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The Limits of the SelfImmunology and Biological Identity$

Thomas Pradeu

Print publication date: 2012

Print ISBN-13: 9780199775286

Published to Oxford Scholarship Online: May 2012

DOI: 10.1093/acprof:oso/9780199775286.001.0001

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(p.275) REFERENCES

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The Limits of the Self
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Oxford University Press

Bibliography references:

Adkins, B., Leclerc, C., and Marshall-Clarke, S. 2004. Neonatal adaptive immunity comes of age. Nature Reviews in Immunology 4: 553–64.

Alder, M. N., et al. 2005. Diversity and function of adaptive immune receptors in a jawless vertebrate. Science 310: 1970–73.

Alizon, S., and van Baalen, M. 2008a. Multiple infections, immune dynamics, and the evolution of virulence. American Naturalist 172(4): E150–68.

———. 2008b. Acute or chronic? Within-host models with immune dynamics, infection outcome, and parasite evolution. American Naturalist 172(6): E244–56.

Aluvihare, V. R., and Betz, A. G. 2006. The role of regulatory T cells in alloantigen tolerance. Immunological Reviews 212: 330–43.

Aluvihare, V. R., Kallikourdis, M., and Betz, A. G. 2004. Regulatory T cells mediate maternal tolerance to the fetus. Nature Immunology 5(3): 266–71.

Anderson, C. C. 2009. Placing regulatory T cells into global theories of immunity: An analysis of Cohn's challenge to integrity (Dembic). Scandinavian Journal of Immunology 69: 306–9.

Anderson, C. C., and Matzinger, P. 2000a. Danger, the view from the bottom of the cliff. Seminars in Immunology 12: 231–38.

———. 2000b. Anderson and Matzinger: Round 2. Seminars in Immunology 12: 277–91.

———. 2000c. Anderson and Matzinger: Round 3. Seminars in Immunology 12: 331–41.

Anderson, M. S., et al. 2002. Projection of an immunological self shadow within the thymus by the Aire protein. Science 298: 1395–401.

Andrian (von), U. H., and Mempel, T. R. 2003. Homing and cellular traffic in lymph nodes. Nature Reviews in Immunology 3: 867–78. (p.276)

Apostolou, I., and von Boehmer, H. 2004. In vivo instruction of suppressor commitment in naive T cells. Journal of Experimental Medicine 199(10): 1401–8.

Aristotle. 1984a. Categories. In The complete works of Aristotle, vol. 1, ed. J. Barnes. Princeton: Princeton University Press.

———. 1984b. Metaphysics. In The complete works of Aristotle, vol. 2, ed. J. Barnes. Princeton: Princeton University Press.

Ashton-Rickardt, P. G., et al. 1994. Evidence for a differential avidity model of T-cell selection in the thymus. Cell 76(4): 651–63.

Atlan, H., and Cohen, I. R., eds. 1989. Theories of immune networks. Berlin: Springer-Verlag.

———. 1998. Immune information, self-organization and meaning. International Immunology 10(6): 711–17.

Bäckhed, F., et al. 2005. Host-bacterial mutualism in the human intestine. Science 307: 1915–20.

Barnes, M. J., and Powrie, F. 2009. Regulatory T cells reinforce intestinal homeostasis. Immunity 31: 401–11.

Barrangou, R., et al. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315: 1709–12.

Beg, A. A. 2002. Endogenous ligands of Toll-like receptors: Implications for regulating inflammatory and immune responses. Trends in Immunology 23: 509–12.

Belkaid, Y., and Oldenhove, G. 2008. Tuning microenvironments: Induction of regulatory T cells by dendritic cells. Immunity 29: 362–71.

Belkaid, Y., and Rouse, B. T. 2005. Natural regulatory T cells in infectious disease. Nature Immunology 6(4): 353–60.

Belkaid, Y., and Tarbell, K. 2009. Regulatory T cells in the control of host-microorganism interactions. Annual Review of Immunology 27: 551–89.

Belkaid, Y., Blank, R. B., and Suffia, I. 2006. Natural regulatory T cells and parasites: A common quest for host homeostasis. Immunological Reviews 212: 287–300.

Belkaid, Y., et al. 2002. CD4+CD25+ regulatory T cells control Leishmania major persistence and immunity. Nature 420: 502–7.

Bendelac, A., Savage, P. B., and Teyton, L. 2007. The biology of NKT cells. Annual Review of Immunology 25: 297–336.

Benson, A., et al. 2009. Gut commensal bacteria direct a protective immune response against Toxoplasma gondii. Cell Host Microbe 6: 187–96.

Bernard, C. [1865] 1927. An Introduction to the study of experimental medicine. New York: Macmillan Company.

Bernstein, E., et al. 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409 (6818): 363–66.

Bettelli, E., Oukka, M., and Kuchroo, V. K. 2007. TH-17 cells in the circle of immunity and autoimmunity. Nature Immunology 8(4): 345–50. (p.277)

Bianchi, D. W., et al. 1996. Male fetal progenitor cells persist in maternal blood for as long as 27 years post partum. Proceedings of the National Academy of Sciences USA 93: 705–7.

Billingham, R. E., Brent, L., and Medawar, P. B. 1953. Actively acquired tolerance of foreign cells. Nature 172: 603–6.

Bindea, G., et al. 2010. Natural immunity to cancer in humans. Current Opinion in Immunology 22: 215–22.

Bingaman, A. W., et al. 2000. Vigorous allograft rejection in the absence of danger. Journal of Immunology 164: 3065–71.

Bischoff, V., et al. 2006. Downregulation of the Drosophila immune response by peptidoglycan-recognition proteins SC1 and SC2. PLoS Pathogens 2(2): e14, 0139–47.

Bluestone, J. A., and Abbas, A. K. 2003. Natural versus adaptive regulatory T cells. Nature Reviews in Immunology 3: 253–57.

Boller, T. 1995. Chemoperception of microbial signals in plant cells. Annual Review in Plant Physiology and Plant Molecular Biology 46: 189–214.

Boller, T., and He, S. Y. 2009. Innate immunity in plants: An arms race between pattern recognition receptors in plants and effectors in microbial pathogens. Science 324: 742–44.

Bonneville, M., O'Brien, R. L., and Born, W. K. 2010. γδ T cell effector functions: A blend of innate programming and acquired plasticity. Nature Reviews in Immunology 10: 467–78.

Boron, W. F. 2005. Physiology … On Our First Anniversary. Physiology 20: 212.

Bouneaud, C., Kourilsky, P., and Bousso, P. 2000. Impact of negative selection on the T cell repertoire reactive to a self-peptide: A large fraction of T cell clones escapes clonal deletion. Immunity 13: 829–40.

Bourtzis, K., and Miller, T. A. 2008. Insect symbiosis. Boca Raton, Fla.: CRC Press.

Breinl, F., and Haurowitz, F. 1930. Chemische Untersuchungen des Präzipitates aus Hämoglobin und anti-Hämoglobin Serum and Bemerkungen über die Natur der Antikörper. Hoppe-Seyler Zeitungschrift 192: 45–57.

Brennan, C. A., and Anderson, K. V. 2004. Drosophila: The genetics of innate immune recognition and response. Annual Review of Immunology 22: 14.1–14.27.

Brent, L. B. 1997. A history of transplantation immunology. San Diego and London: Academic Press.

———. 2001. Tolerance revisited. In Singular selves: Historical and contemporary debates in immunology, ed. A.-M. Moulin and A. Cambrosio, 44–52. Paris: Elsevier.

Bretscher, P., and Cohn, M. 1968. Minimal model for the mechanism of antibody induction and paralysis by antigen. Nature 220: 444–48.

———. 1970. A theory of self-nonself discrimination. Science 169: 1042–49. (p.278)

Brownlie, J. C., and Johnson, K. N. 2009. Symbiont-mediated protection in insect hosts. Trends in Microbiology 17(8): 348–54.

Burnet, F. M. 1929. ‘Smooth-Rough’ variation in bacteria in its relation to bacteriophage. Journal of Pathology and Bacteriology 32: 15–42.

