Scientific literature on the evolutionary origin of the immune system

Supplementary Material

Supplementary Material for: Bottaro, Andrea, Inlay, Matt A., and Matzke, Nicholas J. (2006). "Immunology in the spotlight at the Dover 'Intelligent Design' trial." Nature Immunology. 7(5), 433-435. May 2005. (Subscription no longer required: DOI | Journal | Google Scholar | PubMed | Supplementary Material)

Scientific literature on the evolutionary origin of the immune system

This is the list of books, textbook chapters, and articles that were presented to Defense expert Michael Behe during cross-examination in the Kitzmiller v. Dover Area School District trial about the constitutionality of teaching "intelligent design." The cross-examination was conducted by Pepper-Hamilton attorney Eric Rothschild. Behe summarily dismissed the mass of scientific literature on the evolution of the immune system, despite the fact that it contradicted his previous assertion that the scientific community had "no answers" on the question. This episode was cited in Judge Jones's ruling against intelligent design, and various press accounts.

Sections: BooksTextbook chaptersArticlesNote
See also: Annotated Bibliography | Long Unannotated Bibliography

Books

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 | Amazon | Google Print)

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 | Amazon | Google Print)

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)

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)

Manning, M. J., ed. (1980). Phylogeny of Immunological Memory. Developments in Immunology. Amsterdam, Elsevier/North-Holland Biomedical Press. (Library | Amazon | Google Print)

Marchalonis, J. J. (1976). Immunity in Evolution. Cambridge, Mass., Harvard University Press. (Library | Amazon | Google Print)

Síma, P. and Vetvicka, V. (1990). Evolution of Immune Reactions. Boca Raton, CRC Press. (Library | Amazon | Google Print)

Stewart, J. (1994). The Primordial VRM System and the Evolution of Vertebrate Immunity. Austin, R. G. Landes. (Library | Amazon | Google Print)

Vetvicka, V. and Síma, P. (1998). Evolutionary Mechanisms of Defense Reactions. Basel, Birkhäuser Verlag. (Library | Amazon | Google Print)

Vetvicka, V., Síma, P., Cooper, E. L., Bilej, M. and Roch, P. (1994). Immunology of Annelids. Boca Raton, CRC Press. (Library | Amazon | Google Print)

Warr, G. W. and Cohen, N., eds. (1991). Phylogenesis of Immune Functions. Boca Raton, CRC Press. (Library | Amazon | Google Print)



Textbook chapters

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)

Klein, J. (1986). "Evolution of Mhc." Natural History of the Major Histocompatibility Complex. New York, John Wiley & Sons: 715-762. (Library | Google Print)

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)



Articles

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)

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)

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)

Burnet, F. M. (1971). "Self-recognition in colonial marine forms and flowering plants in relation to the evolution of immunity." Nature 232(5308): 230. (PubMed | DOI | Journal | Google Scholar)

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)

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)

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)

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)

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)

Davis, M. M. (2004). "The evolutionary and structural 'logic' of antigen receptor diversity." Seminars in Immunology 16: 239-243. (PubMed | DOI | Journal | Google Scholar)

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)

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)

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)

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)

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)

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)

Galaktionov, V. G. (2004). "Evolutionary Development of the Immunoglobulin Family." Biology Bulletin 31(2): 101-111. (PubMed | DOI | Journal | Google Scholar)

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)

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)

Holmes, E. C. (2004). "Adaptation and Immunity." PLoS Biology 2(9): 1269-1269. (PubMed | DOI | Journal | Google Scholar)

Hughes, A. L. and Yeager, M. (1997). "Molecular evolution of the vertebrate immune system." BioEssays 19(9): 777-786. (PubMed | Google Scholar)

Janssen, B. J. C., Huizinga, 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)

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)

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)

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)

Kaufman, J. (2002). "The origins of the adaptive immune system: whatever next?" Nature Immunology 3(12): 1124-1125. (PubMed | DOI | Journal | Google Scholar)

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)

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)

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)

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 | Google Scholar)

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, S. M. and Wu, G. E. (2000). "The old and the restless." Journal of Experimental Medicine 191(10): 1631-1636. (PubMed | Journal | Google Scholar)

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)

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)

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 | Google Print)

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)

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)

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 | Google Print)

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)

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)

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, 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)

Nonaka, M. and Yoshizaki, F. (2004). "Evolution of the Complement System." Molecular Immunology 40(12): 897-902. (PubMed | DOI | Journal | Google Scholar)

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 | Google Print)

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)

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)

Plasterk, R. (1998). "Ragtime jumping." Nature 394(6695): 718-719. (PubMed | DOI | Journal | Google Scholar)

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)

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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)

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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)

Stavnezer, J. and Amemiya, C. T. (2004). "Evolution of isotype switching." Seminars in Immunology 16(4): 257-275. (PubMed | DOI | Journal | Google Scholar)

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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)


Note

During his direct testimony, Plaintiffs' expert Kenneth Miller highlighted eight articles on the development and confirmation of the transposon hypothesis for the evolutionary origin of the adaptive immune system. During the cross-examination of Michael Behe, Miller's list was given to Michael Behe first, followed by the rest of the literature. Miller's eight articles partially overlapped with the list of 58 articles in the Behe cross-examination exhibit; they have been combined to produce the articles list above. Also, a few of the available books were not read into the record, being available only as photocopies, or difficult to explain quickly (i.e. Immunology of Annelids).