You are hereAnnotated Bibliography on the Evolutionary Origin of the Vertebrate Immune System
by Nick Matzke
This webpage contains the same articles and books used during the Behe cross-examination that are listed in the Supplementary Material for Bottaro et al. (2006). Here, the citations have been placed in chronological order, and each reference is annotated with a blue box containing a short summary of the significance of the paper, and if relevant, significant quotes from the paper. IntroductionThe purpose of this annotated bibliography is to give the nonspecialist reader some sense of the scholarly weight of the evolutionary immunology literature (here is another method). In particular, this bibliography focuses attention on the scientific work that developed, tested, and established the "transposon hypothesis" for the origin of receptor rearrangement in the adaptive immune system. Contrary to the impression one might get from the ID literature, the transposon hypothesis was not idle speculation, it was not thought up yesterday over breakfast, it is not particularly vague, it is not untestable, and it is not scientifically useless. In contrast, by reading through the bibliography in chronological order, we can see that the transposon hypothesis was explicitly proposed and published in top journals, it was carefully and seriously discussed for decades in the professional literature, it has inspired a very productive research program (both experimental and comparative), it has been tested with diverse evidence by researchers working in many different labs, and it has been dramatically confirmed. In short, it is a classic case of serious, advancing evolutionary science. Without ever getting mentioned in a newspaper article or cable news show, hundreds of PhD scientists have devoted their careers to working out how and why the immune system evolved. Any one of these researchers has quietly produced more research results than the entirety of the intelligent design movement with their collection of op-eds, webpages, in-house publications, books published by InterVarsity Press, one or two books by slightly more rigorous publishers but with dubious peer-review, and one or two review articles slipped into obscure journals. Unlike "intelligent design" proponents, evolutionary immunologists repeatedly published their key work in top journals. For some reason, they have not felt the need to write law review articles, lobby school boards and legislatures to get their view taught, or muck around with state science standards, because they know that scientific hypotheses succeed by convincing other scientists through research. For more along these lines, see Bottaro et al. (2006) and the Why the Immune System?The decision to make the evolution of the immune system a key example in both Kenneth Miller's direct testimony and Michael Behe's cross-examination was based on several factors. First, among the major systems that Behe discusses in Darwin's Black Box, such as the eukaryotic cilium, the bacterial flagellum, the blood-clotting cascade, and the immune system, Behe makes particularly florid claims about the absence of literature on the origin of the immune system -- for example:As scientists we yearn to understand how this magnificent mechanism came to be, but the complexity of the system dooms all Darwinian explanations to frustration. (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)These are claims crying out for refutation. As it happens, there is probably more scientific literature directly on the evolution of the immune system than on the other three systems put together (we can chalk this up to (1) the long tradition of evolutionary and comparative studies in immunology; (2) the age of the discipline (going back to the 1800's); and (3) the massive amount of medical research money available for studies of the immune system, for obvious reasons). So, while Behe makes various mistakes on the other systems, many also discussed at trial, he is most dramatically wrong about the immune system literature. Second, although the immune system is very complex, everyone is familiar with (a) its importance, (b) vaccinations and immunity to disease, and (c) many people have heard of antibodies. So it is actually not so difficult for a nonspecialist, such as a lawyer or judge, to realize the importance of immune system research. Third, those in the community of "creationism watchers" knew that the ID advocates were particularly vulnerable on the immune system, given their past flailings in response to internet challenges. Some of this is mentioned in Bottaro et al. (referencing these Panda's Thumb posts: [1] -- [2]) and Michael Behe's weak response. For an earlier episode often recalled by creationism watchers see this celebrated discussion on an ID bulletin board, where several pro-evolution posters challenged several leaders of the ID movement to admit that Behe's 1996 claim was wrong. Fourth, Behe's dismissal of several famous articles on evolutionary immunology during his deposition also increased confidence that he was not at all familiar with the literature, and instead would brush off any challenges as not meeting his requirement for infinite detail. Fifth, plaintiffs' attorney Eric Rothschild had the strength of will to continue with the immune system gambit, despite Nick Matzke's early attempt at explaining the evolution of V(D)J recombination to him on a whiteboard:
Scientific BackgroundThe annotated bibliography will not make much sense without a little background understanding of immunology. If you can understand this basic terminology, you should be well on your way to understanding the transposon hypothesis:
With that terminology in hand, we can discuss the transposon hypothesis. The transposon hypothesis is based on similarities between transposons and RAGs, and suggests that RAG-1 and RAG-2, and the RSSs, are actually descended from "free-living" transposons. The model states that in an early vertebrate, already equipped with an innate immune system, a transposon inserted into a non-rearranging receptor gene. When this receptor gene was expressed, the transposon was activated, and snipped itself out of the receptor. However, because this excision process was inexact, the resulting receptor would be variable, and therefore some copies of the receptor protein would be better able to recognize new or mutated pathogens. Natural selection would therefore spread this variant. An extended process of gene duplication and diversification would elaborate this basic system into the modern V(D)J recombination system. The transposon hypothesis suggests a number of specific observations that would corroborate the model if found:
All of these observations have been published in the last 10 years. The crowning achievements, and the easiest successes to understand, were the identification of transposon relatives of RAG-1 in sea urchins, lancelets, and cnidarians (Kapitonov and Jurka, 2005) and a RAG1-RAG2 homolog serving a non-immune function in sea urchins (Fugmann et al. 2006). If the above, very short, summary did not completely sink in, other resources are available. For an excellent moderate-length introduction to evolutionary immunology, please see Matt Inlay's online article, "Evolving Immunity." Pay particular attention to the graphics. Next, read our Nature Immunology essay for a brief update on the scientific progress of the transposon hypothesis. See also these Panda's Thumb blogposts by Matt Inlay or Andrea Bottaro: "New discovery of missing link between adaptive immune system and transposons," "The Revenge of Calvin and Hobbes," and "Behe's meaningless complexity." Once you have given those sources a try, take several minutes to work through Figure 1 and Figure 2 of Lewis and Wu's (2000) commentary article, "The Old and the Restless", published in the Journal of Experimental Medicine. Figure 1 is a model of how receptor rearrangement works in modern organisms. Figure 2 is a model of how it evolved.Another introductory survey can be found in the immunology textbook, Immunobiology: the immune system in health and disease. The 5th edition, Janeway et al. (2001), is freely available online in PubMed's textbooks collection. Chapter 4 is "The Generation of Lymphocyte Antigen Receptors" (sections 1, 2, 3, 4, 5). The Afterword to the book, "Evolution of the Immune System: Past, Present, and Future", is written by Janeway, and summarizes the state of knowledge as of 2001 on the evolution of the innate immune system and evolution of the adaptive immune response. The transposon hypothesis naturally plays a large role in the latter. Hopefully, after you have worked through this material you can re-read the above summary and make some headway. How the Bibliography was AssembledThis bibliography was originally developed for the Behe cross-examination in the Kitzmiller case, discussed in Bottaro et al. (2006). The annotations are based on notes that were taken while the bibliography was being assembled (in an all-night session the weekend before Behe testified, it must be said). The annotations have subsequently been revised and updated. While assembling the exhibit, it was very important to make sure it was not vulnerable to some of the critiques that can be leveled against lists of articles that are uncomprehendingly culled from automated literature searches. When one searches online databases for publications that involve the keywords "immune system" and "evolution" -- two immense research topics -- one will get results on a wide variety of topics. These include:
