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Biotech Science

Observing Evolution Over 40,000 Generations 461

Posted by kdawson
from the every-day-in-every-way dept.
Last year we discussed the work of Richard Lenski, who has been breeding E. coli for 21 years in a laboratory in Michigan. Then, the news was that Lenski's lab had caught direct, reproducible evidence of a genetic mutation with functional consequences for an organism. Now Lenski's lab has published in Nature a major study comparing adaptive and random genetic changes in 40,000 generations of E. coli (abstract here). "Early changes in the bacteria appeared to be largely adaptive, helping them be more successful in their environment. 'The genome was evolving along at a surprisingly constant rate, even as the adaptation of the bacteria slowed down,' [Lenski] noted. 'But then suddenly the mutation rate jumped way up, and a new dynamic relationship was established.' By generation 20,000, for example, the group found that some 45 genetic mutations had occurred, but 6,000 generations later a genetic mutation in the metabolism arose and sparked a rapid increase in the number of mutations so that by generation 40,000, some 653 mutations had occurred. Unlike the earlier changes, many of these later mutations appeared to be more random and neutral. The long-awaited findings show that calculating rates and types of evolutionary change may be even more difficult to do without a rich data set."
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Observing Evolution Over 40,000 Generations

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  • fuck that (Score:5, Funny)

    by Anonymous Coward on Sunday October 18, 2009 @05:05PM (#29786921)

    god did it

    • Re:fuck that (Score:5, Insightful)

      by zero.kalvin (1231372) on Sunday October 18, 2009 @05:15PM (#29787003)

      god did it

      Which one of them?

  • by adpe (805723) on Sunday October 18, 2009 @05:07PM (#29786941)
    653 mutations? 1305 missing gaps! Proof of god! Hallelulja!
    • by Idiomatick (976696) on Sunday October 18, 2009 @05:20PM (#29787029)
      Meant as a joke but it will sadly happen like this. It is incredible that we can have this level of clear investigation into evolution. And it is something that people have innately known since early agriculture (replanting grain using the best seeds, genetic engineering). Yet in the US:
      51% of people believe god created man as he is.
      30% said god created us and we can evolve
      15% say humans evolved with out god.

      These figures are a terrifying example of humans ability to deny what should be blatantly obvious. If we can do this imagine how many things people must get completely wrong no matter the level of obviousness.
      • by noundi (1044080) on Sunday October 18, 2009 @05:30PM (#29787127)

        Meant as a joke but it will sadly happen like this. It is incredible that we can have this level of clear investigation into evolution. And it is something that people have innately known since early agriculture (replanting grain using the best seeds, genetic engineering). Yet in the US:
        51% of people believe god created man as he is.
        30% said god created us and we can evolve
        15% say humans evolved with out god.

        These figures are a terrifying example of humans ability to deny what should be blatantly obvious. If we can do this imagine how many things people must get completely wrong no matter the level of obviousness.

        These figures are incredible examples of how much money [virtualtourist.com] you can make on peoples stupidity.

        • More acceptable in the 1600s in a country where religion controlled education system. The US is much better educated :/
        • by caseih (160668)

          You think that people that want to go to the Vatican Museum and see some of the worlds' greatest works of art are stupid? Wow. That is so sad. Guess you've never been to see it. Suffice it to say most people do not go to the vatican museum out of religious zeal. In fact most visitors to the museum are likely not even catholic, or even religious. The Sistine Chapel paintings are simply amazing. Sure you can look at the paintings from a religious point of view, but as artwork they stand just fine witho

      • by EdIII (1114411) * on Sunday October 18, 2009 @07:13PM (#29787881)

        That is not entirely fair.

        30% said god created us and we can evolve
        15% say humans evolved with out god.

        It's more like 45% against the 51% which is far less terrifying than you make it out to be. What about the other 4%?

        I'm all for the impartial analysis of data and I fully recognize that being proven wrong can be just as valuable as being proven right.

        Faith is not the enemy of Science, and therefore, the enemy of logic and reason. I have always believed that Faith is simply the believe in a hypothesis that currently lacks the ability to reach any conclusions. Science is not without Faith in that regard. Faith can be a healthy component of our existence and provide meaning, purpose, and comfort. Regardless of your opinions, it is a well used coping mechanism by the majority of the planet to deal with the very fact we exist and we have questions without answers.

        The problem that you seem to have, and that I have as well, is when people who have Faith (sometimes commonly grouped into the Christian Faith) ignore all evidence in front of them and hold on to beliefs that have already been proven wrong beyond all reasonable doubt. Those people that would belligerently refuse the truth that has been revealed to them because admitting they are wrong somehow destroys their faith.

        More problematic, and downright destructive and counter-productive to human growth, are those that will not only refuse to have a dynamic adaptive Faith that can change with new data and observations, but cannot accept anyone else having a Faith different than their own.

