Tuesday, December 13, 2011

Barry Arrington Explains Irreducible Complexity

The Intelligent Design Creationists are feeling a little bit threatened these days. Some scientists are—believe it or not—actually addressing their main arguments head-on and showing them to be vacuous.

The IDiots don't like this because they are used to posting very silly arguments from amateurs on their blogs and then complaining that scientists are only picking the low-hanging fruit and not addressing the true "experts." Truth is, all of the so-called "expert" arguments have been refuted ages ago.

Here's an example from Barry Arrington who explains the real meaning of irreducible complexity and why it supports intelligent design [Denis Alexander’s Strawman Just as Silly].
No ID theorist has ever argued that evolution is impossible because complex biochemical systems cannot self assemble “all in one go.” This is an absurd caricature of the argument from irreducible complexity (IC).

The basic logic of IC goes like this: (1) By definition, evolution can work only in a stepwise fashion wherein each successive step is “selected for” because it has conferred a selective advantage on the organism. (2) an irreducibly complex system is a system which if one part is removed all function ceases. (3) by definition, therefore, an irreducibly complex system cannot be produced in a stepwise fashion. (4) therefore evolution is not capable of producing an irreducibly complex system.

Starting with this logic the ID proponent argues that certain systems are irreducibly complex and therefore could not have been produced by evolution. The bacterial flagellum and the blood clotting cascade are classic examples of such systems.
I have frequently accused Intelligent Design Creationists of not understanding evolution. For example, one of their heroes, Phillip Johnson, clearly thinks that natural selection is a synonym for evolution in spite of the fact that other mechanisms have been known for almost a century [see This Video Should Be Shown to all Biology Students and Phillip Johnson, One of the Very Best Intelligent Design Creationists].

Jonathan McLatchie defended his hero by saying [Maligning Phil Johnson, with Lots of Rhetoric but Little Substance] ...
This is the type of condescending rhetoric that is so prevalent in anti-ID writings. Does Shallit really think that we haven't heard of processes such as genetic drift and endosymbiosis?
We look forward to hearing again from Jonathan McLatchie about how IDiots like Barry Arrington understand evolution.

Arrington's false premise (#1) isn't the only thing wrong with his argument because one can quite easily construct plausible scenarios where each step in constructing an irreducibly complex system confers a selective advantage. All you have to do is postulate that the intermediate selective advantages are not the same as the final purpose of the system.

This is all been thoroughly debated over a decade ago. It's just not true that the concept of irreducible complexity has so flummoxed evolutionary biologists that they have abandoned evolution.

Barry Arrington also takes on one of my comments from somewhere. I don't remember the context but apparently I questioned whether the definition of "information" from computer science and philosophy could be applied to the "information" in DNA sequences. The problem is that, according to Intelligent Design Creationists, if the DNA information is the same as other kinds of information then it has to be created by an agent like some god or some space alien.

They don't seem to be troubled by such an explanation because they never ask the obvious question ... where did the information in the designer come from?1

Anyway, read Barry's defense of the idea that information in a DNA sequence is the same as other kinds of information that requires a designer [Upright Biped Replies to Dr. Moran on “Information”].

[UPDATE: Apparently that last posting was written by someone called "Upright Biped" and Barry Arrington just posted it under his own name on Uncommon Descent.]

Remember that Barry Arrington is a lawyer from Colorado and one of the regular bloggers on Uncommon Descent. Most IDiots consider him an expert on Intelligent Design Creationism. In other words, this is as good as it gets.


1. It's turtles all the way down, right?

58 comments :

  1. It seems to me that the biggest problem with Barry's syllogism aren't the ones you criticize. (Not that those aren't also valid objections.)

    The major problem is a change in the meaning of "stepwise" in between 1, where it means "small and conferring an advantage", and 3, where it means "adding a part to a set of unvarying parts". That's why IC systems can't evolve by definition: if evolution really were the addition of invariant parts, an IC system could have no function until all the parts were there. (The exception you allow, that it might fill a different function, seems highly unlikely to me given the assumption of invariance.) Allow the parts to vary, though, and it all becomes much easier. For example, part A might initially perform functions x and y. Adding part B, which improves function y, would be advantageous. And A could then gradually specialize entirely in x, while B gradually takes over function y. Etcetera; you know all the scenarios.

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  2. @John Harshman,

    Thanks.

    It's almost trivial to come up with perfectly naturalistic scenarios for the evolution of an irreducibly complex system.

    The IDiots don't see these explanations because they don't have a very good understanding of basic biochemistry and evolution.

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  3. Larry, if you had bothered to read Behe's Darwin's Black Box, you would know that Behe agrees with your statement, "All you have to do is postulate that the intermediate selective advantages are not the same as the final purpose of the system."

    On p.40 he wrote: "Even if a system is irreducibly complex (and thus cannot have been produced diretly), 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."

    As to your claim,"one can quite easily construct plausible scenarios where each step in constructing an irreducibly complex system confers a selective advantage," please do so.

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  4. Oh dear - David "Yes I pad my resume, so what?*" Abel-worshipping 'Upright Biped' explains information to you!?



    *http://davidlabel.blogspot.com/

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  5. Medieval architects built arches out of stone blocks. If you take out any single block from a finished arch, it collapses (ceases to function). Arches are therefor irreproducibly complex and could not have been built in stepwise fashion (By Arrington's logic).

    I wonder how those medieval builders managed to place all the blocks in an arch simultaneously? They must have had divine powers.

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  6. SO many wrongs, so little time:

    (1) By definition, evolution can work only in a stepwise fashion wherein each successive step is “selected for” because it has conferred a selective advantage on the organism.

