Philosophical conjectures and their refutation

Systematic Biology

Volumn 50, Issue 3, 2001, Pages 322-330

  Kluge, Arnold G ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Absolute (logical) probability; Corroboration; Critical evidence; Explanation; Falsificationism; Maximum likelihood; Relative (conditional) probability; Severity of test; Verificationism

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; PHILOSOPHY; PHYLOGENY; STATISTICAL MODEL; SYSTEM ANALYSIS;

LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHILOSOPHY; PHYLOGENY; PROBABILITY THEORY;

EID: 0035527349     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150119615     Document Type: Article

References (38)

1. DE QUEIROZ, K., AND S. POE. 2001. Philosophy and phylogenetic inference: A comparison of likelihood and parsimony methods in the context of Karl Popper's writings on corroboration. Syst. Biol. 50:305-321.
2. EDWARDS, A. W. F. 1972. Likelihood. Cambridge Univ. Press, Cambridge [1992 reprint].
3. FARRIS, J. S. 1983. The logical basis of phylogenetic analysis. Pages 7-36. In Advances in cladistics (N. I. Platnick and V. A. Funk, eds.), volume 2. Columbia Univ. Press, New York.
4. FARRIS, J. S. 1989. Entropy and fruit flies. Cladistics 5:103-108.
5. FARRIS, J. S., A. G. KLUGE, AND J. M. CARPENTER. 2001. