehow the bacteria in this one flask had evolved a way to grow much faster than the other bacteria.

The scientists determined that the bacteria had made a drastic switch: from feeding on the glucose to another compound, called citrate. Citrate is an ingredient in the broth where Lenski’s E. coli grows. It’s not food; instead, it helps keep the minerals in the broth in the right balance for E. coli to grow.

To a microbiologist, the emergence of E. coli that can eat citrate in a lab is deeply weird. E. coli typically can’t feed on citrate in the presence of oxygen. Some strains of E. coli can draw in citrate, but only if there’s no oxygen around. To make the reaction work, they have to pump out another compound called succinate at the same time. The ability of E. coli to feed on citrate in the presence of oxygen is extremely rare; it occurs when E. coli picks up the necessary genes from other species. In its normal environment (inside us), natural selection must not favor these mutants.  Scientists have been studying E. coli in labs for over a century, making it the most intensely studied species, on Earth (as I explain in my book Microcosm).  But in all that time, there has been only a single report of a citrate-feeding E. coli in a lab, back in 1982.

The inability of E. coli to grow on citrate is so stark, in fact, that microbiologists use it as a way to tell whether bacteria they come across are E. coli or not. It was thus a surprise to Lenski and his students to find a flask of E. coli suddenly feeding on citrate. The bacteria had not picked up the genes from another species. Instead, their new ability must have evolved after Lenski started his experiment with a single E. coli. This was not simply a case of natural selection enabling a species to do something better. This was a case of doing something new.

Zachary Blount–then a graduate student in Lenski’s lab and now a post-doctoral researcher there–led the investigation into this strange new development. Blount and his colleagues took away the glucose and found that the E. coli could thrive on citrate alone. They then defrosted the bacteria’s ancestors and fed them citrate to figure out when they acquired the ability. They found that a tiny fraction of the bacteria around generation 31,000 were able to grow very slowly on the citrate. Over a couple thousand generations, they got better at growing on citrate–so good, eventually, that they took over the flask and turned it cloudy.

Blount and Lenski first reported the evolution of the citrate-eaters in 2008. Now, after another four years of painstaking research, they’re back with a new paper that details what happened down at the molecular level. It’s a fascinating look at how new traits evolve by duplicating and recycling old parts.

The scientists found that the evolution took place in three chapters. In the first chapter, the stage was set for the transformation. In the second chapter, the bacteria became citrate feeders. And in the third chapter, they became much better citrate feeders.

It usually makes sense to start a story with Chapter One. But in this case, it’s better to start with Chapter Two: The Birth of the Citrate Feeders.

When E. coli finds itself in the absence of oxygen, it switches on a gene called citT. Like other species (including us), E. coli turns genes on and off by attaching proteins to short stretches of DNA nearby. When E. coli senses a lack of oxygen, proteins clamp onto one of these genetic switches near citT. Once they turn the gene on, it produces proteins that gets delivered to the surface of the cell. There they poke one end out into the environment and pull in citrate, while also pumping out succinate. After the citrate gets inside the microbe, the bacteria can chop it up to harvest its energy.

When E. coli is growing in oxygen, however, no proteins land on the genetic switch near the citT gene, and so it remains silent. The microbe wastes no energy making a protein that won’t help it grow.

Evolution has rewritten this little algorithm in the citrate eaters. As one cell in Lenski’s flask divided, it duplicated its DNA with one fateful mistake. It accidentally copied the citT twice. The new copy ended up near a different genetic switch–a switch that turns on neighboring genes in the presence of oxygen, not the absence.

While citT remained silent in the other bacteria in the flask, in the mutant cell, it switched on. The microbe began sticking citrate transporters on its surface and started drawing in the molecule. This mutation must have occurred by generation 31,500, when Blount found the earliest citrate eaters. The mutation was a crude hack; it produced a microbe that could draw in a little citrate, but not a lot. It still had to feed on glucose to get by.

Thus endeth Chapter Two.

In Chapter Three, life got better for the feeble citrate eaters. They copied the citT gene, along with its oxygen-switch promoter. Now the bacteria could make even more CitT channels, and thus pull in even more citrate. The bacteria made a third copy, and could pull in even more. Blount and his co-authors proved that the extra copies helped the bacteria this way by defrosting bacteria from Chapter Two and inserting copies of citT into them. Those early citrate eaters immediately got much better at feeding.

