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Observing Evolution Over 40,000 Generations

kdawson posted more than 4 years ago | from the every-day-in-every-way dept.

Biotech 461

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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461 comments

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fuck that (5, Funny)

Anonymous Coward | more than 4 years ago | (#29786921)

god did it

Re:fuck that (-1, Offtopic)

Anonymous Coward | more than 4 years ago | (#29786947)

I know this place is full of iphone loving apple suckers. But it seems it's also full of complete retards.

Re:fuck that (5, Insightful)

zero.kalvin (1231372) | more than 4 years ago | (#29787003)

god did it

Which one of them?

Re:fuck that (0)

Anonymous Coward | more than 4 years ago | (#29787033)

Every one... of them

Re:fuck that (0, Offtopic)

noundi (1044080) | more than 4 years ago | (#29787075)

god did it

Haha I thought it was funny.

Re:fuck that (4, Funny)

causality (777677) | more than 4 years ago | (#29787331)

god did it

Haha I thought it was funny.

It reminded me of Bill Hicks, the master of the use of comedy for the opening of minds.

"[The Earth being] 12,000 years old. I asked the guy, c'mon man, dinosaur fossils, what's the deal? He goes, 'God put those here to test our faith'. I think God put you here to test MY faith, dude. I think I figured this out. That's what this guy said -- does that bother anyone here, the idea that GGOODD might be fuckin' with our heads? Anyone have trouble sleeping restfully with that thought in their head? God's runnin' around, burying fossils, 'huh huh huh, we'll see who believes in me now! Huh huh, I'm a prankster God, I am killing me ha ha ha". You die and go before St. Peter, he says 'Did you believe in dinosaurs?' Well yeah, there were fossils everywhere! 'What are you, an idiot, God was fuckin' with you! Giant flyin' lizards, you moron, that's one of God's EASIEST jokes!' It seemed so plausible, aaaahhhhhh!"

Summon Bevets! (0)

Anonymous Coward | more than 4 years ago | (#29787377)

..wait, looks like he is already here!

Re:Summon Bevets! (1)

captjc (453680) | more than 4 years ago | (#29787583)

Fark, it's a trap

Re:fuck that (0)

Anonymous Coward | more than 4 years ago | (#29787669)

Yeah, totally man.

There is absolutely no way to explain how that random mutation happened that suddenly increased the number of mutations.
Damn scientists always lying to us! Why do they deny the power of God!
All hail his noodily appendages.

X MEN?? (0)

Anonymous Coward | more than 4 years ago | (#29787731)

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'

hmmm (1)

zero.kalvin (1231372) | more than 4 years ago | (#29786937)

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.

Re:hmmm (0)

Anonymous Coward | more than 4 years ago | (#29786993)

And there is still idiots who believe evolution is wrong

Not really... they'll just say this is an example of "micro-evolution". (even though there's no such thing)

Re:hmmm (-1, Troll)

Anonymous Coward | more than 4 years ago | (#29787061)

No such thing? Are you retarded or willfully ignorant: http://www.talkorigins.org/faqs/macroevolution.html

If the bacterium are still classifiable as E.Coli. then this is microevolution and doesn't prove anything everyone didn't already know; otherwise it is interesting.

Re:hmmm (4, Insightful)

CyberBill (526285) | more than 4 years ago | (#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 (-1, Flamebait)

ArcherB (796902) | more than 4 years ago | (#29787863)

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).

And the color white was a "defining characteristic" of swans until they found a black one.

Look, I believe in evolution, but never has there been found a parent species to something alive today. In other words, scientists can not point at any two distinct species, living or extinct, plant or animal, and say that this species evolved directly from that one. Sure, they can say that this dog is bigger or a different than it's ancestors, but it's still a dog. Show me the fossils of the prehistoric rodent that evolved directly to today's rabbit or rat and the debate will end.

