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Observing Evolution Over 40,000 Generations
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."
god did it
And there is still idiots who believe evolution is wrong... Anyway I didn't read the article yet, but i would love to see if he was exposing them to different types of pressure and how did they adapted to that pressure.
653 mutations? 1305 missing gaps! Proof of god! Hallelulja!
then again the creationists don't listen to facts so they will naturaly make a dumbass theory in order to feel safe that there is a god.
and consider to a cautionary tale.
"The true measure of a person is how they act when they know they won't get caught." - DSRilk
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?
NewslilySocial News. No lolcats allowed.
in the grim darkness of a petri dish, there is only bacteria?
I am curious to know that why would mutate those germs in a short period of time, in a potentially unchanged lab environment? What are they adapting to by evolutionary mutation?
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.
..wait, looks like he is already here!
do you realize they have been using genetic mutation rates to estimate migration patterns of human and animal history... IE, when did people first move into an area, which groups of people displaced other groups, etc etc etc?
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?
Why can't
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...
Any sufficiently advanced intelligence is indistinguishable from stupidity.
A lot of articles I see about the Lenski lab miss one of the coolest discoveries of the Lenski lab: not only did a line evolve the ability to use citrate as a carbon source, they took 'library copies' they had saved every 500 generations and showed that that particular line had a better chance of re-evolving that trait. In other words, it's evidence for contingency in evolution, that a particular path taken impacts whether/when an adaptation may arise.
just hope we don't have a human civilization genetically predisposed to treachery!
It's not 'you are what you eat' it's 'you are who you are...which makes and shapes what you are'
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 :-)
Table-ized A.I.
While I find some of the reported observations very thought-provoking, I have trouble attaching overwhelming significance to this study due to the way the data is presented. For example, 26 SNPs in the 20k-generational line are non-synonymous. On the surface, I find that a significant departure from the norm, but when you account for 12 total populations and the dataset consisting of only one population, something just feels a bit off.
Now, the authors may really be on to something here, they do raise quite a few questions in my mind (and as I re-read the paper, i'll probably answer some and generate more), so time (and further experimentation) will certainly expand this discussion.
*insert pithy sig here*
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.
Work Safe Porn
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.
I want to delete my account but Slashdot doesn't allow it.
There is a totally fascinating aspect to these findings that should make our thinking about evolution much deeper.
Look at the "adaptive" and "random" mutations they report. Think about it for a minute!
"Adaptive" mutations do not really fit with what we learned in school. We learned that mutations are "random" and by luck a few are adaptive.
Here we see a long stretch (20000 generations) where most mutations are "adaptive"; then a similarly long stretch (another 20000 or so) where most are random. The second half fits the stuff we were taught at school. The first half is a fascinating hint that evolution is not always driven by randomness.
What exactly lies behind this? We do not yet know. As the authors say correctly,this "cautions against categorical interpretations about rates of genomic evolution in nature without specific knowledge of molecular and population-genetic processes".
Science progresses people. We are learning new things here. Evolution is not always driven by randomness...
I'm sure no one here questions micro-evolution (which is an entirely different thing than macro-evolution). However, until the bacteria manage to somehow change the number of chromosomes they have, I will always find it hard to believe that maco-evolution has occurred.
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 constant environment. In particular, beneficial substitutions were surprisingly uniform over time, whereas neutral substitutions were highly variable."
In other words, random mutation ain't the great source of creative, beneficial change we all thought? It's just sorta .. random?
Huh. That is counterintuitive.
"We receive as friendly that which agrees with, we resist with dislike that which opposes us" - Faraday
Its a shame that posts regarding evolution degrade into a "Lets bash knuckle dragging creationists!" affair.
For every KDC, there's a KDE (knuckle dragging evolutionist) that thinks that there is a single evolutionary mechanism that explains everything from the origin of life to how we interact with one another. Both of these KD groups need to calm down, stop drinking the kool-aid and open their minds to the scientific process which is (a) ALWAYS tentative (b) best performed with repeatable, empirical experimentation.