Only the last four topics directly address the evolutionary origin of the immune system, although many of the other topics can have some relevance. Among these four topics, this bibliography focused mostly on topic #11, and included a smattering of work on topics #8, 9, and 10. Within topic #11, the origin of the V(D)J recombination system was emphasized, as it is widely seen as the "key" system, the most remarkable feature of adaptive immunity, and the biggest evolutionary "puzzle" according to ID advocates. This bibliography also focused on the review literature rather than the research literature. First, the research literature is mostly opaque to nonspecialists, and the implications of findings are made much clearer in the review literature. Second, at his deposition, Michael Behe expressed the opinion that if scientists had made any progress worth talking about in evolutionary immunology, he would have expected to see it in the review literature. A few of the most famous research articles were included, but most of the articles are articles reviewing the research literature -- many of the review articles cite several hundred other articles. This literature collection should not be considered comprehensive or complete -- it is merely a sample of the literature on the evolution of the adaptive immune system, focusing on V(D)J recombination, with a small sampling of literature on the evolution of innate immunity, MHC, large-scale comparative immunology, etc. For some idea of how much more scientific literature there is on this topic, see the longer unannotated bibliography. The Larger ContextMatt Inlay (author of "Evolving Immunity" and coauthor of Bottaro et al. 2006) points out that Michael Behe's book Darwin's Black Box was ironically timed. In 1996, the year Darwin's Black Box was was published, research on V(D)J recombination was in the midst of a dramatic upswing:
Inlay has added to the graph boxes showing the chronology of the major research findings supporting the transposon model. The viewer can see that they came fast and furious after 1996, almost as if on cue. Major ThemesThe story told by this bibliography, and by Ken Miller's testimony in Kitzmiller, and by Bottaro et al. (2006), is basically of the proposal, development, testing, and confirmation of Sakano et al.'s 1979 suggestion in Nature that V(D)J recombination might have emerged when a transposon -- a piece of DNA that codes for a protein that can chop out that piece of DNA and insert it somewhere else -- inserted into the middle of a receptor gene. This hypothesis has been gathering steam for awhile, and really took off in the last ten years. A subplot in the story is how evolution has played a key role in immunology throughout its development. Sakano et al.'s hypothesis was not born in a vacuum; it occurred in a field where comparative immunology, informed by evolutionary modeling, had been a core part of the discipline for a hundred years, going back to the work of Metchnikoff in the late 1800s. If one reads chronologically through the bibliography, one will see the researchers themselves telling the same story, and citing the same papers that have been repeatedly cited in the various Behe immune system rebuttals. But you will also see some rather remarkable comments about Sakano et al.'s hypothesis. Some of the best ones will be highlighted. For example, as the transposon hypothesis began to pick up steam in the mid-1990's, it did attract some critisms. E.g., Lewis and Wu (1997) wrote,It is nonetheless worth noting that in spite of various similarities, there are fundamental differences between transposition and V(D)J recombination. For one, there are no reports of a transposase (mutant or otherwise) that is able to mediate site-specific inversion. Conversely, it has never been demonstrated that V(D)J recombination can cause the integration of one piece of DNA into another. (Lewis and Wu 1997, p. 162)However, the very next year, two labs discovered that the RAG proteins actually could cause the integration reaction. In a research article in Nature entitled "Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system", Agrawal et al. write in their abstract, Here we show that RAG1 and RAG2 together form a transposase capable of excising a piece of DNA containing recombination signals from a donor site and inserting it into a target DNA molecule. [...] The results support the theory that RAG1 and RAG2 were once components of a transposable element, and that the split nature of immunoglobulin and T-cell-receptor genes derives from germline insertion of this element into an ancestral receptor gene soon after the evolutionary divergence of jawed and jawless vertebrates.In a commentary article in the same issue of Nature, Plasterk (1998) said, "the authors show that the RAG1 and RAG2 proteins (which mediate V(D)J joining) can still catalyse a full transposition reaction. A similar result has been independently obtained by Martin Gellert and co-workers, and is reported in tomorrow's issue of Cell." This second article was Hiom et al. (1998). In 1999, Schatz reviewed the progress of Sakano et al.'s transposon hypothesis and pronounced it a "prophetic hypothesis": When examined in their germline configuration, the RSSs flanking V and J constitute an inverted repeat, much like that found at the end of transposons, and this realization led to the prophetic hypothesis, in 1979, that insertion of a transposable element into an ancient receptor gene exon was responsible for the generation of split antigen receptor genes during evolution ([Sakano et al., 1979]). (Schatz 1999, p. 170, bold added)Also in 1999, Susanna Lewis -- the same Lewis as Lewis and Wu (1997) -- engaged in a little prophesy of her own. If the RAGs evolved from transposons, she said, it would be really handy to find one: It would be extremely useful if a contemporary version of the original RAG transposon could be identified. A distant cousin, with credentials, would greatly facilitate any attempts to reconstruct the lost history between the time the first RAG element took up residence in the vertebrate genome and the emergence of a developmental recombination system. (Lewis 1999, p. 65)Six years later, exactly this was reported by Kapitonov and Jurka (2005). It is worth pointing out that, apart from the transposon hypothesis, there was no reason whatsoever to suspect that transposons similar to RAG should exist. Annotated Bibliography in Chronological OrderBurnet, F. M. (1971). "Self-recognition in colonial marine forms and flowering plants in relation to the evolution of immunity." Nature 232(5308): 230-235. (PubMed | DOI | Journal | Google Scholar) The author of this article, Sir Frank MacFarlane Burnet, won the 1960 Nobel Prize in Medicine for the discovery of acquired immunological tolerance (http://nobelprize.org/medicine/laureates/1960/). He shared the award with Peter Medawar. Burnet wrote widely on the origin and evolution of the adaptive immune system in the 1960's and 1970's. Although he wrote before the molecular mechanism of recombination was understood he made many perceptive suggestions and is still commonly cited. Marchalonis, J. J. (1976). Immunity in Evolution. Cambridge, Mass., Harvard University Press. (Library | Amazon | Google Print) Early synthesis of knowledge on the evolution of the immune system, published in 1976. The forward, by Frank MacFarlane Burnet, suggests that the book might emerge as "the first definitive statement of the evolutionary origins and development of vertebrate immunity" (p. xx). The author, John Marchalonis, went on to be one of the leaders in the field of immune system evolution (see his articles in this bibliography through 2006). Sakano, H., Hüppi, K., Heinrich, G. and Tonegawa, S. (1979). "Sequences at the somatic recombination sites of immunoglobulin light-chain genes." Nature 280(6): 288-294. (PubMed | DOI | Journal | Google Scholar) Famous article (within the field) that proposed the transposon hypothesis for the origin of the V(D)J recombination system of adaptive immunity. This speculation was based upon the paper's report on the role that RSSs play in the mechanism of V(D)J recombination, a discovery fundamental to modern scientific understanding of the rearrangement mechanism."Evolution of light-chain genesAs of summer 2005, Sakano et al. (1979) had received an extraordinary 735 citations in the scientific literature, according to the Science Citation Index. Manning, M. J., ed. (1980). Phylogeny of Immunological Memory. Developments in Immunology. Amsterdam, Elsevier/North-Holland Biomedical Press. (Library | Amazon | Google Print) Thirty-one chapters by various authors on comparative immunology; Proceedings of the International Symposium on Immunological Memory held at the American Society of Zoologists Meeting in Tampa, Florida, USA, 28-30 December, 1979. Klein, J. (1986). "Evolution of Mhc." Natural History of the Major Histocompatibility Complex. New York, John Wiley & Sons: 715-762. (Library | Google Print) This textbook provides an overview of the Major Histocompatibility Complex (MHC), a