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Evolution of an Irreducibly Complex System – Lenski’s E. Coli

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On another thread we have been discussing abiogenesis in particular, but there was also some discussion about the evolution of an irreducibly complex system. Commenter CHartsil indicated that “we actually watched an IC system evolve” in reference to Lenski’s E. coli research. At my request, he has posted a brief summary of the research and his take, which I am now elevating to a new thread on this important topic.

For those who disagree with CHartsil’s take, strong objections on substantive grounds are of course welcome, whether relating to Lenski’s research or CHartsil’s interpretation of it, but not irrelevant personal attacks. Thank you.

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Guest Post by CHartsil:

This is a pro-ID board so I doubt I need to explain irreducible complexity. When arguing against it, most will bring up Ken Miller or Nick Matzke. They have great points but theirs are indirect and theoretical pathways for systems considered IC. That’s why I’m fond of Lenski’s cit* E. coli.

This particular strain of E. coli evolved the ability to metabolize citrate aerobically. While most E. coli can do this anaerobically, part of the definition of wild-type E. coli is actually the inablity to use citrate as a substrate aerobically. This may not have been a terribly fascinating addition of function if not for the frozen fossil records kept by Lenski et al.

These frozen generations allowed Lenski to determine that this trait was not acquired via a single mutation as it could only be repeated after generation 20,000. Given the distinct cladistic division amongst the populations at the border generation, it was determined that there were at least two potentiating mutations prior to the cit* event.

In this third clade a tandem duplication resulting in a novel regulatory module leading to the aerobic cit* could be repeated and verified. It has been noted since that the fitness of the population has been improving without notable upper limit, increasing based on the number of copies of the new regulatory module.

I find this to be sufficient in warranting the dismissal of the concept irreducible complexity. In Lenski’s E. coli, we observe the rise of a new function resulting from a new gene and new gene regulation. This function is comprised of now interdependent components which demonstrably did not exist in parent generations. It is by definition irreducibly complex and it was observed to evolve.

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Nota bene: for purposes of the above discussion, CHartsil is using the following definition of irreducible complexity: “a system comprised of interdependent parts, the removal of any of which will cause the system to cease functioning.”