———. 1940. Biological aspects of infectious disease. New York: Macmillan.

———. 1941. The production of antibodies. Melbourne: Macmillan.

———. 1957. A modification of Jerne's theory of antibody production using the concept of clonal selection. Australian Journal of Science 20: 67–69.

———. 1959. The clonal selection theory of acquired immunity. Cambridge: Cambridge University Press.

———. 1960. Immunological recognition of self. Nobel Lectures in Physiology or Medicine 3: 689–701.

———. 1962. The integrity of the body: A discussion of modern immunological ideas. Cambridge, Mass.: Harvard University Press.

———. 1967. The impact of ideas on immunology. Cold Spring Harbor Symposia on Quantitative Biology 32: 1–8.

———. 1968. Changing patterns: An atypical autobiography. Melbourne: Heinemann.

———. 1969. Cellular immunology: Self and notself. Cambridge: Cambridge University Press.

———. 1970. Immunological surveillance. Oxford: Pergamon.

———. 1971. ‘Self-recognition’ in colonial marine forms and flowering plants in relation to the evolution of immunity. Nature 232: 230–35.

———. 1976a. Immunology, aging and cancer: Medical aspects of mutation and selection. San Francisco: Freeman and Co.

———, ed. 1976b. Immunology: Readings from Scientific American. San Francisco: W. H. Freeman.

Burnet, F. M., and Fenner, F. 1949. The production of antibodies, 2d ed. Melbourne: Macmillan.

Buss, L. 1987. The evolution of individuality. Princeton: Princeton University Press.

Capron A., et al. 2005. Schistosomes: The road from host–parasite interactions to vaccines in clinical trials. Trends in Parasitology 21(3): 143–49.

Carosella, E. D., et al. 2008. HLA-G: From biology to clinical benefits. Trends in Immunology 29(3): 125–32.

Cash, H. L., et al. 2006. Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science 313: 1126–30.

Caumartin, J., et al. 2007. Trogocytosis-based generation of suppressive NK cells. EMBO Journal 26(5): 1423–33.

Chauvier, S. 2008. Particuliers, individus et individuation. In L'Individu: Perspectives contemporaines, ed. P. Ludwig and T. Pradeu, 11–35. Paris: Vrin. (p.279)

Chen, T.-C., et al. 2004. Generation of anergic and regulatory T cells following prolonged exposure to a harmless antigen. Journal of Immunology 172: 5900–5907.

Chen, W., et al. 2003. Conversion of peripheral CD4+CD25- naive T cells to CD4+CD25+ regulatory T cells by TGF-β induction of transcription factor Foxp3. Journal of Experimental Medicine 198(12): 1875–86.

Chen, Y., et al. 1994. Regulatory T cell clones induced by oral tolerance: Suppression of autoimmune encephalomyelitis. Science 265(5176): 1237–40.

Chen, Y., et al. 1995. Peripheral deletion of antigen-reactive T cells in oral tolerance. Nature 376: 177–80.

Chibani-Chennoufi, S., et al. 2004. Phage-host interaction: An ecological perspective. Journal of Bacteriology 186(12): 3677–86.

Chisholm, S. T., et al. 2006. Host-microbe interactions: Shaping the evolution of the plant immune response. Cell 124: 803–14.

Chomksy, N., 1964. Current issues in linguistic theory. The Hague: Mouton.

Cima, F., Sabbadin, A., and Ballarin, L. 2004. Cellular aspects of allorecognition in the compound ascidian Botryllus schlosseri. Developmental and Comparative Immunology 28: 881–89.

Claas, F. H. J. 2004. Chimerism as a tool to induce clinical transplantation tolerance. Current Opinion in Immunology 16: 578–83.

———. 2005. Transplantation: Changing dogmas in clinical transplantation immunology. Current Opinion in Immunology 17: 533–35.

Clark, W. R. 2008. In defense of self: How the immune system really works. New York: Oxford University Press.

Claverie, J.-M. 1990. Soi et non-soi: Un point de vue immunologique. In Soi et non-soi, ed. J. Bernard, M. Bessis, and C. Debru, 35–53. Paris: Seuil.

Cobbold, S. P., et al. 2006. Immune privilege induced by regulatory T cells in transplantation tolerance. Immunological Reviews 213: 239–55.

Cohen, I. R. 1989. Natural Id-anti-Id networks and the immunological homunculus. In Theories of immune networks, ed. H. Atlan and I. R. Cohen, 6–12. Berlin: Springer-Verlag.

———. 1992a. The cognitive principle challenges clonal selection. Immunology Today 13: 441–44.

———. 1992b. The cognitive paradigm and the immunological homunculus. Immunology Today 13: 490–94.

———. 2000a. Tending Adam's garden: Evolving the cognitive immune self. San Diego: Academic Press.

———. 2000b. Discrimination and dialogue in the immune system. Seminars in Immunology 12: 215–19.

Cohen, I. R., and Werkele, H. 1972. Autosensitization of lymphocytes against thymus reticulum cells. Science 176(41): 1324–25. (p.280)

Cohn, M. 1998a. The self-nonself discrimination in the context of function. Theoretical Medicine and Bioethics 19: 475–84.

———. 1998b. A reply to Tauber. Theoretical Medicine and Bioethics 19: 495–504.

———. 2010. The evolutionary context for a self–nonself discrimination. Cellular and Molecular Life Sciences 67: 2851–62.

Combes, C. 2001. Parasitism: The ecology and evolution of intimate interactions. Chicago: University of Chicago Press.

Coombes, J. L., and Maloy, K. J. 2007. Control of intestinal homeostasis by regulatory T cells and dendritic cells. Seminars in Immunology 19: 116–26.

Coombes, J. L., and Powrie, F. 2008. Dendritic cells in intestinal immune regulation. Nature Reviews in Immunology 8: 435–46.

Coombes, J. L., et al. 2007. A functionally specialized population of mucosal CD103+ DCs induces Foxp3+ regulatory T cells via a TGF-β- and retinoic acid-dependent mechanism. Journal of Experimental Medicine 204(8): 1757–64.

Cooper, E.L., ed. 1974. Invertebrate immunology: Contemporary topics in immunobiology, vol. 4. New York: Plenum Press.

Cooper, E. 2010a. Evolution of immune systems from self/not-self to danger to artificial immune systems. Physics of Life Reviews 7: 55–78.

———. 2010b. Self/not-self, innate immunity, danger, cancer potential. Physics of Life Reviews 7: 85–87.

Coutinho, A., et al. 1984. From an antigen-centered, clonal perspective of immune responses to an organism-centered network perspective of autonomous reactivity of self-referential immune systems. Immunological Reviews 79: 151–68.

Cremer, S., Armitage, S. A. O., and Schmid-Hempel, P. 2007. Social immunity. Current Biology 17: R693–R702.

Cremer, S., and Sixt, M. 2009. Analogies in the evolution of individual and social immunity. Philosophical Transactions of the Royal Society B 364: 129–42.

Crist, E., and Tauber, A. I. 1999. Selfhood, immunity, and the biological imagination: The thought of Frank Macfarlane Burnet. Biology and Philosophy 15(4): 509–33.

Curtis, A. S. G., Kerr, J., and Knowlton, N. 1982. Graft rejection in sponges. Transplantation 33(2): 127–33.

Dakic, A., et al. 2004. Development of the dendritic cell system during mouse ontogeny. Journal of Immunology 172: 1018–27.

Dangl, J. L., and Jones, J. D. G. 2001. Plant pathogens and integrated defence responses to infection. Nature 411: 826–33.

Dausset, J. 1981. The major histocompatibility complex in man. Science 213 (4515): 1469–74.

———. 1990. La Définition biologique du soi. In Soi et non-soi, ed. J. Bernard, M. Bessis, and C. Debru, 19–26. Paris: Seuil. (p.281)

Davis, D. M. 2007. Intercellular transfer of cell-surface proteins is common and can affect many stages of an immune response. Nature Reviews in Immunology 7: 238–43.

Dawkins, R. 1976. The selfish gene. Oxford: Oxford University Press.