system of proteins that help distinguish self from non-self. The final chapter, chapter 10, is entitled "Evolution" and gives a review of self-recognition in various animals. Kelsoe, G. and Schulze, D. H., eds. (1987). Evolution and Vertebrate Immunity: The Antigen-Receptor and MHC Gene Families. Austin, University of Texas Press. (Library | Amazon | Google Print) Twenty-six articles on the evolution of the immune system (71 authors). Very technical. Síma, P. and Vetvicka, V. (1990). Evolution of Immune Reactions. Boca Raton, CRC Press. (Library | Amazon | Google Print) Sima & Vetvicka (Preface, p. iv), begin by saying, "The purpose of this book is to reconstruct the history and evolutionary pathways of immunity among the various forms of life." (p. iv) This book is a survey of the field and all the relevant lineages. It is quite technical although the introduction and conclusion are more accessible."We presume that, in the next few years, the fields of comparative and evolutionary immunology will provide, not only inspiration for further investigations in biomedicine, but also a number of practical applicable results." (p. vii) Warr, G. W. and Cohen, N., eds. (1991). Phylogenesis of Immune Functions. Boca Raton, CRC Press. (Library | Amazon | Google Print) Another technical work dealing with immune systems of both vertebrates and invertebrates. The introduction (p. iii) begins by citing Metchnikoff (1882). Page iii continues:"[I]t can be argued that for a biologist to ignore the evolutionary history either of an organism or a complex system is as much an impediment to comprehending fully that organism or system as it is for a student of society to ignore the history of mankind." (p. iii)In chapter 9, "Evolutionary Origins of Immunoglobulin Genes," (pp. 171-189), Litman et al. write: Dreyfus, D. H. (1992). "Evidence suggesting an evolutionary relationship between transposable elements and immune system recombination sequences." Molecular Immunology 29(6): 807-810. (PubMed | DOI | Journal | Google Scholar) This paper reports sequence similarities between V(D)J recombination signal sequences, and the termini of Tcl-like transposable sequences found in invertebrates. The authors note that this supports Sakano et al.'s 1979 hypothesis:"Sakano et al. (1979) have previously proposed that the vertebrate somatic recombination pathway evolved via the insertion of a transposable element into an ancestral gene encoding an antigen binding molecule, thus accounting for the simultaneous appearance of separated gene segments and a recombination mechanism for their reassembly." (p. 807) Síma, P. and Vetvicka, V. (1992). "Evolution of Immune Accessory Functions." Immune System Accessory Cells. Edited by L. Fornusek and P. Síma. Boca Raton, CRC Press: 1-55. (Library | Amazon | Google Print) Long review of immune system cells across vertebrates and invertebrates. Cites Metchnikoff (1892) on p. 5. Figure 2 (p. 37) depicts the progressive emergence of various aspects of the immune system in the phylogeny of animals."The aim of this overview is to attempt to compare the evolutionary emergence of accessory cellular function and the role of various defense cell types in defense reactions in major natural assemblages of metazoan species." (p. 2)The article begins with a quote from Burnet (1973) in Nature: "Comparative studies which are not made meaningful by use of evolutionary hypotheses are bound to be sterile." Bartl, S., Baltimore, D. and Weissman, I. L. (1994). "Molecular evolution of the vertebrate immune system." Proceedings of the National Academy of Sciences 91(23): 10769-10770. (PubMed | Journal | JSTOR | Google Scholar) This is a short (2 pages) review article. In his 1996 book Darwin's Black Box, Behe critiqued it for vagueness, but even in 1996 there were longer review articles available (e.g. Thompson 1995), and despite the shortness, the basic ideas proposed in this article and elsewhere have been dramatically confirmed in the subsequent decade, as detailed in our 2006 Nature Immunology essay. Beck, G., Cooper, E. L., Habicht, G. S. and Marchalonis, J. J., eds. (1994). Primordial Immunity: Foundations for the Vertebrate Immune System. New York, The New York Academy of Sciences. (Library | PubMed | Publisher | Amazon | Google Print) This volume on comparative and evolutionary immunology resulted from a May 3-5, 1993 conference held in Woods Hole entitled "Primordial Immunity: Foundations for the Vertebrate Immune System." It contains 24 articles and 18 poster summaries, mostly examining the immune systems of various phylogenetically basal organisms. Three of the articles focusing on the origin of adaptive immunity are included in the articles list. Hoffman, J. A., Janeway, C. A. and Natori, S., eds. (1994). Phylogenetic Perspectives in Immunity: The Insect Host Defense. Austin, R. G. Landes Company. (Library | Amazon | Google Print) Fifteen chapters on the immune systems of basal vertebrates and arthropods in an evolutionary perspective. Three of the most relevant chapters are: Marchalonis, J. J. and Schluter, S. F. (1994). "Development of an Immune System." Primordial Immunity: Foundations for the Vertebrate Immune System. Edited by G. Beck, E. L. Cooper, G. S. Habicht and J. J. Marchalonis. New York, New York Academy of Sciences. 712: 1-11. (Library | PubMed | Publisher | Google Print) Overview of the distribution and origin of major pieces of the immune system, and some discussion of the selective pressures that may have been in play. The lead author, Marchalonis, has been working on the evolutionary origin of the immune system since the 1970's. Marchalonis, J. J., Hohman, V. S., Kaymaz, H., Schluter, S. F. and Edmundson, A. B. (1994). "Cell Surface Recognition and the Immunoglobulin Superfamily." Primordial Immunity: Foundations for the Vertebrate Immune System. Edited by G. Beck, E. L. Cooper, G. S. Habicht and J. J. Marchalonis. New York, New York Academy of Sciences. 712: 20-33. (Library | PubMed | Publisher | Google Print) Review of the origin and dramatic diversification of the various immunoglobulins (Igs)."Data obtained recently on gene sequences of Igs of sharks, the ancestors of which diverged from those of mammals more than 400 million years ago, allow us to make detailed comparisons regarding the homologies among Ig V and C domains in evolution." (p. 21) Ohno, S. (1994). "MHC Evolution and Development of a Recognition System." Primordial Immunity: Foundations for the Vertebrate Immune System. Edited by G. Beck, E. L. Cooper, G. S. Habicht and J. J. Marchalonis. New York, New York Academy of Sciences. 712: 13-19. (Library | PubMed | Publisher | Google Print) Argues for a relatively late origin of MHC (self-recognition capability), after the origin of adaptive immunity. This bucks the dominant view and the article explicitly takes a "devil's advocate" approach. Stewart, J. (1994). The Primordial VRM System and the Evolution of Vertebrate Immunity. Austin, R. G. Landes. (Library | Amazon | Google Print) This book is on the origin of the VRM system (VRM = Variable Region Molecules, see p. 9). Vetvicka, V., Síma, P., Cooper, E. L., Bilej, M. and Roch, P. (1994). Immunology of Annelids. Boca Raton, CRC Press. (Library | Amazon | Google Print) Ten chapters on the immunology of annelids (earthworms and relatives). This may seem obscure, but the importance of annelids to evolutionary immunology is explained in Chapter 1, "Comparative Immunology: The Value of Annelids.""[A]ll invertebrates, including annelids, have figured prominently in establishing the field of immunology." (p. 6) Thompson, C. B. (1995). "New insights into V(D)J recombination and its role in the evolution of the immune system." Immunity 3(5): 531-539. (PubMed | DOI | Journal | Google Scholar) A long review article summarizing the early results supporting the transposon model for the origin of adaptive immunity."Current evidence suggests that the ability to mount an antigen-specific immune response arose over a relatively short period of time coincident with the development of the first jawed vertebrates. This has raised the question of how a mechanism as complex as V(D)J recombination arose over such a short evolutionary period. Recent advances in V(D)J recombination suggest a resolution to this issue and allow us to reexamine the role of antigen specificity in shaping the evolution of the immune system." (p. 531) Bernstein, R. M., Schluter, S. F., Bernstein, H. and Marchalonis, J. J. (1996). "Primordial emergence of the recombination activating gene 1 (RAG1): Sequence of the complete shark gene indicates homology to microbial integrases." Proceedings of the National Academy of Sciences 93(18): 9454-9459. (PubMed | Journal | JSTOR | Google Scholar) This study compared RAG1 and RAG2 in sharks and mammals, delineating the highly conserved regions. These conserved regions were found to exhibit homology to bacterial recombinases."Homology domains identified within shark RAG I prompted sequence comparison analyses that suggested similarity of the RAG I and II genes, respectively, to the integrase family genes and integration host factor genes of the bacterial site-specific recombination system. Thus, the apparent explosive evolution (or "big bang") of the ancestral immune system may have been initiated by a transfer of microbial site-specific recombinases." (p. 