    By whose definition? Why do we care about such definition? What about evolution "by its nature"? Evolution is a bunch of natural processes, so starting with "by definition," leaving aside that they go by whatever definition they prefer, imposes a very limited understanding into a complex natural reality. Makes no sense.

    (2) an irreducibly complex system is a system which if one part is removed all function ceases.

    Whatever.

    (3) by definition, therefore, an irreducibly complex system cannot be produced in a stepwise fashion.

    False, that it can't be "reduced" as it stands, does not mean it can't be built in steps. It only implies that how it was built is not obvious.

    (4) therefore evolution is not capable of producing an irreducibly complex system.

    Therefore these guys have no idea of science, nor of logic. They only dismantle their own lack of imagination. I would say pretended lack of imagination. But that would imply that they are dishonest. God forbid.

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  7. Behe's IC-disproves-evolution argument is bullshit on many levels, including some that are obvious to laymen like me. In particular: The steps in an evolutionary stepwise process fall into one of three distinct classes, which are (a) Add a new bit that didn't used to be there, (b) Remove one of the existing bits, or (c) Modify one of the existing bits. It is trivially true that if a system is IC by Behe's definition (I like to specify this because Dr. Dr. Dembski came up with a completely different definition of ID), the final step in its creation/assembly cannot be 'add a new bit', because that would make the penultimate stage of the system's creation/assembly "an IC system with one missing piece", which would, by definition, be nonfunctional. But if the final step is "remove an old bit", the penultimate stage of the system's creation/assembly would be "an IC system plus an extra piece"; if the final step is "modify an existing bit", the penultimate stage of the system's creation/assembly would be "an IC system with one bit changed". It is by no means clear that "an IC system with one extra bit" must be nonfunctional, and it's also not clear that "an IC system with one bit changed" must be nonfunctional. But Behe's IC-disproves-evolution argument crashes and burns unless ABSOLUTELY ALL POSSIBLE evolutionary precursors to an IC system are necessarily nonfunctional!

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  8. IDiots sure aren't expert at science, but they're unsurpassed experts at making fools of themselves.

    Arrington is clueless. I would love to see him try to argue his 'position' in a courtroom, where both sides have to abide by the same rules of procedure (unlike at UD) and where he would have to produce real evidence to support his claims. He wouldn't get very far with his dishonest, delusional, non-evidential assertions.

    ------------------------

    By the way, thanks for the plug Larry. :)

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  9. On reading Arrington's post (via the link) I am struck by the fact that he characterizes the argument against IC as a "strawman"; this seems to be what the ID/Creationist crowd usually themselves - characterize the theory of evolution in a strawman fashion and knock that down, if they can (and of course, every time you mention the modern refinements of the theory which they ignore you are implicitly making that point. Also, I see that he cites the blood cascade as evidence for IC; even an amateur such as I can understand the explanations of the evolution of the blood cascade (I read Ken Miller's at his website) - so naively, one might think that the experts at the Discovery Institute could as well.

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  10. @qetzal:

    I think that an advocate of the IC argument would point out that the architects were intelligent designers, who had a goal in mind when they were making the scaffold for an arch.

    I think that a better example is the case of a natural arch, which is formed by non-directed stepwise processes.


    On a different topic, has any advocate of the IC argument ever looked at the list of precursors given in the Wikipedia article on IC? I think that it is interesting that in the 18th century an argument very much like IC was used to support preformation.

    TomS

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  11. I didn't think the IDiots would ever mention the blood clotting cascade again after Behe's embarrassing performance in Dover where he tried to simultaneously defend the different statements he made about it in Pandas and his book.

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  12. Bilbo,

    Thus, while IDiots present their IC argument as an impossible feat for evolution, the evolution of IC systems is actually merely improbable.

    When Behe says:

    As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously.

    He's right. But how low is enough to make it practically impossible? Behe had at hand morphological examples showing the very kind of circuitous evolution he implied to be near-impossible, such as the evolution of the mammalian ear ossicles. Failing to discuss further those possibilities, the lasting impression from Behe's book is that evolution is supposed to build organisms with Lego blocks.

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  13. 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.

    Hi, Bilbo. One problem with Behe's criticism above is that his neat, clean "direct, uncomplicated" vs. "indirect, thus more complex" comparison doesn't actually occur in real biological systems. "Direct" evolution for a particular purpose would require the ability to look forward, which genes don't have. And unless one claims to be able to know or to scientifically determine the Designer's purposes for various gene mutations, there is no way to say what those purposes were. So the only criterion left to evaluate "direct" vs. "indirect" is to see whether a gene or set of genes has only been used to do one thing ("direct"), or whether what the gene or set of genes produces has changed at one or more points ("indirect"). And what we find when we examine this is that some of the "direct" examples involve considerably more complexity than the "indirect" examples.

    For example, there are species of cold-water fish that use non-coding DNA as a type of antifreeze. (The physical characteristics of the genetic material make it difficult for ice crystals to form in its presence.) That's the only thing this genetic material has ever been used for. But it is just unbelievably chaotic and complicated from a structural point of view (which is what allows it to act as antifreeze).

    On the other hand, there are HOX gene duplications where the "spare" set of HOX genes that originally was used to build one type of structure (e.g., legs) eventually was used to build a different type of structure (e.g., mouth parts). The original duplication was a very straightforward and simple mutation, as were the few mutations that resulted in those genes building something new. Nothing like as complicated as the evolutionary history of the non-coding antifreeze DNA. But these simpler changes would have to be characterized as "indirect," because the genes built legs first before they changed to build mouth parts. So Behe's criticism, which requires that direct=simple, is invalid.

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  14. Bilbo says,

    Larry, if you had bothered to read Behe's Darwin's Black Box, you would know that Behe agrees with your statement, "All you have to do is postulate that the intermediate selective advantages are not the same as the final purpose of the system."

