Advertisement

Acta Biotheoretica

, Volume 57, Issue 1–2, pp 171–186 | Cite as

Explanation and Falsification in Phylogenetic Inference: Exercises in Popperian Philosophy

  • Arnold G. KlugeEmail author
Regular Article

Abstract

Deduction leads to causal explanation in phylogenetic inference when the evidence, the systematic character, is conceptualized as a transformation series. Also, the deductive entailment of modus tollens is satisfied when those kinds of events are operationalized as patristic difference. Arguments to the contrary are based largely on the premise that character-states are defined intensionally as objects, in terms of similarity relations. However, such relations leave biologists without epistemological access to the causal explanation and explanatory power of historical statements. Moreover, the prediction-making to which those kinds of relations are limited in practice can lead to a category error—the mental conversion of an abstraction (the classes defined in terms of similarity relations) into a thing (such as an historical individual). The latter practices and problems characterize pattern cladistics, taxa being interpreted as homeostatic property cluster natural kinds, and other instrumentalist research programs.

Keywords

Evolution Falsification Modus tollens Parsimony Phylogenetics Popper Similarity Transformation series 

Notes

Acknowledgments

Although we may not completely agree, I benefited from the criticisms and editorial suggestions provided by James Carpenter, Prosanta Chakrabarty, Taran Grant, Laura Howard, Alistair McGowan and Francisco Vergara-Silva. Demands for clarification from anonymous reviewers were especially useful. This paper was written and revised at the Cladistics Institute, Harbor Springs, MI.