9454)Figure 5 contains a general phylogenetic tree of the prokaryotic relatives of RAG1, and depicts the hypothesized horizontal transfer event. van Gent, D. C., Mizuuchi, K. and Gellert, M. (1996). "Similarities between initiation of V(D)J recombination and retroviral integration." Science 271(5255): 1592-1594. (PubMed | Journal | JSTOR | Google Scholar) This study reports close similarities between the mechanism of the formation of DNA hairpins during the cutting and assembly of antibody genes, and the processes that occur when transposons and retroviruses insert into DNA."These findings provide support for the speculation that the antigen receptor genes, and the RAG1 and RAG2 proteins that mediate their rearrangement, may have evolved from an ancestral transposon (18). The presence of RSSs facing in opposite directions (the most usual arrangement in the antigen receptor loci) is similar to the inverted repeat architecture of many transposon ends, and the RAG proteins could have developed from genes encoded by the former transposon."Ref. 18 is Thompson (1995). Hughes, A. L. and Yeager, M. (1997). "Molecular evolution of the vertebrate immune system." BioEssays 19(9): 777-786. (PubMed | Google Scholar) Review of the evolution of several key pieces of the immune system (e.g., C3 and the other complement proteins, MHC, RAG & immunoglobulins, etc.), with a focus on the evolutionary mechanisms involved, e.g. various forms of gene duplication vs. block duplication. Ji, X., Azumi, K., Sasaki, M. and Nonaka, M. (1997). "Ancient origin of the complement lectin pathway revealed by molecular cloning of mannan binding protein-associated serine protease from a urochordate, the Japanese ascidian, Halocynthia roretzi." Proceedings of the National Academy of Sciences 94(12): 6340-6345. (PubMed | Journal | Google Scholar) Research paper reporting that key innate immune system genes have been discovered in tunicates, invertebrates related to vertebrates (also known as ascidians or sea-squirts)."The major developments of the complement system, therefore, seem to have occurred in two stages; first, with the emergence in cyclostomes of the alternative pathway to establish a means of amplification, and second, after the divergence of cyclostomes but before the divergence of cartilaginous fish, the emergence of the classical and lytic pathways. This hypothesis would not only explain the evolution of the complement system, but also may help to reevaluate the activation mechanism of the mammalian alternative pathway." (pp. 6344-6345) Lewis, S. M. and Wu, G. E. (1997). "The origins of V(D)J recombination." Cell 88(2): 159-162. (PubMed | DOI | Journal | Google Scholar) Lewis and Wu have authored several reviews on the evolutionary origin of the adaptive immune system. This 1997 review in Cell summarizes the state of the question after several then-recent discoveries. The introductory section, "The Origins of V(D)J Recombination," discusses why the evolutionary question was attracting renewed interest:"Recently V(D)J recombination has been partially reconstituted in vitro (reviewed in Gellert, 1996), and as a result, has been the subject of intense research. A side effect of these efforts has been renewed speculation regarding evolutionary origins. New information bears upon the possibility that this unusual recombination system could have been a transplant from the procaryotic world (Difilippantonio et al., 1996; Spanopoulou et al., 1996, van Gent et al., 1996a)." (p. 159)This article reviews "The Case for a Transposon Progenitor" of RAG (section heading, p. 161), e.g.:"Given that the architecture of a joining signal is transposon-like, this similarity between chemical mechanisms would seem to add weight to the idea that the V(D)J recombination system originally carried out transpositional rearrangements. The transposon theory has in fact been suggested, for various reasons, a number of times over the years." (p. 162)On the other hand, several similarities were missing in 1997:"It is nonetheless worth noting that in spite of various similarities, there are fundamental differences between transposition and V(D)J recombination. For one, there are no reports of a transposase (mutant or otherwise) that is able to mediate site-specific inversion. Conversely, it has never been demonstrated that V(D)J recombination can cause the integration of one piece of DNA into another." (p. 162)Both of these features were soon discovered in lab experiments in following years.[References] Schluter, S. F., Bernstein, R. M. and Marchalonis, J. J. (1997). "Molecular origins and evolution of immunoglobulin heavy-chain genes of jawed vertebrates." Immunology Today 18(11): 543-549. (PubMed | DOI | Journal | Google Scholar) A review of the origins of rearranging immunoglobulins in the light of cartilagenous fish, the most basal vertebrate group possessing classic adaptive immunity. The introduction clearly states the kinds of questions that an evolutionary model must answer."A model for the evolution of the immunoglobulins (Igs) must explain two separate but closely related aspects. The first is the genetic mechanisms by which the diversity of the expressed effector molecules is generated1. This would encompass both the enzymatic mechanism of recombination and the genomic organization of the various elements of the Ig genes. The second is the functional duality of the receptor proteins whereby the variable (V) regions form the antigen-binding sites and the effector activities are mediated through the constant (C) regions2. This article will focus on the latter aspect, particularly the molecular evolutionary origins of the gene segments encoding Ig heavy (H) chains." (p. 543)A model for the origin of the various immunoglobulins is constructed based on the phylogenies reviewed in the paper:"A model for the evolution of the VH genes Agrawal, A., Eastman, Q. M. and Schatz, D. G. (1998). "Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system." Nature 394(6695): 744-751. (PubMed | DOI | Journal | Google Scholar) This study reports a major research finding that supported the transposon hypothesis for the origin of adaptive immunity. The authors found that the rearrangment-activating genes, RAG1+RAG2, could still perform both the excision and the insertion reactions, just like a free-living transposon. Plasterk, R. (1998). "Ragtime jumping." Nature 394(6695): 718-719. (PubMed | DOI | Journal | Google Scholar) Summary of the Nature article Agrawal et al. (1998). While short and nontechnical, it is relevant to some of Behe's "search criteria" as he laid out during his sworn deposition for the Kitzmiller case. During his deposition in May 2005, Behe was quizzed about some of his claims about the immune system, and he was asked how he even knew what was in the literature since he wasn't familiar with the peer-reviewed articles that were presented then. Behe's answers (Behe deposition, pp. 231-233) were basically (1) he relies on other people to email him articles that meet his challenges, (2) articles on the evolution of the immune system would be big news, so he watches out for news articles in major scientific publications, and review articles in review journals and other scientific literature, and (3) he watches out for articles in popular scientific outlets such as the New York Times or Scientific American. Vetvicka, V. and Síma, P. (1998). Evolutionary Mechanisms of Defense Reactions. Basel, Birkhäuser Verlag. (Library | Amazon | Google Print) Vetvicka & Sima systematically review the immune systems of animals, starting with the earliest branches on the animal phylogenetic (sponges), through the various simple and complex invertebrates, the chordate relatives of vertebrates, the early diverging vertebrates such as the lampreys and hagfish, and ending with the "higher" vertebrates and their adaptive immune systems. Highly technical, focuses on immune system organs in addition to the cellular/molecular level. The primary themes are that: (1) immune system evolution must be considered in the context of ecological and morphological change in mammal groups; (2) there is a large degree of diversity in so-called "primitive" organisms, and there are many ways organisms survive without the "required" parts of vertebrate immunity."[B]asic research in comparative and evolutionary immunology has substantially contributed in many ways to the exciting progress that immunology has made in recent decades." (p. 187) Lewis, S. M. (1999). "Evolution of Immunoglobulin and T-Cell Receptor Gene Assembly." Annals of the New York Academy of Sciences 870: 58-67. (PubMed | Journal | Google Scholar) Another detailed review of the RAG transposon hypothesis by Susanna Lewis. It is a clear example of the increasing confidence that researchers in the field have about the transposon hypothesis. E.g., from the introductory section, entitled, "A transposon origin for V(D)J recombination":"How such a singular mechanism for somatic cell differentiation arose has long been a puzzle.6 Although a multiplicity of site-specific recombination systems exist in bacteria, yeast, and protozoa, no other example apart from V(D)J recombination is known to operate in vertebrates. One speculation dating back to the time of the first molecular descriptions of immunoglobulin gene rearrangement is that the V(D)J recombination system may have evolved from a mobile element.7 Now, almost 20 years later, biochemical analyses of RAG1 and RAG2 have uncovered solid clues that this indeed may be the case." (p. 58)Figure 4 contains a summary depiction of the transposon hypothesis. Lewis (1999) is especially noteworthy because it contains an uncannily predictive suggestion in the section suggesting further research avenues:"THE NEXT STEPExactly this was discovered six years later, in 2005 (Kapitonov & Jurka, 2005). Another cousin was discovered in 2006 (Fugmann, S. D., Messier, C., Novack, L. A., Cameron, R. A. and Rast, J. P. (2006). "An ancient evolutionary origin of the Rag1/2 gene locus." Proc Natl Acad Sci U S A 103(10): 3728-3733) Litman, G. W., Anderson, M. K. and Rast, J. P. (1999). "Evolution of antigen binding receptors." Annual Review of Immunology 17: 109-147. (PubMed | DOI | Journal | Google Scholar) This very long (38 pages) and technical review article cites 171 references, surveying all aspects of the origins of adaptive immunity, focusing on the ancestry and phylogeny of the receptors rather than the transposon hypothesis which is taken as confirmed."This review addresses issues related to the evolution of the complex multigene families of antigen binding receptors that function in adaptive immunity. [...] As of yet, homologous forms of antigen binding receptors have not been identified in jawless vertebrates; however, acquisition of large amounts of structural data for the antigen binding receptors that are found in a variety of jawed vertebrates has defined shared characteristics that provide unique insight into the distant origins of the rearranging gene systems and their relationships to both adaptive and innate recognition processes." (p. 109) Schatz, D. G. (1999). "Transposition mediated by RAG1 and RAG2 and the evolution of the adaptive immune system." Immunologic Research 19(2-3): 169-182. (PubMed | Google Scholar) Technical review of the tranposon hypothesis. The abstract summarizes Schatz's main point:"The hypothesis that RAG1 and RAG2 arose in evolution as components of a transposable element has received dramatic support from our recent finding that the RAG proteins are a fully functional transposase in vitro."Noteworthy in the article is Schatz's description of Sakano et al. (1979) as advancing a "prophetic hypothesis":"When examined in their germline configuration, the RSSs flanking V and J constitute an inverted repeat, much like that found at the end of transposons, and this realization led to the prophetic hypothesis, in 1979, that insertion of a transposable element into an ancient receptor gene exon was responsible for the generation of split antigen receptor genes during evolution (5)." (p. 170) Schluter, S. F., Bernstein, R. M., Bernstein, H. and Marchalonis, J. J. (1999). "'Big Bang' emergence of the combinatorial immune system." Developmental and Comparative Immunology 23(2): 107-111. (PubMed | DOI | Journal | Google Scholar) Basic review of the transposon hypothesis. The title and various quotes are the kind of thing that are commonly quote-mined by creationists, e.g., "Thus, the Big Bang must have occurred in the extremely short time of emergence of jawed vertebrates from their ostracoderm ancestors." (p. 107) However, it is worth noting that "extremely short" means about 50 million years in this context. And, the whole point of the article is that the transpson hypothesis, where a prokaryotic transposon jumped into the vertebrate genome, is what explains the "big bang" in question. Du Pasquier, L. (2000). "The Phylogenetic Origin of Antigen-Specific Receptors." Origin and Evolution of the Vertebrate Immune System. Edited by L. Du Pasquier and G. W. Litman. Berlin, Springer. 248: 159-185. (Library | PubMed | Amazon | Google Print) Highly technical review of the origin of the receptor genes, starting with Ig homologs in invertebrates, and then looking at the relationships between the various immune system genes within vertebrates."Fig. 10. Origin and evolution of Igsf members with V and C1 domains. A hypothesis taking into account the genetic linkages and the homologies presented in this chapter." (pp. 178-179) Du Pasquier, L. and Litman, G. W., eds. (2000). Origin and Evolution of the Vertebrate Immune System. Current Topics in Microbiology and Immunology. Berlin, Springer. (Library | Publisher | Amazon | Google Print) This edited book in the Current Topics in Microbiology and Immunology series contains 14 articles by 33 contributors on the evolutionary origin of the immune system. It is a thorough survey of the evolution of the major parts of the immune system as of 2000. Most of the articles are very technical. Despite this, the Preface reads,"This book is by no means comprehensive and can be complemented by reading recent issues of Immunological Reviews (nos. 166, Immune systems of ectothermic vertebrates, and 167, Genomic organisation of the MHC: structure, origin, and function)." (p. vi)Also, from Chapter 1, Section 4, "The Evolution of Complex Systems": Hansen, J. D. and McBlane, J. F. (2000). "Recombination-Activating Genes, Transposition, and the Lymphoid-Specific Combinatorial Immune System: A Common Evolutionary Connection." Origin and Evolution of the Vertebrate Immune System. Edited by L. Du Pasquier and G. W. Litman. Berlin, Springer. 248: 111-135. (Library | PubMed | Amazon | Google Print) This is one of three articles from the volume, "Origin and Evolution of the Vertebrate Immune System," which were included in the article list. The book itself is listed in the book list. The three articles were included in the article bibliography because they were particularly useful summaries of the evolution of key pieces of adaptive and innate immunity. Lewis, S. M. and Wu, G. E. (2000). "The old and the restless." Journal of Experimental Medicine 191(10): 1631-1636. (PubMed | DOI | Journal | Google Scholar) Another review paper on the RAG transposon hypothesis from Lewis and Wu. Figure 2 contains a usefully clear figure depicting the hypothesis. The second paragraph sums up the development of the transposon hypothesis:"As recently as only a few years ago, any real information bearing on the actual genesis of the V(D)J recombination system seemed to be irretrievably lost. However, as more was learned about the molecular genetic and biochemical properties of the V(D)J recombination proteins, termed recombination activating gene (RAG)-1 and RAG-2, tantalizing suggestions of a transposon origin began to emerge. These clues included the following: first, the fact that the genes encoding RAG-1 and RAG-2, which are unrelated in sequence, are tightly linked, and as such share this property with genes that are known to undergo horizontal transfer (4). Second, the chemical mechanism of the recombination reaction, where DNA strand breakage and rejoining is accomplished through one step transesterification reactions, was like that of several well-described mobile elements (5). Finally, a surprising finding further indicated that RAG-1 and RAG-2 might have once been part of a transposon when two groups independently demonstrated that purified RAG-1 and RAG-2 proteins have a latent ability to carry out the transposition of DNA (6, 7)." (p. 1631) Nonaka, M. (2000). "Origin and evolution of the Complement System." Origin and Evolution of the Vertebrate Immune System. Edited by L. Du Pasquier and G. W. Litman. Berlin, Springer. 248: 37-50. (Library | PubMed | Amazon | Google Print) Nonaka regularly authors or coauthors articles reviewing the evolutionary origin of the innate immune system. This article surveys the complement systems of vertebrates and invertebrates and focuses on the origin of the B and C2 proteins which help activate the complement system, and the MASP proteins, mammalian serine proteases which actually have homologs in groups as distant as ascidians."This chapter discusses recent progress in understanding the evolution of the complement system mainly in invertebrates and lower vertebrates." (p. 38) Opal, S. M. (2000). "Phylogenetic and functional relationships between coagulation and the innate immune response." Critical Care Medicine 28(9): S77-S80. (PubMed | Journal | Google Scholar) This article reviews the evolutionary and physiological relationships between the blood-clotting cascade (coagulation) and the the inflammatory cascade which initiates innate immune responses."The simultaneous activation of the inflammatory response and the coagulation system after injury is a phylogenetically ancient, adaptive response that can be traced back to the early stages of eukaryotic evolution." (p. S77) Richards, M. H. and Nelson, J. L. (2000). "The Evolution of Vertebrate Antigen Receptors: A Phylogenetic Approach." Molecular Biology and Evolution 17(1): 146-155. (PubMed | Journal | Google Scholar) This research article explores the phylogeny of somatically rearranging antigen receptors, seeking the most basal groups."It is now clear that indirect, MHC-restricted antigen recognition must be a derived characteristic of [alpha][beta] T cells, while [gamma][beta] T cells exhibit the primitive condition of direct antigen binding. This removes a major stumbling block in several schemes for the evolution of vertebrate immune systems (e.g., Stewart 1992), because it shows that the origins of diverse T-cell