Re:hmmm (2, Informative)

Anonymous Coward | more than 4 years ago | (#29787771)

No such thing? Are you retarded or willfully ignorant: http://www.talkorigins.org/faqs/macroevolution.html

The only difference between macro- and micro- evolution is the time-line.

Each little step/mutation is EVOLUTION, to split the changes into "micro" and "macro" is to diminish the meaning.

You could have dogs evolve into whales, but if you looked at each mutation individually, you could dismiss it as "micro-evolution".

Re:hmmm (-1, Troll)

black3d (1648913) | more than 4 years ago | (#29787011)

While I don't believe in creation, mutations occuring in 40,000 generations (one mutation every 63 generations) of inbred bateria is hardly proof of evolution.

Re:hmmm (2, Insightful)

zach_the_lizard (1317619) | more than 4 years ago | (#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 (2)

black3d (1648913) | more than 4 years ago | (#29787081)

Yes, I was referring primarily to the absence of an external population with which to mediate the process. Allow me to address it from another perspective which is more difficult to answer - in the wild, would the group go through a smaller or greater number of mutations?

Re:hmmm (1)

jack2000 (1178961) | more than 4 years ago | (#29787219)

That would depend on the types and quantity of competition ...

Re:hmmm (1)

noundi (1044080) | more than 4 years ago | (#29787101)

While I don't believe in creation, mutations occuring in 40,000 generations (one mutation every 63 generations) of inbred bateria is hardly proof of evolution.

Well I understand your point. But then what would you suggest is more likely?

Re:hmmm (0)

black3d (1648913) | more than 4 years ago | (#29787211)

Simply, I'd like to see more favorable mutations rather than random ones. The results of this study thus far are that around 10 mutations per population turned out to be advantageous, although randomly spawned. To me, 10 out of 100+ mutations (most of which were neutral or harmful) doesn't seem like a great number. The study shows that the populations are becoming more damaged over time, rather than stronger.

I'd *like to* see an evolutionary study where the majority of binding mutations are advantageous rather than harmful.

Re:hmmm (5, Informative)

stei7766 (1359091) | more than 4 years ago | (#29787319)

ALL mutations are random. If they are advantageous, great, than it is likely that they will be passed along.

Re:hmmm (0)

black3d (1648913) | more than 4 years ago | (#29787347)

Indeed. However when more harmful mutations are being passed along than favorable, do you still call it evolution?

Re:hmmm (2, Insightful)

caerwyn (38056) | more than 4 years ago | (#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?

Re:hmmm (1, Informative)

oldhack (1037484) | more than 4 years ago | (#29787517)

You idiot. More "harmful" mutations would get passed down less, because they are harmful to propagation.

Re:hmmm (0)

Anonymous Coward | more than 4 years ago | (#29787625)

Indeed. However when more harmful mutations are being passed along than favorable, do you still call it evolution?

Absolutely. You seem to misunderstand the concept. It's not magic. For a bad thing to not be passed along, it has to be bad enough to keep the organism from reproducing. Also, the deciding factor for survival can change over time. What may be beneficial or harmful at one point may not necessarily be beneficial or harmful at another point.

Evolution only favors those which can reproduce the most. For instance, in a time of surplus, if a family is prone to having lots of kids, they may very well be able to support them all until they are ready to leave on their own. Over several generations, the amount of descendants will grow exponentially. Families that have fewer kids grow much more slowly, but due to the surplus manage to survive just fine. In that period of time, being prone to having lots of kids is favored, and being prone to few kids is a negative trait.

Now lets say there is a time of shortage, suddenly there is not enough to go around. Families that had grown kids before the shortage started may still be able to bring in enough to support everyone by putting them to work. However, families with many young children may spread their resources too thin, causing them to starve to death (and for whatever reason, no on was willing to share with them). However, families that are prone to having fewer kids can more easily support the small amount of children. Being prone to few kids has now become a positive trait, because the family is less likely to die of starvation.

