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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
653 mutations? 1305 missing gaps! Proof of god! Hallelulja!
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
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.
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.
SSC
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?
"The true measure of a person is how they act when they know they won't get caught." - DSRilk
I don't think you shouldn't participate in any discussions about evolution until you acquire some elementary biology knowledge.
Analogies don't equal equalities, they are merely somewhat analogous.
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.
Sigs are too short to say anything truly profound so read the above post instead.
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.
10 PRINT CHR$(205.5+RND(1)); : GOTO 10
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).
-Bill
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.
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.
Nonsense. Evolution is nothing more than organisms adapting genetically to their environment. These bacteria are doing exactly that.
Sigs are too short to say anything truly profound so read the above post instead.
ALL mutations are random. If they are advantageous, great, than it is likely that they will be passed along.
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.
"The true measure of a person is how they act when they know they won't get caught." - DSRilk
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.
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.
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?
The ringing of the division bell has begun... -PF
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.
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.
The ringing of the division bell has begun... -PF
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.
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".
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."
*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.
"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."
Of course not. That's kind of like pointing to two leaves on a tree and saying one leaf came from the other. It doesn't work that way. They are both on the terminations of the branches, and the node where they branched into two is in the past. Ordinarily, the common ancestor is long dead. The nice thing with these E. coli is that the researchers kept a portion of the ancestral population intact, and the specimens are clones, so while not the actual ancestor of the lineage that kept going, they are genetically identical.
There are plenty of fossils that are close to branch points, and as more fossils are found there are still plenty of gaps left, as there always will be, but the changes necessary to span those gaps get smaller and smaller as the sampling improves. For example, Anchiornis was just discovered in the last couple of years, and a new specimen described a few weeks ago. Dinosaur? Bird? It's rather arbitrary to decide. It's either a wing-clawed, long-tailed, toothed bird like no modern bird, or it is a flight-feathered, gliding dinosaur. As if they were the leaves on a tree, birds and reptiles look distinct now, but follow the branches back far enough and they get mighty blurred together. This is hardly an isolated example.
There are fish that look so tetrapod-like that when the skull was initially found separately they thought it was a tetrapod. Then workers found the rest of the body and realized it was a fish. There are other tetrapod-like fish, such as Tiktaalik . But go back 100 years and these species weren't known at all.
I really don't know what more skeptics are expecting. Perfection? It won't happen. It's not like we'll ever have every twig on the tree. Good fossils are rare. But the statistical pattern with increased sampling is quite robust.
You know, it only took me 10 seconds to google for an example, you could have tried a bit harder. "speciation observed in salamanders":
http://www.santarosa.edu/lifesciences2/ensatina2.htm
A species observed to lose reproductive compatibility between populations separated by geographic barriers.
Not true. You are posing the missing link myth. There are in fact good lines of fossils showing evolutionary trends in species for many different species in the fossil record.
While no we do not and never will have a direct individual by individual line of fossils simply because most creatures that lived on this earth were eaten, rotted and NOT fossilized. Fossilization also did not occur uniformly through all species or stages of evolution, it was collection of many random processes, and thus one would expect gaps in the fossil record. Also most fossils on earth have not been dug up and analyzed by scientists, we only have a small fraction of the record out there and already we can see clear patterns of what is loosely called evolutionary trends.
Also just because one species "evolves" from another doesn't mean that the so-called "parent" species stops evolving.
If you really want an example of diverging species look at the Great Dane and Chihuahua or nearly any other domestic species, such as the cow, that has shown great variations between breeds. In the former example mating is nearly impossible. Don't like that? What about Horses/Donkeys? No we don't have records old enough to historically prove it, but the evidence is there.
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.
And the black swan (Cygnus atratus) is, in fact, a separate species. So even by your own argument-by-analogy, you've agreed that the new bacteria should also be considered a new species, and thus evolution has been observed to occur.
Look, I believe in evolution, but never has there been found a parent species to something alive today.
My grandparents have all passed away, but I'm pretty sure I'm still related to my cousins.
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.
We've had plenty of genetic evidence from preserved material to say exactly that. But the big news about Lenski's experiment is that not only do we have living examples of a species which evolved directly from another species, and not only do we have living examples of that original species, but the scientists actually watched it happen.
Show me the fossils of the prehistoric rodent that evolved directly to today's rabbit or rat and the debate will end.
Rodent ancestors appear is the fossil record around the late Paleocene. We may not be 100% sure the actual individual fossils we have are direct ancestors of currently living rodents; they may be, say, great-great-...-great-uncle rather than great-great-...grandparent. But that doesn't matter since the existence of the latter is logically implied by the existence of the former. The debate, among anyone who actually knows what they are talking about, has been over for a very long time. The only ones claiming otherwise are the creationists.
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.
