Biology & Philosophy

, Volume 22, Issue 1, pp 95–113 | Cite as

The Poverty of Taxonomic Characters

  • Olivier RieppelEmail author
  • Maureen Kearney


The theory and practice of contemporary comparative biology and phylogeny reconstruction (systematics) emphasizes algorithmic aspects but neglects a concern for the evidence. The character data used in systematics to formulate hypotheses of relationships in many ways constitute a black box, subject to uncritical assessment and social influence. Concerned that such a state of affairs leaves systematics and the phylogenetic theories it generates severely underdetermined, we investigate the nature of the criteria of homology and their application to character conceptualization in the context of transformationist and generative paradigms. Noting the potential for indeterminacy in character conceptualization, we conclude that character congruence (the coherence of character statements) relative to a hierarchy is a necessary, but not a sufficient, condition for phylogeny reconstruction. Specifically, it is insufficient due to the lack of causal grounding of character hypotheses. Conceptualizing characters as homeostatic property cluster natural kinds is in accordance with the empirical practice of systematists. It also accounts for the lack of sharpness in character conceptualization, yet requires character identification and re-identification to be tied to causal processes.


Character transformation Developmental systems theory Homology Natural kinds Ontogenetic repatterning 


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We thank Richard Boyd, Richard Richards, and Kim Sterelny for reviewing earlier drafts of this paper. Shannon Hackett provided important opportunities for the discussion of molecular systematics. Research for this paper was funded, in part, through the NSF grant DEB-0235628 (to M.K. and O.R.).