    I have read both of Michael Behe's books and I'm very familiar with his evolving definitions of irreducible complexity [see Irreducible Complexity].

    I presume he will make sure that his colleagues are corrected by explaining to them where they went wrong in their description of irreducible complexity. I'm watching for his comments here on Sandwalk or for a separate posting on one of the IDiot blogs.

    Let me know when you see it, in case I miss it.

    As to your claim,"one can quite easily construct plausible scenarios where each step in constructing an irreducibly complex system confers a selective advantage," please do so.

    One of the best examples is the citric acid cycle [see Irreducible Complexity]. It's clearly an example of irreducible complexity although Behe has tried to wriggle his way out of it [see Behe Responds to Postings in Talk Origins Newsgroup]. His coverage of metabolic pathways in Darwin's Black Box is a blatant attempt to have his cake and eat it too (pp. 150-153).

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  15. Arrington's false premise (#1) isn't the only thing wrong with his argument

    Certainly not. A couple more things wrong:

    (3) is not, as stated, "by definition," but is intended to follow from (2). You say this man is a lawyer?

    (3) does not in fact follow from (2). It is entirely possible for something that currently requires each part to have arisen through a stepwise path. These responses to "irreducible complexity"were all made at least a decade a go.

    Idiot indeed.

    Transcript of testimony at the Dover trial
    in which Michael Behe admits that a weakness in his definition of "irreducible complexity" was pointed out, and that he has never addressed it.

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  16. As far as systems which have evolved despite being complex systems made up of several interacting parts, I think that the "definitive mammalian middle ear" is an excellent example.

    1. The chain of hammer, anvil, and stirrup would not work at all if any one of them were missing.

    2. The fossil evidence is abundant that mammals really did evolve this structure. See also the embryology and genetics.

    TomS

    3. There is pretty good reason to say that natural selection played a role in the evolution.

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  17. It's really astounding that these guys NEVER address this. They just say 'well sure, but if its supermega complex then that wouldn't work'. Or better, it'd be 'improbable', without a valid probability calculation/estimate.

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  18. The fool has said in his heart, "there is no God". Psalm 53

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  19. Larry, you write: "I have read both of Michael Behe's books and I'm very familiar with his evolving definitions of irreducible complexity" and then refer to one of your posts where you quote Behe's definition from p.39 of DBB, where he writes that by definition IC systems cannot evolve directly. You then go on to say the same thing you say in this post: that IC systems can evolve indirectly. But again, you ignored the fact that on p.40 Behe also said that it's possible for IC systems to evolve indirectly.

    As to why Behe does not think metabolic pathways are IC systems:

    If I understand it, metabolic systems are systems where enzymes interact with substrates (I hope that's the correct term) instead of with each other. Thus Enzyme A interacts with substrate A, which is transformed into substrate B, which allows Enzyme B to interact with it, etc. Behe points out in his book that it is possible for such a system to evolve gradually, starting with what is now the last substrate (e.g., substrate D) and working backwards to what is now the first substrate (e.g., substrate A). Thus, it is possible for such a system to evolve one protein at a time, while still producing the same final end product.

    Contrast this with an IC system, where each protein interacts with other proteins, where removing one of them causes the entire system to cease functioning. Now it might still be possible that the remaining proteins might still interact with each other to achieve a different function. And that might be one way of showing that they in fact evolved indirectly.

    So other than the citric acid cycle, which is a metabolic pathway, not an IC system, do you have any other examples?

    Since I doubt that Behe has the time or interest in correcting Barry Arrington, I'll go over to UD and correct him, if it will make you happy.

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  20. Bilbo,

    It might be that Behe said what you say he said. But the fact is that whomever wrote the piece referred to in this Sandwalk post makes several mistakes, both in logic and in science.

    If Behe realizes that IC systems can evolve indirectly, I don't see why should any of us find the examples for you. Can you explain your rationale?

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  21. Compare and contrast the clearly established evolution of the definitive mammalian middle ear with any "irreducibly complex" feature of Homo sapiens which challenges the common descent with modification (that is, evolution) of humans and any other Hominid (or Primates or Mammals).

    Compare and contrast the argument from IC against evolution with the serious use of IC in the 18th century as an argument from IC against reproduction (and in favor of preformation).

    TomS

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  22. NE: "If Behe realizes that IC systems can evolve indirectly, I don't see why should any of us find the examples for you. Can you explain your rationale?"

    Behe argues that even though it is possible for IC systems to evolve indirectly, it is too improbable that they did so.

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  23. TomS, I think Behe would call the auditory system a compound system (made up of several simple systems), and so would not make a good example of an IC system, which, by definition, is a single system.

    That's why, for example, Behe does not try to refute the evolution of the eye (a compound system), but he does offer the biochemistry of vision as an IC system, and a challenge to Darwinian evolution.

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  24. Qetzal, if I understand how arches are constructed, one first constructs a simple, one-piece arch, which acts as the scaffolding for the stones which are then placed on it. Once all the stones are in place, the original scaffolding is removed.

    If there were an multi-part IC system in a cell that originally was performed by one single part, then the multi-part system wasn't really IC. Is there such a system?

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  25. If there were an multi-part IC system in a cell that originally was performed by one single part, then the multi-part system wasn't really IC. Is there such a system?

    The immunological cascade in humans, which Behe called IC, was shown to be performed with some of the steps removed in (if memory serves) lobsters. I don't know if Behe has admitted this renders the human immunological cascade not IC. It does cause one to wonder on what scientific basis Behe determines processes, structures, etc., to be IC, since obviously much depends on getting this right. If there is no scientifically rigorous way to determine what is IC, then the edifice of ID is built on a scientifically shaky foundation, yes?