The scientists also found other mutations that arose during Chapter Three. While they have yet to figure out what those mutations did, the evidence they’ve gathered so far suggests the mutations allowed the bacteria to break down citrate more efficiently so they could get more energy from their food.

The most intriguing part of the story, however, is the first– Chapter One: Setting the Stage.

When Lenski and Blount first began to study the citrate eaters, they wondered what would happen if they wound back the evolutionary tape and let the bacteria re-evolve. Would the citrate feeding evolve again?

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

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

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

And thus a history takes shape:

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

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

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

It’s remarkable how this experiment contains many elements of evolution that scientists have noted in other species. It’s common for genes to get duplicated, and for the new copy to be rewired for a new job. Snake venom, to pick one example, also evolved when genes were accidentally copied and then rewired. A gene that originally produced a digestive enzyme in the pancreas, for instance, now started making that enzyme in a snake’s mouth. It turned out to be a crude but effective venom. Later mutations fine-tuned the new venom gene until it became wickedly good.

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

Reference: Blount et al, “Genomic analysis of a key innovation in an experimental Escherichia coli population.” Nature, September 19 2012.

Comments (60)

  1. Good example of pre-adaptation at the molecular level. Also good evidence for molecular vestigialism – they abandon the glucose mechanism after gaining the citrate mechanism, but presumably there is DNA residue of that pathway.

    Beautiful piece of science.

  2. Amos Zeeberg (Discover Web Editor)

    I’m curious about how the other 11 strains developed—whether they went through some of the same chapters as the one that evolved to eat citrate, or whether that one went off in an entirely different direction in evolution space.

    [CZ: None of the other 11 lines evolved citrate metabolism.]

  3. Do they have any idea what the mutations are that ‘set the stage’ for citT? That seems equally interesting (possibly coming in a future paper!).

    [CZ: The mutations are catalogued in the supplementary material, but the scientists can’t say yet which one (or ones) set the stage, or how.]

  4. Dr. Lenski’s research has been extremely valuable for the field of evolutionary biology. Evolutionary and ecological biology need more resources and incentives to conduct long-term research.

  5. Mark

    Fascinating. I try to remain sceptical of experiments with amazing results, but no reason for scepticism here (none that I see, anyway). I can’t wait to watch this experiment over the next few decades. I’d really love to see what adaptations come up (in all 12 samples)

  6. Avi Burstein

    Wow. Amazing story. Thanks!

  7. Paul

    So, what evolved were changes in the number of genes and control of the expression of the genes, but not alterations to the proteins themselves?

    [CZ: All of the above.]

  8. D. Kim

    It would be even more interesting to continue to fund this research for an even longer period — dare I say hundreds of years more? — and see what new developments occur.

    Could a new species present itself? Perhaps even the rise of a multicellular form? Now THAT would be a giant leap for evolutionary biology.

  9. Scott

    Cool experiment! So much hard work must have gone into it.

    I have a couple questions:
    1) Would the generation 1 E coli outcompete the citrate E coli in a glucose rich environment?

    2)In some ways, shouldn’t we expect more? I mean, after 55, 000 generations of a huge number of E coli in a very controlled environment perfectly suited for evolution and really all we get is a change in promoters and some duplications of that. Nothing really new is added; all the pieces of citrate metabolism were there beforehand.

    Maybe you should try putting E coli in an environment that they truly are not able to utilize at and see if they will eventually evolve to create a completely novel digestion system?

  10. sparc

    Creationsts will not accept this research. They will state that adding citrate to the media was an intervention in the frst place that influenced the outcome of the experiments. “Methinks it is like a weasel”, Dawkins, latching, in 3 … 2 … 1 …

  11. Ramesh

    If such a wonderful evolution occurred and was so rigorously scrutinised,the genesis of life itself starts looking lesser surprising!

  12. A really nice piece on one of the iconic studies in experimental evolution. I totally agree with Christopher Moore – there has to be security of funding for long-term studies. The most exciting thing here is Chapter One (because we don’t understand it and it could only be studied with an experiment like this), but you could imagine someone with a business-minded attitude to science saying “20,000 generations and no results. That’s not cost-effective so we’ll stop the funding”. Every long-term study I know of has produced important results, almost as if running a study for a long time is a sure way to make the findings important. Probably a low risk strategy in funding terms!