Also, there is a fundamental need for everyone to understand how to think about and discuss evolution. Evolution happens, and that life changes over time is the "fact of evolution," but how does life change and to what extent? The "how" part is what we refer to as the theory of evolution, of which there are many, but most lay people are only familiar with Neo-Darwinian theory of evolution, otherwise known as Random Mutation and Natural Selection.
Anyway, regarding Lenski's work, why is it significant, and what do Lenski's most qualified critics have to say about it? For some reason, in the field of evolutionary biology, open criticism is not as tolerated as it is in other fields. There's the fear that KDC will get their foot in the door, and there are also the metaphysical aspects of evolutionary biology that tend to stray far from fundamental science. Even if the critic has a stellar research track record, he has a tremendous challenge when it comes to questioning the power of purely Darwinian mechanisms. There may be some other mechanism, but such mechanisms typically assume some external source of information, which has different metaphysical assumptions than does those of purely Darwinian evolution. Consequently, evolutionary biologists are restricted to mechanisms that are purely naturalistic, even if there is a better explanation that is not entirely naturalistic.
To put it another way, imagine that some aspect of life was designed, perhaps the mechanisms of DNA and protein replication, for example. But, because of your a-priori commitment to naturalism, you had to look for how such a machine could have come about via random mutation and natural selection. If you have trouble thinking that the machinery of DNA was designed, then think about the computer you are reading this on. It WAS designed. We don't have to resort to forensics to determine that, we KNOW it was designed. But, how could you show scientifically that it was designed and did not come about naturalistically? That's the problem that the intelligent design proponents have.
So, what does the most credible skeptic, Dr. Michael Behe, of Lenski's work have to say? Read it here:
http://www.amazon.com/gp/blog/post/PLNK3U696N278Z93O
...we evolved from something and perhaps a so called rule of evolutionary order or screw up caused us to become what we are. Was God involved in the process? Yes, no, maybe? Maybe all three called the trinity!!!!
I've always been curious about how random mutations really are. Not from a creation / evolution perspective but from a generational perspective. Is there an n-generational component to mutation? Can a mutation in generation 1 deterministically cause a mutation in a later generation, say 101? This seems like a good data set for analysis.
http://www.answersingenesis.org/articles/aid/v2/n1/a-poke-in-the-eye
"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 example of evolution, this theme will keep coming up. The information was already there, it just needed to be flipped on or off or the genes reconfigured or recombined.
Selah.ca. Pause, and calmly think on that.
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.
Give this man (and his colleagues) the Nobel prize already! This is some freaking impressive science.
I think the only reason we say mutations are random is because we we really don't have a good understanding of how life actually works. I would be willing to bet that, if you got down to the brass tacks of it, that some mutations are actually more likely than others, simply because the various molecules that make up the proteins would be more likely to fold or split in one path in response to a stimulus, more than an other. In fact, I bet evolution is actually not only going to be found to be predictable, but managable, and that social and cultural definitions will effect physical evolution as much as any other. So, even though atheists might well successfully prove to most folks that there is no god, they will be stuck with the thorny fact that story of life is, to some degree, pre-ordained.
This is my sig.
People like to follow whoever gives them the most good news. When religion made people feel more comfortable with their place in a terrifying world, religion was popular. When science gave people the means the control the world, science became popular. When science started doling out all sorts of bad news - that people will have to have a lesser lifestyle due to environmental issues, that many medical breakthroughs are being undone by new virii and bacteria, and even once safe things are now unsafe, well, religion becomes more popular. It's really that simple.
This is my sig.
What we are really seeing is natural selection or an organism changing to better meet its environment.
That may be a form of evolution, but it actually does little to prove that a complex organism can change into another totally different complex organism.
That study is similar to observing the eating habits of a bunch of meat intolerant people who are locked in a slaughter house.
Some will die and some will adapt.
Does that mean God created us? No.
Does that mean God didn't create us? No.
If I read things right, it took over 40,000 generations to make a single functional change. To extrapolate, 40,000 human generations is approaching 1 million years. That is a very long time, however there are a lot of unknowns and the rate of mutations was not constant. If the rate was increased by a factor of 100 or better what environmental differences would be needed to make different rate of change? I know any answer will be speculation because we don't have a rich data set, but I am curious.
