Homology: A Philosophical and Biological Perspective

  • Olivier Rieppel
Living reference work entry


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.


Natural Kind Causal Process Natural Kind Term Transformation Series Common Evolutionary Origin 
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.


  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. Guillaume Cavellat, ParisGoogle Scholar
  3. Bock WJ (1974) Philosophical foundations of classical evolutionary classification. Syst Zool 22:375–392Google Scholar
  4. Boyd R (1991) Realism, anti-foundationalism and the enthusiasm for natural kinds. Philos Stud 61:127–148Google Scholar
  5. Boyd R (1999) Homeostasis, species, and higher taxa. In: Wilson RA (ed) Species; new interdisciplinary essays. The MIT Press, Cambridge, pp 141–185Google Scholar
  6. Brandon RN (1999) The units of selection revisited: the modules of selection. Biol Philos 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 131:85–98Google 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 7:367–394Google Scholar
  11. Devitt M, Sterelny K (1999) Language and reality. An introduction to the philosophy of language. The MIT Press, CambridgeGoogle Scholar
  12. Dupré J (1993) The disorder of things. Metaphysical foundations of the disunity of science. Harvard University Press, CambridgeGoogle Scholar
  13. Dupuis C (1984) Willi Hennig’s impact on taxonomic thought. Annu Rev Ecol Syst 15:1–24Google 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, SunderlandGoogle 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, San Diego, pp 435–454Google 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 20:23–31Google 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, 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, San Diego, pp 1–19Google 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 68:497–503Google 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, San Diego, pp 339–368Google Scholar
  30. Hull DL (1976) Are species really individuals? Syst Zool 25:174–191Google 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, ChicagoGoogle 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, 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 1:327–361Google Scholar
  35. Keller RA, Boyd RN, Wheeler QD (2003) The illogical basis of phylogenetic nomenclature. Bot Rev 69:93–110Google 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 38:7–25Google Scholar
  39. Kluge AG (1997) Testability and the refutation and corroboration of cladistic hypotheses. Cladistics 13:81–96Google Scholar
  40. Kluge AG (2003a) The repugnant and the mature in phylogenetic inference: atemporal similarity and historical identity. Cladistics 19:356–368Google Scholar
  41. Kluge AG (2003b) On the deduction of species relationships: a précis. Cladistics 19:233–239Google Scholar
  42. Kluge AG (2004) On total evidence: for the record. Cladistics 20:205–207Google Scholar
  43. Körner S (1970) Erfahrung und Theorie. Suhrkamp, Frankfurt a.MGoogle Scholar
  44. Kripke S (2002) Naming and necessity. Blackwell, OxfordGoogle Scholar
  45. La Porte J (2004) Natural kinds and conceptual change. Cambridge University Press, CambridgeGoogle Scholar
  46. 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):34–43Google 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, BerlinGoogle Scholar
  50. Mayhall CW (2002) On Carnap. Wadsworrth/Thomson, BelmontGoogle 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 29:177–190Google 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 52:853–864PubMedGoogle 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, 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, San Diego, pp 21–62Google Scholar
  58. Patterson C (1982) Morphological characters and homology. In: Joysey KA, Friday AE (eds) Problems of phylogenetic reconstruction. Academic, 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 28:537–546Google Scholar
  62. Platts M (1997) Ways of meaning. An introduction to a philosophy of language, 2nd edn. The MIT Press, CambridgeGoogle Scholar
  63. Quine WV (1964) Word and object. The MIT Press, CambridgeGoogle Scholar
  64. Quine WV (1994) Natural kinds. In: Stalker D (ed) Grue. The new riddle of induction. Open Court, La Salle, 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, pp 450–462Google 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. Evol Dev 2:102–113PubMedGoogle 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 27:1–32Google 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 52:259–271PubMedGoogle Scholar
  75. Rieppel O (2003b) Semaphoronts, cladograms, and the roots of total evidence. Biol J Linn Soc 80:167–186Google Scholar
  76. Rieppel O (2004a) The language of systematics, and the philosophy of ‘total evidence’. Syst Biodiv 2:9–19Google 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, 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 75:59–82Google Scholar
  80. Roth VL (1984) On homology. Biol J Linn Soc 22:13–29Google Scholar
  81. Ruse M (1988) Philosophy of biology today. State University of New York Press, AlbanyGoogle 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 Biotheor 38:303–315Google 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 edition. Oxford University Press, Oxford, pp 358–380Google Scholar
  86. Shubin NH (1994) The phylogeny of development and the origin of homology. In: Grande L, Rieppel O (eds) Interpreting the hierarchy of nature. Academic, San Diego, pp 201–225Google Scholar
  87. Shubin N, Tabin C, Carroll S (1997) Fossils, genes and the evolution of animal limbs. Nature 388:639–648PubMedGoogle 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 University Press, OxfordGoogle 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 40:147–176Google Scholar
  92. Sober E (1984) Discussion: sets, species, and evolution. Comments on Philip Kitcher’s ‘species’. Philos Sci 51:334–341Google Scholar
  93. Sober E (1985) A likelihood justification of parsimony. Cladistics 1:209–233Google Scholar
  94. Sterelny K (1994) The nature of species. Philos Books 35:9–20Google Scholar
  95. Swoyer C (2000) Properties. In: Zalta EN (ed) The Stanford encyclopedia of philosophy, Winter 2000 edn.
  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, pp 101–125Google Scholar
  97. Wagner GP (1989) The biological concept of homology. Ann Rev Ecol Syst 20:51–69Google Scholar
  98. Wagner GP (1994) Homology and the mechanisms of development. In: Hall BK (ed) Homology. The hierarchical basis of comparative biology. Academic, San Diego, pp 273–299Google Scholar
  99. Wagner GP (1996) Homologues, natural kinds and the evolution of modularity. Am Zool 36:36–43Google Scholar
  100. Wagner GP (2001) Characters, units, and natural kinds. In: Wagner GP (ed) The character concept in evolutionary biology. Academic, San Diego, pp 1–10Google 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 243–251Google Scholar
  104. Wiesemüller G, Rothe H, Henke W (2003) Phylogenetische Systematik. Springer, BerlinGoogle 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, Lawrence, Special Publication No. 19Google 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, pp 191–224Google Scholar
  107. Wilson EO (1965) A consistency test for phylogenies based on contemporaneous species. Syst Zool 14:214–220Google Scholar
  108. Wilson RA (1999) Realism, essence and kind: resuscitating species essentialism? In: Wilson RA (ed) Species; new interdisciplinary essays. The MIT Press, Cambridge, pp 187–207Google Scholar
  109. Winther RG (2001) Varieties of modules: kinds, levels, origins, and behaviors. J Exp Zool (Mol Dev Evol) 291:116–129Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  1. 1.Department of GeologyThe Field MuseumChicagoUSA

Personalised recommendations