Advertisement

6 Homology: A Philosophical and Biological Perspective

  • Olivier Rieppel
Reference work entry

Abstract

Current discussions of the concept of homology center on metaphysical and epistemological issues: what are homologs, and how can they be discovered? Homology is the relation of common ancestry shared by homologs. Homologs are the “same” parts of two or more organisms under every variation of form or function that are shared due to inheritance from a common ancestor. Homology is the key to phylogeny reconstruction, because the hierarchy of homologs/homologies is isomorphic with the phylogenetic hierarchy of taxa. Consequently, the discussion of homologs as evolving entities shares many parallels with the discussion of species evolution. Homologs are conceptualized as tokens of natural kinds that engage in causal processes of ontogeny, phylogeny, and physiology. Operational criteria for the discovery of homology are the topological relations (connectivity) shared by homologs. These operational criteria are (at least to some degree) grounded in ontogeny, where developmental modules may share the relation of homology. In that sense, the operational criteria for the discovery of homology are aligned with the structure of the causal processes in which the homologs qua tokens of natural kinds engage. The discussion of concepts of partial homology and the complementarity of static (taxic, hierarchical) versus dynamic (developmental, transformational) approaches to homology reveals empirical as well as a semantic components.

Keywords

Natural Kind Causal Process Phylogeny Reconstruction Natural Kind Term Transformation Series 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

The content of this paper profited much from discussions with Maureen Kearney and Richard A Richards, which is not to say that they agree with all the views expressed here. Support from the National Science Foundation is greatly acknowledged (grant # DEB-0235618, to M.K. and O.R.).