  1. Belon P. (1555). L’Histoire de la Nature des Oyseaux. Guillaume Cavellat, ParisGoogle Scholar
  2. Boyd R. (1991). Realism, anti-fondationalism and the enthusiasm for natural kinds. Philos. Stud. 61:127–148Google Scholar
  3. Boyd R. (1999). Homeostasis, species, and higher taxa. In: Wilson R.A. (eds), Species: New Interdisciplinary Essays. MIT Press, Cambridge, MA, pp. 141–185Google Scholar
  4. Brandon R.N. (1999). The units of selection revisited: the modules of selection. Biol. Philos. 14:67–180Google Scholar
  5. Burke A.C. (1989). Development of the turtle carapace: implications for the evolution of a novel bauplan. J. Morphol. 199:363–378Google Scholar
  6. Burke A.C. (1991). The development and evolution of the turtle body plan: inferring intrinsic aspects of the evolutionary process from experimental embryology. Am. Zool. 31:616–627Google Scholar
  7. Caldwell M.W., Lee M.S.Y. (1997). A snake with legs from the marine Cretaceous of the Middle East. Nature 386:705–709Google Scholar
  8. Carroll R.L. (1988). Vertebrate Paleontology and Evolution. W.H. Freeman & Co., New YorkGoogle Scholar
  9. Coates M., Ruta M. (2000). Nice snakes, shame about the legs. Trends Ecol. Evol. 15: 503–507Google Scholar
  10. Cohn M.J., Tickle C. (1999). Developmental basis of limblessness and axial patterning in snakes. Nature 399:474–479Google Scholar
  11. Darwin Ch. (1859). The Origin of Species. John Murray, LondonGoogle Scholar
  12. Devitt M. (1997). Realism and Truth, Second Edition. Princeton University Press, Princeton New JerseyGoogle Scholar
  13. Disney R.H.L. (2003). Is not Hennig’s method of producing cladograms as defensible as those derived from parsimony algorithms?. Bonner zoologische Beiträge 50:305–311Google Scholar
  14. Dobzhansky Th. (1973). Nothing in biology makes sense except in the light of evolution. Am. Biol. Teach. 35:125–129Google Scholar
  15. Dupré J. (1993). The Disorder of Things. Metaphysical Foundations of the Disunity of Science. Harvard University Press, Cambridge, MAGoogle Scholar
  16. Dupuis C. (1990). Hennig, Emil Hans Willi. In: Holmes F.L. (eds), Dictionary of Scientific Biography Vol 17 (Suppl 2). Charles Scribner’s Sons, New York, pp. 407–410Google Scholar
  17. Estes R., deQuieroz K., Gauthier J. (1988) Phylogenetic relationships within Squamata. In: Estes R., Pregill G. (eds), Phylogenetic Relationships of the Lizard Families. Stanford University Press, Stanford, pp. 119–281Google Scholar
  18. Field H. (1973). Theory change and the indeterminacy of reference. J. Philos. 70:462–481Google Scholar
  19. Gilbert S.F., Loredo G.A., Brukman A., Burke A.C. (2001). Morphogenesis of the turtle shell: the development of a novel structure in tetrapod evolution. Evol. Dev. 3:47–58Google Scholar
  20. Gilbert S.F., Cebra-Thomas J.A., Fraser T. (2004). Working hypothesis for the origin of the turtle shell. Journal of Morphology 260:294 (abstract)Google Scholar
  21. Goodman N. (1965). Fact, Fiction, and Forecast, Second Edition. Bobbs-Merrill, New YorkGoogle Scholar
  22. Goodman N. (1972). Seven strictures on similarity. In: Goodman N. (eds), Problems and Projects. The Bobbs-Merrill Company, Indianapolis IN, pp. 437–447Google Scholar
  23. Gould S.J. (1977). Ontogeny and Phylogeny. The Belknap Press at Harvard University Press, Cambridge, MAGoogle Scholar
  24. Grant T., Kluge A.G. (2004). Transformation series as an ideographic character concept. Cladistics 20:32–31Google Scholar
  25. Greene H.W., Cundall D. (2000). Limbless tetrapods and snakes with legs. Science 287:1939–1941Google Scholar
  26. Griffiths P.E. (1999). Squaring the circle: natural kinds with historical essences. In: Wilson R.A. (eds), Species. New Interdisciplinary Essays. The MIT Press, Cambridge, MA, pp. 209–228Google Scholar
  27. 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
  28. Hennig W. (1950). Grundzüge einer Theorie der Phylogenetischen Systematik. Deutscher Zentralverlag, BerlinGoogle Scholar
  29. Hennig W. (1966). Phylogenetic Systematics. University of Illinois Press, UrbanaGoogle Scholar