———. 1982. The extended phenotype. Oxford: Oxford University Press.

Dedeine, F., et al. 2001. Removing symbiotic Wolbachia bacteria specifically inhibits oogenesis in a parasitic wasp. Proceedings of the National Academy of Sciences USA 98(11): 6247–52.

De Tomaso, A. W., et al. 2005. Isolation and characterization of a protochordate histocompatibility locus. Nature 438(24): 454–59.

DeYoung, B. J., and Innes, R. W. 2006. Plant NBS-LRR proteins in pathogen sensing and host defense. Nature Immunology 7: 1243–49.

Di Giacinto, C., et al. 2005. Probiotics ameliorate recurrent Th1-mediated murine colitis by inducing IL-10 and IL-10-dependent TGF-β-bearing regulatory cells. Journal of Immunology 174: 3237–46.

Ding, S.-W. 2010. RNA-based antiviral immunity. Nature Reviews in Immunology 10: 632–44.

Doolittle, W. F., and Bapteste, E. 2007. Pattern pluralism and the Tree of Life hypothesis. Proceedings of the National Academy of Sciences USA 104(7): 2043–49.

Dubois, B., et al. 2005. Oral tolerance and regulation of mucosal immunity. Cellular and Molecular Life Sciences 62: 1322–32.

Dunbar, H. E., et al. 2007. Aphid thermal tolerance is governed by a point mutation in bacterial symbionts. PLoS Biol 5(5): 1006–15.

Dunn, G. P., Koebel, C. M., and Schreiber, R. D. 2006. Interferons, immunity and cancer immunoediting. Nature Reviews Immunology 6: 836–48.

Dunn, G. P., Old, L. J., and Schreiber, R. D. 2004. The immunobiology of cancer immunosurveillance and immunoediting. Immunity 21: 137–48.

Dunn, G. P., et al. 2002. Cancer immunoediting: From immunosurveillance to tumor escape. Nature Immunology 3(11): 991–98.

Eberl, G., and Lochner, M. 2009. The development of intestinal lymphoid tissues at the interface of self and microbiota. Mucosal Immunology 2(6): 478–85.

Ehrlich, P. [1897] 1957. The assay of the activity of diphtheria-curative serum and its theoretical basis. In The collected papers of Paul Ehrlich, vol. 2, ed. F. Himmelweit, 107–25. Oxford: Pergamon.

———. 1900. On immunity with special reference to cell life. Proceedings of the Royal Society 66: 424–48.

Ehrlich, P., and Morgenroth, J. 1901. Über Hämolysine: fünfte Mittheilung. Berlin klin Wochenschr 38, 251–56. In The collected papers of Paul Ehrlich, vol. 2, ed. F. Himmelweit, 246–55. Oxford: Pergamon.

Elliott, M. R., et al. 2009. Nucleotides released by apoptotic cells act as a find-me signal to promote phagocytic clearance. Nature 461: 282–6. (p.282)

Engelhorn, M. E., et al. 2006. Autoimmunity and tumor immunity induced by immune responses to mutations in self. Nature Medicine 12: 198–206.

Falk, R. 2000. The gene—a concept in tension. In The concept of the gene in development and evolution: Historical and epistemological perspectives, ed. P. Beurton, R. Falk, and H.-J. Rhenberger, 317–48. Cambridge: Cambridge University Press.

Fehr, T., and Sykes, M. 2004. Tolerance induction in clinical transplantation. Transplant Immunology 13: 117–30.

Fire, A., et al. 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806–11.

Flor, H. H. 1971. Current status of the gene-for-gene concept. Annual Review of Phytopathology 9: 275–96.

Folse, H. J., and Roughgarden, J. 2010. What is an individual organism? A multilevel selection perspective. Quarterly Review of Biology 85(4): 447–72.

Frank, S. A. 1996. Host control of symbiont transmission: The transmission of symbionts into germ and soma. American Naturalist 148(6): 1113–24.

———. 2007. Dynamics of cancer: Incidence, inheritance, and evolution. Princeton and Oxford: Princeton University Press.

Freitas, A. A., and Rocha, B. 1999. Peripheral T cell survival. Current Opinion in Immunology 11: 152–56.

Friedl, P., den Boer, A. T., and Gunzer, M. 2005. Tuning immune responses: Diversity and adaptation of the immunological synapse. Nature Reviews in Immunology 5: 532–45.

Fuchs, E. J., Ridge, J. P., and Matzinger, P. 1996. Immunological tolerance: Response to A. M. Silverstein. Science 272(5267): 1407–8.

Gajewski, T. F. 2007. The expanding universe of regulatory T cell subsets in cancer. Immunity 27(2): 185–87.

Gallimore, A., et al. 1998. Induction and exhaustion of lymphocytic choriomeningitis virus-specific cytotoxic T lymphocytes visualized using soluble tetrameric major histocompatibility complex class I–peptide complexes. Journal of Experimental Medicine 187(9): 1383–93.

Gallucci, S., Lolkema, M., and Matzinger, P. 1999. Natural adjuvants: Endogenous activators of dendritic cells. Nature Medicine 5(11): 1249–55.

Gardner, A., and Grafen, A. 2009. Capturing the superorganism: A formal theory of group adaptation. Journal of Evolutionary Biology 22(4): 659–71.

Gasser, S., and Raulet, D. H. 2006. Activation and self-tolerance of natural killer cells. Immunological Reviews 214: 130–42.

Gayon, J. 1996. The individuality of the species: A Darwinian theory? From Buffon to Ghiselin, and back to Darwin. Biology and Philosophy 11: 215–44.

Ghiselin, M. T. 1974. A radical solution to the species problem. Systematic Zoology 23: 536–44. (p.283)

———. 1987. Species concepts, individuality, and objectivity. Biology and Philosophy 2: 127–43.

Gilbert, S. F. 2002. The genome in its ecological context. Annals of the New York Academy of Science 981: 202–18.

———. 2010. Developmental biology, 9th ed. Sunderland, Mass.: Sinauer Associates.

Gilbert, S. F., and Epel, D. 2009. Ecological developmental biology: Integrating epigenetics, medicine and evolution. Sunderland, Mass.: Sinauer Associates.

Godfrey, W. R., et al. 2005. Cord blood CD4+CD25+-derived T regulatory cell lines express FoxP3 protein and manifest potent suppressor function. Blood 105(2): 750–58.

Godfrey-Smith, P. 2009. Darwinian populations and natural selection. Oxford: Oxford University Press.

Goldstein, K. [1934] 1939. The organism: A holistic approach to biology derived from pathological data in man. New York: American Book Company.

Gordon, J. I., et al. 2005. Extending our view of self: The human gut microbiome initiative. 〈http://genome.gov/10002154〉.

Gottesman, S. 2004. The small RNA regulators of Escherichia coli: Roles and mechanisms. Annual Reviews of Microbiology 58: 303–28.

Goubier, A., et al. 2008. Plasmacytoid dendritic cells mediate oral tolerance. Immunity 29: 464–75.

Gould, S. J. 1998. Gulliver's further travels: The necessity and difficulty of a hierarchical theory of selection. Philosophical Transactions: Biological Sciences 353(1366): 307–14.

———. 2002. The structure of evolutionary theory. Cambridge, Mass.: Harvard University Press.

Gould, S. J., and Lloyd, E. 1999. Individuality and adaptation across levels of selection: How shall we name and generalize the unit of Darwinism? Proceedings of the National Academy of Sciences USA 96(21): 11904–9.

Graca, L., Cobbold, S. P., and Waldmann, H. 2002. Identification of regulatory T cells in tolerated allografts. Journal of Experimental Medicine 195(12): 1641–46.

Graca, L., et al. 2005. Dominant tolerance: Activation thresholds for peripheral generation of regulatory T cells. Trends in Immunology 26(3): 130–35.

Green, D. R., et al. 2009. Immunogenic and tolerogenic cell death. Nature Reviews in Immunology 9: 353–63.

Greenberg, J. T. 1996. Programmed cell death: A way of life for plants. Proceedings of the National Academy of Sciences USA 93: 12094–97.