Comments
Collin
Is it true that what happened is that there was a system that transported oxygen and a system that metabolized citrate and that the oxygen transport got duplicated and mashed together with the citrate metabolism system?
No, that is not what occurred in the Lenski long-term expt. Perhaps have a go at reading the published literature from Lenski's lab to see what the expt. was/is all about.
Argument from ignorance. If you’re claiming that it was guided, the onus is on you to show that.
Not only that is estimated that every nucleotide in the bacteria strain used in this expt was mutated at least once and that the total single point mutations were on the magnitude of billion.......doesn't really sound like a directed process at all....at least not that could be differentiated from chance alone.franklin
March 6, 2015
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If I knew more about molecular biology I could engage more. But let me ask this question: Is it true that what happened is that there was a system that transported oxygen and a system that metabolized citrate and that the oxygen transport got duplicated and mashed together with the citrate metabolism system? I figure that this issue is important enough that Behe needs to address it himself if he wants to defend his idea. I certainly can't do it for him.Collin
March 6, 2015
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"If this is an example of IC, and I doubt that it is, it is minimal IC at best." No true Scotsman "And no one can say if unguided evolution did it so it doesn’t do anything to Behe’s argument" Argument from ignorance. If you're claiming that it was guided, the onus is on you to show that.CHartsil
March 6, 2015
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"If this is an example of IC, and I doubt that it is, it is minimal IC at best." No true Scotsman "And no one can say if unguided evolution did it so it doesn’t do anything to Behe’s argument." Argument from ignorance. If you're claiming that it was guided, the onus is on you to show that.CHartsil
March 6, 2015
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If this is an example of IC, and I doubt that it is, it is minimal IC at best. And no one can say if unguided evolution did it so it doesn't do anything to Behe's argument.Joe
March 6, 2015
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box
Okay Franklin, you insist on calling it a “newly evolved transport system”. I find that utterly ridiculous.
I call it a newly evolved citrate transport system because that is what it is. Are you suggesting that the E coli strain used in the Lenski expt. had the ability to aerobically transport citrate across the cell membrane? Previously, you acknowledged that the strain did not possess this ability. Are you now retracting that acknowledgment? If it did not exist in this strain previously and arose, through mutation mechanisms, then how is it NOT a new transport system? Your apparent denial of this basic result of the expt. is truly absurd. box
Therefor I see no point in discussing this any further. Let’s agree to disagree.
The results of the expt. are clear cut and fit the definition of a newly evolved IC system as per Behe which you regard so highly.franklin
March 6, 2015
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How was it determined that gene duplication is a blind watchmaker process?Joe
March 6, 2015
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Okay Franklin, you insist on calling it a "newly evolved transport system". I find that utterly ridiculous. Therefor I see no point in discussing this any further. Let's agree to disagree.Box
March 6, 2015
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box
However there is a transport system for citrate across the cell in place, it just lacks a promoter that works in the presence of oxygen
That is a significant absence of function. IN fact it is so significant it is used as a diagnostic test to differentiate between E coli and other pathogenic bacteria. box
This pre-existing ready-made transport system is being utilized in the end
No, the preexisting system is not being utilized. The anaerobic citrate transport system remains intact and is a separate system than the aerobic citrate system. box
IOW we are not talking about a newly evolved transport system
Of course we are talking about a newly evolved transport system. You've already acknowledged that the aerobic transport system did not exist at the start of the expt. If it did not exist previously and now it does it is a new transport system. box
Are we in agreement so far?
No. box
I more or less did all that in post #16. Let me know if you find anything missing.
There appears to be a great deal missing in your #16 partial summary. I don't see any mention of potentiating mutations nor activating mutations. They are part of the evolutionary details of the evolution of this new and novel transport system in E coli. box
On the IC-issue, why do you keep ignoring my argument that a piece of DNA is not a “single system” – which is part of Behe’s definition of IC?
What components, in your mind, constitute the aerobic citrate transport system?
franklin
March 6, 2015
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Franklin,
Franklin: E. coli, at the start of the Lenski expt., did not posses the ability to transport citrate across the cell membrane in the presence of oxygen.
True. However there is a transport system for citrate across the cell in place, it just lacks a promoter that works in the presence of oxygen. This pre-existing ready-made transport system is being utilized in the end. IOW we are not talking about a newly evolved transport system. Are we in agreement so far? And BTW we are also not talking about a newly evolved promoter; this also pre-exists.
Franklin: As I have suggested several times (which for some reason you appear to be ignoring) is that you list each step of the evolutionary pathway that led to this ability and then we can compare it to your Behe requirements for IC evolution and see how it matches up. That seems like a straight forward way to settle this issue. How about it, Box, does that sound OK to you?
I more or less did all that in post #16. Let me know if you find anything missing. On the IC-issue, why do you keep ignoring my argument that a piece of DNA is not a "single system" - which is part of Behe's definition of IC?Box
March 6, 2015
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box
the simple point is that the citrate transporter is a pre-existing mechanism and not something newly evolved.
E. coli, at the start of the Lenski expt., did not posses the ability to transport citrate across the cell membrane in the presence of oxygen. In fact the very commonly used citrate test is a test used to differentiate between E. coli and other pathogenic bacteria because of the well known inability of E coli to transport citrate across the cell membrane in the presence of oxygen. There is absolutely no question that this is a new, novel, ability for E coli to possess and the mutational path leading to this ability, i.e., evolution, has been clearly delineated by Lenski's group. As I have suggested several times (which for some reason you appear to be ignoring) is that you list each step of the evolutionary pathway that led to this ability and then we can compare it to your Behe requirements for IC evolution and see how it matches up. That seems like a straight forward way to settle this issue. How about it, Box, does that sound OK to you? box
IOW we are talking about modification of pre-existing elements.
If you think that is the case which elements of the anaerobic citrate transporter was modified and how? Also if the aerobic citrate transport system ( a new and novel trait for this species of bacteria) is not IC which parts can be removed and still have the aerobic transport function retained?franklin
March 6, 2015
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CHartsil:
The do a search on the evolution of said systems.
Been there, done that and there isn't any evidence that unguided evolution can produce any of those. Did you have a point?Joe
March 6, 2015
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Hangonasec:
And I seriously doubt that any of those papers has one word to say about IC,
They don't have anything to say about unguided evolution. The IC part can be gleaned by the details of the structure.Joe
March 6, 2015
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Franklin, the simple point is that the citrate transporter is a pre-existing mechanism and not something newly evolved. All the machinery for citrate metabolism is already in place. IOW we are talking about modification of pre-existing elements. WRT the IC claim. I think it's not an "single system"; see #279, #280.Box
March 6, 2015