    BTW, at the risk of being called self-promoting, this very result features on the cover of October’s Trends in Ecology and Evolution along with a major review on experimental evolution for anyone who wants to read more about the potential of this approach.

  13. What is all the hype about? Even YEC’s baraminology is OK with the type of “evolution” Lenski is observing and studying.

    Also there is no way you can determine that the bacteria “accidentally” rewired” their genome.

  14. John Kwok

    Sorry Joe G, I think you missed the importance of Lenski’s work, especially with the likelihood that he and his team witnessed a “speciation event” in the strain that began metabolizing citrate. I agree with Paul Craze that this ongoing experiment by the Lenski team should be viewed as one of the “iconic studies of experimental evolution”.

  15. John Kwok,

    Baraminology is OK with speciation. The problem is you and your ilk still believe darwin’s strawman that your opposition preaches the fixity of species.

  16. sparc sez:
    Creationsts will not accept this research.

    Why is that? That research does absolutely nothing to undermine anything Creationists have said.

  17. I first read about this wonderful experimente on Richard Dawkins book about evolution. That information really got my attention, specially for me that already worked with many species on research lab. Sometimes is difficult to explain concepts of evolution to lay person by just showing comparing biology and “history” (fossil evidence). That paper will certainly help me to better explain evolution because of approximation to a “human time”

    Darwin by himself made the same experiment using pigeons, but he hadn’t the genetic tools available today. Nevertheless he could demonstrate how evolution path let to evolution by natural selection (in this case “natural” was manipulated).

    Can anyone send me this paper ?

    Thanks

  18. Vinny Lynch

    I find it really amazing that almost half of the new citT promoters are (likely) derived from mobile genetic elements (IS3). Transposons and regulatory innovation a la McClintock.

  19. Ryan W

    @Joe G “there is no way you can determine that the bacteria ‘accidentally rewired’ their genome.” – Yes there is. If the experiment is repeated and we continue to get the same results, then we can’t really call it an accident as much as we can call it an evolutionary force pulling in a certain direction. This force was already demonstrated by this experiment and the results have already been reproduced.

    Also, baraminology was created in the 90s and is a pseudoscience, just like people who claim to converse with the non-living, so we don’t really care about what claims baraminologists make and whether or not they are OK with speciation; it doesn’t matter.

    Nice troll, though! :)

  20. Ryan W-

    Unfortunately the only way to determine is was an accident is to determine living organisms arose from non-living matter via accidents. Otherwise Dr Spetner’s non-random evolutionary hypothesis is the inference, meaning if point mutations only didit, then you might have a point.

    As for baraminology, umm that dates back to scriptures and after that to Linneaus, who was attempting to dtermine the Created kinds when he formulated his taxonomy, which was based on a common deign.

    As for pseudoscience, well that would be evolutionism which relies on eons of time to get from the slight changes observed in Lenski’s experiments and the untestable claim that accumulations of genetic accidents produced the diversity of life observed.

    But do keep humping your cartoon version of your opponents…

  21. Vinny Lynch

    “accumulations of genetic accidents produced the diversity of life observed” is a perfectly testable hypothesis.

  22. Vinny Lynch-

    Please tell us about this alleged testable hypothesis then.

  23. Re @20:

    So you really want to argue, in essence, that it’s impossible for many small changes to add up to large differences?

    That’s at the heart of the anti-evolution argument you’re making, and when you state it clearly, it looks quite foolish.

  24. Ryan W

    “Unfortunately the only way to determine is was an accident is to determine living organisms arose from non-living matter via accidents. Otherwise Dr Spetner’s non-random evolutionary hypothesis is the inference, meaning if point mutations only didit, then you might have a point.” -The first sentence here is just word soup and this study already illustrates pretty clearly that it wasn’t only point mutations which produced the observed results, but that genes migrated to different parts within the genome and as a result, this migration was beneficial to survival and thus, selected for. Did you read this article?

    You also make some pretty refutable claims when you use phrases like, “the only way,” because it’s not very…. creative. :)

    Evolution a pseudoscience? Interesting, I thought a baraminologist would be more creative than funny! I shouldn’t have made such strong assumptions.

  25. Eric R

    Joe G: strangely, this research was not done in order to tell us anything about creationism. It was done in order to help us understand how evolution works. You’d think that evolution scientists are as engaged in fighting creationism as creationists are in fighting evolution scientists, but that is not the case – because the scientists are too busy doing actual research. Creationism and its proponents are simply irrelevant here (as they are everywhere else where science is being done).

