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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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  • by black3d (1648913) on Sunday October 18, 2009 @05:12PM (#29786979)
    and consider to a cautionary tale.
  • 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?

  • Re:hmmm (Score:3, Insightful)

    by zach_the_lizard (1317619) on Sunday October 18, 2009 @05:20PM (#29787031)
    I thought most bacteria did not engage in sexual reproduction, but instead basically cloned themselves for each successive generation. If that's the case with this particular species, I don't think it would be entirely fair to call this group inbred, considering all of them would be clones, not just this group.
  • Re:hmmm (Score:5, Insightful)

    by arose (644256) on Sunday October 18, 2009 @05:27PM (#29787105)

    inbred bateria

    I don't think you shouldn't participate in any discussions about evolution until you acquire some elementary biology knowledge.

  • 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.

  • Re:uhh? (Score:2, Insightful)

    by noundi (1044080) on Sunday October 18, 2009 @05:33PM (#29787169)

    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.

  • Re:hmmm (Score:5, Insightful)

    by CyberBill (526285) on Sunday October 18, 2009 @05:39PM (#29787221)
    They already demonstrated the E.Coli bacterium evolving the ability to metabolize citric acid... that makes it a new kid of bacterium (the inability of E.Coli to metabolize citric acid is one of its defining characteristics).
  • Re:hmmm (Score:3, Insightful)

    by wizardforce (1005805) on Sunday October 18, 2009 @05:46PM (#29787279) Journal

    Nonsense. Evolution is nothing more than organisms adapting genetically to their environment. These bacteria are doing exactly that.

  • Re:uhh? (Score:3, Insightful)

    by Sparky McGruff (747313) on Sunday October 18, 2009 @05:55PM (#29787355)
    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 thousands of dollars. "Fine mapping" a mutation by PCR sequencing the candidate clones for generations between the ones that you have full sequence data on (and to confirm the mutations in the whole genome reads) would run at least $5-7, not counting labor costs. Then there's the analysis of the data to consider.

    Let's see you make 40,000 generations of disk-to-disk copies on a 1.44 Mb floppy disk, "diff" them all to figure out when every bit flip happened, analyze the significance of each bit flip to the data and executables on the disk, and then get back to us. That would be several orders of magnitude easier than this analysis was.
  • Re:hmmm (Score:3, Insightful)

    by caerwyn (38056) on Sunday October 18, 2009 @06:17PM (#29787513)

    If more harmful mutations are being passed along than favorable, then either you're misclassifying mutations are harmful or your population is, in fact, evolving to a dead end that may result in population death.

    If it doesn't, then what's the basis for the "harmful" classification?

  • by Anonymous Coward on Sunday October 18, 2009 @06:18PM (#29787529)

    You've got the cause and effect a bit wrong, here. Evolution is never intentional - it's just a side effect. Mutations happen all the time, and there's no good way to avoid them. As for why, well: The copying machinery isn't perfect, radiation can knock things around, unexpected chemicals can throw things out of sync.

    And of course, E.Coli as it was added at the start of the experiment is not The Perfect Bacteria for these specific conditions. The food source is limited, so there's strong competition - and there's a chemical present they couldn't use as food when the experiment started.

    In other words, there is mutation (unavoidable), selection (as mentioned, strong competition), and inheritance (obviously - bacteria clone themselves for reproduction). When you've got that combination, evolution is just what happens. The bacteria with negative mutations tend to do badly, and those with beneficial ones tend to do better ... and that's all there is to it. :)

  • 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.

  • by Gothmolly (148874) on Sunday October 18, 2009 @07:23PM (#29787951)

    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 EdIII (1114411) * on Sunday October 18, 2009 @08:44PM (#29788421)

    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 evidence for that and the statement has no scientific grounds whatsoever, then who does it harm? I don't even believe that I personally am being harmed by such a belief. I am perfectly cognizant of the fact that I cannot prove that Unicorns exist and that my belief exists solely for my own comfort.

    Moreover, sometimes there can be a hypothesis that lacks any experimental methods to obtain data, and then form conclusions. However, that can provide a sense of purpose and motivation to create those experiments, draw your conclusions, and then present them to others so they can be peer reviewed.