characteristics, such as antigen recognition and effector functions, may be separate, independent evolutionary events. Continued phylogenetic analysis of TCR and Ig relationships, especially as more suitable outgroup sequences are obtained from organisms such as cyclostomes or sharks, should continue to improve our understanding of immune system evolution." (p. 154)The reference to Stewart is: Stewart, J. 1992. Immunoglobulins did not arise in evolution to fight infection. Immunology Today 13:396-399. Stewart is also the author of the 1994 book The Primordial VRM System and the Evolution of Vertebrate Immunity. Roth, D. B. (2000). "From lymphocytes to sharks: V(D)J recombinase moves to the germline." Genome Biology 1(2): 1014.1011-1014.1014. (PubMed | DOI | Journal | Google Scholar) This article reviews the transposon model for the origin of rearranging receptors, and also explores the impact that the V(D)J recombinase may have had as an evolutionary force."Early on, it was suggested that the V(D)J recombination system might have arisen by the fortuitous integration of a transposable element into an ancestral antigen-receptor gene [14]. This hypothesis was strengthened by the discovery that the RAG genes are tightly linked [7], and by the finding that the RAG proteins can act as a transposase. Thus, a plausible model for the acquisition of the V(D)J recombination system during vertebrate evolution is the integration of a transposable element carrying the linked RAG genes into a primordial antigen-receptor gene in an ancestral jawed vertebrate, approximately 450 million years ago (reviewed in [1,11]). Presumably, this initial integration event created the first rearranging antigen-receptor gene; subsequent gene duplication events then created the multiple immunoglobulin and T-cell receptor loci." (p. 1014.2) Vaandrager, J.-W., Schuuring, E., Philippo, K. and Kluin, P. M. (2000). "V(D)J recombinase-mediated transposition of the BCL2 gene to the IGH locus in follicular lymphoma." Blood 96(5): 1947-1952. (PubMed | Journal | Google Scholar) The results of this research article give indirect evidence that transposition reactions mediated by RAGs can occur not just in vitro, but within mammalian cells, further supporting the transposon hypothesis. Du Pasquier, L. (2001). "The immune system of invertebrates and vertebrates." Comparative Biochemistry and Physiology Part B Biochemistry & Molecular Biology 129(1): 1-15. (PubMed | DOI | Journal | Google Scholar) Review of current comparative immunology. Excellent figures show the variability and repeated themes (due to duplication and combination of genes) in various immune systems. Fig. 3 shows the repeated use of proteins in the immunoglobulin superfamily in invertebrates. Nonaka, M. and Miyazawa, S. (2001). "Evolution of the Initiating Enzymes of the Complement System." Genome Biology 3(1): 1001.1001-1001.1005. (PubMed | DOI | Journal | Google Scholar) Technical review of the origin of the innate (non-adaptive) immune system. Cannon, J. P., Haire, R. N. and Litman, G. W. (2002). "Identification of diversified genes that contain immunoglobulin-like variable regions in a protochordate." Nature Immunology 3(12): 1200-1207. (PubMed | DOI | Journal | Google Scholar) A key research article finally presenting evidence of a non-rearranging receptor closely related to the vertebrate rearranging receptors, in the lancelet (a cephalochordate which lacks adaptive immunity). This is important because it provides one of the homologs that scientists had been seeking for years. It also shows that even without rearranging receptor capability, selection favored diverse receptors:"Thus, multigenic families encoding diversified V regions exist in a species lacking an adaptive immune response." (p. 1200) Kaufman, J. (2002). "The origins of the adaptive immune system: whatever next?" Nature Immunology 3(12): 1124-1125. (PubMed | DOI | Journal | Google Scholar) In this News & Views article in Nature Immunology, Kaufman expresses wonderment at the results of Cannon et al. (2002)."Indeed, the initial event that enabled the emergence of the adaptive immune system is thought to have been the insertion of a transposon into a previously undisrupted V-like exon of an Ig domain-containing gene2,3,5. But in which Ig gene did the insertion occur?" (p. 1124) Krem, M. M. and Di Cera, E. (2002). "Evolution of enzyme cascades from embryonic development to blood coagulation." Trends in Biochemical Sciences 27(2): 67-74. (PubMed | DOI | Journal | Google Scholar) Article reviews the evolutionary and physiological relationships between the blood-clotting cascade and the complement cascade of the innate immune system."Here, it is proposed that a single ancestral developmental/immunity cascade gave rise to the protostome and deuterostome developmental, clotting, and complement cascades. Extensive similarities suggest that these cascades were built by adding enzymes from the bottom of the cascade up and from similar macromolecular building blocks." (p. 67)Figure 2 (p. 71) shows proposed relationships."Fig. 2. Evolutionary changes producing developmental, immune and clotting cascades." Laird, D. J. (2002). "Immune System." Encyclopedia of Evolution. Edited by M. Pagel. Oxford, Oxford University Press. 2: 558-564. (Library | Publisher | Amazon | Google Print) Basic introduction to the immune system, but in a thoroughly evolutionary context. Figure 4 (p. 563) depicts the progressive aquisition of features as one moves closer to mammals in the vertebrate phylogeny. It is noteworthy that the transposon hypothesis is sufficiently well-accepted, and well-known, to make it into a general encyclopedia on evolution. Furthermore, this is another example of the secondary literature that is readily available to anyone seriously looking into evolutionary immunology."Structures of the Vertebrate Immune System. Despite the quantity of immune receptors, signalling molecules, and serum factors that carry out antigen recognition and the accompanying inflammatory response, these structures share much in common. Protein motifs such as the immunoglobulin fold, which appears in Ig, TCR, natural killer (NK) cell receptors, MHC receptors, complement proteins, and adhesion molecules, imply extraordinary recycling and even a common origin during evolution. The hypothesis that a primordial immunoglobulinlike receptor gave rise to the rearranging receptors of lymphocytes has inspired the study of Ig, TCR, and other immune receptors of primitive vertebrates. This section focuses on the evolution of the main components of the adaptive immune system, unique to jawed vertebrates." (p. 559) Marchalonis, J. J., Jensen, I. and Schluter, S. F. (2002). "Structural, antigenic and evolutionary analyses of immunoglobulins and T cell receptors." Journal of Molecular Recognition 15(5): 260-271. (PubMed | DOI | Journal | Google Scholar) Long review of the work of the Marchalonis lab."This laboratory has focused upon the structure, function and evolution of antibodies and T cell receptors for more than 25 years." (p. 260)Evolution played a key role in the lab's study of antigen receptors. The article is interesting because it highlights the interrelationship between structural and evolutionary studies -- homology and phylogeny allow structural knowledge gained in one lineage (e.g., sharks) to be applied to another that is more medically relevant (such as humans). The authors also note that sharks were chosen as the study organisms of choice because any features conserved across the evolutionary distance between sharks and humans is likely to be functionally important:"We have studied antibodies, antibody production and cellular immunity in representatives of all the vertebrate classes, but we have chosen to concentrate our studies of antibody and T cell receptor structure on a comparison between the genes and molecules of sharks and humans because these two species represent the most evolutionarily divergent organisms to express the complete combinatorial immune system consisting of immunoglobulins, major histocompatability complex antigens, T cell receptors, and recombination activator genes (DuPasquier and Flajnik, 1999; Litman et al., 1999; Marchalonis and Schluter, 1998; Marchalonis et al., 1998a)." (p. 261) Marchalonis, J. J., Kaveri, S., Lacroix-Desmazes, S. and Kazatchkine, M. D. (2002). "Natural recognition repertoire and the evolutionary emergence of the combinatorial immune system." FASEB Journal 16(8): 842-848. (PubMed | Journal | Google Scholar) Technical review of several aspects of the origin of adaptive immunity, including the capacity for receptor diversity and its selective value, and the importance of clonal selection during maturation of specific antibodies. The quick review of the transposon hypothesis is quoted below:"The complete [Combinatorial Immune Response, CIR] ensemble is present in all jawed vertebrates (8-10). The system emerged rapidly and accidentally in evolution (3, 14, 18) probably as the result of horizontal transfer of microbial genes for site-specific recombination (4-6, 18, 19). Ab initio, the CIR was neither a defense mechanism nor part of an internal regulatory system (20), but its unparalleled capacity to generate recognition molecules in real time gave it the potential to function effectively in both contexts. The CIR co-opted