Over on the opposingviews.com website, Casey Luskin of the DI tries to rebut the Kitzmiller decision by re-fighting Behe’s spectacular implosion on the issue of the evolution of the vertebrate immune system. To review, in his 1996 book Darwin’s Black Box, Behe claimed that:
“As scientists we yearn to understand how this magnificent mechanism came to be, but the complexity of the system dooms all Darwinian explanations to frustruation.” (Darwin’s Black Box, p. 139)
“We can look high or we can look low, in books or in journals, but the result is the same. The scientific literature has no answers to the question of the origin of the immune system.” (Darwin’s Black Box, p. 138)
As the debate over “irreducible complexity” developed in the next decade, the most detailed arguments would go basically like this:
ID: Gradual evolution by natural selection can’t produce IC structures because any structure missing a part would be nonfunctional
Evo: You are ignoring cooption of structures with different functions, which has a been a major feature of the evolutionary explanation of complex structures ever since the Origin of Species.
ID: Cooption explanations are too improbable.
ID: Because we say so.
Evo: But homology evidence shows that “IC systems” lacking parts can still have other functions, and therefore your claim that structures missing parts would be nonfunctional is wrong
ID: OK well I don’t have a comeback on that point, so instead I will claim that evolutionary cooption explanations aren’t detailed & tested enough to satisfy me.
Evo: Here’s a bunch of detailed & tested research papers on the evolution of system X.
ID: Not detailed enough. I need every single mutation & selection pressure before I admit that evolution produced this IC system rather than ID.
At this point the ID proponent has abandoned the original argument and therefore lost, even though he won’t admit it. Knowing all of this before the Kitzmiller trial, we devised ways to bring this point to the attention of the judge. The most famous example was the fabled “immune system cross”. A large amount of evidence was submitted that showed how the key feature of the vertebrate adaptive immune system, rearranging immune receptors (antibodies), evolved. The adaptive immune system produces diverse antibodies by recombination of different immunoglobin (Ig) domains. In Darwin’s Black Box, Behe argued that the gradual evolution of this system was impossible because the three crucial parts (antibody genes, recombination signal sequences, and recombination-activating genes (RAGs)) could not provide minimal function unless they were all assembled at once:
“In the absense of the [RAG] machine, the parts never get cut out and joined. In the absense of the signals, it’s like expecting a machine that’s randomly cutting paper to make a paper doll. And, of course in the absence of the message for the antibody itself, the other components would be pointless.” (Darwin’s Black Box, p. 130).
The scientific literature on the origin of this system was well-known in the evolution/ID-creationism debate, primarily because various PT posters like Matt Inlay and Andrea Bottaro had been waving it in the faces of the ID guys for several years. The responses of Dembski (“ID is not a mechanistic theory, and it’s not ID’s task to match your pathetic level of detail in telling mechanistic stories”) and Behe were pitiful, always involving retreating to an impossible, unscientific requirement for infinite evolutionary detail before evolution was accepted and ID rejected.
So, in court in the Kitzmiller case, the obvious thing to do was take Behe through the above steps of the immune system argument, and when he reached the point of asserting there was not enough detail – and confirming that he still believed his 1996 statements about how the literature had “no answers” on the evolution of the immune system – a large body of literature on just this question was presented to Behe. Behe hemmed and hawed – he couldn’t just dismiss a pile of peer-reviewed research in top journals, but he also couldn’t admit that it was good enough to answer his question because then his whole position was sunk. So he asserted that the literature was not detailed enough. Telling himself this tale may have helped Behe get to sleep that night, but to any objective observer this was a ludicrous and laughable response. If hundreds of pages of peer-reviewed research specifically on the origin and evolution of the vertebrate immune system, proposing, testing, and verifying a detailed model (called the transposon model) for its origin, was not enough for Behe, then clearly nothing could ever be enough and Behe was only maintaining his position by a stubborn refusal to seriously deal with the data (and he still has not dealt with the evolutionary immunology literature in any detail). Basically, Behe’s verbal victory worked in his own head but was a spectacular defeat in the eyes of anyone with a vaguely rational view of what appropriate standards of evidence in science might be (that is: when you propose and test hypotheses you have good science, when you demand impossible levels of proof before accepting anything you are engaging in pseudoscience). When this was coupled to Behe’s nonanswers to questions like “Well, Dr. Behe, where is the detailed, testable ID explanation for the origin of the immune system?” it was all over. The details are here.