  26. amphiox

    It would be even more interesting to continue to fund this research for an even longer period — dare I say hundreds of years more? — and see what new developments occur.
    Could a new species present itself?

    Since the inability to metabolize citrate in the presence of oxygen is part of the species definition of E. coli (being a non-sexually reproducing organism, the interfertility criteria does not apply), quite arguably, a new species already has.

    These citrate metabolizing E. coli actually AREN’T E. coli by the definitions that microbiologists have used to define what E. coli is.

  27. Zachary Blount

    Hello everyone!

    I am the first author on the paper discussed in Carl’s post. If anyone has any specific questions on our findings, or about the Long-term Evolution Experiment in general, please feel free to ask. I can’t promise that I will be able to answer everyone’s questions, or that I will necessarily be timely. (I’m serving jury duty this week in addition to the usual everything else.) I will, however, do my best!

    Thanks,
    Zachary

  28. Zachary Blount

    For those who are really interested, the BEACON Center for the Study of Evolution in Action just posted my doctoral defense presentation from last March. It might answer some of your questions:

    http://beacon-center.org/blog/2012/09/20/zachary-blount-shows-us-evolution-in-action-in-e-coli/

  29. Daniel J. Andrews

    As Joe points out many YEC don’t hold to a fixedness of species. They can evolve within the constraints of their own “kind”. It is important to address the beliefs of the person in front of you, not the ones of the one who came before (yes, some YEC do believe what Joe says is a straw an argument, so Joe, don’t call it a straw man argument because there will be a number of people who hold to it, and would tell you that you are being deceived if you argue against them).

    This constraints within “kinds” runs into another big problem though. It requires the “kinds” coming off the ark to evolve/change at an incredibly rapid impossible rate to produce the diversity of shapes, forms, habitat adaptations, genomic differences even within each “kind”.

    The solution here sometimes falls back on the no true Scotsman fallacy–that is, if a difference between the same “kind” is too great, then it is not the same “kind”. Which the leads to the question, “what exactly is the definition of a kind, and what criteria do you use to identify different kinds?”. To this question I have not received any good answers. And what answers I do receive are sometimes contradictory.

    These items were just a few of the many issues I wrestled with as a YEC. The many inconsistencies, poor arguments, the misrepresenting of what the science actually said led me to rejecting YEC over a 10-15 yr period. Half my good friends and most of my family and in-laws are YEC, and I enjoy listening to their discussions on the subject as they grapple with some of the questions I once had.

  30. Daniel Andrews-

    Dr Spetner’s non-random evoltionary hypothesis takes care of rapid speciation- that is the ability to adapt was programmed in and the new/ open niches provided the opportunity.

    And no, educated YECs do not hold to the fixity of species. As I said Linne was a Creationist who put the “kind” at the genus level- over 200 years ago.

    But anyway if this is all “evolution” can do after 55, 000 genreations, there is no hope for evolution once sex hits the scene as it would take many more generations to do the same thing.

  31. Zachary Blount

    @Kevin T Keith

    Just to clarify, none of the Cit+ we have looked at in any generation has lost the ability to grow on glucose. As we discuss in the 2008 PNAS paper, the Cit+ at 33,000 generations appear to not grow quite as well on glucose as Cit-, but they do still grow on it. Indeed, in the DM25 medium in which we grow the Long-terms Cit+ grows on the citrate only after growing on the glucose.

  32. SteveF

    Zachary,

    Many thanks for answering questions and all your hard work on this wonderful ongoing experiment. I hate to bring up the creationist response to exciting evolutionary biology work like this, however one vaguely substantial point has possibly been made (though I’m not really sure how it supports creationism).

    Michael Behe published a paper in the Quarterly Review of Biology arguing that work such as yours and related papers by Richard Lenski and others shows that most mutations involve loss of function (the creationist implication presumably being that this isn’t an effective way to generate complexity). The paper can be found here:

    http://www.lehigh.edu/~inbios/pdf/Behe/QRB_paper.pdf

    Jerry Coyne had some initial thoughts on this paper:

    http://whyevolutionistrue.wordpress.com/2010/12/12/behes-new-paper/

    as did Jim Bull:

    http://whyevolutionistrue.wordpress.com/2010/12/20/an-experimental-evolutionist-replies-to-behe/

    I was wondering if you or Prof Lenski had any thoughts?