Griffiths, P. E. 2001. Genetic information: A metaphor in search of a theory. Philosophy of Science 68(3): 394–412. (p.284)

Grmek, M. D. 1996. L’âge héroïque: les vaccins de Pasteur. In L'aventure de la vaccination, ed. A. M. Moulin, 143–159. Paris: Fayard.

Grossman, Z., and Paul, W. E. 2000. Self-tolerance: Context-dependent tuning of T cell antigen recognition. Seminars in Immunology 12: 197–203.

Guillet, J.-G., et al. 1987. Immunological self-nonself discrimination. Science 235: 865–70.

Ha, E.-M., et al. 2009. Coordination of multiple dual oxidase–regulatory pathways in responses to commensal and infectious microbes in drosophila gut. Nature Immunology 10(9): 949–58.

Haeckel, E. 1866. Generelle Morphologie der Organismen. Berlin: Georg Reimer.

Hamburger, J. [1976] 1978. Discovering the individual. New York: Norton & Company.

Hemmrich, G., Miller, D. J., and Bosch, T. C. G. 2007. The evolution of immunity: A low-life perspective. Trends in Immunology 28(10): 449–54.

Henrickson, S. E., et al. 2008. T cell sensing of antigen dose governs interactive behavior with dendritic cells and sets a threshold for T cell activation. Nature Immunology 9(3): 282–91.

Herrath (von), M. G., and Homann, D. 2008. Organ-specific autoimmunity. In Fundamental immunology, 6th ed., ed. W. E. Paul, 1331–74. Philadelphia: Lippincott Williams & Wilkins.

Hildemann, W. H., et al. 1979. Immunocompetence in the lowest metazoan phylum: Transplantation immunity in sponges. Science 204: 420.

Holt, P. G., et al. 2008. Regulation of immunological homeostasis in the respiratory tract. Nature Reviews in Immunology 8: 142–52.

Hooper, L. V. 2004. Bacterial contributions to mammalian gut development. Trends in Microbiology 12(3): 129–34.

———. 2005. Resident bacteria as inductive signals in mammalian gut development. In The influence of cooperative bacteria on animal host biology, ed. M. J. McFall-Ngai, B. Henderson, and E. G. Ruby, 249–64. Cambridge: Cambridge University Press.

Hooper, L. V., and Gordon, J. I. 2001. Commensal host-bacterial relationships in the gut. Science 292: 1115–18.

Hooper, L. V., et al. 2003. Angiogenins: A new class of microbicidal proteins involved in innate immunity. Nature Immunology 4(3): 269–73.

Horvath, P., and Barrangou, R. 2010. CRISPR/Cas, the immune system of bacteria and archaea. Science 327: 167–70.

Houghton, A. N. 1994. Cancer antigens: Immune recognition of self and altered self. Journal of Experimental Medicine 180: 1–4.

Howes, M. 2000. Self, intentionality, and immunological explanation. Seminars in Immunology 12: 249–56. (p.285)

Huang, F.-P., and MacPherson, G. 2001. Continuing education of the immune system: Dendritic cells, immune regulation and tolerance. Current Molecular Medicine 1: 457–68.

Hull, D. L. 1974. Philosophy of biological science. Englewood Cliffs, N.J.: Prentice-Hall.

———. 1978. A matter of individuality. Philosophy of Science 45(3): 335–60.

———. 1980. Individuality and selection. Annual Review of Ecology and Systematics 11: 311–32.

———. 1981. Units of evolution: A metaphysical essay. In The philosophy of evolution, ed. U. L. Jensen and R. Harré, 23–44. Brighton: Harvester Press.

———. 1988. Science as a process: An evolutionary account of the social and conceptual development of science. Chicago: Chicago University Press.

———. 1989. The metaphysics of evolution. New York: State University of New York Press.

———. 1992. Individual. In Keywords in evolutionary biology, ed. E. Fox-Keller and E. Lloyd, 181–87. Cambridge, Mass.: Harvard University Press.

Hunt, J. S. 2006. Stranger in a strange land. Immunological Reviews 213: 36–47.

Huxley, J. 1912. The individual in the animal kingdom. New York: Cambridge University Press.

Huxley, Thomas H. 1852. Upon animal individuality. Proceedings of the Royal Institution 1: 184–89. Reprinted in M. Foster and W. R. Lankester, eds., The scientific memoirs of Thomas Henri Huxley (London: Macmillan, 1892), 146–51.

Innes, R. W. 2011. Activation of plant nod-like receptors: How indirect can it be? Cell Host & Microbe 9: 87–89.

Ishii, K. J., and Akira, S. 2006. Innate immune recognition of, and regulation by, DNA. Trends in Immunology 27(11): 525–32.

Jacob, F., and Monod, J. 1961. On the regulation of gene activity. Cold Spring Harbor Symposia on Quantitative Biology 26: 193–211.

Jain, R., Rivera, M. C., and Lake, J. A. 1999. Horizontal gene transfer among genomes: The complexity hypothesis. Proceedings of the National Academy of Sciences USA 96: 3801–6.

Janeway, C. A. 1989. Approaching the asymptote? Evolution and revolution in immunology. Cold Spring Harbor Symposia on Quantitative Biology 54: 1–13.

———. 1992. The immune system evolved to discriminate infectious nonself from noninfectious self. Immunology Today 13(1): 11–16.

———. 2001. How the immune system protects the host from infection. Microbes and Infection 3: 1167–71.

Janeway, C. A., Goodnow, C. C., and Medzhitov, R. 1996. Immunological tolerance: Danger—pathogen on the premises! Current Biology 6(5): 519–22.

Janeway, C. A., and Medzhitov, R. 2002. Innate immune recognition. Annual Review of Immunology 20: 197–216. (p.286)

Janeway, C. A., Travers, P., Walport, M., and Shlomchik, M. J. 2005. Immunobiology: The immune system in health and disease. New York: Garland Science Publishing.

Janzen, D. H. 1977. What are dandelions and aphids? American Naturalist 111(979): 586–89.

Jeannin, P., Jaillon, S., and Delneste, Y. 2008. Pattern recognition receptors in the immune response against dying cells. Current Opinion in Immunology 20: 530–37.

Jerne, N. K. 1955. The natural selection theory of antibody formation. Proceedings of the National Academy of Sciences USA 41: 849–57.

———. 1967. Waiting for the end. Cold Spring Harbor Symposia on Quantitative Biology 32: 591–603.

———. 1974. Towards a network theory of the immune system. Annales d'immunologie 125 C: 373–89.

———. 1976. The immune system: A network of lymphocyte interactions. In The immune system, ed. F. Melchers and K. Rajewski, 259–66. Berlin: Springer Verlag.

———. 1984. Idiotypic networks and other preconceived ideas. Immunological Reviews 79: 5–24.

———. 1985. The generative grammar of the immune system. Science 229(4718): 1057–59.

Jiang, H., and Chess, L. 2009. How the immune system achieves self–nonself discrimination during adaptive immunity. Advances in Immunology 102: 95–133.

Joffre, O., et al. 2009. Inflammatory signals in dendritic cell activation and the induction of adaptive immunity. Immunological Reviews 227(1): 234–47.

Jonuleit, H., et al. 2000. Induction of interleukin 10-producing, nonproliferating CD4+ T cells with regulatory properties by repetitive stimulation with allogeneic immature human dendritic cells. Journal of Experimental Medicine 192: 1213–22.

Kahan, B. D. 2003. Individuality: The barrier to optimal immunosuppression. Nature Reviews Immunology 3: 831–8.

Kant, I. [1790] 2000. Critique of the power of judgement. Translated by P. Guyer and E. Matthews. Cambridge: Cambridge University Press.

Kappler, J. W., Roehm, N., and Marrack, P. 1987. T cell tolerance by clonal elimination in the thymus. Cell 49: 273–80.

Kärre, K. 1985. Role of target histocompatibility antigens in regulation of natural killer activity: A reevaluation and a hypothesis. In Mechanisms of NK mediated cytotoxicity, ed. D. Callewert and R. B. Herberman, 81–91. San Diego, Calif.: Academy Press.