        That 30% do not fall into that category necessarily are certainly not the most destructive. They are acknowledging that evolution as a process is real and observable. I cannot see how that is denying anything you hold to be "blatantly obvious". Neither you or I can prove that God does not exist and currently we have no data or observations that can disprove that God did not set into motion the creation of the Earth, and through evolutionary processes, all life on Earth. Of course, I think we have reasonably disproved the whole so-called 7 day "theory" and that Earth is only a few thousand years old. However, to me that only proves the Bible was a book created by a bunch of men with vivid imaginations. Disproving the Bible, in whole or in part, does not disprove the existence of diving being(s).

        Your post is rather insulting to that 30%. I don't think they are your "enemies" in this case or part of the problem. Heck, the very fact they are willing to acknowledge Evolution means they are meeting you half way and can be reasoned with.

        The 51% are probably a lost cause. That is not intended as an insult, but people can take that for what's it worth. When Faith cannot change because it has been delivered by Doctrine, than it is not really their Faith at all. I agree with you and those people concern me greatly since they seem to like laws that legislate their Faith upon others which is deeply and tragically ironic considering that my country (USA) was ostensibly founded with opposition to such behavior.

        • I have no problem with people who's faith doesn't collide with science, but:

          I have always believed that Faith is simply the believe in a hypothesis that currently lacks the ability to reach any conclusions.

          The problem is, why chose _that_ particular hypothesis, if there is no ground to sustain it? On the other hand, we have respected scientist calling for hipothesis like the future changing the present [arxiv.org], so it's doesn't t

          That's one thing I like in the Dalai Lama:

          "My confidence in venturing into science lies in my basic belief that as in science, so in Buddhism, understanding the nature of reality is pursued by means of critical investigation."

          "If scientific analysis were conclusively to demonstrate certain claims in Buddhism to be false," he says, "then we must accept the findings of science and abandon those claims."

          • Re: (Score:2, Insightful)

            by EdIII (1114411) *

            The problem is, why chose _that_ particular hypothesis, if there is no ground to sustain it?

            Because it makes me feel good?

            I would ask the question why not? What are the reasonable grounds to sustain a hypothesis in your opinion? There are a great many aspects of spirituality and religion which certainly seem to have no scientific ground to sustain them. Yet, that in of itself does not make those beliefs negative.

            Let's say I want to believe that Unicorns exist. As long as I realize that there is no evide

      • http://www.answersingenesis.org/articles/aid/v2/n1/a-poke-in-the-eye [answersingenesis.org]

        "Previous research has shown that wild-type E. coli can utilize citrate when oxygen levels are low."

        In some of my previous posts, I've tried to convey the idea that perhaps we're not seeing new characteristics generate - rather we're seeing a reconfiguration / recombination / whatever of existing information.

        As the quote says, it already knew how to use citrate. Creationists are fine with that. I think when you look closely at each exampl

      • Re: (Score:3, Insightful)

        by ShakaUVM (157947)

        51% of people believe god created man as he is.
        30% said god created us and we can evolve
        15% say humans evolved with out god.

        These figures are a terrifying example of humans ability to deny what should be blatantly obvious.

        If it is so blatantly obvious, what is your discrimination criteria between the last two options?

        I mean, most people say that they can't tell, but since you take the opposite approach, I'm curious what your data is?

        Oh? Just your presupposition that God doesn't exist proves that God doesn't

    • by Yvanhoe (564877) on Sunday October 18, 2009 @05:52PM (#29787329) Journal
      And indeed, this very person had a very good email dialogue with some crationists a few years ago about this work on E.Coli.

      http://rationalwiki.com/wiki/Lenski_affair [rationalwiki.com]
  • and consider to a cautionary tale.
  • uhh? (Score:2, Interesting)

    by blhack (921171)

    Forgive me, as I am not a biologist, but...

    What does he have to do to "prove" that genetic mutations have occurred beyond:

    1) Sequence DNA from original strain
    2) Sequence DNA from current strain
    3) diff strain1 strain2

    Wasn't easy DNA sequencing supposed to be one of the new technological advancements that was changing the world?

    Am I missing something here?

    • Re:uhh? (Score:5, Informative)

      by wizardforce (1005805) on Sunday October 18, 2009 @05:32PM (#29787151) Journal

      Yes. You are missing the fact that this experiment has been running for the last 20+ years. Time is the major factor here. Furthermore, they did a bit more than simply comparing the DNA from the current strain to the original strain. THey kept samples of strains of the bacteria every 500 generations or so and compared them. Even running parallel experiments using these stored strains allowing them to effectively repeat the experiment in order to understand the evolution of the new metabolic pathway allowing for the utilisation of Citrate.