    As an example take the Greek philosopher Democritus. His hypothesis that all matter was ultimately indivisible lacked any experiments that could be performed while he was alive. In his time, I would argue that such a hypothesis had no grounds to sustain itself. Yet he had faith that this was the truth. It was not a faith that was lacking in reason or logic either.

    Just as Democritus never lived to see any of the experiments regarding his hypothesis, or the conclusions that have been drawn from them (we have actual pictures of atoms now), I may never live to see any experiments that prove my ancestors live in a different state of existence and never actually "met oblivion".

    I like what you quoted about the Dalai Lama. It sums up my feelings about Faith and Science quite nicely. I do consider myself to be a man of Faith and Science and the two are not in conflict with each other at all. Faith does not always equal a major religion either. When I mention Faith I am referring to deeply personal journey and one in which the principles of my Faith are not dictated to me by others, but are truths that I have come to hold true for myself.

    When I discuss my own Faith with others I am careful to never claim that elements of my Faith are necessarily correct at all. If any element of my Faith was correct, than by its very nature, it would cease to be a matter of my Faith and would in fact be a matter of Science.

    In that fashion, I believe that Democritus's faith was ultimately changed into Scientific theory, and then Scientific Fact.

    So once again, why would I hold a belief in a hypothesis that has no grounds to sustain it?

    It provides me comfort, purpose, and just makes me feel good while I have to experience a life full of mostly questions, few answers, too much pain, goatse, and music by Britney Spears.

  • by Maeric (636941) on Sunday October 18, 2009 @09:12PM (#29788581)
    I may be missing something and if I am I'm sure somebody will point it out but I fail to see the evolution in this article. From my reading E. Coli still continued to be E. Coli. It certainly mutated, but I do not see any quoted evidence of evolution.
  • Re:hmmm (Score:2, Insightful)

    by ArcherB (796902) on Sunday October 18, 2009 @09:33PM (#29788701) Journal

    what you are asking for is exactly what this studied proved.

    No. What this study provided are variations of E-coli.

  • 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.
  • Re:hmmm (Score:1, Insightful)

    by Anonymous Coward on Sunday October 18, 2009 @11:49PM (#29789651)

    This will sound offensive, but will counter the main point you espouse in this post...

    You must not exist, because I can go and find the bones of your grandparents.

    --
    Why would you think that just because a fossil is formed, that the creature in question did not pass on its genes to a long line of progeny?

    However, it is not possible to prove that any given fossil represents a common ancestor of modern creatures. It can only be shown that the fossil was related. Perhaps this is what you meant?

  • by CTachyon (412849) <chronos.chronos-tachyon@net> on Monday October 19, 2009 @12:30AM (#29789999) Homepage

    Richard Lenski could have saved himself a lot of time if he had asked himself "was any new information created when it mutated" . The answer of course is NO!

    Even though you're a troll, I'm feeling generous today. This is completely and utterly wrong, and if you understood what information was, you'd agree with me — and all of biology — that evolution occurs within a species. (Speciation will have to wait for another day.)

    Claude Shannon, of Bell Labs fame, invented Information Theory in the late 1940s for the utterly practical purpose of cramming more data onto copper wires. What he discovered, with a bit of a shock quite soon after, was that the equations were identical to those describing thermodynamic entropy. In fact, thermodynamic entropy turned out to be a special case of Information Theory. After discovering this, Shannon took to calling his discovery "information entropy".

    Fundamentally, thermodynamic entropy is the unpredictableness of a physical system. The more unpredictable a physical system is, the more information it takes to describe the system. This was the link between the two.

    About 10 years later in computer science, two researchers named Kolmogorov and Chaitin [wikipedia.org] independently invented a hypothetical measure for the complexity of any arbitrary data: measure the length of the shortest possible computer program that can produce that data. Again, random data has the highest complexity: if the data has a pattern, then a short program can compute the pattern starting from a tiny piece of the data; but if there is no pattern in the data, the program must be large enough to duplicate a full copy of the data.

    Getting back to biology: mutations add randomness to DNA. Therefore, they make the DNA less predictable, and therefore they add information and complexity to the DNA. After that, natural selection acts on that mutation: if the mutation was harmful for the cell, the cell makes fewer copies of itself; if the mutation was beneficial for the cell, the cell makes more copies of itself.