Kelly, D., Conway, S., and Aminov, R. 2005. Commensal gut bacteria: Mechanisms of immune modulation. Trends in Immunology 26(6): 326–33. (p.287)

Kelly, D., et al. 2004. Commensal anaerobic gut bacteria attenuate inflammation by regulating nuclear-cytoplasmic shuttling of PPAR-γ and RelA. Nature Immunology 5: 104–12.

Khosrotehrani, K., et al. 2004. Transfer of fetal cells with multilineage potential to maternal tissue. Journal of the American Medical Association 292(1): 75–80.

Khush, R. V., Leulier, F., and Lemaitre, B. 2002. Pathogen surveillance—The flies have it. Science 296: 273–75.

Kiers, T. E., et al. 2003. Host sanctions and the legume-rhizobium mutualism. Nature 425: 78–81.

Klein, J. 1982. Immunology: The science of self-nonself discrimination. New York: Wiley. Second edition Boston: Blackwell Scientific Publications, 1990.

Kocks, C., et al. 2005. Eater, a transmembrane protein mediating phagocytosis of bacterial pathogens in Drosophila. Cell 123: 335–46.

Koebel, C. M., et al. 2007. Adaptive immunity maintains occult cancer in an equilibrium state. Nature 450: 903–8.

Kourilsky, P., and Claverie, J.-M. 1986. The peptidic self model: A hypothesis on the molecular nature of the immunological self. Annales d'immunologie 137: 3–21.

Kovats, S., et al. 1990. A class I antigen, HLA-G, expressed in human trophoblasts. Science 248: 220–23.

Kretschmer, K., et al. 2005. Inducing and expanding regulatory T cell populations by foreign antigen. Nature Immunology 6(12): 1219–27.

Kurtz, J., and Armitage, S. A. O. 2006. Alternative adaptive immunity in invertebrates. Trends in immunology 27(11): 493–96.

Kurtz, J., and Franz, K. 2003. Evidence for memory in invertebrate immunity. Nature 425: 37–38.

Ladyman, J., and Ross, D. 2007. Every thing must go: Metaphysics naturalized. New York: Oxford University Press.

Lafferty, K. J., and Cunningham, A. 1975. A new analysis of allogenic interactions. Australian Journal of Experimental Biology and Medical Science 53: 27–42.

Laird, D. J., De Tomaso, A. W., and Weissman, I. L. 2005. Stem cells are units of natural selection in a colonial ascidian. Cell 123: 1351–60.

Langman, R. E. 1989. The immune system: Evolutionary principles guide our understanding of this complex biological defense system. San Diego, Calif.: Academic Press.

Langman, R. E., and Cohn, M. 2000. Editorial Introduction. Seminars in Immunology 12(3): 159–62.

Lanier, L., and Sun, J. 2009. Do the terms innate and adaptive immunity create conceptual barriers? Nature Reviews Immunology 9: 302–3.

Lederberg, J. 2000. Infectious history. Science 288(5464): 287–93. (p.288)

Lee, H. K., and Iwasaki, A. 2007. Innate control of adaptive immunity: Dendritic cells and beyond. Seminars in Immunology 19: 48–55.

Leibniz, G. W. [1765] 1996. New essays on human understanding. Translated and edited by P. Remnant and J. Bennett. Cambridge: Cambridge University Press.

Lemaitre, B., and Hoffmann, J. 2007. The host defense of Drosophila melanogaster. Annual Review of Immunology 25: 697–743.

Lemaitre, B., Reichhart, J.-M., and Hoffmann, J. 1997. Drosophila host defense: Differential induction of antimicrobial peptide genes after infection by various classes of microorganisms. Proceedings of the National Academy of Sciences USA 94: 14614–19.

Lemaitre, B., et al. 1996. The dorsoventral regulatory gene cassette Spätzle/Toll/cactus controls the potent antifungal response in Drosophila adults. Cell 86: 973–83.

Lemaoult, J., et al. 2004. HLA-G1-expressing antigen-presenting cells induce immunosuppressive CD4+ T cells. Proceedings of the National Academy of Sciences USA 101(18): 7064–69.

Lemaoult, J., et al. 2007. Immune regulation by pretenders: Cell-to-cell transfers of HLA-G make effector T cells act as regulatory cells. Blood 109(5): 2040–48.

Leulier, F., and Royet, J. 2009. Maintaining immune homeostasis in fly gut. Nature Immunology 10(9): 936–38.

Levy, O. 2007. Innate immunity of the newborn: Basic mechanisms and clinical correlates. Nature Reviews in Immunology 7: 379–90.

Lewin, K. 1922. Der Begriff der Genese. Berlin: Springer.

Lewontin, R. 1970. The units of selection. Annual Review of Ecology and Systematics 1: 1–18.

———. 1983. The organism as the subject and object of evolution. Scientia 118: 63–82.

———. 1994. Inside and outside: Gene, environment and organism. Worcester, Mass.: Clark University Press.

———. 2000. The triple helix: Gene, organism and environment. Cambridge, Mass.: Harvard University Press.

Ley, R. E., Peterson, D. A., and Gordon, J. I. 2006. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124: 837–48.

Litman, G. W. 2005. Colonial match and mismatch. Nature 438(7067): 437–39.

———. 2006. How Botryllus chooses to fuse. Immunity 25(1): 13–15.

Litman, G. W., and Cooper, M. D. 2007. Why study the evolution of immunity? Nature Immunology 8(6): 547–48.

Lloyd, E. A. 2007. Units and levels of selection. In The Cambridge companion to the philosophy of biology, ed. D. L. Hull and M. Ruse, 44–65. Cambridge: Cambridge University Press. (p.289)

Locke, J. [1690] 1979. An essay concerning human understanding. Edited by P. H. Nidditch. Oxford: Clarendon Press & New York: Oxford University Press.

Loeb, J. 1916. The organism as a whole from a physiochemical viewpoint. New York: G. P. Putnam's sons.

Loeb, L. 1930. Transplantation and individuality. Physiological Review 10: 547–616.

———. 1937. The biological basis of individuality. Science 86(2218): 1–5.

———. 1945. The biological basis of individuality. Springfield, Ill.: Thomas.

Löwy, I. 1991. The immunological construction of the self. In Organism and the origins of self, ed. A. I. Tauber, 3–75. Boston Studies in the Philosophy of Science, no. 129. Dordrecht: Kluwer.

Lu, L.-F., et al. 2006. Mast cells are essential intermediaries in regulatory T-cell tolerance. Nature 442: 997–1002.

McFall-Ngai, M. J. 2002. Unseen forces: The influence of bacteria on animal development. Developmental Biology 242: 1–14.

Macpherson, A. J., and Harris, N. L. 2004. Interactions between commensal intestinal bacteria and the immune system. Nature Reviews in Immunology 4: 478–85.

Makarova, K. S., et al. 2006. A putative RNA-interference-based immune system in prokaryotes: Computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biology Direct 1(7).

Margulis, L. 1970. Origin of eukaryotic cells. New Haven: Yale University Press.

Margulis, L., ed. 1991. Symbiosis as a source of evolutionary innovation: Speciation and morphogenesis. Cambridge, Mass.: MIT Press.

Margulis, L., and Sagan, D. 2002. Acquiring genomes: A theory of the origins of species. New York: Basic Books.

Marks, B. R., et al. 2009. Thymic self-reactivity selects natural interleukin 17–producing T cells that can regulate peripheral inflammation. Nature Immunology 10: 1125–32.

Marshak-Rothstein, A. 2006. Toll-like receptors in systemic autoimmune disease. Nature Reviews in Immunology 6: 823–35.

Maturana, H. R., and Varela, F. J. 1980. Autopoiesis and cognition: The realization of the living. Boston Studies in the Philosophy of Science, no. 42. Boston: D. Reidel.

Matzinger, P. 1994. Tolerance, danger, and the extended family. Annual Review of Immunology 12: 991–1045.

———. 1998. An innate sense of danger. Seminars in Immunology 10: 399–415.