When this guy gets in front of a crowd for a press release or announcement, a pulsating brain slug hat would be a nice touch. And a deadpan monotone "there was no evolutionary leap as some speculated, now kindly don this protective hat so we may give you a tour" would make it perfect.
You have the right to remain sentient. If you give up the right to remain sentient, you will be elected to public office
It must take a certain amount of doublethink to be an American and to believe in the usefulness of science.
Given all the experimental evidence for evolution, it seems that either Jefferson or Feynman was wrong. It's either that God is not our "Creator", or that the scientific method is not useful in general, but only for some things. I think that most Americans solve the contradiction by putting either creationism or science in such a sandbox. A majority seem to put science in the sandbox and let creationism be the real truth.
Actually, I think this fallacy is the core elements of the problem in the U.S. People believe faith and science cannot coexist, so they reject one or the other.
In fact there is nothing about a belief in a creator which negates the idea of evolution. If a being created the entire universe, then this being also created the rules which govern it. Creating a world in which evolution will take place and certain kinds of life will emerge is simply one means of creating that life.
It is the fallacy that faith and science are incompatible which has led to this conflict. The faithful (some of them, I mean) mistakenly feel science undermines their belief, so they violently reject it... Or, more recently, seek to infiltrate and undermine it by pushing for acceptance of their philosophy as "science" within education - a campaign of propaganda... Fans of science (again, some of them) thus see faith as harmful and reject it in turn... But examination of the mechanism by which life develops does not negate the philosophical question of why this world exists - and belief in a creator does not invalidate the study of the means by which creation occurred.
Bow-ties are cool.
Sorry, they're saving the next Nobel Prize in Medicine for Obama...
Lawrence Person (lawrencepersonh@gmailh.com (remove all "h"s to mail)
http://www.lawrenceperson.com/
Quite coincidentally, I was just reading Dawkins' new book in which this very experiment was explained in some detail. This is pretty amazing for proving evolution by natural selection as a process involved in life all around us. Creationist history-deniers are pretty foolish if they actually deny the process of evolution as a fact of life, for it is scientific fact at this point. What could be debated is the origin of life, or maybe different processes by which evolution occurs, but no argument can be made that evolution doesn't actually happen.
Why the bloody hell is this tagged "badscience"?
Impressive. Microevolution has never been so successfully illustrated. I hope the day comes when we can try this with Macroevolution and put that to the test. *crosses fingers and hopes for a time dilation field*
They would be dead end only of they died before having offspring. Once they have had offspring, then they can die, or live forever until today, it does not matter. I can only imagine you took this "every fossil=dead end" from a creationist web site. To give you an analogy, once your grand parent gave birth to your parent, whether they continue to live or not, they were not a dead end : your parents lived, and gave birth to you. And you did not disappear if (sadly) your parents have died/or will die, chance is that you will survive your parents, and maybe have offspring of your own. It make no sense whatsoever to think all fossile we found were dead end.
C. Sagan : A demon haunted world:
http://www.amazon.com/gp/product/0345409469/
visit randi.org
In other words, every fossil was from a creature that was an evolutionary dead end.
Either I don't understand what you are saying - or you are wrong.
You and I are not dead ends - every creature between us and our bacterial forebears was an evolutionary success. The "aunts" and "uncles" that didn't reproduce are evolutionary dead ends - but that does mean their successful siblings were.
And there is nothing that says that once you reproduce you can't be fossilized. And on the flip side, you cannot say that those that were fossilized didn't reproduce...
Dinosaurs eggs are definitely evolutionary dead ends - but dinosaur adults are not (necessarily).
Genesis 1:32 And God typed
So let me get this right. They thought this was going to prove their theory. Things were clipping along fine, then things suddenly went random. That produced "counterintuitive results" that didn't match their theory. So rather than that proving the theory incorrect, it proved that this was "more complex" than previously realized.
Anyone with a little intelligence should struggle with evolution. There are 350 billion galaxies on one end of the complexity scale. There are hundreds of intricately complex systems within the human body. To believe this all occurred by random mutations passed on through natural selection would take more faith than religion.