Re:hmmm (3, Informative)

ZombieWomble (893157) | more than 4 years ago | (#29787353)

These bacteria were probably exposed to little or no selection pressure - this means that "beneficial" or "not beneficial" mutations are not selected for, as all bacteria are allowed to multiply. As a result, only catastrophically poor mutations will be selected out.

Evolution is a two-step process - the first part is the production of mutations, which is a random process (and, given how finely balanced organisms are, the majority of these random events will probably be negative, on balance). The second part is selection - if there is genuine competition between these strains, then the beneficial mutations will be selected, so the fact that they are relatively rare will have little effect on their eventual domination of the population.

Re:hmmm (1)

dvice_null (981029) | more than 4 years ago | (#29787433)

> The study shows that the populations are becoming more damaged over time, rather than stronger.

I think that the study shows that when there is no competition, mutations become more likely.

Now imagine this: An island, no-one lives there, except rabbits. No competition, except from other members of the same population. Now, based on evolution theory, those rabbits that can eat most of the grass, will succeed. But even more successful would be a "rabbit" which would eat something else, what other rabbits can't eat. E.g. other rabbits, or fish or insects.

So in this kind of an environment, it would be best for the genes, to mutate rapidly.

But the question is: Is the mutation speed random, or can the population/genes notice when the situation is more favorable for rapid mutation and when it is not? E.g. does the amount of stress hormones reveal this?

Re:hmmm (0)

Anonymous Coward | more than 4 years ago | (#29787437)

I see your point, but you're significantly missing the point of evolution.

Negative mutations don't all stick around. If they're really bad, the bacterium will just die. If they're negative, but not fatal, the affected bacteria will get out-competed quite fast, in an environment as competitive as the one we're looking at.

Positive changes increase the chance a given bacterium will do well (Imagine if one single cell is the only one that can use the only food source that's left - it'll dominate in short order).

These two effects downplay negative effects and emphasise the good ones. It's not impossible to imagine the net result being that positive effects accumulate faster than negative ones - and indeed, that's what seems to be happening.

Re:hmmm (0)

Anonymous Coward | more than 4 years ago | (#29787465)

Simply, I'd like to see more favorable mutations rather than random ones.

You may have misunderstood this evolution thing, or maybe said something you didn't mean to say...

Re:hmmm (4, Insightful)

arose (644256) | more than 4 years ago | (#29787105)

inbred bateria

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

Re:hmmm (1)

black3d (1648913) | more than 4 years ago | (#29787163)

Isolation is the bacterial form of inbreeding. Without external competition increasing the available gene pool for reproduction (asexual in this case), mutations are going to occur no matter what. From the study - "populations developed defects in their ability to repair DNA, greatly increasing the rate of additional mutations in those strains". The emphasis is, this would NOT have occured in the wild, in mixed populations.

Re:hmmm (1)

caerwyn (38056) | more than 4 years ago | (#29787541)

Err. No.

Any given mutation would have the same chance of occurring in the wild. It may be more likely that said mutations would result in their carriers being outcompeted in the wild, but that does not in any way shape or form indicate that such mutations would not appear (and potentially persist for a period of time) in the wild.

Re:hmmm (2, Insightful)

wizardforce (1005805) | more than 4 years ago | (#29787279)

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

Re:hmmm (2)

black3d (1648913) | more than 4 years ago | (#29787333)

Indeed evolution is. However, the individual I was quoting suggested that anyone was an idiot who didn't fully believe in evolution purely on the basis of a controlled group of bacteria, forced to undergo mutation through lack of natural competition, in a controlled environment. I'm not arguing against evolution or the results of the experiment, I'm arguing against parent who couldn't even be bothered to read far enough to find out what the mutations were or which what percentage of fixated mutations were beneficial or anything.

Point is - the parent to my reply is just as short-sighted as those creationists he seeks to ridicule. He doesn't actually care for proof, didn't bother reading article or study results. In other words - he's just as idiotic as those he calls such.