———. 2002. The danger model: A renewed sense of self. Science 296: 301–5. (p.290)

———. 2003. The real function of the immune system or tolerance and the four D's (danger, death, destruction and distress), online publication: 〈http://glamdring.ucsd.edu〉.

———. 2007. Friendly and dangerous signals: Is the tissue in control? Nature Immunology 8: 11–13.

Matzinger, P., and Kamala, T. 2011. Tissue-based class control: The other side of tolerance. Nature Reviews in Immunology 11: 221–30.

Mayer, L., and Shao, L. 2004. Therapeutic potential of oral tolerance. Nature Reviews in Immunology 4: 407–19.

Maynard-Smith, J., and Szathmary, E. 1995. The major transitions in evolution. Oxford and New York: W. H. Freeman Spektrum.

Mayr, E. 1961. Cause and effect in biology. Science 134: 1501–6.

———. 1987. The ontological status of species: Scientific progress and philosophical terminology. Biology and Philosophy 2: 145–66.

Mazumdar, P. H. 1995. Species and specificity: An interpretation of the history of immunology. Cambridge: Cambridge University Press.

Medawar, P. B. 1944. The behavior and fate of skin autografts and skin homografts in rabbits. Journal of Anatomy 78: 176–99.

———. 1953. Some immunological and endocrinological problems raised by evolution of viviparity in vertebrates. Symposia of the Society for Experimental Biology 7: 320–28.

———. 1957. The uniqueness of the individual. Londres: Methuen.

———. 1960. Immunological tolerance. Nobel Lectures in Physiology or Medicine 3: 704–15.

Medzhitov, R. 2001. Toll-like receptors and innate immunity. Nature Reviews in Immunology 1: 135–45.

Medzhitov, R., and Janeway, C. A. 1997. Innate immunity: The virtues of a nonclonal system of recognition. Cell 91: 295–98.

———. 2002. Decoding the patterns of self and nonself by the innate immune system. Science 296: 298–300.

Melamed, D., et al. 1998. Developmental regulation of B lymphocyte immune tolerance compartmentalizes clonal selection from receptor selection. Cell 92: 173–82.

Mellor, A. L., and Munn, D. H. 2004. Policing pregnancy: Tregs help keep the peace. Trends in Immunology 25: 563–65.

———. 2006. Immune privilege: A recurrent theme in immunoregulation? Immunological Reviews 213: 5–11.

Metchnikoff, E. 1884. Researches on the intracellular digestion of invertebrates. Quarterly Journal of Microscopical Science 24: 89–111.

———. [1892] 1893. Lectures on the comparative pathology of inflammation. Translated by F. A. Starling and E. H. Starling. London: Kegan, Pauls Trench Trubner. (p.291)

———. [1901] 1905. Immunity in infective diseases. Translated by F. G. Binnie. Cambridge: Cambridge University Press.

Michel, T., et al. 2001. Drosophila Toll is activated by Gram-positive bacteria through a circulating peptidoglycan recognition protein. Nature 414: 756–9.

Michod, R. E. 1999. Darwinian dynamics. Evolutionary transitions in fitness and individuality. Princeton: Princeton University Press.

Miller, J. F. A. P. 1962. Effect of neonatal thymectomy on the immunological responsiveness of the mouse. Proceedings of the Royal Society of London 156B: 410–28.

Moalem, G., et al. 1999. Autoimmune T cells protect neurons from secondary degeneration after central nervous system axotomy. Nature Medicine 5: 49–55.

Moffet-King, A. 2002. Natural killer cells and pregnancy. Nature Reviews in Immunology 2: 656–63.

Morange, M. 1998. A history of molecular biology. Cambridge, Mass.: Harvard University Press.

———. 2005. The ambiguous place of structural biology in the historiography of molecular biology. Symposium History and Epistemology of Molecular Biology and Beyond: Problems and Perspectives. Max Planck Institute for the History of Science, October 2005.

———. 2008. Life explained. Translated by M. Cobb and M. DeBevoise. New Haven: Yale University Press.

Moulin, A. M. 1990. La Métaphore du soi et le tabou de l'auto-immunité. In Soi et non-soi, ed. J. Bernard, M. Bessis, and C. Debru, 55–68. Paris: Seuil.

———. 1991. Le Dernier Langage de la médecine: Histoire de l'immunologie de Pasteur au Sida. Paris: PUF.

Murphy, J. B. 1913. Transplantability of tissues to the embryo of foreign species. Journal of Experimental Medicine 17: 482–92.

Neill, J. D., and Benos, D. J. 1993. Relationship of molecular biology to integrative physiology. News in Physiological Sciences 8: 233–35.

Nossal, G. J. V. 1989. Immunologic tolerance: Collaboration between antigen and lymphokines. Science 245(4914): 147–53.

———. 1991. Molecular and cellular aspects of immunologic tolerance. European Journal of Biochemistry 202: 729–37.

Noverr, M. C., and Huffnagle, G. B. 2004. Does the microbiota regulate immune responses outside the gut? Trends in Microbiology 12(12): 562–68.

Nurnberger, T., et al. 2004. Innate immunity in plants and animals: Striking similarities and obvious differences. Immunological Reviews 198: 249–66.

Nyholm, S. V., et al. 2006. Fester: A candidate allorecognition receptor from a primitive chordate. Immunity 25: 163–73.

O'Hara, A. M., and Shanahan, F. 2006. The gut flora as a forgotten organ. EMBO Reports 7(7): 688–93. (p.292)

O'Neill, S. L., et al. 1997. Influential passengers: Inherited microorganisms and arthropod reproduction. New York: Oxford University Press.

Okasha, S. 2006. Evolution and the levels of selection. New York: Oxford University Press.

Oldroyd, G. E. D., Harrison, M. J., and Paszkowski, U. 2009. Reprogramming plant cells for endosymbiosis. Science 324: 753–54.

Owen, R. D. 1945. Immunogenetic consequences of vascular anastomoses between bovine twins. Science 102: 400–405.

Oyama, S. [1985] 2000. The ontogeny of information. Durham, N.C.: Duke University Press.

Pacholczyk, R., et al. 2007. Nonself-antigens are the cognate specificities of Foxp3+ regulatory T cells. Immunity 27: 493–504.

Palmer, C., et al. 2007. Development of the human infant intestinal microbiota. PLoS Biology 5(7): 1556–73.

Pancer, Z., et al. 2004. Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey. Nature 430: 174–80.

Pardoll, D. 2003. Does the immune system see tumors as foreign or self? Annual Review of Immunology 21: 807–39.

Parker, A. S., et al. 2010. Optimization algorithms for functional deimmunization of therapeutic proteins. BMC Bioinformatics 11:180.

Paul, P., et al. 1998. HLA-G expression in melanoma: A way for tumor cells to escape from immunosurveillance. Proceedings of the National Academy of Sciences USA 95: 4510–15.

Pauling, L. 1940. A theory of the structure and process of formation of antibodies. Journal of the American Chemical Society 62: 2643–57.

Plasterk, R. H. A. 2002. RNA silencing: The genome's immune system. Science 296: 1263–65.

Pohl, U. 2005. Physiology without borders. Physiology 20: 148.

Pradeu, T. 2009. Immune system: “Big Bang” in question. Science 325: 393.

Pradeu, T., and Carosella, E. D. 2004. Analyse critique du modèle immunologique du soi et du non-soi et de ses fondements métaphysiques implicites. Comptes rendus de l'Académie des Sciences Biologies 327: 481–92.

———. 2006a. The self model and the conception of biological identity in immunology. Biology and Philosophy 21(2): 235–52.

———. 2006b. On the definition of a criterion of immunogenicity. Proceedings of the National Academy of Sciences USA 103(47): 17858–61.

Qin, S., et al. 1993. “Infectious” transplantation tolerance. Science 259(5097): 974–77.

Queller, D. C. 2000. Relatedness and the fraternal major transitions. Philosophical Transactions of the Royal Society B 355: 1647–55.