Well, this particular point, more than almost anything else except perhaps the discovery of the cdesign proponentsists, really really stung the ID guys. The fact that it made it into the Kitzmiller decision and numerous books, articles, and the Nova reenactment only made it worse. It is just too painful for them to contemplate it unemotionally and admit that they lost on a crucial scientific point, so occasionally ID advocates will pop up with pitiful responses that try to fix the damage. What follows is one that was really pitiful. Casey Luskin has developed a line of argument that he thinks is clever and serious, but is actually a product of the very same problem that afflicted Behe: a failure to engage seriously with the literature on evolutionary immunology and deal with the massively inconvenient facts.
In the opposingviews.com essay, Casey Luskin writes (a fair bit down the page; the opposingviews format is pretty confusing so I reproduce the relevant bit here),
In another finding which was both wrong and irrelevant, Judge Jones ruled that “Dr. Miller presented peer-reviewed studies refuting Professor Behe’s claim that the immune system was irreducibly complex.”(24) Moreover, Judge Jones found that Behe’s claims that the immune system was irreducibly complex were refuted by a large stack of papers dumped upon him during cross-examination:
“[O]n cross-examination, Professor Behe was questioned concerning his 1996 claim that science would never find an evolutionary explanation for the immune system. He was presented with fifty-eight peerreviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system.”(25)
Yet Behe never claimed that no papers or books are “about the evolution of the immune system”–indeed in Darwin’s Black Box, Behe wrote that “[t]here are other papers and books that discuss the evolution of the immune system.”(26) On the contrary, Behe actually testified:
“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.”(27)
Thus, what Behe actually requested was, “a step-by-step mutation by mutation analysis” of the evolution of the immune system, for Behe said he is “quite skeptical” that the papers in the literature dump “present detailed rigorous models for the evolution of the immune system by random mutation and natural selection.”(28) Judge Jones misquoted Behe and twisted his views about the state of evolutionary literature on the origin of the immune system.
One of the 58 articles dumped on Behe was an authoritative article published in Nature the year before the Kitzmiller trial which conceded that there were major questions about step-by-step accounts of the evolution of the adaptive immune system. In that recent and authoritative paper, Max Cooper, one of the fathers of immunology, wrote that the evolutionary origin of one of the most important components of the higher vertebrate “adaptive immune system,” the immunoglobulin (IG) domain containing antibody, is currently “untraceable”:
“In contrast, the deployment of immunoglobulin domains as core components of jawed vertebrate recombinatorial lymphocyte receptors represents an intriguing although as yet untraceable evolutionary innovation, as immune recognition of pathogens and allografts by means of immunoglobulin superfamily members have been shown only in the jawed vertebrates.”(29)
IG domains perform a primary structural function in antibodies of the “adaptive immune system” used by all jawed vertebrates (such as sharks, reptiles, birds, and mammals). The paper discovered that the antibody-equivalent in the lamprey (a jawless vertebrate fish) is highly dissimilar, both in structure and how they are assembled. In fact, the lamprey uses a completely different type of protein domain for its antibody-equivalent structures. This paper therefore calls the origin of anitibodies that utilize IG domains presently “untraceable.”
Furthermore, when these authors say that the usage of IG domains is “untraceable,” they are not asking the question “from what were these materials co-opted during evolution?” IG domains are found throughout biology from bacteria to humans and thus it is simple to imagine where higher vertebrates might have co-opted such domains. Rather, this paper is talking about the type of deeper question Behe raises: by what Darwinian pathway did IG domains evolve into the type of IG domain used by antibodies in the adaptive immune system of higher vertebrates?
This paper had no answer to that question, yet Judge Jones claimed that Miller provided evidence demonstrating that “[b]etween 1996 and 2002, various studies confirmed each element of the evolutionary hypothesis explaining the origin of the immune system.”(30) Did Judge Jones read these 58 papers plus books and other literature dumped during the trial to verify his claim? I highly doubt it. After all, Judge Jones’ discussion on the immune system was copied nearly verbatim from an ACLU brief.(31) But a cursory look at one of those papers reveals that Judge Jones’ finding was a bluff, and Behe’s arguments were never refuted.
In the end, most of Kenneth Miller’s arguments about the evolution of the immune system were based upon observing mere sequence similarity or functional similarity between proteins used by our immune system and some found in lower organisms. In other words, some of the starting material might be crudely present elsewhere in biology, but Miller did not testify about any step-by-step Darwinian pathways as Behe requested, nor did Miller testify about the vast differences between our adaptive immune system and immune systems used by lower organisms like the Lamprey.(32) Behe was never refuted, and Judge Jones’ strong findings based upon such hypothetical arguments demonstrate his uncritical acceptance of the plaintiffs’ literature-dump bluffs.