References

  1. Audi R (2003) Epistemology. A contemporary introduction to the theory of knowledge, 2nd edn. Routledge, LondonGoogle Scholar
  2. Belon P (1555) L'Histoire de la Nature des Oyseaux. Paris, Guillaume CavellatGoogle Scholar
  3. Bock WJ (1974) Philosophical foundations of classical evolutionary classification. Syst Zool 22: 375––392CrossRefGoogle Scholar
  4. Boyd R (1991) Realism, anti-fondationalism and the enthusiasm for natural kinds. Philos Stud 61: 127–148CrossRefGoogle Scholar
  5. Boyd R (1999) Homeostasis, species, and higher taxa. In: Wilson RA (ed) Species; New interdisciplinary essays. The MIT Press, Cambridge MA, pp 141–185Google Scholar
  6. Brandon RN (1999) The units of selection revisited: the modules of selection. Biology and philosophy 14: 67–180Google Scholar
  7. Brower AVZ, Schawaroch V (1996) Three steps of homology assessment. Cladistics 12: 265–272Google Scholar
  8. Cain AJ, Harrison GA (1958) An analysis of the taxonomist's judgment of affinity. Proc Zool Soc Lond 131: 85–98CrossRefGoogle Scholar
  9. Darwin C (1859) The Origin of Species. John Murray, LondonGoogle Scholar
  10. dePinna MCC (1991) Concepts and tests of homology in the cladistic paradigm. Cladistics 7: 367–394CrossRefGoogle Scholar
  11. Devitt M, Sterelny K (1999) Language and reality. An introduction to the philosophy of language. The MIT Press, Cambridge MAGoogle Scholar
  12. Dupré J (1993) The disorder of things. Metaphysical foundations of the disunity of science. Harvard University Press, Cambridge MAGoogle Scholar
  13. Dupuis C (1984) Willi Hennigs impact on taxonomic thought. Annu Rev Ecol Syst 15: 1–24CrossRefGoogle Scholar
  14. Farris SJ (1983) The logical basis of phylogenetic analysis. In: Platnick NI, Funk VA (eds) Advances in cladistics, vol 2. Columbia University Press New, York, pp 7–36Google Scholar
  15. Gilbert SF (1988) Developmental biology, 2nd edn. Sinauer Ass, Sunderland MAGoogle Scholar
  16. Gilbert SF, Bolker JA (2001) Homologies of process and molecular elements of embryonic construction. In: Wagner GP (ed) The character concept in evolutionary biology. Academic Press, San Diego, pp 435–454CrossRefGoogle Scholar
  17. Goodman (1972) Seven strictures on similarity. In: Goodman N (ed) Problems and projects. The Bobbs-Merrill Company, Indianapolis, pp 437–447Google Scholar
  18. Grant T, Kluge AG (2004) Transformation series as an ideographic character concept. Cladistics 20: 32–31CrossRefGoogle Scholar
  19. Griffiths PE (1999) Squaring the circle: natural kinds with historical essences. In: Wilson RA (ed) Species; New interdisciplinary essays. The MIT Press, Cambridge MA, pp 209–228Google Scholar
  20. Haack S (1998) Evidence and inquiry. Towards reconstruction in epistemology. Blackwell, OxfordGoogle Scholar
  21. Hall BK (1994) Introduction. In: Hall BK (ed) Homology. The hierarchical basis of comparative biology. Academic Press, San Diego, pp 1–19CrossRefGoogle Scholar
  22. Hall BK (1995) Homology and development. Evol Biol 28: 1–37Google Scholar
  23. Hanson NR (1961) Patterns of discovery. An inquiry into the conceptual foundations of science. Cambridge University Press, CambridgeGoogle Scholar
  24. Härlin M (1999) The logical priority of the tree over characters and some of its consequences for taxonomy. Biol J Linn Soc 68: 497–503CrossRefGoogle Scholar
  25. Hennig W (1950) Grundzüge einer Theorie der Phylogenetischen Systematik. Deutscher Zentralverlag, BerlinGoogle Scholar
  26. Hennig W (1957) Systematik und Phylogenese. In: Hannemann HJ (ed) Bericht über die Hundertjahrfeier der Deutschen Entomologischen Gesellschaft Belin. Akademie Verlag, Berlin, pp 50–71Google Scholar
  27. Hennig W (1966) Phylogenetic systematics. University of Illinois Press, UrbanaGoogle Scholar
  28. Hey J (2001) Genes, categories, and species. Oxford University Press, OxfordGoogle Scholar