I may have misunderstood the findings, but the rate that these bacteria evolve sounds an awful lot like data to support the theory of punctuated equilibrium. I would sure like to hear fellow /.'s opinions about this, rather than the same old creationist metadiscussion that we have every single time there's an article about evolution up.
You will note that none of the bacteria changed into a fish or anything else. This shows that micro-evolution can occur but so far no one has proof of macro-evolution.
Let the flames begin!
"E. Coli" is an arbitrary name that people gave to "those organisms with the following list of qualities..." If it becomes useful to give a different name for "the ones who can eat X" or "the ones who aren't killed by Y" or "the ones who behave like Z" then they'll get a new name. At what point they are a "new organism" is really a judgment call.
To put it another way, saying "the group of E. Coli that can eat X" is no more or less arbitrary a distinction as "the group of mammals that lay eggs." We could call every human a different species, because we all have unique DNA - and maybe that would be useful if there were clones. On the opposite end of the spectrum, we could divide the world into "makes its own food" and "eats other creatures" and not get any more specific than that. ("Run! It's a giant Eats-Other-Creatures!") It's all about what names are useful to us.
Not so. Organisms can change their mutation rate and type in response to their environment. There is even a word for it. That order arises from disorder is more than just a first-order effect, in particular for life systems sharing millions of generations of refinement.
I suppose one of these days I should sit down and spend a year studying evolutionary theory in all its various forms (eg. micro, macro) so I can properly debate these idiots instead of going on what I can remember from high school (which was awhile ago and the field has moved on). The problem is, it would be pointless. You can't have a debate on any topic with an authoritarian/fundamentalist because you can't have a debate with them at all - they simply don't have the tools. Insults aside and nevertheless, here goes...
.
...and some remarkably bad design decisions. What sane engineer would put the reproductive and excretory systems in the same pipe (I'm misquoting somebody)? Why don't humans have rotatable ears like cats? I want my tail back!!!
They thought this was going to prove their theory.
OK, which theory? All of evolutionary theory (your last paragraph implies that's your target)? Punctuated Equilibrium (note other discussion)? Survival of the fittest? Darwin's Finches?
Things were clipping along fine, then things suddenly went random.
Sounds like a working description of Punctuated Equilibrium as I (probably incorrectly) understand it.
So rather than that proving the theory incorrect, it proved that this was "more complex" than previously realized.
Here's what the article actually says...
Rather than a plodding equilibrium, even in a consistent environment, the interplay between these two kinds of genomic changes "is complex and can be counterintuitive,"
So rather than that proving the theory incorrect, it proved that this was "more complex" than previously realized.
No. It says that the overall theory is "complex and can be counterintuitive". So is General Relativity but I consider it pretty much a given - nuclear reactors work. The overall theory of "evolution" is a mainstay in biology - Darwin's theories were confirmed when genetics and DNA/RNA came along.
What you're doing is a "straw man". You have a mental concept you're calling "evolution", which you haven't even stated (but presumably is some variation on "plodding equilibrium" or other cast-by-the-wayside theory (is it??)), then proclaim that this particular experiment destroys your theory. Guess what? It does. That's straw man at its finest.
Anyone with a little intelligence should struggle with evolution.
ROFL!!!! Oh, stop it. Really!! An "appeal to intelligence"??? I would have thought you'd gone with "any idiot can see evolution is a crock".
There are hundreds of intricately complex systems within the human body.
I'll leave the complexity debate to better hands. Random mutation? May I remind you about the bright shiny thing in the big blue room? It's the ultimate random event generator. We're having one tonight (SOHO predicts a CME - watch for Northern Lights).
To believe this all occurred by random mutations passed on through natural selection would take more faith than religion.
It's not a matter of faith. It's a matter of what I'm going to base my decision-making on. Here's two examples.
It's flu shot season. My understanding of evolutionary theory (bad as it is) leads me to believe there's some nasty bugs out there (eg. H1N1) that mutate over time. That time is long enough that this season's flu shot will be relevant, but last year's might noy. I'm getting my shots, thank you very much.