Re:hmmm (1)

wizardforce (1005805) | more than 4 years ago | (#29787495)

suggested that anyone was an idiot who didn't fully believe in evolution purely on the basis of a controlled group of bacteria,

That isn't quite true. The individual that you responded to did not suggest that our evidence for evolution was solely this experiment. That would be extraordinarily ignorant. We have in fact enough evidence of evolution that the books written on the subject alone would crush any creationist standing underneath their shear mass.

Re:hmmm (1)

SpinyNorman (33776) | more than 4 years ago | (#29787405)

Huh?

Genetic mutations are by definition evolution.

Maybe what you meant was that it's not proof of what creationists like to term "macro evolution" (a scientifically meaningless term which I gather roughly means evolution of new species).

The only functionally useful definition of new species is ability to interbreed which make me wonder how you are guageing that in a species (ecoli) that predominantly reproduces asexually!

I wonder if the starting and ending strains were unable to reproduce by conjugation you would then accept them as separate species? I wonder are you at all impressed by the rather trivial changes in our lineage over the last 250,000 generations (5 million years)?

http://bioweb.uwlax.edu/bio203/s2008/moder_just/reproduction.htm [uwlax.edu]

Re:hmmm (-1, Troll)

Anonymous Coward | more than 4 years ago | (#29787291)

And there is still idiots who fucking suck at grammar too aren't there...

Re:hmmm (0)

Anonymous Coward | more than 4 years ago | (#29787443)

But here's the real question.... did any of the mutations ever result in more information being encoded into the structure of the virus? My understanding is that such a mutation has yet to be ever directly observed... that is, we can only infer that it's even possible in nature by pre-assuming that Darwinian evolution is actually completely correct.

I'm not saying the theory of evolution is totally bogus, nor that it's impossible for more information to ever come from less, but the likelihood of it happening is certainly unlikely to the extreme, and I wouldn't be at all surprised if even over the lifetime of the universe (which is pretty damn long, but still a finite age), the likelihood is still not very appreciable when it comes to the probability of forming intelligent life.

So in the end, I guess we're just really damn lucky. That luck isn't something that the theory evolution explains particularly well, which I think may be why some people who would consider themselves to have a scientific outlook have difficulties with the theory.

Re:hmmm (2, Informative)

caerwyn (38056) | more than 4 years ago | (#29787577)

You missed the evolution of the ability to metabolize citric acid.

There's no luck involved here- there's just a mindbogglingly high number of mutations and tests of those mutations over the course of history. You say "even over the lifetime of the universe", but it's unclear to me that you really understand just how large a number of generations there have been even since the rise of life on Earth, let alone the entire span of the universe. That's a lot of individuals, a lot of generations, a *lot* of mutations, and therefore an enormous well of opportunities for change.

Creationists response: (4, Funny)

adpe (805723) | more than 4 years ago | (#29786941)

653 mutations? 1305 missing gaps! Proof of god! Hallelulja!

Re:Creationists response: (4, Informative)

Idiomatick (976696) | more than 4 years ago | (#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.

Re:Creationists response: (5, Insightful)

noundi (1044080) | more than 4 years ago | (#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:Creationists response: (1)

Idiomatick (976696) | more than 4 years ago | (#29787413)

More acceptable in the 1600s in a country where religion controlled education system. The US is much better educated :/

Re:Creationists response: (0)

Anonymous Coward | more than 4 years ago | (#29787641)

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.

Well, that is an incredible piece of art though.

Re:Creationists response: (3, Insightful)

EdIII (1114411) | more than 4 years ago | (#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.

Re:Creationists response: (0)

Anonymous Coward | more than 4 years ago | (#29787095)

Or even better: The Darwinian's respsone:
Organisms are dynamic! Proof there is no God!

Re:Creationists response: (0)

Anonymous Coward | more than 4 years ago | (#29787153)

I played that video game. I don't recall the Darwinian's saying anything like that.