preexisting cellular and humoral mechanisms for activation, differentiation, and destruction of bound targets including the NF[kappa]B pathway, the IL-1/TOLL receptor complex, and interaction with more ancient complement components to initiate cytolysis, killing, and trigger inflammation (12-15)." (p. 843) Clatworthy, A. E., Valencia, M. A., Haber, J. E. and Oettinger, M. A. (2003). "V(D)J recombination and RAG-mediated transposition in yeast." Molecular Cell 12(2): 489-499. (PubMed | DOI | Journal | Google Scholar) This paper showed for the first time that RAG1 and RAG2 can act as a bona fide transposase in eukaryotic (yeast) cells, mediating the integration in the genome of an excised DNA fragment. The results confirmed another long-sought prediction of the transposon hypothesis:"Here, we show that expression in Saccharomyces cerevisiae of murine RAG1 and RAG2, the lymphoid-specific components of the V(D)J recombinase, is sufficient to induce V(D)J cleavage and rejoining in this lower eukaryote." (p. 489) Flajnik, M. F., Miller, K. and Du Pasquier, L. (2003). "Evolution of the Immune System." Fundamental Immunology. Edited by W. E. Paul. Philadelphia, Lippincott Williams & Wilkins: 519-570. (Library | Amazon | Google Print) This 51-page review of evolutionary immunology references 213 citations. Technical, but very useful tables and graphics showing how the major features of the vertebrate immune system are gradually acquired in organisms getting closer in the phylogenetic tree to vertebrates."As predicted over 10 years ago by Zasloff (2), it is informative from both intellectual and applied viewpoints to understand how all living things defend themselves; few would argue against the premise that studies of Drosophila humoral immunity has fueled great interest in innate immunity, both for its own sake and in the way it regulates adaptive immunity (R3)." (p. 521)Regarding the transposon hypothesis for the origin of the Recombination-Activating Genes, RAG1 and RAG2, Flajnik et al. write,"It seems that a 'horizontal' acquisition of a RAG-laden transposon occurred at some point during the history of the vertebrates (R156, 202). The structure of the receptor gene itself, in the region where rearrangements occur, suggests the introduction of a transposon." (p. 562)The article also suggests future research directions:"Further molecular studies in hagfish and lamprey and in non-vertebrate deuterostomes will perhaps permit a better understanding of the events leading to the emergence of the adaptive immune system." (p. 566)Note that in May 2005, a "free-living" transposon relative of RAG1 was discovered in a tunicate, a non-vertebrate deuterostome (Kapitonov and Jurka, 2005). Market, E. and Papavasiliou, F. N. (2003). "V(D)J Recombination and the Evolution of the Adaptive Immune System." PLoS Biology 1(1): 24-27. (PubMed | DOI | Journal | Google Scholar) A short review of recombination, and its evolutionary origin from a transposon. Included in the very first issue (volume 1, number 1) of the journal Public Library of Science: Biology. The entire contents of this journal are available free online. Messier, T. L., O'Neill, J. P., Hou, S.-M., Nicklas, J. A. and Finette, B. A. (2003). "In vivo transposition mediated by V(D)J recombinase in human T lymphocytes." The EMBO Journal 22(6): 1381-1388. (PubMed | DOI | Journal | Google Scholar) Messier and coworkers show that in human T lymphocytes, the excised DNA fragments from VDJ recombination can be reintegrated in genomic DNA, in this case causing disruption of the gene for a metabolic enzyme. Like Clathworthy et al (2003, in this bibliography), this paper provides strong evidence for a role of RAG1/2 as a functional transposase. Cannon, J. P., Haire, R. N., Rast, J. P. and Litman, G. W. (2004). "The phylogenetic origins of the antigen-binding receptors and somatic diversification mechanisms." Immunological Reviews 200(1): 12-22. (PubMed | DOI | Journal | Google Scholar) Detailed review of the origin of adaptive immunity. It takes the transposon hypothesis for granted and deals mostly with the "setting" for the transposon insertion -- the ancestral receptors and cells, etc."A mechanism that most likely gave rise to the adaptive immune system has been identified (1, 2) and is discussed elsewhere in the text. However, to understand the evolution of vertebrate adaptive immunity in detail, the characteristics of the immune systems of pre-adaptive ancestors must be reconstructed. Davis, M. M. (2004). "The evolutionary and structural 'logic' of antigen receptor diversity." Seminars in Immunology 16: 239-243. (PubMed | DOI | Journal | Google Scholar) Article on the evolutionary advantages of immune system receptor diversity. Highly technical. Eason, D. D., Cannon, J. P., Haire, R. N., Rast, J. P., Ostrov, D. A. and Litman, G. W. (2004). "Mechanisms of antigen receptor evolution." Seminars in Immunology 16: 215-226. (PubMed | DOI | Journal | Google Scholar) Detailed review of the evolutionary origin of adaptive receptors. All of the figures are useful summaries of various points. Flajnik, M. F. and Du Pasquier, L. (2004). "Evolution of innate and adaptive immunity: can we draw a line?" Trends in Immunology 25(12): 640-644. (PubMed | DOI | Journal | Google Scholar) New developments in the study of the evolution of adaptive immunity, especially noting that the lines between "innate" and "adaptive" immunity are becoming blurred as more organisms are studied. Representative quotes:"Particularly exciting are the discoveries of a new gene rearrangement mechanism in lampreys and a somatic diversification of mollusk immune genes." (p. 640) Galaktionov, V. G. (2004). "Evolutionary Development of the Immunoglobulin Family." Biology Bulletin 31(2): 101-111. (PubMed | DOI | Journal | Google Scholar) Reviews the evolutionary origin of immunoglobulins, particularly how the immunoglobulin domain has been reused in many different receptors."It is believed that RAG was originally introduced by a retrovirus into the genome of ancestral vertebrates, specifically, into the region occupied by the single V gene." (p. 110) Gould, S. J., Hildreth, J. E. and Booth, A. M. (2004). "The evolution of alloimmunity and the genesis of adaptive immunity." Quarterly Review of Biology 79(4): 359-382. (PubMed | DOI | Journal | Google Scholar) A long review article in the prestigious general biology journal Quarterly Review of Biology. Stephen J. Gould (a different one than the famous paleontologist) argues that alloimmunity (recognition of self vs. nonself) evolved first, allowing the slightly later evolution of the hypervariable adaptive immune system (the variability creates the risk of accidentally attacking self-cells, so preexisting alloimmunity would ameliorate this)."Given that alloimmunity arose more than 550 million years ago, at the dawn of animal evolution, and that adaptive immunity arose approximately 100 million years later at the origin of the jawed vertebrates (Schatz 1999), the most parsimonious explanation for why the two systems share so many features is that adaptive immunity evolved from a preexisting alloimmune system. We propose that hypervariable alloimmunity was exapted for adaptive immune responses soon after its genesis, an evolutionary event that could be selected by virtually any pathogen, even HAAPs." (p. 373) Holmes, E. C. (2004). "Adaptation and Immunity." PLoS Biology 2(9): 1269-1269. (PubMed | DOI | Journal | Google Scholar) This short primer article in PLoS Biology discusses the well-known adaptive value of having diverse antigen receptor genes, and the evolutionary arms race between immune system cells attempting to detect pathogens, and the pathogens attempting to avoid detection."It is therefore little wonder that the host and pathogen genes that control infection and immunity frequently show high levels of genetic diversity and present some of the best examples of positive selection (adaptive evolution) reported to date (Yang and Bilawski 2000). In particular, rates of nonsynonymous substitution per site (resulting in an amino acid change; dN) often greatly exceed those of synonymous substitution per site (silent change; dS), as expected if most mutations are fixed becuase they increase fitness." (p. 1267) Jones, J. M. (2004). "The taming of a transposon: V(D)J recombination and the immune system." Immunological Reviews 200(1): 233-248. (PubMed | DOI | Journal | Google Scholar) Review exploring the diversity of transposon systems and their relationship to V(D)J recombination."The study of V(D)J recombination has been continually informed by research into other systems, and it is now apparent that V(D)J recombination shares a particularly close relationship with the family of transposons that includes Ac/Ds. These similarities support the hypothesis that V(D)J recombination evolved from a primordial transposon." (pp. 233-234) Nonaka, M. and Yoshizaki, F. (2004). "Evolution of the Complement System." Molecular Immunology 40(12): 897-902. (PubMed | DOI | Journal | Google Scholar) Technical review of the origin of the innate (non-adaptive) immune system."Here, we discuss an early evolution of the complement components, both the non-modular C3 family and the other modular components, revealed by recent molecular analysis of possible complement genes from [a] variety of animals and the recently