There's also the whole issue of GM wheat. I don't know where those genes came from or what's been done to them. I'd like to sit through a few generations (its or mine) and see what happens. For all I know they could cause something that makes gluten issues pale by comparison.
--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.--
Yeah, and we are evolving fast that direction. So one day, maybe in our lifetime, a specimen might be caught 10' in height and weigh 900lbs. It's amazing what size a corn fed naturally selected human can become. Now, intelligence seems to be selected out during this process because of lack of breeding between smart people.
It was those damn aliens that did it all going back to the big bang even though you can't hear it.
It would be interesting to look at the types of Bacteriophages Virues in the mix. Bacteriophages Virues infect bacteria and change their DNA.
Some people think virus are the catalyst to evolution.
... is not my job.
Look, I'm not by any means a radical atheist - if you want to believe in God, you're welcome to, and I won't waste my time and yours by trying to change your mind. But statements like the above have an obvious logical problem: the existence of a magic man in the sky who created the entire universe out of nothing, and is variously attributed to have other "magical" powers, is an extraordinary claim. Anyone who makes a claim like this can't pass off the problem of proof to the skeptics - it's on you to convince US that God exists. If I were to claim that there was a pink unicorn in my backyard that commanded me to dance naked on top of the birdbath, you'd think I was nuts. But if I said "but you can't prove there's no pink unicorn"... you'd still think I was nuts. The point here is that you don't get to enter the argument assuming that God is real, and I have to disprove it.
... your claim that a magic man in the sky is extraordinary, and requires evidence. My claim that there is no such magic man does not. In other words, it's your job to prove that God exists, not mine to prove that he doesn't.
Actually, I surprised that there was so much beneficial change. Think back to the days in using Basic - ever write a program where you wrote a program that randomly POKE'd changes into the system? Were any of the changes beneficial to the program? Obviously, DNA is a lot more redundant than a BASIC program, and has repair mechanisms that would fix a lot of potentially lethal problems, but still - random changes in your operating program are generally going to be neutral, sometimes fatal, and more rarely, useful. This doesn't seem counterintuitive at all to me.
Thanks for clearing that up. I'll keep it in mind. Also, props to whoever modded me funny earlier. That said, there are certainly other examples of the same principle. The fact that HCl exists in our digestive system fits this category. I'm no med student, but from what I read on the back of "Anatomy for Dummies", there is a mucus membrane in the stomach that prevents the HCl from wreaking havoc in the rest of the body. A stomach with neither HCl nor mucus wouldn't be terribly useful, HCL with no mucus wouldn't last long, mucus with no HCL also would serve little purpose, until you have all three in the proper combination. Even at that it's not a once-and-out job, both parts require contant replenishing in order for them to provide an evolutionary advantage. As such, they require other pieces to support them, etc. Sure, you could correctly argue that the systems could have evolved in order such that everything would have remained dormant until everything functioned properly, but while that's a stretch at best with the digestive system, a dormant-until-fully-functional reproductive system is at odds with the concept of gradual evolution.
Additionally, I apologize for the lack of specificity earlier. I tend to lump "gradual-change-over-time" and "from-big-bang-to-2009AD" and refer to them intergangeably as evolution, which is indeed inaccurate. My comments regarding abiogenesis were in reference to the latter, not the former.
they didn't evolve into a substantially different organism.
...nobody went for the X-Men angle...I mean, c'mon, is this /. or what?
Spontaneous. Unexplained. Accelerated. Mutation. Rate.
So when can I expect my grandkids to start shooting fireballs out their bums?
"I love animals! Some are cute, others are tasty, what's not to like?" - Betsy Schroeder, Jeopardy contestant
Pffft... "direct, reproducible evidence of a genetic mutation with functional consequences for an organism" - wow you mean like the white and black moths? Umm big deal? I can't believe this has in the title "Observing Evolution" and how so many nerds here are posting "aha more proof of evolution" comments... Keep bombarding those thousands of generations with gamma rays folks... the likes of slashdot will help boost your self belief and even funding perhaps...
The fossil record documents the evolution of several species (whales, horses, and us of course).
IANAL but write like a drunk one.