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  26. Bilbo, arguing about arches is stupid. It's just an analogy. Stop obfuscating. Although, I will play along enough to point out that you have not dealt with natural arches, nor have you justified your assertion that a form must be a single piece. Not that it matters in anycase.

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  27. @Bilbo:

    The definitive mammalian middle ear has a chain of three bones, the hammer, the anvil, and the stirrup. If any of those bones is missing, then there is no chain of bones, and that path of transmission of sound does not work at all.

    TomS

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  28. Is this the same Barry Arrington that claimed that the Columbine school shootings were the result of darwinism?

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  29. Bilbo,

    Behe argues that even though it is possible for IC systems to evolve indirectly, it is too improbable that they did so.

    Too improbable why?

    Then there are at least two scenarios I can think of right now where things can evolve "directly":

    First: components come and go, which allows for the evolution of the system in steps. Some components later disappear rendering the current system as it appears in some organism as IC. You can't take any component out without disrupting the function. But that does not mean it did not develop by steps. Only that it is IC as you found it. Right?

    Second way: systems evolving under different circumstances. For instance, the blood clotting cascade is much smaller in different organisms. Some have just a few of the components we have and they are all right, the blood clots and all. That would indicate that the system is not IC. Then, let us say for the sake of discussion, that we did experiments in rats, and any component missing makes blood clotting fail in the rat. Well, it would still be possible for the system to evolve in steps if ancestors did not need all the components, right?

    So, let me summarize:
    1. IC systems can evolve independently (meaning, apparently for you and Behe, doing something else).
    2. In order to claim that systems have a very low probability to evolve "indirectly" you need some basis. What's that basis?
    3. A system might evolve in steps if not all steps are IC in ancestral organisms, either because the system exchanges components during its evolution, or because some functions are not necessary in different environments.

    -NE

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  30. Bilbo,

    That's why, for example, Behe does not try to refute the evolution of the eye (a compound system), but he does offer the biochemistry of vision as an IC system, and a challenge to Darwinian evolution.

    Which means that Behe is looking for gaps in knowledge to put his god there. Nothing but the same old god-of-the-gaps argument after all. Hardly a challenge to any evolution (what the hell does "Darwinian" mean?).

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  31. Jud: "The immunological cascade in humans, which Behe called IC, was shown to be performed with some of the steps removed in (if memory serves) lobsters. I don't know if Behe has admitted this renders the human immunological cascade not IC."

    I think the lobster example was offered by Ken Miller, and I think (though I'm not sure) it was the blood-clotting cascade. I think Behe's response was that it was irrelevant to the human blood-clotting cascade. If most or all of the parts in the lobster's system are the same as the human system, then I think there would be quite a bit of relevance. I'll have to go back and look through Miller's book (Finding Darwin's God).

    Anon: "...you have not dealt with natural arches, nor have you justified your assertion that a form must be a single piece. Not that it matters in anycase."

    Am I mistaken in thinking that natural arches form when softer rock below is washed out and the harder rock above is left in tact? And I guess a form could be (and is?) made of more than one piece. But the form is still an arch, is it not? Not that it matters in any case.

    TomS: "The definitive mammalian middle ear has a chain of three bones, the hammer, the anvil, and the stirrup. If any of those bones is missing, then there is no chain of bones, and that path of transmission of sound does not work at all."

    Yes, but the bones are just one of several systems involved in the auditory system. Behe defines IC systems as strictly involving one single system. He's more interested in biochemical systems, at the cellular or intra-cellular level.

    Negative Entropy: "[Behe argues indirect evolution is] Too improbable why?"

    Until recently, I think most biologists would say that if a system only required one protein to evolve at a time before it could function, then this was within the reach of naturalistic means of evolution. But if more than one protein needed to evolve before there was a new function, then it was beyond the reach of evolution.

    So let's say we had system A, which functioned with 5 proteins and performed function X. Now let's say that we had system B, which functioned with 7 proteins (five of them the exact same as in system A) and performed function Y. We would suspect that system B evolved from system A. But we would need an explanation for how the additional two proteins came into existence. At this point, I think most biologists wouldn't consider this a major challenge. But suppose the difference between the two systems is not two proteins, but ten. And there do not appear to be any intermediate systems using any of the additional proteins. Now, I think, the challenge becomes more severe. And that, in a nutshell, is Behe's point.

    But I'm running out of time. Be back tomorrow, after I look up Miller's lobster.

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  32. Bilbo:

    "Qetzal, if I understand how arches are constructed, one first constructs a simple, one-piece arch, which acts as the scaffolding for the stones which are then placed on it. Once all the stones are in place, the original scaffolding is removed.

    If there were an multi-part IC system in a cell that originally was performed by one single part, then the multi-part system wasn't really IC. Is there such a system?"


    Not according to the definition in the post:

    "(2) an irreducibly complex system is a system which if one part is removed all function ceases. (3) by definition, therefore, an irreducibly complex system cannot be produced in a stepwise fashion."

    Note that an arch made of stone blocks perfectly meets point (2). Remove any single block, and it collapses. Yet such arches clearly can be produced in stepwise fashion. Thus, (3) does not follow from (2).

    Of course, you're free to offer a different definition of IC. But if your definition makes IC compatible with stepwise evolution, then what's the point?

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  33. Bilbo,

    suppose the difference between the two systems is not two proteins, but ten. And there do not appear to be any intermediate systems using any of the additional proteins. Now, I think, the challenge becomes more severe. And that, in a nutshell, is Behe's point.