Re:Creationists response: (1)

adpe (805723) | more than 4 years ago | (#29787229)

Well, no. That's exactly the difference between us. We don't draw illogical conclusions. We conclude that evolution is true, that's it. There's no mention of god anywhere. Theists see god everywhere and immideately consider it proof.

Re:Creationists response: (1, Funny)

Anonymous Coward | more than 4 years ago | (#29787441)

No, the difference is that 'Theist' ( with exception of course ) open their heart to all things, without prejudice, without conclusion. They feel God's influence( because they are humble enough to accept it ), and don't draw simple conclusions about their reality. Those that only believe in what they can 'prove' lack imagination and are the more close minded of the two.

Re:Creationists response: (1, Flamebait)

caerwyn (38056) | more than 4 years ago | (#29787589)

No, the difference is that the Theist makes shit up.

Everyone else relies on this little thing called logic to understand reality, rather than making up fairy tales.

Re:Creationists response: (4, Informative)

Yvanhoe (564877) | more than 4 years ago | (#29787329)

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]

Re:Creationists response: (-1, Troll)

Nigel No Mates (1659303) | more than 4 years ago | (#29787553)

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! Mutations almost always reusult in a REDUCTION of information therefore NO NEW SPECIES every results from adaptation or natural selection although new abilities often result.An ecoli bacteria will ALWAYS be a ecoli bacteria until information has been exhausted to the degree that it can no longer be sustained. (I would call that Devolution if anything!By the way, evolutionist don't own the term 'Natural Selection' it was around long before Darwin and can be explained easily within the creationist view.)

goodbye creationists (0)

Anonymous Coward | more than 4 years ago | (#29786945)

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.

Re:goodbye creationists (2, Informative)

Dracos (107777) | more than 4 years ago | (#29787009)

Not yet.

The creationists will blindly and steadfastly cling to their mysticism-based pseudoscience until two chimps mate and produce a homo sapiens offspring.

Which of course is not how evolution works.

Re:goodbye creationists (-1, Flamebait)

hierofalcon (1233282) | more than 4 years ago | (#29787067)

Not at all. We will simply say that it is still e-coli. Marginally different, yes, but still e-coli. When he turns it into a buffalo, he'll have something.

Re:goodbye creationists (1)

odourpreventer (898853) | more than 4 years ago | (#29787477)

> When he turns it into a buffalo, he'll have something.

Wow, ignorant and condescending. Less bible studies and more high school biology for you, I think.

Re:goodbye creationists (0, Troll)

hierofalcon (1233282) | more than 4 years ago | (#29787753)

Sorry, the buffalo comment was not necessary - but was in the slashdot tradition and just as wild as the other comments directed towards us creationists around it.

The fact remains that after 40,000 generations, what the scientist has is a marginally more efficient strain of E. coli than he started with. He can track all the mutations to see how it has changed. He can see how and when those changes occurred - which is indeed fascinating, but at the end, he still has an E. coli. His very statements were that the later changes were not as drastic as the first which leads away from an evolution argument.

If he is making other claims, then the linked abstracts don't make that clear.

I'd say it was a great study in the work of natural selection, but a weak study in evolution until it crosses the border into some other definitely recognizable bacteria. High school biology was a long time ago - I let my wife handle the micro-biology today - she has a degree in it.

Someone needs to tag this "Inbreeding".. (2, Insightful)

black3d (1648913) | more than 4 years ago | (#29786979)

and consider to a cautionary tale.

Re:Someone needs to tag this "Inbreeding".. (0)

pclminion (145572) | more than 4 years ago | (#29787015)

What the hell does inbreeding have to do with MUTATION rate?

Re:Someone needs to tag this "Inbreeding".. (2, Informative)

black3d (1648913) | more than 4 years ago | (#29787039)

Is that are joke or are you intentionally dense? http://en.wikipedia.org/wiki/Inbreeding [wikipedia.org]

"Inbreeding has a variety of consequences. Allele exposure can cause genes to be expressed that are not otherwise expressed. This fact, combined with the fact that most mutations are recessive may indicate that inbreeding drives evolution. Speciation, a key process in evolution, depends on reproductive barriers, a necessary feature of which is inbreeding."