These episodes provide vivid illustrations why it is dangerous for courts to try to settle these scientific debates. Legal scholars agree with this basic point.
(24) Kitzmiller 400 F.Supp.2d at 741.
(25) Id, at 741.
(26) Michael J. Behe Darwin’s Black Box, pg. 138.
(27) Transcript of Testimony of Michael Behe 19 Kitzmiller, No. 4:04-CV-2688 (M.D. Pa., Oct. 19, 2005).
(28) Id. at 19, 23
(29) Nature, Vol. 430: 174-180 (July 8, 2004) Z. Pancer, Z., C. T. Amemiya, G. R. A. Ehrhardt, J. Ceitlin, G. L. Gartland, M. D. Cooper, “Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey”
(30) Kitzmiller 400 F.Supp.2d at 741.
(31) A Comparison of Judge Jones’ Opinion in Kitzmiller v. Dover…
(32) Transcript of Testimony of Kenneth R. Miller
“The significant similarity between the transib transpases and RAG core, the common structure of these transpases and others, as well as the similar size of these basically catalyzed by these enzymes directly support the 25-year-old hypothesis of a transposon related origin of the VDJ machinery.” 30-31, Kitzmiller, No. 4:04-CV-2688 (M.D. Pa., Sept. 26, 2005).
A shorter version of this argument is provided in a law review article coauthored by Luskin (David K. DeWolf, John West, Casey Luskin. “Intelligent Design will Survive Kitzmiller v. Dover,” 68 Montana Law Review 7 (Winter, 2007)):
Judge Jones ruled that a pile of fifty-eight papers dumped upon the witness stand during Behe’s cross-examination refuted the claim that “science would never find an evolutionary explanation for the immune system.” Kitzmiller v. Dover Area Sch. Dist, 400 F. Supp. 2d 707, 741 (M.D. Pa. 2005). Judge Jones provided no reference for that claim. Behe merely requested a reasonable standard of evolutionary proof of “detailed rigorous models for the evolution of the immune system by random mutation and natural selection.” Transcr. of Procs. Afternoon Sess. at 23 (Oct. 19, 2005), Kitzmiller, 400 F. Supp. 2d 707. Did the fifty-eight papers meet that standard? One of the papers, an authoritative article recently published in Nature, reveals the answer is “no,” as it clearly discussed the lack of step-by-step accounts of the evolution of key components of the immune system: “In contrast, the deployment of immunoglobulin domains as core components of jawed vertebrate recombinatorial lymphocyte receptors represents an intriguing although as yet untraceable evolutionary innovation, as immune recognition of pathogens and allografts by means of immunoglobulin superfamily members [IG domains] have been shown only in the jawed vertebrates.” Z. Pancer et al., Somatic Diversification of Variable Lymphocyte Receptors in the Agnathan Sea Lamprey, 430 Nature 174, 179 (2004) (emphasis added). Immunoglobu lin (IG) domains are a common structure in proteins found throughout biology from bacteria to humans. Id. at 174. When the paper found that the evolution of IG domains is “untraceable,” it was therefore not asking “from what might these structures have been borrowed during evolution?” It was asking the deeper question Behe raises: by what detailed, step-by-step pathway did IG domains come into their critical function in the adaptive immune system? Judge Jones said “each element of the evolutionary hypothesis explaining the origin of the immune system” had been “confirmed.” Kitzmiller, 400 F. Supp. 2d at 741. Yet Pancer’s recent, authoritative paper reveals that Judge Jones’s finding merely recapitulated the plaintiffs’ literature-dump bluff, and that Behe’s actual arguments were never refuted.
When this came out, I noted its sillyness in private, but no one ever got around to rebutting it in public, so apparently Luskin figured he’d made a good point and put even more weight on it in the opposingviews.com debate.
(An aside: if you’re not up on your evolutionary immunology, antibodies are basically Y-shaped receptors made up of a series of Ig-domains; different domains get switched around via V(D)J recombination to generate zillions of different antibodies that can bind almost any invader; the transposon hypothesis suggests that V(D)J recombining receptors evolved from non-recombining receptors by insertion of a transposon that would snip itself out, rejoining the receptor segments in different ways. Duplication & elaboration of this basic system produced the modern system. See the figures/discussion here and here)
Luskin’s argument doesn’t make sense even if his facts were right
Here’s the short version of Luskin’s argument: Luskin claims that Pancer et al. (2004) showed there was a big gap in the origin of the vertebrate immune system – that is, where did an Ig domain involved in immune recognition come from?