Queller, D. C., and Strassmann, J. E. 2009. Beyond society: The evolution of organismality. Philosophical Transactions of the Royal Society B 364: 3143–55. (p.293)

Quine, W. V. O. 1951. Two dogmas of empiricism. Philosophical Review 60: 20–43.

———. 1969. Epistemology naturalized. In Ontological Relativity and Other Essays. New York: Columbia University Press.

Rairdan, G., and Moffett, P. 2007. Brothers in arms? Common and contrasting themes in pathogen perception by plant NB-LRR and animal NACHT-LRR proteins. Microbes and Infection 9: 677–86.

Rakoff-Nahoum, S., et al. 2004. Recognition of commensal microflora by Toll-like receptors is required for intestinal homeostasis. Cell 118: 229–41.

Ramet, M. 2001. Drosophila scavenger receptor CI is a pattern recognition receptor for bacteria. Immunity 15: 1027–38.

Raulet, D. H., Vance, R. E., and McMahon, C. W. 2001. Regulation of the natural killer cell receptor repertoire. Annual Review of Immunology 19: 291–330.

Reichenbach, H. [1928] 1958. The philosophy of space and time. Translated by M. Reichenbach and J. Freund. New York: Dover Publications.

———. 1938. Experience and prediction: An analysis of the foundations and the structure of knowledge. Chicago: University of Chicago Press.

Rescigno, M., et al. 2001. Dendritic cells express tight junction proteins and penetrate gut epithelial monolayers to sample bacteria. Nature Immunology 2: 361–67.

Ridge, J. P., Fuchs, E. J., and Matzinger, P. 1996. Neonatal tolerance revisited: Turning on newborn T cells with dendritic cells. Science 271(5256): 1723–26.

Rosengaus, R. B., et al. 1999. Immunity in a social insect. Naturwissenschaften 86: 588–91.

Rouas-Freiss, N., et al. 1997. Direct evidence to support the role of HLA-G in protecting the fetus from maternal uterine natural killer cytolysis. Proceedings of the National Academy of Sciences USA 94, 11520–25.

Rouas-Freiss, N., et al. 2007. Tolerogenic functions of human leukocyte antigen G: From pregnancy to organ and cell transplantation. Transplantation 84(1 Suppl): S21–S25.

Round, J. L., and Mazmanian, S. K. 2009. The gut microbiota shapes intestinal immune responses during health and disease. Nature Reviews in Immunology 9: 313–23.

Rudolph, M. G., Stanfield, R. L., and Wilson, I. A. 2006. How TCRs bind MHCs, peptides, and coreceptors. Annual Review of Immunology 24: 419–66.

Ryals, J. A., et al. 1996. Systemic acquired resistance. Plant Cell 8: 1809–19.

Saha, N. R., Smith, J., and Amemiya, C. T. 2010. Evolution of adaptive immune recognition in jawless vertebrates. Seminars in Immunology 22: 25–33.

Sakaguchi, S. 2005. Naturally arising Foxp3-expressing CD25+CD4+ regulatory T cells in immunological tolerance to self and non-self. Nature Immunology 6: 345–52. (p.294)

———. 2006. Regulatory T cells: Meden agan. Immunological Reviews 212: 5–7.

Saleh, C., et al. 2009. Antiviral immunity in Drosophila requires systemic RNA interference spread. Nature 458: 346–51.

Santelices, B. 1999. How many kinds of individuals are there? Trends in Ecology and Evolution 14(4): 152–55.

Sapp, J. 1994. Evolution by association: A history of symbiosis. New York: Oxford University Press.

Savill, J., et al. 2002. A blast from the past: Clearance of apoptotic cells regulates immune responses. Nature Reviews in Immunology 2: 965–75.

Schmidt, O., Theopold, U., and Beckage, N. E. 2008. Insect and vertebrate immunity: Key similarities versus differences. In Insect Immunology, ed. E. Beckage. San Diego: Academic Press.

Scofield, V. L., et al. 1982. Protochordate allorecognition is controlled by a MHC-like gene system. Nature 295: 499–502.

Shao, F., et al. 2003. Cleavage of Arabidopsis PBS1 by a bacterial type III effector. Science 301: 1230–33.

Shevach, E. M. 2006. From vanilla to 28 flavors: Multiple varieties of T regulatory cells. Immunity 25: 195–201.

———. 2009. Mechanisms of Foxp3+ T regulatory cell-mediated suppression. Immunity 30: 636–45.

Silverstein, A. M. 1985. A history of theories of antibody formation. Cellular Immunology 91: 263–83.

———. 1989. A history of immunology. New York: Academic Press.

———. 1991. The dynamics of conceptual change in twentieth century immunology. Cellular Immunology 132: 515–31.

———. 1996. Immunological tolerance. Science 272: 1405.

———. 1999. Paul Ehrlich's passion: The origins of his receptor immunology. Cellular Immunology 194: 213–21.

———. 2001. Autoimmunity versus horror autotoxicus: The struggle for recognition. Nature Immunology 2: 279–81.

———. 2003. Darwinism and immunology: From Metchnikoff to Burnet. Nature Immunology 4(1): 3–6.

Silverstein, A. M., and Rose, N. R. 1997. On the mystique of the immunological self. Immunological Reviews 159: 197–206.

Simpson, E. 2006. A historical perspective on immunological privilege. Immunological Reviews 212: 12–22.

Smith, D. W., and Nagler-Anderson, C. 2005. Preventing intolerance: The induction of nonresponsiveness to dietary and microbial antigens in the intestinal mucosa. Journal of Immunology 174: 3851–57.

Smits, H. H., et al. 2005. Different faces of regulatory DCs in homeostasis and immunity. Trends in Immunology 26(3): 123–29. (p.295)

Snell, G. D. 1948. Methods for the study of histocompatibility genes. Journal of Genetics 49: 87–108.

Sober, E. 1991. Organisms, individuals and units of selection. In Organism and the origins of self, ed. A. I. Tauber, 275–96. Boston Studies in the Philosophy of Science, no. 129. Dordrecht: Kluwer.

———. [1993] 2000. Philosophy of biology. Boulder, Colo.: Westview Press.

Sober, E., and Lewontin, R. C. 1982. Artifact, cause and genic selection. Philosophy of Science 49(2): 157–80.

Sober, E., and Wilson, D. S. 1999. Unto others: The evolution and psychology of unselfish behavior. Cambridge, Mass.: Harvard University Press.

Somerset, D. A., et al. 2004. Normal human pregnancy is associated with an elevation in the immune suppressive CD25+ CD4+ regulatory T-cell subset. Immunology 112: 38–43.

Sontheimer, E. J., and Carthew, R. W. 2005. Silence from within: Endogenous siRNAs and mi RNAs. Cell 122(1): 9–12.

Spörri, R., and Reis e Sousa, C. 2005. Inflammatory mediators are insufficient for full dendritic cell activation and promote expansion of CD4+ T cell populations lacking helper function. Nature Immunology 6(2): 163–70.

Steinman, R. M., and Nussenzweig, M. C. 2002. Avoiding horror autotoxicus: The importance of dendritic cells in peripheral T cell tolerance. Proceedings of the National Academy of Sciences USA 99(1): 351–58.

Steinman, R. M., Hawiger, D., and Nussenzweig, M. C. 2003. Tolerogenic dendritic cells. Annual Review of Immunology 21: 685–711.

Steinman, R. M., et al. 2000. The induction of tolerance by dendritic cells that have captured apoptotic cells. Journal of Experimental Medicine 191(3): 411–16.

Sterelny, K. 2001. Niche construction, developmental systems, and the extended replicator. In Cycles of contingency: Developmental systems and evolution, ed. S. Oyama, P. E. Griffiths, and R. D. Gray, 333–49. Cambridge, Mass.: MIT Press.

Sterelny, K., and Griffiths, P. E. 1999. Sex and death: An introduction to philosophy of biology. Chicago: University of Chicago Press.

Sterelny, K., Smith, K. C., and Dickison, M. 1996. The extended replicator. Biology and Philosophy 11: 377–403.