The mutation process here is driven by inbreeding and keeping the population isolated.

Re:Someone needs to tag this "Inbreeding".. (1)

Lando242 (1322757) | more than 4 years ago | (#29787461)

I don't know how something that doesn't have sex can inbreed, care to explain? They reproduce asexually, its kind of like natures cloning (big oversimplification, I know). Even so, if the initial population is large and diverse enough (and they "bred", which E. Coli does not) inbreeding wouldn't be an issue. Not like its hard to fit a couple trillion bacteria anyplace.

Re:Someone needs to tag this "Inbreeding".. (1)

arose (644256) | more than 4 years ago | (#29787119)

More importantly, what does inbreeding have to do with bacteria?

Re:Someone needs to tag this "Inbreeding".. (1)

black3d (1648913) | more than 4 years ago | (#29787237)

Isolation is the asexual bacterias equivalent of inbreeding. Which is why these same mutation rates are not seen in the wild. But you're right - I should use the term "Inhibited Reproductive Variety" instead.

Re:Someone needs to tag this "Inbreeding".. (0)

Anonymous Coward | more than 4 years ago | (#29787795)

If you knew anything about bacteria, you would know they do share DNA even if they are not into the whole "let's become one" thing.
In this case it would appear they did, as "random mutations with no apparent effect" wouldn't have selected the crazy mutation lovers over the conservatives.
Of course, the researchers might have just failed to discover that E. Coli has a mechanism to go into mutation orgy mode in a controlled way when the need arises.

uhh? (1, Interesting)

blhack (921171) | more than 4 years ago | (#29787013)

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? (0)

Anonymous Coward | more than 4 years ago | (#29787077)

Don't forget that even for bacterium like this, just over 96% of its DNA is useless. It's present, but changes have no observable effect.

So there can be billions of differences, but none of them affect the DNA in a way that can be considered a "mutation" (that is, a DNA change that produces an observable change in the structure or behavior of the host).

This is what makes the analysis of DNA so difficult and time consuming. There's a whole lot of chaff to thresh from the grains.

Re:uhh? (0)

Anonymous Coward | more than 4 years ago | (#29787239)

Mutation is not: "a DNA change that produces an observable change in the structure or behavior of the host."

http://en.wikipedia.org/wiki/Mutation [wikipedia.org]

Re:uhh? (0)

Anonymous Coward | more than 4 years ago | (#29787309)

Sorry, but that's actually entirely wrong.
One of the significant differences between bacterial and eucaryotic DNA is that the bacteria tend to have a much higher gene density, and no introns. If I'm not mistaken, a typical amount of noncoding DNA in a bacterial genome is closer to 15% than 95%.

Re:uhh? (4, Informative)

wizardforce (1005805) | more than 4 years ago | (#29787151)

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.

Re:uhh? (4, Informative)

Trepidity (597) | more than 4 years ago | (#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:uhh? (1, Insightful)

noundi (1044080) | more than 4 years ago | (#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:uhh? (0)

Anonymous Coward | more than 4 years ago | (#29787609)

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.

(Too lazy to log in) Comply with religion? Really? It's probably a good idea, actually. I mean, hell, we wouldn't want scientific work to offend anyone. Gosh, I mean, what if present social and/or scientific paradigms were challenged? We can't have that now, can we? Gotta keep that pesky science chugging along in parallel to the [current (dominant)((whatever that happens to be))] religious ideology...wouldn't want to ruffle anybody's feathers, now would we?

Re:uhh? (1)

timeOday (582209) | more than 4 years ago | (#29787197)

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 relatedness of different species and the time frames involved if the rate of mutation were constant. But it isn't, so, too bad. I think this was already pretty well accepted from the fossil record, but I guess directly observing it under controlled conditions is a nice confirmation.