  29. Hillis AL (1994) Homology in molecular biology. In: Hall BK (ed) Homology. The hierarchical basis of comparative biology. Academic Press, San Diego, pp 339–368CrossRefGoogle Scholar
  30. Hull DL (1976) Are species really individuals? Syst Zool 25: 174–191CrossRefGoogle Scholar
  31. Hull DL (1988) Science as a process. An evolutionary account of the social and conceptual development of science, The University of Chicago Press, ChicagoCrossRefGoogle Scholar
  32. Hull DL (1997) The ideal species concept—and why we cannot get it. In: Claridge MF, Dawah HA, Wilson MR (eds) Species: The units of biodiversity. Chapman & Hall, London, pp 358–380Google Scholar
  33. Hull DL (1999) On the plurality of species: questioning the party line. In: Wilson RA (ed) Species; New interdisciplinary essays. The MIT Press, Cambridge MA, pp 23–48Google Scholar
  34. Jardine N (1969) The observational and theoretical components of homology: a study based on the morphology of the dermal skull roofs of rhipidistian fishes. Biol J Linn Soc 1: 327–361CrossRefGoogle Scholar
  35. Keller RA, Boyd RN, Wheeler QD (2003) The illogical basis of phylogenetic nomenclature. Bot Rev 69: 93–110CrossRefGoogle Scholar
  36. Kitcher P (1993) The advancement of science. Science without legend, objectivity without illusions. Oxford University Press, OxfordGoogle Scholar
  37. Kitching IJ, Forey PL, Humphries CJ, Williams DM (1998) Cladistics, 2nd edn. Oxford University Press, OxfordGoogle Scholar
  38. Kluge AG (1989) A concern for evidence, and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst Zool 38: 7–25CrossRefGoogle Scholar
  39. Kluge AG (1997) Testability and the refutation and corroboration of cladistic hypotheses. Cladistics 13: 81–96CrossRefGoogle Scholar
  40. Kluge AG (2003a) The repugnant and the mature in phylogenetic inference: atemporal similarity and historical identity. Cladistics 19: 356–368CrossRefGoogle Scholar
  41. Kluge AG (2003b) On the deduction of species relationships: a précis. Cladistics 19: 233–239CrossRefGoogle Scholar
  42. Kluge AG (2004) On total evidence: for the record. Cladistics. 20: 205–207CrossRefGoogle Scholar
  43. Körner S (1970) Erfahrung und Theorie, Suhrkamp, Frankfurt a.M.Google Scholar
  44. Kripke S (2002) Naming and necessity. Blackwell, OxfordGoogle Scholar
  45. Lankester ER (1870) On the use of the term homology in modern zoology, and the distinction between homogenetic and homoplastic agreements. Ann Mag Nat Hist (4)6: 43–43Google Scholar
  46. La Porte J (2004) Natural kinds and conceptual change. Cambridge University Press, CambridgeGoogle Scholar
  47. Lipton P (2004) Inference to the best explanation, 2nd edn. Routledge, LondonGoogle Scholar
  48. Luntley M (1999) Contemporary philosophy of thought. Blackwell, OxfordGoogle Scholar
  49. Mahner M, Bunge M (1997) Foundations of biophilosophy. Springer, BerlinCrossRefGoogle Scholar
  50. Mayhall CW (2002) On Carnap. Wadsworrth/Thomson, Belmont CAGoogle Scholar
  51. McMullin E (2002) A case for scientific realism. In: Balashov Y, Rosenberg A (eds) Philosophy of science. Contemporary readings. Routledge, London, pp 248–281Google Scholar
  52. Mindell DP, Meyer A (2001) Homology evolving. Tree 16: 434–440Google Scholar
  53. Mitter C (1980) The thirteenth annual numerical taxonomy conference. Syst Zool 29: 177–190CrossRefGoogle Scholar
  54. Nagel E (1961) The structure of science. problems in the logic of scientific explanation. Hartcourt, Brace & World Inc., New YorkGoogle Scholar
  55. O'Leary MA, Gatesy J., Novacek MJ (2003) Are the dental data really at odds with the molecular data? Morphological evidence for whale phylogeny (re)reexamined. Syst Biol 52: 853–564PubMedCrossRefGoogle Scholar
  56. Oyama S, Griffiths PE, Gray RD (2001) Introduction: what is developmental systems theory? In: Oyama S, Griffiths PE, Gray RD (eds) Cycles of contingency. developmental systems and evolution. The MIT Press, Cambridge MA, pp 1–11Google Scholar