This question wasn’t answered by 2005, claims Luskin, and therefore (this argument resembles the “Underpants Gnomes” business plan from South Park) Judge Jones was wrong to rule that “various studies confirmed each element of the evolutionary hypothesis explaining the origin of the immune system” and therefore “Behe’s arguments were never refuted.”
Again, this sort of thing makes the ID proponent feel better and lets them sleep at night, but it’s wrong on several levels as a scientific argument.
1. First of all, the “as yet untraceable” remark in Pancer et al. 2004 was just an aside from the main point of the paper, which was about how lampreys have their own adaptive immune system which is different from the adaptive immunity of jawed vertebrates. Evolution is used throughout the methods and analysis of the paper, so it is rather strange to attempt to use it as evidence against evolution. The paper did not do a thorough search for Luskin’s “missing” Ig domain, it just mentioned as an aside that it had not been found yet.
2. Second, it is not clear exactly what Pancer et al. actually meant in their parenthetical remark. They cite Kaufman (2002), which reports on the discovery of V-type domains in Amphioxus, but notes various differences which indicate that that particular molecule was not a super-close relative of the non-rearranging ancestor of the V(D)J receptor. So a possible interpretation, the one which Luskin adopts, is that they are still searching for a close relative of a non-rearranging V-type receptor. But Pancer et al. might merely have been saying that they didn’t detect VDJ recombination in lampreys, which is unsurprising because the system much have originated at some point, and the common view has always been that it originated after jawed vertebrates diverged from lampreys. The whole point of the transposon model is to explain how that system originated.
3. Third, even if it were true that the origin of an Ig domain with an immune function was (currently) untraceable, Luskin admits that Ig domains with other functions are well-known and widespread, so there is not really much of a “leap” left. There is no requirement in the scenario that the ancestor of the rearranging antibody had an immune function as opposed to some other binding function, although probably most immunologists thought that this was the most likely option, being a particularly gradual pathway. As previously mentioned, not just Ig domains, but specifically V-type domains were discovered in Amphioxus in 2002 (see: Kaufman, J. (2002). “The origins of the adaptive immune system: whatever next?” Nature Immunology 3(12): 1124-1125. This article was in the Kitzmiller immune system exhibit, so there is a summary in the Annotated Bibliography).
4. Fourth, even in 2005 it wasn’t true to say that non-rearranging V-type Ig domains, with immune functions, in organisms diverging before jawed vertebrates, were unknown. PT poster Ian Musgrave comments:
Even by 2004 several Ig-like molecules had been identified in amphioxus and sea squirts that could play the role of the ancestor of Ig. In sea squirts there are Ig fold proteins (nectin and Junctional Adehesion Molecules) with an Ig fold and a Constant-Variable domain architecture just like the immunoglobulins. Also in amphioxus there is an Ig protein which is used in innate immunity (the Variable Domain Chitin Binding proteins) that was known in 2002 (in 2006 a protein that is a very similar to the TCR and is involved in innate immunity was found in the amphioxus, but here I’m dealing with 2004 knowledge).
The most one can say is that, in 2004, non-rearranging V-type Ig domains, with immune functions, had not yet been found specifically in lampreys.
5. Fifth, nothing about a missing Ig receptor impeaches any of the other evidence that was discovered in the literature and presented at trial. To wit:
* the VVVVVVV DDDDDD JJJJJJ arrangements found in the genomes of bony fish and land vertebrates, and the VDJ VDJ VDJ VDJ VDJ VDJ VDJ VDJ arrangements found in sharks and relatives, indicated that the common ancestor was a much simpler VDJ arrangement that was elaborated by duplication.
* the hypothesis that the recombination genes (RAG) were descended from a transposon was dramatically confirmed by the discovery of just such a transposon in the wild, a transposon which we had no reason to suspect existed, except for the transposon hypothesis for the origin of recombination.
* numerous other discoveries mentioned here
The transposon model for the origin of the vertebrate immune system was literally standard textbook material by 2005 and was strengthened even further by several discoveries in 2005. As with any complex historical process there will always be various gaps in our knowledge, but none of this weakens the major collection of positive scientific discoveries supporting the transposon model. All of the positive evidence is still there whether or not a particular gene has yet been discovered in a particular organism. Only ID proponents think that they can turn ignorance into scientific support for their position.
6. Sixth, in 2005 we didn’t even have a genome sequence for lampreys and other relevant early-diverging organisms. Claiming that a missing homology is a problem is particularly dumb if the relevant sequencing hasn’t even been accomplished yet.