    Then Behe's point is but a god-of-the-gaps argument compounded with ignorance. Note this: we have plenty of systems, and I mean plenty, where we might as well suppose, for the sake of argument, that they are all IC as they stand. Yet, we see the proteins "shared" among systems so much, that taking a bunch from one system to work in another, does not seem like a problem whatsoever. So, suppose we have one as the one you describe. Ten proteins with no homologs anywhere so far found. The challenge is not for "naturalistic" evolution. The challenge is for us to ever be able to figure out how that particular system evolved. That's it. After all, other systems, similar to ancestral systems, using those proteins might have gone extinct, or might be there in some organism we have not looked at yet. So, with plenty of clear examples, why doubt that the unclear ones did evolve just as naturally?

    Have fun reading Miller's book. I have not read it. Nor do I think I will.

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  34. @Bilbo:Yes, but the bones are just one of several systems involved in the auditory system. Behe defines IC systems as strictly involving one single system. He's more interested in biochemical systems, at the cellular or intra-cellular level.
    I am interested in systems which leave behind a fossil record, because there the traces of the intermediate forms are more likely to be preserved in a way that is obvious to the layperson.
    To go back to what I had to say: Do you have an example of a difference which is "irreducibly complex", a difference between the human body and the body of a chimp, or of any other ape, a difference to which the IC argument shows that there is no likelihood of common descent with modification? Something to which "irreducibly complex" applies more appropriately than the definitive mammalian middle ear?
    Or, again to repreat myself, do you have an example better than those given by the 18th century advocates of preformation?

    TomS

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  35. Bilbo writes:

    I think the lobster example was offered by Ken Miller, and I think (though I'm not sure) it was the blood-clotting cascade. I think Behe's response was that it was irrelevant to the human blood-clotting cascade. If most or all of the parts in the lobster's system are the same as the human system, then I think there would be quite a bit of relevance. I'll have to go back and look through Miller's book (Finding Darwin's God).

    Sorry, clotting cascade and immune system. It was regarding the immune system where during cross-examination in Kitzmiller Dr. Behe said over 100 articles in the peer reviewed literature plus textbooks, together amounting to a pile about two feet high, were all irrelevant.

    Regarding the clotting cascade, in his cross-examination in Kitzmiller Dr. Behe could not even consistently pin down the components of the clotting cascade that were supposed to be IC, admitting if the system were reduced to the components he'd named in Darwin's Black Box that in fact it would not function in humans, but on the other hand it would function in puffer fish.

    You don't have to go to Ken Miller's book, just read Dr. Behe's own cross examination in Kitzmiller.

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  36. > The immunological cascade in humans, which Behe called IC, was shown to be performed with some of the steps removed in (if memory serves) lobsters.

    For those who are interested, here is a reply by Behe to critics of his book, and here is a development by Miller of his immune-system argument.

    "Although embedded in a lengthy description of how blood clotting and other systems work, Professor Miller's actual explanation for how the vertebrate clotting cascade evolved consists of one paragraph. It is a just-so story that doesn't deal with any of the difficulties the evolution of such an intricate system would face." (Behe)

    It does seem that even Miller's detailed scenario has this problem. For example, it still does not address the critical tuning of blood clotting amplification. Too little, and we bleed to death, too much, and all our blood clots.

    "But why would natural selection favor a mutation like this in B's active site? Simple: it would increase the efficiency of the clotting process by producing a 2-level cascade." (Miller)

    It's simple? Only if we leave out control of the system, it seems.

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  37. > Regarding the clotting cascade, in his cross-examination in Kitzmiller Dr. Behe could not even consistently pin down the components of the clotting cascade that were supposed to be IC, admitting if the system were reduced to the components he'd named in Darwin's Black Box that in fact it would not function in humans, but on the other hand it would function in puffer fish.

    Reference, please? I'm finding no mention of puffer fish here.

    > Jud: It was regarding the immune system where during cross-examination in Kitzmiller Dr. Behe said over 100 articles in the peer reviewed literature plus textbooks, together amounting to a pile about two feet high, were all irrelevant.

    And here is Behe's response from (I believe) his erstwhile Amazon.com blog about the pile of papers:

    The point was "here is this mound of evidence confronting Professor Behe". But something does not jive here … I talked a great deal about the immune system … I pointed out that a paper published in 2005 ["The Descent of the … Immune System by Gradual Evolution" – Kline and Nicholaidis], and I showed that in the paper, the authors say that "according to a currently popular view, the 'big bang' hypothesis, the adaptive immune system arose suddenly, within a relatively short time interval, in association with the postulated genome-wide duplication." I pointed out to the court that here was a paper published in 2005, which says that the standard view of how the immune system came about, in a rapid burst, in a rapid appearance, was wrong, and that instead, they were proposing a different view of how the immune system might have come about. … and I was directly addressing the testimony of the other side [e.g. Kenneth Miller]."

    So did Behe produce an argument here? it seems he did, instead of just saying "irrelevant!"

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  38. Bilbo,

    According to Behe, a compound system is one that it is made up of more than a single IC system. Could you identify at least two of the IC systems involved in the transmission of vibrations from the tympanum to the fenestra ovalis?

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  39. lee merrill writes:

    Reference, please? I'm finding no mention of puffer fish here.

    Lee, you'll find the discussion of the puffer fish during Behe's cross-examination here:

    http://www.talkorigins.org/faqs/dover/day12am2.html

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  40. lee merrill says Behe denied on Amazon.com that he said the books and articles he was asked about during cross examination (amounting to a two foot high pile) were irrelevant.

    Here is a quote from Behe's cross examination during the afternoon of day 12 of the trial:

    "Q. Is that your position today that these articles aren't good enough, you need to see a step-by-step description?

    "A. These articles are excellent articles I assume. However, they do not address the question that I am posing. So it's not that they aren't good enough. It's simply that they are addressed to a different subject."

    Thus Behe quite clearly said at trial the books and articles weren't relevant, regardless of the explanations/justifications he chose to offer at Amazon when not under oath and not subject to cross examination.