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Box
Franklin, if you happen to find a car key by pure chance, which happens to fit the Lamborghini in front of your house, are you claiming that chance brought about an “entire new car”?
Huh? In your tortured analogy which part corresponds to which part of the evolution of the aerobic transport of citrate in the Lenski expt.? You'll need to flesh this out a bit since it makes no sense in its present form. Alternately, you can outline the documented steps in the evolution of the aerobic citrate transporter system in E. Coli and we can compare that to the Behe requirements you posted earlier.. OK? If the aerobic transport of citrate in E coli is not IC which part(s) can be removed and have E. coli retain this ability? If no parts can be removed then would you agree this is a IC system that evolved in E coli?franklin
March 5, 2015
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Franklin, if you happen to find a car key by pure chance, which happens to fit the Lamborghini in front of your house, are you claiming that chance brought about an "entire new car"?Box
March 5, 2015
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box
Nonsense. Of course, there is no newly evolved “transporter system for citrate across the cell membrane” – don’t be silly.
If that was the case why were the E coli unable to transport oxygen across the cell membrane in the presence of oxygen? box
This transporter system, which normally transports citrate in the absence of oxygen, was already in place.
Of course we are discussing the transport of citrate across the cell membrane in the presence of oxygen. Did the E. coli have the ability to transport citrate across the cell membrane, in the presence of oxygen, at the start of the expt? If it did not how did this ability arise? Evolution perhaps? If not that could you outline the steps that led to the ability to transport citrate across the cell membrane in the presence of oxygen? What Joe describes is the evolution of a new and novel pathway to transport citrate across the cell membrane in the presence of oxygen. A decidedly advantageous development to the E coli. If you think this is not a IC system which parts may be removed and have the E coli maintain the ability to transport citrate across the cell membrane in the presence of oxygen. List the evolutionary steps which were documented and led to this ability and we can compare them to your Behe requirements and see how they match up. OK?franklin
March 5, 2015
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Collin: But couldn’t you say that EVERYTHING is part of a larger system?
You have a point. However it's obvious to anyone that a flagellum is more a "single system" than a piece of DNA-code.Box
March 5, 2015
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Franklin: except that the IC system that was documented to have evolved in the Lenski long-term expt is the aerobic transporter system for citrate across the cell membrane.
Nonsense. Of course, there is no newly evolved "transporter system for citrate across the cell membrane" - don't be silly. This transporter system, which normally transports citrate in the absence of oxygen, was already in place. In post #82 Joe gives the perfect summation of what happened.
Joe: It is a duplicate of an existing gene that was placed under the control of an existing regulatory system.
Box
March 5, 2015
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box
CHartsil’s “aerobic citrate metabolizing system” is not a single system
except that the IC system that was documented to have evolved in the Lenski long-term expt is the aerobic transporter system for citrate across the cell membrane. If you think that system is not IC tell us which part can be removed and have the function of aerobic transport of citrate into the cell maintain function......in leui of that you can just acknowledge that the Lenski expt. did document the evolution of a IC system as per Behe requirements that you posted above.franklin
March 5, 2015
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Joe
Read any paper on ATP synthase- or any bacterial flagellum- or any blood clotting system- asexual reproduction- sexual reproduction- the list is long.
And I seriously doubt that any of those papers has one word to say about IC, so unless you can give a cite, I'd say you are blowing hot air. It's no good just naming things in biology. Biological organisms and their systems are known to be integrated, and parts non-optional now. But that does not prove their non-optional relations the day the system came into being. Demonstration of 'true' IC is not a trivial matter. There are probably more bits that can't be chopped out now than can, so that is obviously not the way to do it. It has to be separated from apparent IC, of which there are several potential mechanisms of formation. And no, I don't have to demonstrate their formation by incremental change in order to prove they are not IC. You have to demonstrate they are IC. That's what you said has been done. Not just asserted to be, shown to be. So back it up.Hangonasec
March 5, 2015
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Box, But couldn't you say that EVERYTHING is part of a larger system?Collin
March 5, 2015
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Zachriel, Helpers to what? A system that is already functional? An already irreducably complex system?Collin
March 5, 2015
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Behe: An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. Such systems can be produced; for example, by the addition of helpers that become essential through optimization; or through duplication followed by functional migration.Zachriel
March 5, 2015
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//follow up #279// CHartsil's "aerobic citrate metabolizing system" is not a single system - see Behe's definition of irreducible complexity #279. It goes without saying that it's a small part of a much larger system.Box
March 5, 2015
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// irreducible complexity //
By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on. Even if a system is irreducibly complex (and thus cannot have been produced directly), however, one can not definitively rule out the possibility of an indirect, circuitous route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously. And as the number of unexplained, irreducibly complex biological systems increases, our confidence that Darwin's criterion of failure has been met skyrockets toward the maximum that science allows. In the abstract, it might be tempting to imagine that irreducible complexity simply requires multiple simultaneous mutations—that evolution might be far chancier than we thought, but still possible. Such an appeal to brute luck can never be refuted. Yet it is an empty argument. One may as well say that the world luckily popped into existence yesterday with all the features it now has. Luck is metaphysical speculation; scientific explanations invoke causes. It is almost universally conceded that such sudden events would be irreconcilable with the gradualism Darwin envisioned. Richard Dawkins explains the problem well:
Evolution is very possibly not, in actual fact, always gradual. But it must be gradual when it is being used to explain the coming into existence of complicated, apparently designed objects, like eyes. For if it is not gradual in these cases, it ceases to have any explanatory power at all. Without gradualness in these cases, we are back to miracle, which is simply a synonym for the total absence of explanation.
[Behe, Darwin's Black Box, p. 39/40]
Box
March 5, 2015
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CHartsil @275:
The[n] do a search on the evolution of said systems.
This is a great suggestion. What you will find are speculations, hypotheticals, "what-if's", wild guesses, question-begging assumptions and the like. What you will not find is any empirical evidence that such systems can arise via blind, undirected processes.Eric Anderson
March 5, 2015
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CHartsil, re-read #260. You misunderstand irreducible complexity. As well as fundamental lesson of Lenski's experiments.Eric Anderson
March 5, 2015
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We have observation that a system which cannot be deconstructed can evolve. You have inference that it can't. We winCHartsil
March 4, 2015
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"Read any paper on ATP synthase- or any bacterial flagellum- or any blood clotting system- asexual reproduction- sexual reproduction- the list is long." The do a search on the evolution of said systems.CHartsil
March 4, 2015
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