  30. Hennig W. (1978). Die Stellung der Systematik in der Biologie. Entomol. Germ. 4:193–199Google Scholar
  31. Hillis A.L. (1994). Homology in molecular biology. In: Hall B.K. (eds), Homology. The Hierarchical Basis of Comparative Biology. Academic Press, San Diego, pp. 339–368Google Scholar
  32. Hull D.L. (1988). Science as a Process. An Evolutionary Account of the Social and Conceptual Development of Science. The University of Chicago Press, ChicagoGoogle Scholar
  33. Hull D.L. (1999). On the plurality of species: questioning the party line. In: Wilson R.A. (eds), Species. New Interdisciplinary Essays. The MIT Press, Cambridge, MA, pp. 23–48Google Scholar
  34. Iordansky N.N. (1978). On the origin of snakes. Zool. Zh. 57:888–898 (in Russian)Google Scholar
  35. Iwabe N., Hara Y., Kumazawa Y., Shibamoto K., Saito Y., Miyata T., Katho K. (2005). Sister group relationship of turtles to the bird-crocodilian clade revealed nuclear DNA-coded proteins. Mol. Biol. Evol. 22:810–813Google Scholar
  36. Janich P. (1993). Der Vergleich als Methode in den Naturwissenschaften. In: Weingarten M., Gutmann W.F. (eds), Geschichte und Theorie des Vergleichs in den Biowissenschaften, Aufsätze und Reden Nr. 40 der Senckenbergischen Naturforschenden Gesellschaft. Verlag Waldemar Kramer, Frankfurt a.M., pp. 13–27Google Scholar
  37. Kearney, M. (In press). Philosophy and phylogenetics: historical and current connections. In: Hull, D. and Ruse, M. (eds), Cambridge Companion to the Philosophy of BiologyGoogle Scholar
  38. Keller R.A., Boyd R.N., Wheeler Q.D. (2003). The illogical basis of phylogenetic nomenclature. Bot. Rev. 69:93–110Google Scholar
  39. Kitcher P. (1993). The Advancement of Science. Science without Legend, Objectivity without Illusions. Oxford University Press, OxfordGoogle Scholar
  40. Kley N., Hilton E.J., Richmond E.J. (2002). Comparative morphology of the pelvic apparatus of snakes. Integr. Comp. Biol. 42:1257 (abstract)Google Scholar
  41. Kluge A.G. (2003). The repugnant and the mature in phylogenetic inference: atemporal similarity and historical identity. Cladistics 19:356–368Google Scholar
  42. Kluge A.G. (2004). On total evidence: for the record. Cladistics 20:205–207Google Scholar
  43. Kühne W. (1978). Willi Hennig 1913–1976: Die Schaffung einer Wissenschaftstheorie. Entomol. Germ. 4:374–376Google Scholar
  44. Kuraku S., Usuda R., Kuratani S. (2005). Comprehensive survey of carapacial ridge-specific genes in turtle implies co-option of some regulatory genes in carapace evolution. Evolution & Development 7:3–17Google Scholar
  45. LaPorte J. (2004). Natural Kinds and Conceptual Change. Cambridge University Press, CambridgeGoogle Scholar
  46. Lee M.S.Y. (1993). The origin of the turtle body plan: bridging a famous morphological gap. Science 261:1716–1720Google Scholar
  47. Lee M.Y.S., Scanlon J.D. (2002). Snake phylogeny based on osteology, soft anatomy, and ecology. Biol. Rev. 77:333–401Google Scholar
  48. Lipton P. (2004). Inference to the Best Explanation. Second Edition. Routledge, LondonGoogle Scholar
  49. Lycan W.G. (2000). Philosophy of Language. A Contemporary Introduction. Routledge, New YorkGoogle Scholar
  50. Mahner M., Bunge M. (1997). Foundations of Biophilosophy. Springer, BerlinGoogle Scholar
  51. Nagel E. (1961). The Structure of Science. Problems in the Logic of Scientific Explanation. Hartcourt, Brace & World Inc., New YorkGoogle Scholar
  52. O’Leary M.A., Gatesy J., Novacek M.J. (2003). Are the dental data really at odds with the molecular data? Morphological evidence for whale phylogeny (re)reexamined. Syst. Biol. 52:853–564Google Scholar
  53. Oyama S., Griffiths P.E., Gray R.D. (2001). Introduction: what is developmental systems theory?. In: Oyama S., Griffiths P.E., Gray R.D. (eds), Cycles of Contingency. Developmental Systems and Evolution. The MIT Press, Cambridge, MA, pp. 1–11Google Scholar
  54. Panchen A.L. (1994) Richard Owen and the concept of homology. In: Hall B.K. (eds), Homology. The Hierarchical Basis of Comparative Biology. Academic Press, San Diego, pp. 21–62Google Scholar