  57. Panchen AL (1994) Richard Owen and the concept of homology. In: Hall BK (ed) Homology. The hierarchical basis of comparative biology. Academic Press, San Diego, pp 21–62CrossRefGoogle Scholar
  58. Patterson C (1982) Morphological characters and homology. In: Joysey KA, Friday AE (ed) Problems of phylogenetic reconstruction. Academic Press, London, pp 21–74Google Scholar
  59. Patterson C (1988) Homology in classical and molecular biology. Mol Biol Evol 5: 603–625PubMedGoogle Scholar
  60. Peckham M (1959) The origin of species by Charles Darwin. A variorum text. University of Pennsylvania Press, PhiladelphiaGoogle Scholar
  61. Platnick NI (1978) Philosophy and the transformation of cladistics. Syst Zool 28: 537–546CrossRefGoogle Scholar
  62. Platts M (1997) Ways of meaning. An introduction to a philosophy of language, 2nd edn. The MIT Press, Cambridge MAGoogle Scholar
  63. Quine WV (1964) Word and object. The MIT Press, Cambridge MAGoogle Scholar
  64. Quine WV (1994) Natural kinds In: Stalker D (ed) Grue. The new riddle of induction, open court, La Salle IL, pp 42–56Google Scholar
  65. Quine WV (2001) Two dogmas of empiricism In: Martinich AP, Sosa D (eds) Analytic philosophy, an anthology, Blackwell MS, Malden, pp450–462Google Scholar
  66. Raff RA (1996) The shape of life. Genes, development, and the evolution of animal form. The University of Chicago Press, ChicagoGoogle Scholar
  67. Raff RA, Sly BJ (2000) Modularity and dissociation in the evolution of gene expression territories in development. evolution & development 2: 102–113CrossRefGoogle Scholar
  68. Reichert C (1837) Über die Visceralbogen der Wirbelthiere im allgemeinen und deren Metamorphosen bei den Vögeln und Säugethieren. Arch Anat Physiol Wiss Med 1837: 120–222Google Scholar
  69. Remane A (1952) Die Grundlagen des Natürlichen Systems der Vergleichenden Anatomie und der Phylogenetik. Akademische Verlagsgesellschaft, LeipzigGoogle Scholar
  70. Riedl R (1977) Die Ordnung des Lebendigen. Systembedingungen der Evolution. Paul Parey, HamburgGoogle Scholar
  71. Rieppel O (1988) Fundamentals of comparative biology. Birkhäuser Verlag, BaselGoogle Scholar
  72. Rieppel O (1993) The conceptual relationship of ontogeny and phylogeny: The taxic approach. Evol Biol 27: 1–32CrossRefGoogle Scholar
  73. Rieppel O (2001) Georges-Louis Leclerc, Compte de Buffon (1707–1788). In: Jahn I, Schmitt M. (eds) Darwin & Co. Eine Geschichte der Biologie in Porträts. C.H. Beck Verlag, München, pp 157–175Google Scholar
  74. Rieppel O (2003a) Popper and systematics. Syst Biol 52: 259–271PubMedCrossRefGoogle Scholar
  75. Rieppel O (2003b) Semaphoronts, cladograms, and the roots of total evidence. Biol J Linn Soc 80: 167–186CrossRefGoogle Scholar
  76. Rieppel O (2004a) The language of systematics, and the philosophy of ‘total evidence’. Syst Biodiv 2: 9–19CrossRefGoogle Scholar
  77. Rieppel O (2004b) What happens when the language of science threatens to break down in systematics—A Popperian perspective. In: Williams DM, Forey PL (eds) Milestones in systematics. CRC Press, Boca Raton FL, pp 5–100Google Scholar
  78. Rieppel O (2004c) Modules, kinds, and homology. J Exp Zool (Mol Dev Evol) 304B: 18–27Google Scholar
  79. Rieppel O, Kearney M (2002) Similarity. Biol J Linn Soc 75: 59–82CrossRefGoogle Scholar
  80. Roth VL (1984) On homology. Biol J Linn Soc 22: 13–29CrossRefGoogle Scholar
  81. Ruse M (1988) Philosophy of Biology Today. State University of New York Press, Albany NYGoogle Scholar
  82. Russell ES (1982) Form and Function. With a New Introduction by George V. Lauder. Chicago University Press, ChicagoGoogle Scholar
  83. Sattler R (1990) Towards a more dynamic plant morphology. Acta Biotheoretica 38: 303–315CrossRefGoogle Scholar
  84. Sattler R (1996) Classical morphology and continuum morphology: opposition and continuum. Ann Bot 69: 249–262Google Scholar
  85. Shoemaker S (2003) On what there are. In: Shoemaker S (ed) Identity, cause, and mind, expanded esdition. Oxford University Press, Oxford, pp 358–280Google Scholar