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  41. lee merrill,

    You are but typing unless and inept noise.

    the adaptive immune system arose suddenly, within a relatively short time interval

    Creationists don't seem prone to check the meaning of "suddenly" and of "relatively short interval." They assume these to mean a couple seconds, while for scientists talking about evolution it can easily mean millions of years. Can you clarify what those terms meant in K & N's paper? Can you also clarify how such a quotation changes anything about Behe ignoring all the data on the evolution of the immune system?

    ----
    For example, it still does not address the critical tuning of blood clotting amplification. Too little, and we bleed to death, too much, and all our blood clots.

    Really? Wow, add me to the list of new converts! If any detail is not explained by Miller it must mean that there is no successful research on the evolution of blood clotting whatsoever, and that evolution could not do it! There! And I was here concluding that ID was merely a god-of-the-gaps argument ... wait! It is a god-of-the-gaps argument!

    Once Miller explains to you about such "critical tuning" (after all, "critical tuning" is not defined by creationists either, who prefer to leave them alone for rhetorical effect), will you deny the possibility because he did not explain to you the evolution of these processes at the atomic detail?

    Please. Think then type.

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  42. Whoops, looks like Moran made another boo boo.

    Larry Moran: "I'm a Darwinist and I speak for all Canadians"

    ReplyDelete
  43. Sorry for not getting back sooner. I couldn't get to a library this weekend, where I use the computer to go online. I forget who brought up the lobster example, but Miller admits that they are different proteins than are used in the human blood-clotting cascade. So I think Behe is right in claiming that there isn't much relevance.

    qetzal: "Note that an arch made of stone blocks perfectly meets point (2). Remove any single block, and it collapses. Yet such arches clearly can be produced in stepwise fashion. Thus, (3) does not follow from (2)."

    But the original scaffolding was already an arch. If you can show that an IC system was made from a simpler system that accomplished the same purpose, and then was replaced, part by part, by the new IC system, then, yes, you have succeeded in showing how an IC system can evolve directly. Do you know of such a biological system?

    Negative Entropy: "Ten proteins with no homologs anywhere so far found. The challenge is not for "naturalistic" evolution. The challenge is for us to ever be able to figure out how that particular system evolved. That's it. After all, other systems, similar to ancestral systems, using those proteins might have gone extinct, or might be there in some organism we have not looked at yet. So, with plenty of clear examples, why doubt that the unclear ones did evolve just as naturally?"

    Even if we have homologous proteins, the problem is figuring out how they became part of a new IC system. Was it one at a time? Then what use were they until all were in place? Was it in one fell swoop? That sounds possible, but what would the probability be of that happening?

    "Have fun reading Miller's book. I have not read it. Nor do I think I will."

    I read it a number of years ago. I think Miller offered a very good way to reconcile Darwinian evolution with Christianity. But I don't think his arguments against Behe were very good.

    TomS: "Do you have an example of a difference which is "irreducibly complex", a difference between the human body and the body of a chimp, or of any other ape, a difference to which the IC argument shows that there is no likelihood of common descent with modification?"

    Behe accepts and even argues in favor of common descent (in his second book). What he argues against is that all of the modifications are by random mutations. He argues that at least some of them are non-random.

    Jud: "You don't have to go to Ken Miller's book, just read Dr. Behe's own cross examination in Kitzmiller."

    When I get a chance. You wouldn't have a link, would you?

    Lee: Thanks for the links.

    Geoxus: "Could you identify at least two of the IC systems involved in the transmission of vibrations from the tympanum to the fenestra ovalis?"

    Is that all that is involved in the auditory system?

    Jud: http://www.talkorigins.org/faqs/dover/day12am2.html

    Thanks for the link, Jud.

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  44. > Jud: Lee, you'll find the discussion of the puffer fish during Behe's cross-examination here...

    So here is the result of the discussion:

    Q. Well, you spent a lot of time trashing Dr. Doolittle and his work, his article in the Boston Review. Your mistake here is quite a bit more substantial than misinterpreting a mice study, isn't it?

    A. I'm not even quite sure what you are referring to as my mistake.

    Q. I'll withdraw that question, Professor Behe.

    > Jud: Thus Behe quite clearly said at trial the books and articles weren't relevant...

    But the point you were making was seeming to imply that's all he did, and it wasn't. He addressed Miller's points. Are were the books and articles relevant? If so, which ones?

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  45. > Negative Entropy: Can you clarify what those terms meant in K & N's paper?

    Well, Behe's point is that the Doolittle scenario is being rejected by some authors. The matter is a matter of some dispute, thus "all these papers" won't carry the day.

    > Lee: For example, it still does not address the critical tuning of blood clotting amplification.
    >
    > NE: If any detail is not explained by Miller it must mean that there is no successful research on the evolution of blood clotting whatsoever, and that evolution could not do it!

    Well, no, the point is that Miller's scenario is inadequate if he leaves this aspect out.

    Especially after Behe has pointed out the problem, then to present this as a solution borders on deception.

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  46. But the original scaffolding was already an arch.

    No ... it was a hump. It only becomes an arch if there is a gap beneath. Consider a simple hill of solid rock. If you drive a tunnel through it, you have also made an arch. Alternatively, if you lay blocks over the hill surface and then remove all the original rock, you have used the hill as support during the construction of a separate arch. In neither case was it 'already an arch' - it became one upon removal of support.

    If you can show that an IC system was made from a simpler system that accomplished the same purpose, and then was replaced, part by part, by the new IC system, then, yes, you have succeeded in showing how an IC system can evolve directly. Do you know of such a biological system?

    Do you know of any IC biological system? The point of arch analogies is to show that lost information - the removed rock in the above example - forms a vital part of the evolutionary pathway. ID proponents insist that the burden of proof lies with the mainstream to show what the nature of such 'lost' information is. But to demonstrate IC, one would have to eliminate the possibility of such 'lost' intermediate states.