  55. Patterson C. (1977). Cartilage bones, dermal bones and membrane bones, or the exoskeleton versus the endoskeleton. In: Andrews S.M., Miles R.S., Walker A.D. (eds), Problems in Vertebrate Evolution. Academic Press, London, pp. 77–121Google Scholar
  56. Patterson C. (1982). Morphological characters and homology. In: Joysey K.A., Friday A.E. (eds), Problems of Phylogenetic Reconstruction. Academic Press, London, pp. 21–74Google Scholar
  57. Patterson C. (1987). Introduction. In: Patterson C. (eds), Molecules and morphology in evolution: conflict or compromise. Cambridge University Press, Cambridge, pp. 1–22Google Scholar
  58. Patterson C. (1988). Homology in classical and molecular biology. Mol. Biol. Evol. 5:603–625Google Scholar
  59. Platnick N.I. (1978). Philosophy and the transformation of cladistics. Syst. Zool. 28:537–546Google Scholar
  60. Putnam H. (1996). The meaning of ‘meaning’. In: Pessin A., Goldberg S. (eds), The Twin Earth Chronicles. Twenty Years of Reflection on Hilary Putnam’s “The Meaning of ‘Meaning”’. M.E. Sharpe, Armonk, NY, pp. 3–52Google Scholar
  61. Quine W.V. (1964). Word and Object. Cambridge MA, The MIT PressGoogle Scholar
  62. Quine W.V. (1994). Natural kinds. In: Stalker D. (eds), Grue. The New Riddle of Induction. Open Court, La Salle, IL, pp. 42–56Google Scholar
  63. Raff R.A. (1996). The Shape of Life. Genes, Development, and the Evolution of Animal Form. The University of Chicago Press, ChicagoGoogle Scholar
  64. Rage J.-C. and Escuillié F. 2003. The Cenomanian: stage of hindlimbed snakes, Carnets de Géologie, Article 2003/01:1–11Google Scholar
  65. Remane A. (1952). Die Grundlagen des Natürlichen Systems, der Vergleichenden Anatomie und der Phylogenetik. Akademische Verlagsgesellschaft, LeipzigGoogle Scholar
  66. Richards R. (2002). Kuhnian values and cladistic parsimony. Perspect. Sci.10:1–27Google Scholar
  67. Richards R. (2003). Character individuation in phylogenetic inference. Philos. Sci. 70:264–279Google Scholar
  68. Riedl R. (1978). Order in Living Organisms. John Wiley & Sons, ChichesterGoogle Scholar
  69. Rieppel O. (1993a). The conceptual relationship of ontogeny and phylogeny: the taxic approach. Evol. Biol. 27:1–32Google Scholar
  70. Rieppel O. (1993b). Studies on skeleton formation in reptiles. II. The postembryonic development of the skeleton in Chamaeleo hoehnelii (Reptilia: Chamaeleoninae). Herpetologica 49:66–78Google Scholar
  71. Rieppel O. (2001). Turtles as hopeful monsters. BioEssays 23:987–991Google Scholar
  72. Rieppel O. (2003). Semaphoronts, cladograms, and the roots of total evidence. Biol. J. Linn. Soc. 80:167–186Google Scholar
  73. Rieppel O. (2004). The language of systematics, and the philosophy of ‘total evidence’. Syst. Biodivers. 2:9–19Google Scholar
  74. Rieppel O. (2005a). The philosophy of total evidence and its relevance for phylogenetic inference. Papéis Avulsos Zool. 45:77–89Google Scholar
  75. Rieppel O. (2005b). Modules, kinds, and homology. J. Exp. Zool. (Mol. Dev. Evol.) 304B:18–27Google Scholar
  76. Rieppel O., Kearney M. (2001). The origin of snakes: limits of a scientific debate. Biologist 48: 110–114Google Scholar
  77. Rieppel O., Kearney M. (2002). Similarity. Biol. J. Linn. Soc. 75:59–82Google Scholar
  78. Rieppel O., Reisz R.R. (1999). The origin and early evolution of turtles. Annu. Rev. Ecol. Syst. 30:1–22Google Scholar
  79. Rieppel O., Zaher H., Tchernov E., Polcyn M.J. (2003). The anatomy and relationships of Haasiophis terrasanctus, a fossil snake with well-developed hind limbs from the mid-Cretaceous of the Middle East. J. Paleontol. 77:336–358Google Scholar
  80. Romer A.S. (1956). Osteology of the Reptiles. Chicago University Press, ChicagoGoogle Scholar
  81. Rowe T. (1987). Definition and diagnosis in the phylogenetic system. Syst. Zool. 36:208–211Google Scholar
  82. Ruse M. (1988). Philosophy of Biology Today. State University of New York Press, Albany, NYGoogle Scholar
  83. Sanger T.J., Gibson-Brown J.J. (2004). The developmental bases of limb reduction and body elongation in squamates. Evolution 58:2103–2106Google Scholar
  84. Scanlon J.D., Lee M.Y.S. (2000). The Pleistocene serpent Wonambi and the early evolution of snakes. Nature 403:416–420Google Scholar