    Many thanks.

  33. “There is no hope for evolution once sex hits the scene as it would take many more generations to do the same thing.”

    That is the wrongest thing that I have read this week. Which, given that I’ve been reading a lot of political reporting as well, is really saying something.

  34. Hi Alex Merz-

    What I say has the support of geneticist Giusppe Sermonti who wrote:

    Sexuality has brought joy to the world, to the world of the wild beasts, and to the world of flowers, but it has brought an end to evolution. In the lineages of living beings, whenever absent-minded Venus has taken the upper hand, forms have forgotten to make progress. It is only the husbandman that has improved strains, and he has done so by bullying, enslaving, and segregating. All these methods, of course, have made for sad, alienated animals, but they have not resulted in new species. Left to themselves, domesticated breeds would either die out or revert to the wild state—scarcely a commendable model for nature’s progress.

    (snip a few paragraphs on peppered moths)

    Natural Selection, which indeed occurs in nature (as Bishop Wilberforce, too, was perfectly aware), mainly has the effect of maintaining equilibrium and stability. It eliminates all those that dare depart from the type—the eccentrics and the adventurers and the marginal sort. It is ever adjusting populations, but it does so in each case by bringing them back to the norm. We read in the textbooks that, when environmental conditions change, the selection process may produce a shift in a population’s mean values, by a process known as adaptation. If the climate turns very cold, the cold-adapted beings are favored relative to others.; if it becomes windy, the wind blows away those that are most exposed; if an illness breaks out, those in questionable health will be lost. But all these artful guiles serve their purpose only until the clouds blow away. The species, in fact, is an organic entity, a typical form, which may deviate only to return to the furrow of its destiny; it may wander from the band only to find its proper place by returning to the gang.

    Everything that disassembles, upsets proportions or becomes distorted in any way is sooner or later brought back to the type. There has been a tendency to confuse fleeting adjustments with grand destinies, minor shrewdness with signs of the times.

    It is true that species may lose something on the way—the mole its eyes, say, and the succulent plant its leaves, never to recover them again. But here we are dealing with unhappy, mutilated species, at the margins of their area of distribution—the extreme and the specialized. These are species with no future; they are not pioneers, but prisoners in nature’s penitentiary.

  35. amphiox

    Michael Behe published a paper in the Quarterly Review of Biology arguing that work such as yours and related papers by Richard Lenski and others shows that most mutations involve loss of function (the creationist implication presumably being that this isn’t an effective way to generate complexity).

    This is true. Most mutations that are not neutral do involve a loss of function.

    It is also completely irrelevant. Because SOME mutations DO involve gain of function, and that is all that is required.

    (There are also multiple examples of mutations that produce a “loss” of function at the protein level which end up producing a GAIN of function at the phenotype level.)

  36. Zachary Blount

    @SteveF

    I will need to confer a bit with Rich before saying anything about the general issue. However, I can say something about the specific instance of Cit+ evolution. Aerobic citrate utilization is a novel trait for E. coli, and it is one that evolved spontaneously in the Ara-3 population that I study. (By this I mean that it did not come from the acquisition of foreign DNA like a plasmid carrying a citrate transporter into the cell line from outside.) Moreover, the actualization stage that produced the qualitative switch to Cit+ did not involve any loss of gene function! As Carl explained so well, actualization involved a duplication mutation that produced two copies of a segment of DNA that 2933 bp long. These two copies are in a tandem, head-to-tail orientation, and placed a copy of the citT gene under the control of a copy of the promoter element that normally controls when the rnk gene is turned on – this is what we call the “rnk-citT module”. (I know, I know, incredibly catchy!) As rnk is turned on when oxygen is present, the copy of its promoter in the new rnk-citT module likewise turns on citT when oxygen is present. Voila! There you have a new element formed in the way that evolution so often innovates – by making the new from the old. (A process that Gould called exaptation, but that Darwin actually mentioned in the 1859 first edition of the Origin, and then discussed a good bit more in the 1872 sixth edition.) Is the material that went into the new element fundamentally new? No. But to deny that the new module is new is like saying that a new word is nothing new merely because it was formulated from pre-existing letters. Now something that I found to be really interesting about this mode of innovation is that it wouldn’t eliminate any pre-existing function. The duplication generates the new rnk-citT module, but there ends up remaining in the genome complete copies of rnk under the control of the rnk promoter, as well as of the cit operon as it existed before the duplication took place. The duplication thus added a new regulatory element while not actually disrupting any pre-existing regulatory modules. I think that gets to the issue you brought up, however.