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  47. > Lee: Well, no, the point is that Miller's scenario is inadequate if he leaves this aspect out.

    I need to correct my comment, Miller's book leaves this out, Miller's expanded article discusses controlling the clotting:

    "... just as soon as the occasional clot becomes large enough to present health risks, natural selection would favor the evolution of systems to keep clot formation in check. And where would these systems come from? From pre-existing proteins, of course, duplicated and modified. The tissues of the body produce a protein known as a1-antitrypsin which binds to the active site of serine proteases found in tissues and keeps them in check. So, just as soon as clotting systems became strong enough, gene duplication would have presented natural selection with a working protease inhibitor that could then evolve into antithrombin, a similar inhibitor that today blocks the action of the primary fibrinogen-cleaving protease, thrombin."

    Right, these components are in place, but how do you evolve them as a system? This is the complexity that presents the problem, too much clotting is very important to control, and the control has to evolve together with the clotting amplification. And an added level of amplification would provide a quantum leap in clotting, as indeed Miller says, this means control would be rather urgent.

    "In similar fashion, plasminogen, the precursor to a powerful clot-dissolving protein now found in plasma, would have been generated from duplicates of existing protease genes, just as soon as it became advantageous to develop clot-dissolving capability."

    But all this takes time. If my clotting is out of control, I'm going to have trouble waiting for a gene duplication and a fortuitous mutation.

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  48. Bilbo: But the original scaffolding was already an arch. If you can show that an IC system was made from a simpler system that accomplished the same purpose, and then was replaced, part by part, by the new IC system, then, yes, you have succeeded in showing how an IC system can evolve directly. Do you know of such a biological system?

    The original scaffolding need not be an arch. It could be two separate scaffolds, each supporting one side of the nascent arch.

    In any case, you seem to be missing the point. Whoever wrote the original piece made a positive claim about IC systems - that they can't be made in stepwise fashion (and therefore couldn't be generated by conventional evolution). I was simply showing that their claim is trivially wrong, and therefore does not disprove evolution.

    I'm not trying to argue that existing biological IC systems evolved by the particular stepwise mechanism you're suggesting, or by any other. I'm merely arguing that there ARE stepwise mechanisms by which a biological system could, at least hypothetically, evolve to be "IC" without having to come together all at once. Proving whether any given system DID evolve by such a mechanism is a different discussion. An interesting one, no doubt, but not one I care to engage at the moment.

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  49. Allan Miller: "But to demonstrate IC, one would have to eliminate the possibility of such 'lost' intermediate states."

    How do we go about eliminating possibilities, exactly?

    qetzal: "Proving whether any given system DID evolve by such a mechanism is a different discussion. An interesting one, no doubt, but not one I care to engage at the moment."

    Let me know if you decide to engage in it.

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  50. Lee,

    I asked:
    Can you clarify what those terms meant in K & N's paper?

    You answer:
    Well, Behe's point is that the Doolittle scenario is being rejected by some authors. The matter is a matter of some dispute, thus "all these papers" won't carry the day.

    So you can't clarify what those terms meant in K & N's paper, and you still think that the quote means something?

    How on Earth does a quote with neither clarifications as of what those terms mean, nor the data that support (or not) the quote, can be construed to mean that some authors don't agree with Doolittle? Who said that all those papers were written by Doolittle? Do you really think that the research on the evolution of any system is done by putting together meaningless quotes with no data nor evidence whatsoever? Do you really think that whatever Miller writes, or Doolittle, is all there is to the current understanding of how those systems have evolved?

    I should not be surprised. But I am.

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  51. Bilbo,

    So now you move the goal posts? I agree that the question as to how those proteins go from one system to form another is important and interesting. Don;t get me wrong. But can we say that your first "problem," the hypothetical case where we might not know where those ten protein came from, was answered?

    As to how proteins are recruited from one system into another. There are several clues. But it would take me a good while to explain here. I can tell you, without pretending that my words will convince you, but so that you understand my stance, that some examples are clear cut. Some more complicated than others, and so on. Not all cases are clear. Sure there must be other clear but complicated cases that have been solved and I have not read about. But I bet there are many for which we might never have a clue of how they evolved. Yet again, since we have clear examples, I don't see why we should propose that the unclear ones need an "intelligent designer," rather than propose that the evolutionary steps leading to those systems might have been lost in the confines of the history of life on Earth. Do you understand why I see your IC stuff as nothing but a god-of-the-gaps argument?

    Best for your holidays.

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  52. Lee,

    Well, no, the point is that Miller's scenario is inadequate if he leaves this aspect out.

    It is only inadequate if you expect Miller to cover each and every detail you care to toss at him. It is much easier to come up with further questions than to answer them. Just how much research do you think it took to figure out the kinds of clotting cascades existing across organisms? Just in humans? It is thus bullshitting around to think that because you can come up with detail questions that Miller did not answer it means that IC carries any weight as an argument for creationism (by whichever name you want to call it). You are showing it to be nothing but a god-of-the-gaps argument.

    Especially after Behe has pointed out the problem, then to present this as a solution borders on deception.

    No. Because then all Behe has to do is continue moving the goalposts. From "there is nothing indicating the evolution of this system" to "but what about this detail?" to "what about this other detail?" Until Behe stands on "that does not explain the atomic detail behind every mutation." Thus because Miller's explanations will always "fall short" of Behe's capacity to continue demanding detail, you will conclude that it is Miller who is wrong there? I would say that the strategy of moving the goal posts is what "borders on deception."

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  53. Is that all that is involved in the auditory system?

    Certainly not, and that's irrelevant*, but if I sidetrack to explain why, I find much more interesting point.