Re:uhh? (3, Informative)

ceoyoyo (59147) | more than 4 years ago | (#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:uhh? (2, Insightful)

Sparky McGruff (747313) | more than 4 years ago | (#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:uhh? (0)

Anonymous Coward | more than 4 years ago | (#29787661)

A diff is useful. It's more useful if:

4) you figure out what the diff does.

E. coli 40k (0)

Anonymous Coward | more than 4 years ago | (#29787165)

in the grim darkness of a petri dish, there is only bacteria?

Re:E. coli 40k (1)

jack2000 (1178961) | more than 4 years ago | (#29787275)

Burn the heretical citrate, purge the mutant strain!

Re:E. coli 40k (0)

Anonymous Coward | more than 4 years ago | (#29787339)

For the Amoeba!

Why would they mutate? (0)

Anonymous Coward | more than 4 years ago | (#29787259)

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?

Re:Why would they mutate? (1)

quantaman (517394) | more than 4 years ago | (#29787489)

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?

There's two reasons.

First it is a somewhat different environment than they evolved in. Particularly if this was the same bacteria as the previous article I think they were also exposed to a new nutrient (citrate?) that they learned to metabolize. This trait evolving could be the reason that their mutation rate jumped up as they adapted to their new condition.

Second, even if there wasn't any adaptive pressure there's still evolutionary drift as unimportant changes show up and propagate through sheer chance.

Re:Why would they mutate? (1, Insightful)

Anonymous Coward | more than 4 years ago | (#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. :)

Yes, that Lenski (4, Interesting)

JoshuaZ (1134087) | more than 4 years ago | (#29787277)

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] .

Re:Yes, that Lenski (3, Informative)

Foobar of Borg (690622) | more than 4 years ago | (#29787397)

Conservapedia is down right now, but here is the link to the Conservapedia-Lenski dialog [conservapedia.com] . His first response is very polite, but when Schafly pigheadedly and insultingly keeps at him, Lenski rips him a new asshole with this powerful thing called "facts" (which naturally have a liberal bias). The exchange is on Conservapedia since Lenski basically threatened to put it all over the web if they didn't include the entire exchange unedited.

Re:Yes, that Lenski (1)

black3d (1648913) | more than 4 years ago | (#29787455)

LOL - I love all his PPPPPS's at the end of the letter. A very good article, thanks for linking this. :)

yawn? wtf? (0)

Anonymous Coward | more than 4 years ago | (#29787415)

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?

Evolutive pressure? (1)

cowboy76Spain (815442) | more than 4 years ago | (#29787493)

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?

Re:Evolutive pressure? (1)

Tubal-Cain (1289912) | more than 4 years ago | (#29787601)

Did the mutations change the fenotype (the external aspect/behaviour) to something more adapted?

They can now digest citric acid.

Re:Evolutive pressure? (1)

caluml (551744) | more than 4 years ago | (#29787821)

Your signature is amusingly apt for this story:

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

Re:Evolutive pressure? (2, Informative)

Machupo (59568) | more than 4 years ago | (#29787877)

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 revived from frozen stocks by growth overnight in LB medium. After dilution and 24 h of re-growth in Davis minimal medium supplemented with 25 mg l-1 glucose, we inoculated 24 replicate 10-ml cultures of Davis minimal medium with 250 mg l-1 glucose with 100–1,000 cells. After 24 h of growth to stationary phase, these cultures were concentrated by centrifugation and plated on LB agar containing 20 mug ml-1 nalidixic acid."

A very interesting thought, (2, Interesting)

Hurricane78 (562437) | more than 4 years ago | (#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...

Missing the Awesomeness (0)

Anonymous Coward | more than 4 years ago | (#29787629)

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.

Not Convincing to Public (2, Interesting)

Tablizer (95088) | more than 4 years ago | (#29787749)

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 :-)
   

Significance? (1)

Machupo (59568) | more than 4 years ago | (#29787819)

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.

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