This is not entirely true, E. Coli is known to be able to metabolise glucose. The bacteria were "grown" in a solution that included glucose as it's main component. There were also many populations of the bacteria that were being evolved seperately (they NEVER mixed). Suddenly, in one population, a bacteria emerged that could metabolise citrate. This gave that bacteria a massive advantage, because it could now consume two types of food and it had no competition for the citrate (unlike glucose, which all the other bacteria could consume as well).
This also allowed the total population in that group to explode (there's now more food in total, glucose + citrate).
Another cool thing is that this smashes the "Irreducible Complexity" argument. The ability to metabolise citrate is developed by two separate mutations, which, on their own achieve nothing. Some of the populations developed the first mutation and some developed the second one, but none of them had previously developed both. This shows that the "preliminary" mutations were not harmful to the bacteria, so they just "hung around" until one of them was lucky enough to get the second mutation too.
Anyway, look up Lenski's work, I'm sure his papers (and those of his students/colleagues) are better at explaining it all than me...
1178161 is prime...
Give this man (and his colleagues) the Nobel prize already! This is some freaking impressive science.
Perhaps you should define as to what you think evolution is, before you say you don't see any.
I thought I did. E. Coli still remainds E. Coli. Perhaps I should have said I don't see anything significant about this study. I have no problem accepting that genetic mutations occur. However, it seems that this study is inferring that this is the first witnessed proof for evolution. I would be interested at the lead researchers definition of evolution.
It's a fair request that you ask. I looked it up. Good ol' Google:
http://www.talkorigins.org/faqs/evolution-definition.html
I looked at other pages as well but it seems the most standard definition I could find was on the above page and read:
"Evolution is a process that results in heritable changes in a population spread over many generations."
Also reading further into other articles about this study it would seem that Richard Lenski and many other evolutionists hold this study as a holy grail (in comparison to other studies before it) in the debate of creation vs. evolution. If all evolution is defined as being is the heritable change in a population spread over many generations then why would there be any debate at all?
Perhaps the debate is mearly by what process did life evolve. If this study holds any significance in that debate I am not seeing one. If this study is of significance in the study of mutation then I suggest there are more clear and abundant examples elsewhere.
20 years of study for what?
I digress a bit from the original request of a definition but I believe you should now understand the point I am making.
If you logically think about what you said the answer would become apparent. For a common ancestor to be both in its original form as a bookmark for when a species split off AND still alive today it would mean that the niche it occupies (and has adapted to) has not changed since whenever the species split off. This is very unlikely as the co-evolution between itself and the environment (including new creatures that come into play) is quite rapid (on an evolutionary time-scale). There are always new opportunities to exploit - and species that don't go extinct.
Your statement that every fossil is from an evolutionary dead end is wrong however - as there are plenty of 'missing-link' fossils that are found that have a (very likely) lineage (as a species rather than individuals) to current species.
Control is an illusion, order our comforting lie. From chaos, through chaos, into chaos we fly
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/
The standard method of identification of bacterial species is to determine what compounds they can eat. E. coli is defined as not being able to eat citrate. They evolved something from E. coli which can eat citrate. The new bacteria is not E. coli by the standard method of identification.
But I guess you're right... it's still just some random nigh-invisible animalcule that nobody really cares about. I mean it didn't turn into a dolphin, did it?
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.
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!
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.
To use an analogy, let's compare the evidence to a murder trial:
Wait, can you put that in a filesystem developer analogy?
Harald
*kisses karma goodbye*
My issue in general here (yes, I am a creationist...I'm a delusional moron, I know) is that while 40,000 generations of E. Coli did show some form of usable mutation, it doesn't account for many other inconsistencies with evolution as the be-all and end-all for how we got where we were. My biggest issue is that, to my knowledge, there has never been a documented observance of life coming from non-life.
But the one more relevant to your point about this disproving the concept of irreducible complexity has problems of its own. Yes, there was indeed an evolution of the bacteria being able to process citrate. However, that's a smaller step than, say, if E. Coli bacteria started to be able to perform photosynthesis, or vice versa. There are other extremely wide gaps (asexual reproduction to sexual reproduction, live birth vs. egg laying, visual and audible processing, etc. etc.) that are still a challenge for gradual, incremental evolution to explain. The most immediately memorable example of this for me is the bombardier beetle. The system it's got in place to ward off predators relies on a series of chemicals and an expulsion system that incremental evolution can't account for. If any of those pieces evolved improperly, there would be no fossil record because the beetle would have a Fourth-of-July special internally before it ever got to reproduce.
I'm not one of those crazed creationists who believe that everything we see today is exactly how God created it, but full-blown, evolved-over-billions-of-years-from-a-singularity-filled-with-energy evolution is still a challenge for me to accept. If that makes me $DEROGATORY_COMMENT, well, I already said goodbye to my karma points.