      • Not entirely related: These guys [youtube.com] observed the evolution of long-living flies for 20 years (google talk). Although I do have some reservations about their ethics and patents.

      • by astar (203020)

        what is the difference between adaptive mutations and random mutations? My understanding of evolutionary theory is that it says evolution is driven first by random mutations, and then the adaptive ones are preserved. So I see a distinction, but the naming here seems a little off-center.

        Now I further figure that if the mutations are random, then their adaptiveness is random. Was adaptiveness potential less used up at the beginning of the experiment, thus it was more likely for a random mutation to be adap

    • Re:uhh? (Score:5, Informative)

      by Trepidity (597) <delirium-slashdo ... org minus author> on Sunday October 18, 2009 @05:33PM (#29787157)

      A main purpose of the study is to investigate evolution of phenotypes, not just genomes--- i.e. how the functions and capabilities of bacteria change over generations due to evolution. Just showing there was a change in the genetic sequence doesn't do that, since it might be a change that isn't expressed.

    • Re: (Score:2, Insightful)

      by noundi (1044080)

      What does he have to do to "prove" that genetic mutations have occurred beyond:

      Present it in a way that nobody gets offended. Meaning it should comply with religion so that people can go on living their lies.

    • by timeOday (582209)
      The parent provided its own nonstandard definition of "mutation" under which the question makes sense, in fact it's the point of the Nature article - which in the abstract is called "genomic vs adaptive evolution." Some mutations matter to the fitness of the organism, and some don't, and some can change the mutation rate itself, so it would be wrong to assume uniform rates of either genomic or adaptive evolution. This has implications for phylogenetics, where it would be a lot easer to infer the relatedne
    • Re:uhh? (Score:4, Informative)

      by ceoyoyo (59147) on Sunday October 18, 2009 @05:44PM (#29787267)

      That would be one way to go about it, all right. There are a couple of problems though. Current state of the art DNA sequencing runs somewhere in the range of a few tens of thousands per (for humans, perhaps a bit less for something like E Coli). That's a technological advancement, all right, considering when they first started sequencing genomes it was a billion dollar project. It's also not instantaneous. Much faster than it used to be (years or decades) but not instant. Note that the samples he's looking at are ones that have been frozen periodically over the last twenty years. Apparently the price of sequencing genomes has dropped to the point where his lab has the funding to actually do it now.

      The diff part isn't trivial either. The genome for E. Coli is around 5 million base pairs long, which doesn't sound like much, if you're just looking for point mutations. The problem is, there are lots of other things that can happen to a genome besides point mutations. Genes can hop around or get copied into the wrong location, which you might count as no mutation, or one mutation, but either way you still have to figure out where it came from. Also, although E. Coli reproduce asexually, they do share genetic information through conjugation, so you get gene shuffling that way. There's also at least some genetic diversity in the colony, meaning you'll be dealing with several different genomes.

      Once you've worked all that out, it's not all that interesting just to look at now vs. then. If you wanted to do that you could go dig frozen bacteria out of ice cores or something. The point of this experiment was to be able to watch as the genome changed. So you have to do lots and lots of comparisons, from samples taken at different times (every 500 generations, IIRC, meaning about 80 timepoints). Oh, and there were multiple, isolated populations.

      On top of all that, what's really interesting is functional changes. Counting mutations is fine and all, but you really want to know what (if anything) those mutations are doing. The headline event was a mutation that allowed the E Coli to metabolize citrate, for example.

    • Re: (Score:3, Insightful)

      The problem with your quick dismissal -- "Easy DNA sequencing" isn't that easy. It's a hell a lot easier and cheaper than it was 20 years ago, but it's neither cheap nor effortless.

      "Easy" DNA sequencing (e.g. short-read sequencing systems) are still rather expensive, and require a good deal of skill. Even archiving and preparing 40,000 samples would be an enormous challenge. The costs for a "full genome" read of an E.Coli genome (say, 1 or 2 lanes on an Illumina short-read sequencer) would run in the
  • Yes, that Lenski (Score:5, Interesting)

    by JoshuaZ (1134087) on Sunday October 18, 2009 @05:46PM (#29787277) Homepage
    This is the same Richard Lenski whom Conservapedia (the right-wing Christian alternative to Wikipedia because Wikipedia is evil) repeatedly attacked. Apparently his work is such strong evidence of evolution, that Conservapedia's response was to more or less accuse him of faking the data. See http://scienceblogs.com/pharyngula/2008/06/lenski_gives_conservapdia_a_le.php [scienceblogs.com].
  • There is a step from "DNA mutation" to "Evolution", and that is adaptation to the medium. Did the mutations change the fenotype (the external aspect/behaviour) to something more adapted? Were set certains goals (for example, putting them in a medium less than ideal for the original strain, but to which its survivors have adapted) or the surviving changes did not affect at all at the species?
    • by caluml (551744)
      Your signature is amusingly apt for this story:

      I'm a signature virus. Please copy me to your signature so I can replicate.