    I also think it worth nothing that another really interest aspect of the Cit+ story is that it was actually rather a complex process. Potentiation involved at least 2 mutations, actualization at least one more, and refinement, which is an ongoing process, even more. Even taking the minimum numbers, the process involved at least 4 mutations, and undoubtedly considerably more. (Ara-3 is at generation 56,000 now, meaning that Cit+ have been adapting to being Cit+ for about 24,500 generations at this point. There may well be a dozen or more refining mutations that have accumulated over that time.) Moreover, this isn’t the first instance of such complexity observed in the lab. Justin Meyer, a former graduate student of Rich’s, published a paper earlier this year in which he described the evolution of a novel function in a phage that involved four mutations! (See: http://www.sciencemag.org/content/335/6067/428.full ) (Carl’s story in the New York Times on Justin’s research: http://www.nytimes.com/2012/01/27/science/in-real-time-a-virus-learns-a-new-way-to-infect.html)

    Zachary

  37. SteveF

    Zachary,

    Thanks very much for the informative reply. Interesting to see that loss of function wasn’t involved. If I remember rightly, Behe was pretty confident in his writings for creationist publications that it would be when your initial results came out (I’ll try and find the link later), although he was more circumspect in his QRB paper:

    “If the phenotype of the Lenski Cit strain is caused by the loss of the activity of a normal genetic regulatory element, such as a repressor binding site or other FCT, it will, of course, be a loss-of-FCT mutation, despite its highly adaptive effects in the presence of citrate. If the phenotype is due to one or more mutations that result in, for example, the addition of a novel genetic regulatory element, gene-duplication with sequence divergence, or the gain of a new binding site, then it will be a noteworthy gain-of-FCT mutation.”

    On the more general point, I’d be very interested to hear your thoughts. In the piece I linked to earlier, Jim Bull wrote about Behe’s paper:

    “My own view of the MB paper is that it has done a service to the study of evolution by pointing out where the next generation of experients should focus. We don’t yet have many studies on the long term evolution of protein novelty (to get extreme divergence), and the types of selection used are typically extreme. Answers to these problems aren’t yet available simply because we simply have not applied much effort.”

    I wonder if you agree and if you do agree whether you have any thoughts on starting this next generation of experiments.

  38. amphiox

    An interesting thing note here is that the mechanism for citrate import involves exporting succinate. Since succinate and citrate are both part of the TCA cycle this means that succinate is actually required in order to metabolize citrate fully. So the bacteria, in order to get a nutrient, must give up another nutrient, and one that it actually needs as part of the metabolic pathway for processing the nutrient it gains.

    Ultimately this works because citrate has 6Cs and succinate just four, so there is a net gain of carbon.

    But if you think about it, this is a remarkably klugey way of doing things, and certainly not something any sensible designer would do if tasked with developing a method of citrate metabolism from scratch.

    But of course this sort of kluginess is precisely what we expect to see and often see when looking at the products of evolutionary processes.

  39. Childermass

    Joe G @ 13: “What is all the hype about? Even YEC’s baraminology is OK with the type of “evolution” Lenski is observing and studying.”

    And yet creationists have been attacking the observation that the culture line evolved a means to metabolize citrate ever since it was announced. This is mainly because many of them said this sort of thing could not happen. This is evolution of a new function involving multiple mutations. It certainly involves new “information” by any reasonable definition of the word.

  40. amphiox

    What is all the hype about? Even YEC’s baraminology is OK with the type of “evolution” Lenski is observing and studying.

    YEC’s baraminology is OK with absolutely anything the creationist using it wants it to be, and not OK with absolutely anything the creationist using it doesn’t want it to be, because there is no coherent definition of the boundaries of a “baramin”.

    That’s why it is both useless and irrelevant.

    This is mainly because many of them said this sort of thing could not happen. This is evolution of a new function involving multiple mutations.

    It is a gain of function random mutation, an increase in biological information due to random mutation and natural selection, and the observed evolution in real time of an irreducibly complex system.

    All three of which are things creationists and IDers have been insisting to be impossible without direct involvement of a designer.