References

  1. Ball IR (1982) Implication, conditionality and taxonomic statements. Bijdr Dierk 52:186–190Google Scholar
  2. Cartmill M (1981) Hypothesis testing and phylogenetic reconstruction. Z f zool Systematik u Evolutionsforschung 19:73–96Google Scholar
  3. Cleland CE (2002) Methodological and epistemic differences between historical science and experimental science. Philos Sci 69:474–496. doi: 10.1086/342455 CrossRefGoogle Scholar
  4. de Queiroz K (2004) The measurement of test severity, significance tests for resolution, and a unified philosophy of phylogenetic inference. Zool Scr 33:463–473CrossRefGoogle Scholar
  5. Edwards AWF (1972) Likelihood. Johns Hopkins University Press, Baltimore [1992 reprint]Google Scholar
  6. Faith DP, Trueman JH (2001) Towards an inclusive philosophy for phylogenetic inference. Syst Biol 50:331–350. doi: 10.1080/106351501300317969 CrossRefGoogle Scholar
  7. Farris JS (1967) The meaning of relationship and taxonomic procedure. Syst Zool 16:44–51. doi: 10.2307/2411515 CrossRefGoogle Scholar
  8. Farris JS (1983) The logical basis of phylogenetic analysis. In: Platnick NI, Funk VA (eds) Advances in cladistics II. Columbia University Press, New York, pp 7–36Google Scholar
  9. Fitzhugh K (2006a) The abduction of phylogenetic hypotheses. Zootaxa 1145:1–110Google Scholar
  10. Fitzhugh K (2006b) The philosophical basis of character coding for the inference of phylogenetic hypotheses. Zool Scr 35:261–286. doi: 10.1111/j.1463-6409.2006.00229.x CrossRefGoogle Scholar
  11. Fitzhugh K (2006c) The ‘requirement of total evidence’ and its role in phylogenetic systematics. Biol Philos 21:309–351. doi: 10.1007/s10539-005-7325-2 CrossRefGoogle Scholar
  12. Gaffney ES (1979) An introduction to the logic of phylogeny reconstruction. In: Cracraft J, Eldredge N (eds) Phylogenetic analysis and paleontology. Columbia University Press, New York, pp 79–111Google Scholar
  13. Gattei S (2003) Reply to Olivier Rieppel. Cladistics 19:172. doi: 10.1016/S0748-3007(03)00002-1 CrossRefGoogle Scholar
  14. Ghiselin MT (1966a) An application of the theory of definition to systematic principles. Syst Zool 15:127–130. doi: 10.2307/2411630 CrossRefGoogle Scholar
  15. Ghiselin MT (1966b) On psychologism in the logic of taxonomic controversies. Syst Zool 15:207–215. doi: 10.2307/2411392 CrossRefGoogle Scholar
  16. Grant T (2002) Testing methods: the evaluation of discovery operations in evolutionary biology. Cladistics 18:94–111. doi: 10.1111/j.1096-0031.2002.tb00142.x CrossRefGoogle Scholar
  17. Grant T, Kluge AG (2003) Data exploration in phylogenetic inference: scientific, heuristic, or neither. Cladistics 19:379–418. doi: 10.1111/j.1096-0031.2003.tb00311.x CrossRefGoogle Scholar
  18. Grant T, Kluge AG (2004) Transformation series as an ideographic character concept. Cladistics 20:23–31. doi: 10.1111/j.1096-0031.2004.00003.x CrossRefGoogle Scholar
  19. Grant T, Kluge AG (2007) Ratio of explanatory power (REP): a new measure of group support. Mol Phylo Evol 44:483–487. doi: 10.1016/j.ympev.2006.11.027 CrossRefGoogle Scholar
  20. Grant T, Kluge AG (2008a) Credit where credit is due: the Goodman–Bremer support metric. Mol Phylo Evol 49:405–406. doi: 10.1016/j.ympev.2008.04.023 CrossRefGoogle Scholar
  21. Grant T, Kluge AG (2008b) Clade support measures and their adequacy. Cladistics 24:1051–1064. doi: 10.1111/j.1096-0031.2008.00231.x CrossRefGoogle Scholar
  22. Hennig W (1966) Phylogenetic systematics. University of Illinois Press, UrbanaGoogle Scholar
  23. Howson C, Urbach P (1993) Scientific reasoning: the Bayesian approach, 2nd edn. Open Court, ChicagoGoogle Scholar
  24. Hull DL (1967) Certainty and circularity in evolutionary taxonomy. Evol 21:174–189. doi: 10.2307/2406751 CrossRefGoogle Scholar
  25. Hull DL (1974) Biology and philosophy of science. Prentice-Hall, Englewood CliffsGoogle Scholar
  26. Hull DL (1999) The use and abuse of Sir Karl Popper. Biol Philos 14:481–504. doi: 10.1023/A:1006554919188 CrossRefGoogle Scholar
  27. Kearney M (2007) Philosophy and phylogenetics: historical and current connections. In: Hull DL, Ruse M (eds) The Cambridge companion to the philosophy of biology. Cambridge University Press, New York, pp 211–232Google Scholar
  28. Kearney M, Rieppel O (2006) Rejecting “the given” in systematics. Cladistics 22:369–377. doi: 10.1111/j.1096-0031.2006.00110.x CrossRefGoogle Scholar
  29. Kluge AG (1997) Testability and the refutation and corroboration of cladistic hypotheses. Cladistics 13:81–96. doi: 10.1111/j.1096-0031.1997.tb00242.x CrossRefGoogle Scholar
  30. Kluge AG (2001a) Parsimony with and without scientific justification. Cladistics 17:199–210. doi: 10.1111/j.1096-0031.2001.tb00117.x CrossRefGoogle Scholar