  85. Schank J.C., Wimsatt W.C. (2000). Evolvability: adaptation and modularity. In: Singh R., Krimbas C., Beatty J., Pauls D. (eds), Thinking about Evolution: Historical, Philosophical, and Political Perspectives. Cambridge University Press, Cambridge, pp. 322–335Google Scholar
  86. Shoemaker S. (2003). Causality and properties. In: Shoemaker S. (eds), Identity, Cause, and Mind; Expanded Edition. Oxford University Press, Oxford, pp. 206–233Google Scholar
  87. Simpson G.G. (1961). Principles of Animal Taxonomy. Columbia University Press, New YorkGoogle Scholar
  88. Sober E. (1981). Evolutionary theory and the ontological status of properties. Philos. Stud. 40:147–176Google Scholar
  89. Sober E. (1984). Discussion: sets, species, and evolution. Comments on Philip Kitcher’s ‘species’. Philos. Sci. 51:334–341Google Scholar
  90. Sterelny K., Griffiths P.E. (1999). Sex and Death. An Introduction to Philosophy of Biology. The University of Chicago Press, ChicagoGoogle Scholar
  91. Tchernov E., Rieppel O., Zaher H., Polcyn M.J., Jacobs L.J. (2000). A new fossil snake with limbs. Science 287:2010–2012Google Scholar
  92. Underwood G. (1957). On lizards of the family Pygopodidae, a contribution to the morphology and phylogeny of the Squamata. J. Morphol. 100:207–268Google Scholar
  93. Vane-Wright R.I. (2001). Taxonomy, methods of. In: Levin S. (eds), Encyclopedia of Biodiversity Vol 5. Academic Press, New York, pp. 589–606Google Scholar
  94. Wägele K. (2004). Hennig’s phylogenetic systematics brought up to date. In: Williams D.M., Forey P.L. (eds), Milestones in Systematics. CRC Press, Boca Raton, FL, pp. 101–125Google Scholar
  95. Wagner G.P. (1994). Homology and the mechanisms of development. In: Hall B.K. (eds), Homology. The Hierarchical Basis of Comparative Biology.Academic Press, San Diego, pp. 273–299Google Scholar
  96. Wagner G.P. (1996). Homologues, natural kinds and the evolution of modularity. Am. Zool. 36:36–43Google Scholar
  97. Wagner G.P. (2001). Characters, units, and natural kinds. In: Wagner G.P. (eds), The Character Concept in Evolutionary Biology. Academic Press, San Diego, pp. 1–10Google Scholar
  98. West-Eberhard M.J. (2003). Developmental Plasticity and Evolution. Oxford University Press, OxfordGoogle Scholar
  99. Wheeler W. (2001a). Homology and DNA sequence data. In: Wagner G.P. (eds), The Character Concept in Evolutionary Biology. Academic Press, San Diego, pp. 303–317Google Scholar
  100. Wheeler W. (2001b). Homology and the optimization of DNA sequence data. Cladistics 17:S1–S11Google Scholar
  101. Wickler W. (1967). Vergleichende Verhaltensforschung und Phylogenetik. In: Heberer G. (eds), Die Evolution der Organismen, 3. Auflage, Band I. G. Fischer, Stuttgart, pp. 420–508Google Scholar
  102. Wiley E.O. (1981). Phylogenetics. The Theory and Practice of Phylogenetic Systematics. John Wilery & Sons, New YorkGoogle Scholar
  103. Williams D.M. (2004). Homologues and homology, phenetics and cladistics: 150 years of progress. In: Williams D.M., Forey P.L. (eds), Milestones in Systematics. CRC Press, Boca Raton, FL, pp. 191–224Google Scholar
  104. Wilson R.A. (1999). Realism, essence, and kind: resuscitating species essentialism?. In: Wilson R.A. (eds), Species. New Interdisciplinary Essays. The MIT Press, Cambridge, MA, pp. 187–207Google Scholar
  105. Wimsatt W.C. (1986). Developmental constraints, generative entrechment and the innate-acquired distinction. In: Bechtel W. (eds), Integrating Scientific Disciplines. Martinus Nijhoff, Dordrecht, pp. 185–208Google Scholar
  106. Winther R.G. (2001). Varieties of modules: kinds, levels, origins, and behaviors. J. Exp. Zool. (Mol. Dev. Evol.) 291:116–129Google Scholar
  107. Zaher H., Rieppel O. (2000). A brief history of snakes. Herpetol. Rev. 31:73–76Google Scholar

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© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  1. 1.Department of GeologyThe Field MuseumChicagoUSA
  2. 2.Department of ZoologyThe Field MuseumChicagoUSA

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