  41. Childrmass:

    And yet creationists have been attacking the observation that the culture line evolved a means to metabolize citrate ever since it was announced.

    Reference please.

    It certainly involves new “information” by any reasonable definition of the word.

    That has nothing to do with creation arguments and it is false. It is using the same information it had it different ways.

  42. amphiox-

    1- No one knows that the mutations were random in any sense of the word.

    2- Creationsust do NOT argue agaisnst gain of function mutations, neither does ID

    3- No IC system evolved

  43. Can anyone send me that paper ? my e-mail is rafaelbrm@yahoo.com.br

  44. Alan Fox

    Zachary Blount is unequivocal!

    Aerobic citrate utilization is a novel trait for E. coli, and it is one that evolved spontaneously in the Ara-3 population that I study. (By this I mean that it did not come from the acquisition of foreign DNA like a plasmid carrying a citrate transporter into the cell line from outside.) Moreover, the actualization stage that produced the qualitative switch to Cit+ did not involve any loss of gene function!

    What a beautiful demonstration of the power of natural selection at work. Professor Lenski and his team are to be congratulated on their persistence, patience and the results of this elegant mega-experiment..

  45. amphiox

    1- No one knows that the mutations were random in any sense of the word.

    Only someone who does not actually comprehend the meaning of the word “random”, or is deliberately lying about it, can say the above with a straight face.

    2- Creationsust do NOT argue agaisnst gain of function mutations, neither does ID

    Only someone who does not know anything at all about what Creationists or ID argues against, or someone deliberately lying about it, can say this with a straight face.

    3- No IC system evolved

    Only someone who does not know what an IC system is, or deliberately lying about it, or, alternatively, does not have the foggiest clue as to what “evolved” actually means, or is lying about it, can say this with a straight face.

  46. amphiox-

    I get it- you are clueless and forced to spew false accusations.

    Nice job- or can you support your spewage? I know I can support what I posted…

  47. 1- No one knows that the mutations were random in any sense of the word.

    Foir example, take a look at any bus on a computer’s mother board. The 1s and 0s appear to be random, however we know they are not. The are directed by the program.

    Dr Spetner goes over mutations in “Not By Chance” and there isn’t any justification for saying gene duplications are random/ chance events.

    - Creationsust do NOT argue agaisnst gain of function mutations, neither does ID

    That is a fact that not even amphiox can refute. But it sure can spew a false accusation.

    3- No IC system evolved

    Another fact- and it is very noticeable that amphiox couldn’t produce any evidence that an IC system evolved via blind and undirected processes. Ya see “evolved” just means descent with modification/ a change in allele frequency over time. It says NOTHING about any mechanism. Meaning evolved by design is perfectly OK.

  48. Alan Fox:

    What a beautiful demonstration of the power of natural selection at work.

    Umm the environment was artificially selected. And no one knows if the mutations were random.

    So in what way was natural selection at work?

    Professor Lenski and his team are to be congratulated on their persistence, patience and the results of this elegant mega-experiment..

    Yes, congratulated by Creationists because it supports their position and casts serious doubts on evolutionism.

  49. Rob E

    @ Joe G —
    a quick internet search will show you several examples of YEC’s and their ilk attacking this research, just as Childermass has said
    http://www.conservapedia.com/Richard_Lenski
    http://creation.com/bacteria-evolving-in-the-lab-lenski-citrate-digesting-e-coli

    Only posting two. Twenty second of searching through google results will show you a great deal more. But then, I don’t actually expect you to bother with troublesome things like fact.

  50. Umm Rob E-

    Your first link just questions the research/ has questions about it and the second just tells it like it is. How is this attacking the research?

  51. ben

    @22 Mark C Chu-Carroll: “That’s at the heart of the anti-evolution argument you’re making, and when you state it clearly, it looks quite foolish.”

    Foolish? Remember you’re talking about Joe Gallien, who will argue until he’s blue in the face that ICE IS NOT WATER and that you can calculate the CSI content of a cake by counting the number of letters in the recipe. He’s got the foolish market cornered.

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The Loom

A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.

About Carl Zimmer

Carl Zimmer writes about science regularly for The New York Times and magazines such as DISCOVER, which also hosts his blog, The LoomHe is the author of 12 books, the most recent of which is Science Ink: Tattoos of the Science Obsessed.

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