    A "subsystem" is as much of a proper system as the whole system. Let's be reminded that a "system" is a subset of all the structures and interactions that's arbitrarily delimited by us for explanatory purposes. There is not a single "correct" way of breaking apart an organism into systems. And there is not a single "correct" way of breaking a system into parts either**. So the identification of IC is dependant on the way we chose to describe things. Isn't this a problem?

    * TomS specifically mentioned the mammalian middle ear, not the whole auditory system.

    ** There might be more appropriate ways of breaking things apart depending on the problem at hand. If that's the case for IC, I'd like to know what are the criteria.

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  54. Negative Entropy: "Yet again, since we have clear examples, I don't see why we should propose that the unclear ones need an "intelligent designer," ....

    Which clear examples do we have?

    Best holidays to you, also, NE.

    ReplyDelete
  55. > Negative Entropy: So you can't clarify what those terms meant in K & N's paper, and you still think that the quote means something?

    Well, from here it seems we're talking about animals at the base of the evolutionary tree, just past multicellular organisms. So quickly, on a timescale relative to all of life's history, which yet might be millions of years.

    But the point is that there is disagreement about fundamentals in evolution of the immune system. This is not quibbling about details. A search just turned up: Immune System: "Big Bang" in Question, Pradeu, T.,
    Science, vol. 325, issue 5939, pp. 393-393, four years after the Dover trial.

    > How on Earth does a quote with neither clarifications as of what those terms mean, nor the data that support (or not) the quote...

    But none of these questions pertain to my view here. What makes you think that for instance, I believe Miller and Doolittle wrote everything on this subject?

    > From "there is nothing indicating the evolution of this system" to "but what about this detail?"

    Well, here, let me propose to you that I have written a history of the development of the motorcycle, but I only mark out plainly the development of the engine.

    You might suggest that my history would be lacking. The question is whether control of amplification is a critical aspect of the system, clearly it is, like the brakes and the throttle on a motorbike.

    Happy holidays,
    Lee

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  56. Ugh -- neither side of the "big bang in (vertebrate) immune system evolution" question doubts that the immune system evolved, nor that there are numerous known relatives of the vertebrate immune system proteins in invertebrates, nor that the key RAG genes are derived ultimately from transposons, nor hundreds of more detailed established facts about the evolutionary origins of the vertebrate immune system.

    The "big bang" idea basically suggested that the transposon insertion event was the key event in the whole process, which kicked off a whole cascade of evolutionary events producing modern-ish vertebrate immune systems in the ancestors of sharks + higher vertebrates.

    The criticism of the "big bang" idea is that the immune system is really about a lot more than the RAG gene adaptive system, and that many/most/virtually all of these other components can be found in more distant relatives. If this is the case, the "big bang" language seems to be an inaccurate description, so criticism of it has increased in recent years.

    I'm pretty sure, Lee, that you would be completely unable to explain even the basics of this debate, and you are simply relying on Behe's word on this, and that he would be similarly unable to describe what this debate is about and why it constitutes evidence that evolutionary theory is completely unable to explain something like the immune system. The kind of silliness from ID guys will never, ever impress serious scientists.

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  57. Here's the referenced letter from 2009:


    ====================
    Science 24 July 2009:
    Vol. 325 no. 5939 p. 393
    DOI: 10.1126/science.325_393a

    Letters

    Immune System: “Big Bang” in Question

    J. Travis's News Focus story “On the origin of the immune system” (1 May, p. 580) strengthens the idea that there exists a “Big Bang” in the evolution of the immune system, namely the move from innate to adaptive immunity. Yet evidence accumulated during the past 10 years has shown that this idea requires caution, for at least three reasons: (i) Immune memory, supposedly a characteristic of adaptive immunity and therefore of higher vertebrates, does in fact exist in invertebrates (1, 2). (ii) Nonvertebrate immunity no longer appears to be “unspecific”; many forms of immune specificity exist in animals, and even in plants (3). (iii) The adaptive immune system never works on its own [a little-known fact first revealed 20 years ago (4) but subsequently neglected]. An antigen that is recognized by the adaptive immune system but not by the innate immune system will not, in general, trigger an immune response (5).

    These studies show that immunity is ubiquitous in nature and that the boundary between adaptive and innate immunity is not as clear cut as has been claimed for decades (6). In light of these results, looking for evidence for the immunological “Big Bang” is probably an inadequate strategy for studying the evolution of immunology.

    Thomas Pradeu

    Institut d'Histoire et de Philosophie des Sciences et des Techniques, Paris-Sorbonne University, Paris, 75006, France.

    E-mail: thomas.pradeu@paris-sorbonne.fr

    References


    J. Kurtz,
    K. Franz
    , Nature 425, 37 (2003).
    UC-eLinksCrossRefMedline

    K. Kurtz,
    S. A. O. Armitage
    , Trends Immunol. 27, 493 (2006).
    UC-eLinksCrossRefMedlineWeb of Science

    B. J. DeYoung,
    R. W. Innes
    , Nat. Immunol. 7, 1243 (2006).
    UC-eLinksCrossRefMedlineWeb of Science

    C. A. Janeway
    , Cold Spring Harbor Symp. Quant. Biol. 54, 1 (1989).
    Abstract/FREE Full Text

    R. M. Steinman,
    D. Hawiger,
    M. C. Nussenzweig
    , Annu. Rev. Immunol. 21, 685 (2003).
    UC-eLinksCrossRefMedlineWeb of Science

    E. Vivier,
    B. Malissen
    , Nat. Immunol. 6, 17 (2005).

    ====================

    Which is in reply to Travis's (2009) popular article in Science, on the history of research into the evolution of the immune system. (And it favorably cites the Dover immune cross)

    http://www.sciencemag.org/content/324/5927/580.full

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