It gets worse for ID
So Luskin’s argument is excruciatingly bad even if he had his facts right. But as it turns out, he didn’t have his facts right. As Luskin noted, Pancer et al. (2004) said, in an article coauthored by “Max Cooper, one of the fathers of immunology”, that:
“immune recognition of pathogens and allografts by means of immunoglobulin superfamily members have been shown only in the jawed vertebrates”
Luskin and other ID proponents seem to think that such ignorance, once admitted in science, is permanent and irrevocable, and is forever a stain on an evolutionary model for a particular system.
Unfortunately for them, though, science doesn’t stay still. Have a look at this paper:
Yes, those coauthors include the very same Pancer who was the lead author on Luskin’s favorite paper, as well as “Max Cooper, one of the fathers of immunology.” And what do they say?
Abstract Immunoglobulins (Igs) and T cell antigen receptors (TCRs) that undergo somatic diversification have not been identified in the two extant orders of jawless vertebrates, which occupy essential positions in terms of understanding the evolution of the emergence of adaptive immunity. Using a single motif-dependent PCR-based approach coupled with a vector that allows selection of cDNAs encoding secretion signal sequences, four different genes encoding Ig V-type domains were identified in the sea lamprey (Petromyzon marinus).
Whoops. It appears that once someone had a good hard look for V-domains in agnathans, they found them. Who would have thunk it? In the conclusion, the paper also notes:
The recent description of a non-rearranging single copy gene sequence in lamprey that can be modeled to a TCR V suggests that other molecules that are related to the combinatorial antigen binding receptors may exist in jawless vertebrates (Pancer et al. 2004b).
What’s that? A homolog to another V-domain was discovered in 2004 as well? The referenced paper is:
Pancer Z, Mayer WE, Klein J, Cooper MD (2004b) Prototypic T cell receptor and CD4-like coreceptor are expressed by lymphocytes in the agnathan sea lamprey. Proc Natl Acad Sci USA 101:13273-13278
Hey look, our buddies Pancer and “Max Cooper, one of the fathers of immunology” again! And what do they say in this 2004 paper? If “prototypic T cell receptor” wasn’t clear enough for you, here’s the abstract:
All jawed vertebrates have highly diverse lymphocyte receptors, which allow discrimination between self and nonself antigens as well as the recognition of potential pathogens. Key elements of the anticipatory recombinatorial immune system in jawed vertebrates are the TCR, Ig, and MHC genes, but their ancestral genes have not been found in more basal vertebrates. In this study, we extended our analysis of the transcriptome of lymphocyte-like cells in the lamprey to identify the TCR-like and CD4-like genes. The structural features of these genes and their preferential expression in lymphocytes make them attractive candidates for ancestral TCR and CD4 genes. The TCR-like gene contains both V (variable) and J (joining) sequences in its first exon and exists as a single-copy gene that is invariant. Thus, the TCR-like gene cannot account for the receptor diversity that is required for the immune responses reported for lamprey, but it could have been easily modified to serve as an evolutionary precursor of modern TCR and Ig genes.
So basically, the authors answered Luskin’s question in an article published in the research literature in the very same year as the paper which Luskin has been citing at opposingviews.com, in a comprehensive pro-ID law review article, and probably elsewhere.
But, how could poor Casey Luskin have known about this discovery? I mean, after all, he is not “one of the fathers of immunology,” is he? (say, I wonder what a father of immunology would say about Behe’s argument?) Well, as it happens, Cannon et al. 2005 is sitting right there in the friggin list of articles given to Behe! Pancer et al. 2004b is not (an oversight on the part of the Kitzmiller plaintiffs’ team – we beg forgiveness: there is so much evolutionary immunology literature, it was hard to get even a decent sample of it together!), but it was cited by Cannon et al. (2005).
Earth to Luskin and ID guys: you screwed up. Your very best (and basically only) scientific counterargument to Behe’s immune system debacle fell apart as soon as someone took a mildly close look at the situation. You relied on scientific ignorance to maintain some smidgen of credibility for the ID movement’s rejection of massive positive evidence for evolution, and, predictably, you got burned. Again. Good job.
(Even worse, we had to catch the mistake for you, proving (again) that within the entire ID community there is no one with the knowledge/gumption/scientific spirit to read just a few measly articles on evolutionary immunology to double-check a key Luskin assertion.)
Thanks to Ian Musgrave, Andrea Bottaro, and the PT crew for helpful comments.