    (Aside: It helps that DNA duplication is a fairly common event, especially in kingdoms like the animal kingdom where virus-like transposons infect all of our genomes. If you're a cell, and you have two copies of a gene, and one copy is mutated into something useless by a mutation, then nothing bad happens to you. In fact, if having the extra copy was a bad thing, making the copy shut up or do something else is a good thing. A lot of new proteins arose because the gene coding for them was copied then modified until it finally did something useful again, like the mammal blood clotting cascade or the photoreceptor pigments for color vision.)

    Natural selection provides a filter: it layers meaning on top of the information in the DNA, in much the same way that "English" is a filter that layers meaning on top of "light-emitting screen that displays funny squiggly marks". If information "A" means "cell lives", and information "B" means "cell dies", then natural selection is the process that distinguishes between "A" and "B" by giving them meaning. Information is complexity. Information is unpredictability. Information is randomness. Information is not meaning. Meaning is something you do with information, not something the information inherently has.

    Once you understand the difference between "information" and "meaning", you necessarily realize that DNA was the final, unequivocal proof that microevolution logically must exist in biology and that it's silly to argue otherwise. Your beliefs are contradicted by reality itself.

  • Re:hmmm (Score:5, Insightful)

    by smoker2 (750216) on Monday October 19, 2009 @12:40AM (#29790083) Homepage Journal

    In other words, every fossil was from a creature that was an evolutionary dead end. We have never found the fossil from a creature whose offspring evolved into something that's still around. If the strong survive and the weak die off, it makes sense that the strong would survive long enough to evolve. Shouldn't there be MORE of these fossils? Why do we only find the dead end?

    Explain crocodiles. According to the fossil record they have hardly changed from their ancestors millions of years ago. But they *have* changed. And we don't "only find the dead end". There is no dead end if there are descendants. What you're forgetting is that fossilisation only happens in relatively rare circumstances, so the vast majority of the record is not preserved at all. That unfortunately is where the step by step evolution would be easily recognised. But you can still fill in the gaps with insight and close examination. After all, the current generation came from somewhere, and it's pretty unlikely it started from scratch as is.

    Regarding crocodiles, the current species get to between 20 and 30 feet in length. Crocs in the Cretaceous period were around 40 feet in length. But back then they were dealing with prey much larger than is available today. Overall, most species on earth are smaller than their ancestors, except of course humans, who have no real predators and are able to take advantage of a wider range of foods.

    We have played our part in the destruction of the chain of evidence too. If you buy fish, you may have seen a halibut on the counter. Maybe it's a couple of feet long, probably less. But specimens have been caught that are 7.5 feet long and weigh over 621 pounds. They only get that big through long life, and these days we are catching them before they ever get that big. Future paleontologists will wonder why the "giant halibut" died out relatively suddenly, but there will be no missing link fossils because we ate them.

  • by ShakaUVM (157947) on Monday October 19, 2009 @04:53AM (#29791301) Homepage Journal

    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 exist? Got it, thanks.

  • Re:Micro vs Macro (Score:3, Insightful)

    by koiransuklaa (1502579) on Monday October 19, 2009 @06:55AM (#29791899)

    Yeah, I agree. I've been following physics lately and it's weird how the "scientists" only test micro-gravity -- it's like they are trying avoid building planet size objects for their tests even though it's clearly required before their theory could be taken seriously. "Theory of Gravity", hah!

  • Re:hmmm (Score:2, Insightful)

    by mayko (1630637) on Monday October 19, 2009 @09:08AM (#29792833)
    One thing I want to point out: Natural fossilization is very rare. The circumstances have to be perfect, then the fossil has to survive conditions until we actually find it. Those who point to our lack of fossil evidence are not pointing out a flaw in the other side's argument, they are pointing to an unfortunate fact of life on this planet. Assuming these species which may not have been prosperous for very long (before adapting into something we have found, or is still alive today) would all be fossilized is naive at best.

    I am interested to know (but too lazy to look) are their extensive fossil records of the animal species we see today? Or are we also assuming the earth is a 'young' earth? Either way, if their isn't extensive fossil records for all the species we see today, as we see them today. Then I think you see my point.

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