    • Re: (Score:2, Informative)

      by Machupo (59568)

      There is a step from "DNA mutation" to "Evolution", and that is adaptation to the medium. Did the mutations change the fenotype (the external aspect/behaviour) to something more adapted? Were set certains goals (for example, putting them in a medium less than ideal for the original strain, but to which its survivors have adapted) or the surviving changes did not affect at all at the species?

      I think what you're trying to ask is: "Was the selective pressure determined to be in response to stimuli versus a random occurance?"

      The authors cover the difference between neutral drift and selective mutations which increase fitness throughout the paper.

      Specifically in answer to your question, though, is the following from the expanded methods & materials:

      "We performed Luria–Delbrück fluctuation tests33 to confirm that the Ara-1 population evolved an elevated mutation rate. Bacteria were re

  • by Hurricane78 (562437) <deleted@s[ ]hdot.org ['las' in gap]> on Sunday October 18, 2009 @06:19PM (#29787539)

    would be, if you could say, that there are parallels to human evolution.

    At first, E. coli adapted to the environment. But when there was nothing to adapt to, because nothing changed anymore, mutation almost switched to a different "mode", where random changes got bigger. My guess: In the battle to stand out of the crowd and become dominant.

    Now the parallel would be, that humanity also now dominates the planet, and very little can eradicate whole humanity. So for all of humanity, the risk is very close to zero. Which could mean that now, we also rather fight ourselves, in the battle to stand out and become dominant.

    I mean after all, even with "global peace" (something that will never happen), "everyone is equal", and all that stuff, it's still an evolutionary game, where those with even the slightest advantages, will in the end "win".

    Just that now we are perhaps evolving in a "mode" where it's not for the best of whole humanity anymore, because that became insignificant.
    My guess here, is that this is, how diversification into different species (at the very beginning) starts to happen...

  • by Tablizer (95088) on Sunday October 18, 2009 @06:50PM (#29787749) Homepage Journal

    This is not "dramatic" enough to convince the general public of the power of evolution. A more interesting experiment would involve the Mud-skipper fish; a fish that can hop on land for short durations but has no close relationships to amphibians or lung-fish, being the "fan ray" fin type.

    I'd like to see an attempt to breed them via nation-wide contests to evolve the fish into a more efficient walker or hopper. Races could be held at high-schools and colleges, and the winners would be bread with other regional winners to produce a more land-friendly next generation. The gradual process could be observed by all.

    I discarded the chimp version of this after watching Planet of the Apes :-)
       

  • by KalvinB (205500) on Sunday October 18, 2009 @07:22PM (#29787937) Homepage

    took millions of years. Nobody with eyeballs doubts that things change over time. What we're finding out finally is just how long it actually takes for things to change.

  • Everyone assumes that the E. coli bacteria "evolved" its way into better dealing with adverse conditions (citric acid, etc.). Not true - the ones who HAPPENED to be able to withstand and metabolyze citric acid DIDNT DIE - the survivors didn't evolve to metabolize it, they already could. Animals don't genetically adapt to change - the ones already predisposed to tolerate the change survive.

    • by MWoody (222806) on Sunday October 18, 2009 @07:57PM (#29788131)

      Congratulations! You've just described the process of evolution.

    • by s7uar7 (746699)
      I think you're on to something there. I'm not sure what you'd call it though; maybe 'survival of the fittest' or something like that.
    • Gold star for you! I also sometimes forget this. Anyone who doesn't get this doesn't really understand evolution. Evolution is NOT a magical force that changes organisms.
    • Re: (Score:3, Informative)

      by MozeeToby (1163751)

      On this particular subject, and I know this is unrealistic on slashdot, it would be good to read the article. The techniques used in this study were brilliant, they are specifically designed to investigate the criticisms that are usually leveled on studies of evolution and they do so beautifully. I'll try for a quick explanation of why your criticism is invalid.

      First, how the experiment worked. They put E. Coli. into dishes with a growth medium of glucose and other nutrients with glucose as the limiting

  • From the summary,

    "...genomic evolution was nearly constant for 20,000 generations. Such clock-like regularity is usually viewed as the signature of neutral evolution, but several lines of evidence indicate that almost all of these mutations were beneficial. This same population later evolved an elevated mutation rate and accumulated hundreds of additional mutations dominated by a neutral signature. Thus, the coupling between genomic and adaptive evolution is complex and can be counterintuitive even in a con

  • Nobel? (Score:3, Insightful)

    by Jonny_eh (765306) on Sunday October 18, 2009 @09:41PM (#29788733)
    Give this man (and his colleagues) the Nobel prize already! This is some freaking impressive science.

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