  86. Shubin N, Tabin C, Carroll S (1997) Fossils, genes and the evolution of animal limbs. Nature 388: 639–648PubMedCrossRefGoogle Scholar
  87. Shubin NH (1994) The phylogeny of development and the origin of homology. In: Grande L, Rieppel O (eds) Interpreting the hierarchy of nature. Academic Press, San Diego, pp 201–225Google Scholar
  88. Sneath PHA, Sokal RR (1973) Numerical taxonomy. WH Freeman, San FranciscoGoogle Scholar
  89. Soames S (2002) Beyond rigidity. The unfinished semantic agenda of naming and necessity. Oxford, Oxford University PressCrossRefGoogle Scholar
  90. Soames S (2003) Philosophical analysis in the twentieth century, vol 1. The dawn of analysis. Princeton University Press, PrincetonGoogle Scholar
  91. Sober E (1981) Evolutionary theory and the ontological status of properties. Philos Stud 40: 147–176CrossRefGoogle Scholar
  92. Sober E (1984) Discussion: sets, species, and evolution. Comments on Philip Kitcher's ‘species’. Philos Sci 51: 334–341CrossRefGoogle Scholar
  93. Sober E (1985) A likelihood justification of parsimony. Cladistics 1: 209–233CrossRefGoogle Scholar
  94. Sterelny K (1994) The nature of species. Philos Books 35: 9–20CrossRefGoogle Scholar
  95. Swoyer C (2000) “Properties.” The Stanford Encyclopedia of Philosophy (Winter 2000 edn., Edward N. Zalta (ed), URL: http://plato.stanford.edu/archives/win2000/entries/properties/
  96. Wägele K (2004) Hennig's phylogenetic systematics brought up to date. In: Williams DM, Forey PL (eds) Milestones in systematics. CRC Press, Boca Raton FL, pp 101–125CrossRefGoogle Scholar
  97. Wagner GP (1989) The biological concept of homology. Ann Rev Ecol Syst 20: 51–69CrossRefGoogle Scholar
  98. Wagner GP (1994) Homology and the mechanisms of development. In: Hall BK (ed) Homology. The hierarchical basis of comparative biology. Academic Press, San Diego, pp 273–299CrossRefGoogle Scholar
  99. Wagner GP (1996) Homologues, natural kinds and the evolution of modularity. Am Zool 36: 36–43CrossRefGoogle Scholar
  100. Wagner GP (2001) Characters, units, and natural kinds. In: Wagner GP (ed) The character concept in evolutionary biology. Academic Press, San Diego, pp 1–10CrossRefGoogle Scholar
  101. West-Eberhard MJ (2003) Developmental plasticity and evolution. Oxford University Press, OxfordGoogle Scholar
  102. Westen PH (2000) Process morphology from a cladistic perspective. In: Scotland R, Pennington RT (eds) Homology and systematics. Taylor and Francis, London, pp 124–144Google Scholar
  103. Wheeler WC (1998) Alignment characters, dynamic programming and heuristic solutions. In: DeSalle R, Schierwater B (eds) Molecular approaches to ecology and evolution, 2nd edn, Birkhäuser, Basel, pp 243–251CrossRefGoogle Scholar
  104. Wiesemüller G, Rothe H, Henke W (2003) Phylogenetische Systematik. Springer-Verlag BerlinCrossRefGoogle Scholar
  105. Wiley EO, Siegl-Causey D, Brooks DR, Funk VA (1991) The Compleat Cladist. A primer of phylogenetic procedures. The University of Kansas Museum of Natural History Special Publication No. 19, LawrenceGoogle Scholar
  106. Williams DM (2004) Homologues and homology, phenetics and cladistics: 150 years of progress. In: Williams DM, Forey PL (eds) Milestones in systematics. CRC Press, Boca Raton FL, pp 191–224CrossRefGoogle Scholar
  107. Wilson EO (1965) A consistency test for phylogenies based on contemporaneous species. Syst Zool 14: 214–220CrossRefGoogle Scholar
  108. Wilson RA (1999) Realism, essence and kind: resuscitating species essentialism? In: Wilson RA (ed) Species; New interdisciplinary essays. The MIT Press, Cambridge MA, pp 187–207Google Scholar
  109. Winther RG (2001) Varieties of modules: kinds, levels, origins, and behaviors. J Exp Zool (Mol Dev Evol) 291: 116–129CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg New York 2007

Authors and Affiliations

  • Olivier Rieppel

There are no affiliations available

Personalised recommendations