published genome analysis of an ascidian, [a tunicate or sea squirt], Ciona intestinalis." (p. 897) Pancer, Z., Amemiya, C. T., Ehrhardt, G. R. A., Ceitlin, J., Gartland, G. L. and Cooper, M. D. (2004). "Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey." Nature 430(6996): 174-180. (PubMed | DOI | Journal | Google Scholar) Evidence of a different system of adaptive immunity in an early-diverging vertebrate, the sea lamprey."Different evolutionary strategies were thus used to generate highly diverse lymphocyte receptors through rearrangement of LRR modules in agnathans (jawless fish) and of immunoglobulin gene segments in gnathostomes (jawed vertebrates)." (p. 174) Rothenberg, E. V. and Pant, R. (2004). "Origins of lymphocyte developmental programs: transcription factor evidence." Seminars in Immunology 16(4): 227-238. (PubMed | DOI | Journal | Google Scholar) Origins of lymphocytes (vertebrate immune system cells). Highly technical. Schatz, D. G. (2004). "Antigen receptor genes and the evolution of a recombinase." Seminars in Immunology 16(4): 245-256. (PubMed | DOI | Journal | Google Scholar) Reviews the transposon hypothesis for the origin of rearranging receptors. Fig. 3 (p. 250) gives the RAG transposon model. The evidence is also reviewed in detail on p. 250. Stavnezer, J. and Amemiya, C. T. (2004). "Evolution of isotype switching." Seminars in Immunology 16(4): 257-275. (PubMed | DOI | Journal | Google Scholar) Long, technical review of the evolution of an aspect of the adaptive immune system (CSR, class switch recombination) apparently restricted to tetrapods (amphibians, reptiles, mammals, birds)."This chapter will review the evolution of the ability to express antibodies, or immunoglobulins (Igs) of different classes or isotypes." (p. 257)Figure on p. 258 shows diversity of immune system gene organization. Zhou, L., Mitra, R., Atkinson, P. W., Hickman, A. B., Dyda, F. and Craig, N. L. (2004). "Transposition of hAT elements links transposable elements and V(D)J recombination." Nature 432: 995-1001. (PubMed | DOI | Journal | Google Scholar) Discovery of a transposon with mechanistic and sequence similarities to the RAG genes."It had been suggested that the V(D)J recombination system may have evolved from an ancient transposable DNA element12, 50. Our findings here of such a close mechanistic relationship between hAT transposition and V(D)J recombination...and the related active sites of hAT tranposases and RAG1 provides strong support for the view that V(D)J recombination evolved from transposable elements." (p. 1000) Klein, J. and Nikolaidis, N. (2005). "The descent of the antibody-based immune system by gradual evolution." Proceedings of the National Academy of Sciences 102(1): 169-174. (PubMed | DOI | Journal | Google Scholar) Argues against the "big bang" model of immune system evolution which asserts that the main features of the immune system came together "suddenly", i.e., in less than 50 million years. Instead, it argues that the processes was more graduated and step-by-step. Given that the research community seems to agree that the introduction of RAG clearly was a key step and would be "sudden" compared to other forms of genetic change, but also agrees that many other more common evolutionary processes and precursors were also involved in the origin of adaptive immunity, it can be argued that debating the "big bang" label is not particularly illuminating. Regardless, in doing so Klein and Nikolaidis re-emphasize some useful points:"We argue that the AIS [Antibody-based Immune System] has been assembled from elements that have primarily evolved to serve other functions and incorporated existing molecular cascades, resulting in the appearance of new organs and new types of cells." (p. 169)Figure 2 shows how many organisms lack many of the parts found in the most sophisticated systems. Cannon, J. P., Haire, R. N., Pancer, Z., Mueller, M. G., Skapura, D., Cooper, M. D. and Litman, G. W. (2005). "Variable Domains and a VpreB-like molecule are present in a jawless vertebrate." Immunogenetics 56(12): 924-929. (PubMed | DOI | Journal | Google Scholar) This paper describes a family of non-rearranging receptors in sea lampreys that are closely related to modern immunoglobulins and, together with papers by Cannon et al (2002, in this bibliography) and Suzuki et al (2005, Journal of Immunology, 174:2885-91) constitutes strong evidence of the existence of multiple, diverse families of immunoglobulin-like proteins predating the rearranging antigen receptors found in jawed vertebrates."This is the first indication of a molecule related to the B cell receptor (BCR) complex in a species that diverged prior to the jawed vertebrates in which RAG-mediated adaptive immunity is first encountered." (p. 924) Kapitonov, V. V. and Jurka, J. (2005). "RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons." Public Library of Science Biology 3(6): e181:0001-0014. (PubMed | DOI | Journal | Google Scholar) Reports the discovery of homologs of RAG1 in several non-chordate phyla -- this is the direct evidence of a free-living transposon suggested by Lewis in 1999. The summary figure was used by Ken Miller during his trial testimony."Even prior to the discovery of RAG1 and RAG2, it had been suggested that the first two RSSs were originally terminal inverted repeats (TIRs) of an ancient transposon whose accidental insertion into a gene ancestral to BCR and TCR, followed by gene duplications, triggered the emergence of the V(D)J machinery [4]. Later, this model was expanded by the suggestion that both RAG1 and RAG2 might have evolved from a transposase (TPase) that catalyzed transpositions of ancient transposons flanked by TIRs that were precursors of RSSs [9]. This model has received additional support through observations of similar biochemical reactions in transposition and V(D)J recombination [10,11]. Finally, it was demonstrated that RAG1/2 catalyzed transpositions of a DNA segment flanked by RSS12 and RSS23 in vitro [12,13] and in vivo in yeast [14]. In vertebrates, in vivo RAG-mediated transpositions are strongly suppressed, probably to minimize potential harm to genome function. So far, only one putative instance of such a transposition has been reported [15]. However, given the lack of significant structural similarities between RAGs and known TPases, the "RAG transposon" model [9,12,13,16] remained unproven. Here we demonstrate that the RAG1 core and RSSs were derived from a TPase and TIRs encoded by ancient DNA transposons from the Transib superfamily [17]." (pp. e181-e182) Du Pasquier, L. (2005). "Meeting the demand for innate and adaptive immunities during evolution." Scandinavian Journal of Immunology 62(s1): 39-48. (PubMed | DOI | Journal | Google Scholar) Detailed review of the total immune responses across metazoa, focusing on the demands imposed by natural selection, and the evolution of cooperation between adaptive and nonadaptive systems."Immunoglobulins and T-cell receptors Janssen, B. J. C., Huizinga1, E. G., Raaijmakers, H. C. A., Roos, A., Daha, M. R., Nilsson-Ekdahl, K., Nilsson, B. and Gros, P. (2005). "Structures of complement component C3 provide insights into the function and evolution of immunity." Nature 437(7058): 505-511. (PubMed | DOI | Journal | Google Scholar) The authors report the crystal structure of the key innate immunity protein, C3, and deduce certain features of the evolutionary origin of the protein, such as internal domain duplications. This research came out the week before trial and was cited in Kenneth Miller's direct testimony. Cohn, M. (2006). "What are the commonalities governing the behavior of humoral immune recognitive repertoires?" Developmental and Comparative Immunology 30(1-2): 19-42. (PubMed | DOI | Journal | Google Scholar) Long review of selection-related issues in the evolution of immunity."The evolution of the immune system has been reviewed over the years from several points of view [1-10]. I will try to take a different tack by stressing selectable function rather than structure, genealogy, sequence, homology, gene dynamics, etc., the basic tools of comparative immunologists. This is not to downplay the importance of these analyses, which are, in fact, fundamental and indispensable, but rather to see whether another approach will confirm our present views or, hopefully, give us new insights." (p. 19) Marchalonis, J. J., Adelman, M. K., Schluter, S. F. and Ramsland, P. A. (2006). "The antibody repertoire in evolution: Chance, selection, and continuity." Developmental and Comparative Immunology 30(1-2): 223-247. (PubMed | DOI | Journal | Google Scholar) Massive review with 177 references. Deals with mutation and selection explicitly."At the onset, we emphasize that evolution is a stochastic or accidental process building upon the spontaneous generation of mutations followed by natural selection based upon survival to reproduce under external/environmental conditions." (p. 224) AcknowledgementsThanks to Andrea Bottaro, Matt Inlay, and the Panda's Thumb crew for suggestions and corrections. Any mistakes that remain are my own. |
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Judgment Day: Intelligent Design on Trial, produced by Nova
Kitzmiller decision (2005) McLean v. Arkansas Documentation Project Books 
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