Stoner, D. S., Rinkevich, B., and Weissman, I. 1999. Heritable germ and somatic cell lineage competitions in chimeric colonial protochordates. Proceedings of the National Academy of Sciences USA 96: 9148–53.

Strassman, J. E., and Queller, D. C. 2007. Insect societies as divided organisms: The complexities of purpose and cross-purpose. Proceedings of the National Academy of Sciences USA 104: 8619–26.

Strawson, P. F. 1959. Individuals: An essay in descriptive metaphysics. London: Methuen & Co. (p.296)

Strober, W. 2009. The multifaceted influence of the mucosal microflora on mucosal dendritic dell responses. Immunity 31: 377–88.

Stuart, L. M., and Ezekowitz, R. A. B. 2005. Phagocytosis: Elegant complexity. Immunity 22: 539–50.

Suber, F., Carroll, M. C., and Moore, Jr., F. D. 2007. Innate response to self-antigen significantly exacerbates burn wound depth. Proceedings of the National Academy of Sciences USA 104(10): 3973–7.

Suffia, I. J., et al. 2006. Infected site-restricted Foxp3+ natural regulatory T cells are specific for microbial antigens. Journal of Experimental Medicine 203: 777–88.

Sykes, M. 2001. Mixed chimerism and transplant tolerance. Immunity 14: 417–24.

Tafuri, A., et al. 1995. T cell awareness of paternal alloantigens during pregnancy. Science 270: 630–33.

Taiz, L., and Zeiger, E. [1991] 2006. Plant physiology, 4th ed. Sunderland: Sinauer Associates.

Talmage, D. W. 1957. Allergy and immunology. Annual Reviews of Medicine 8: 239–56.

Tauber, A. I. 1994. The Immune Self: Theory or Metaphor? Cambridge: Cambridge University Press.

———. 1997. Historical and philosophical perspectives on immune cognition. Journal of the History of Biology 30: 419–40.

———. 1999. The elusive immune self: A case of category errors. Perspectives in Biology and Medicine 42(4): 459–74.

———. 2000. Moving beyond the immune self? Seminars in Immunology 12: 241–48.

———. 2009 [2002]. The biological notion of self and non-self. Stanford Encyclopedia of Philosophy (online).

Tauber, A. I., and Chernyak, L. 1991. Metchnikoff and the origins of immunology. New York: Oxford University Press.

Taylor, P. R., et al. 2005. Macrophage receptors and immune recognition. Annual Review of Immunology 23: 901–44.

Thomas, L. 1959. Discussion. In Cellular and humoral aspects of the hypersensitive states, ed. H. S. Lawrence, 529–32. New York: Hoeber-Harper.

Tonegawa, S. 1983. Somatic generation of antibody diversity. Nature 302: 5009–15.

Tonegawa, S., et al. 1974. Evidence for somatic generation of antibody diversity. Proceedings of the National Academy of Sciences USA 71(10): 4027–31.

Traniello, J. F. A., Rosengaus, R. B., and Savoie, K. 2002. The development of immunity in a social insect: Evidence for the group facilitation of disease resistance. Proceedings of the National Academy of Sciences USA 99: 6838–42. (p.297)

Turnbaugh, P. J., et al. 2007. The Human microbiome project. Nature 449: 804–10.

Vaishnava, S., et al. 2008. Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host-microbial interface. Proceedings of the National Academy of Sciences USA 105:20858–63.

van der Biezen, E. A., and Jones, J. D. G. 1998. Plant disease-resistance proteins and the gene-for-gene concept. Trends in Biochemical Sciences 23: 454–56.

van der Oost, J., et al. 2009. CRISPR-based adaptive and heritable immunity in prokaryotes. Trends in Biochemical Sciences 34(8): 401–7.

Vance, R. E. 2000. A Copernican revolution? Doubts about the danger theory. Journal of Immunology 165: 1725–28.

Varela, F. J., et al. 1988. Cognitive networks: Immune, neural, and otherwise. In Theoretical immunology (Part Two), ed. A. S. Perelson, 359–75. Redwood City: Addison-Wesley Publishing Co.

Vaz, N. M., and Varela, F. J. 1978. Self and non-sense: An organism-centered approach to immunology. Medical Hypotheses 4: 231–67.

Venkatesan, K., et al. 2009. An empirical framework for binary interactome mapping. Nature Methods 6(1): 83–90.

Vidal, M. 2001. A biological atlas of functional maps. Cell 104: 333–39.

Vivier, E., and Malissen, B. 2005. Innate and adaptive immunity: Specificities and signaling hierarchies revisited. Nature Immunology 6(1): 17–21.

Voinnet, O. 2001. RNA silencing as a plant immune system against viruses. Trends in Genetics 17(8): 449–59.

von Boehmer, H. 2003. Dynamics of suppressor T cells: In vivo veritas. Journal of Experimental Medicine 198(6): 845–49.

Waldmann, H. 2002. Reprogramming the immune system. Immunological Reviews 185(1): 227–35.

Waldmann, H., et al. 2004. Regulatory T cells and organ transplantation. Seminars in Immunology 16: 119–26.

Waldmann, H., et al. 2006. Regulatory T cells in transplantation. Seminars in Immunology 18: 111–19.

Wang, X.-H., et al. 2006. RNA interference directs innate immunity against viruses in adult Drosophila. Science 312: 452–54.

Wells, H. G., Huxley, J. S., and Wells, G. P. [1929] 1934. The science of life. New York: Literary Guild.

West-Eberhard, M. J. 2003. Developmental plasticity and evolution. Oxford: Oxford University Press.

Wheeler, W. M. 1911. The ant-colony as an organism. Journal of Morphology 22: 307–25.

Wiggins, D. [1980] 2001. Sameness and substance renewed. Oxford: Basil Blackwell.

Williams, G. C. 1966. Adaptation and natural selection: A critique of some current evolutionary thought. Princeton: Princeton University Press. (p.298)

Wilson, D. 1971. The science of self: A report of the new immunology. Essex: Longman.

Wilson, D. S, and Sober, E. 1989. Reviving the superorganism. Journal of Theoretical Biology 136: 337–56.

Wilson, J. 1999. Biological individuality: The identity and persistence of living entities. Cambridge: Cambridge University Press.

———. 2000. Ontological butchery: Organism concepts and biological generalizations. Philosophy of Science (Proceedings) 67: S301–S311.

Wilson, R. 2004. Genes and the agents of life: The individual in the fragile sciences (Biology). Cambridge: Cambridge University Press.

Wodarz, D. 2006. Ecological and evolutionary principles in immunology. Ecology Letters 9: 694–705.

Wolvekamp, H. P. 1966. The concept of the organism as an integrated whole. Dialectica 20: 196–214.

Wood, K. J., and Sakaguchi, S. 2003. Regulatory T cells in transplantation tolerance. Nature Reviews Immunology 3: 199–210.

Wraith, D. C. 2006. Avidity and the art of self non-self discrimination. Immunity 25: 191–93.

Xu, J. 2007. Evolution of symbiotic bacteria in the distal human intestine. PLoS Biology 5(7): 1574–86.

Xu, J., and Gordon, J. I. 2003. Honor thy symbionts. Proceedings of the National Academy of Sciences USA 100(18): 10452–59.

Xu, J., et al. 2004. Message from a human gut symbiont: Sensitivity is a prerequisite for sharing. Trends in Microbiology 12(1): 21–28.

Yokota, T., et al. 2006. Tracing the first waves of lymphopoiesis in mice. Development 133: 2041–51.

Yong, Z., et al. 2007. Role and mechanisms of CD4+CD25+ regulatory T cells in the induction and maintenance of transplantation tolerance. Transplant Immunology 17: 120–29.

Zaidman-Remy, A., et al. 2006. The Drosophila amidase PGRP-LB modulates the immune response to bacterial infection. Immunity 24: 463–73.

Zinkernagel, R. M. 2004. Credo 2004. Scandinavian Journal of Immunology 60: 9–13.

Zinkernagel, R. M., et al. 1978. On the thymus in the differentiation of “H-2 self-recognition” by T cells: Evidence for dual recognition? Journal of Experimental Medicine 147: 882–96.