  31. Kluge AG (2001b) Philosophical conjectures and their refutation. Syst Biol 50:322–330. doi: 10.1080/10635150119615 CrossRefGoogle Scholar
  32. Kluge AG (2003a) On the deduction of species relationships: a précis. Cladistics 19:233–239Google Scholar
  33. Kluge AG (2003b) The repugnant and the mature in phylogenetic inference: atemporal similarity and historical identity. Cladistics 19:356–368. doi: 10.1111/j.1096-0031.2003.tb00379.x CrossRefGoogle Scholar
  34. Kluge AG (2005) What is the rationale for ‘Ockham’s razor’ (a.k.a. parsimony) in phylogenetic inference? In: Albert VA (ed) Parsimony, phylogeny, and genomics. Oxford University Press, Oxford, pp 15–42Google Scholar
  35. Kluge AG (2007) Completing the neo-Darwinian synthesis with an event criterion. Cladistics 23:613–633Google Scholar
  36. Kluge AG (2008) Caveat emptor. Cladistics 24:623–624. doi: 10.1111/j.1096-0031.2007.00196.x CrossRefGoogle Scholar
  37. Kluge AG, Grant T (2006) From conviction to anti-superfluity: old and new justifications of parsimony in phylogenetic inference. Cladistics 22:276–288Google Scholar
  38. Lewontin RC (1980) Theoretical population genetics in the evolutionary synthesis. In: Mayr E, Provine WB (eds) The evolutionary synthesis. Perspectives on the unification of biology. Harvard University Press, Cambridge, pp 58–68Google Scholar
  39. Notturno MA (2000) Science and the open society: the future of Karl Popper’s philosophy. CEU Press, BudapestGoogle Scholar
  40. Popper KR (1957) The poverty of historicism. Routledge, New York [1994 reprint]Google Scholar
  41. Popper KR (1959) The logic of scientific discovery. Harper Torchbook, Harper and Row, New York [1968 reprint]Google Scholar
  42. Popper KR (1972) Objective knowledge. Clarendon Press, Oxford [1979 revised edition]Google Scholar
  43. Popper KR (1974) 9. Kneale on my alleged exclusion of nonuniversal hypotheses. In: Schilpp PA (ed) The philosophy of Karl Popper. Part three: the philosopher replies. Karl Popper: "Replies to my critics". Library Living Philosophers, vol XIV book II. Open Court, La Salle, Illinois, pp 987–989Google Scholar
  44. Popper KR (1983) Realism and the aim of science. Routledge, New York [1992 reprint]Google Scholar
  45. Richards R (2002) Kuhnian values and cladistic parsimony. Perspect Sci 10:1–27. doi: 10.1162/106361402762674780 CrossRefGoogle Scholar
  46. Richards R (2003) Character individuation in phylogenetic inference. Philos Sci 70:264–279. doi: 10.1086/375467 CrossRefGoogle Scholar
  47. Rieppel O (1983) Kladismus oder die Legende vom Stammbaum. Birkhäuser Verlag, BaselGoogle Scholar
  48. Rieppel O (1996) Testing homology by congruence: the pectoral girdle of turtles. Proc R Soc Lond B Biol Sci 263:1395–1398. doi: 10.1098/rspb.1996.0204 CrossRefGoogle Scholar
  49. Rieppel O (2003) Popper and systematics. Syst Biol 52:259–271. doi: 10.1080/10635150390192762 CrossRefGoogle Scholar
  50. Rieppel O (2004) 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 57–100Google Scholar
  51. Rieppel O (2005) Proper names in twin worlds: monophyly, paraphyly, and the world around us. Org Divers Evol 5:89–100. doi: 10.1016/j.ode.2004.03.003 CrossRefGoogle Scholar
  52. Rieppel O (2006) The merits of similarity reconsidered. Syst Biodivers 4:137–147. doi: 10.1017/S1477200005001830 CrossRefGoogle Scholar
  53. Rieppel O (2007a) The nature of parsimony and instrumentalism in systematics. J Zoological Syst Evol Res 45:177–183. doi: 10.1111/j.1439-0469.2007.00426.x CrossRefGoogle Scholar
  54. Rieppel O (2007b) The metaphysics of Hennig’s phylogenetic systematics: substance, events and laws of nature. Syst Biodivers 5:345–360. doi: 10.1017/S1477200007002575 CrossRefGoogle Scholar
  55. Rieppel O (2007c) Species: kinds of individuals or individuals of a kind. Cladistics 23:373–384. doi: 10.1111/j.1096-0031.2007.00152.x CrossRefGoogle Scholar
  56. Rieppel O, Kearney M (2002) Similarity. Biol J Linn Soc Lond 75:59–82. doi: 10.1046/j.1095-8312.2002.00006.x CrossRefGoogle Scholar
  57. Rieppel O, Rieppel M, Rieppel L (2006) Logic in systematics. J Zoological Syst Evol Res 44:186–192. doi: 10.1111/j.1439-0469.2006.00370.x CrossRefGoogle Scholar
  58. Siddall ME, Kluge AG (1997) Probabilism and phylogenetic inference. Cladistics 13:313–336. doi: 10.1111/j.1096-0031.1997.tb00322.x CrossRefGoogle Scholar
  59. Sober E (1988) Reconstructing the past: parsimony, evolution and inference. MIT Press, CambridgeGoogle Scholar
  60. Sober E (1994) Let’s razor Ockham’s razor. In: Knowles D (ed) Explanation and its limits. Roy Instit Philos suppl 27. Cambridge University Press, Cambridge, pp 73–93Google Scholar
  61. Williams DM, Ebach MC (2006) The data matrix. Geodivers 28:409–420Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  1. 1.Ann ArborUSA

Personalised recommendations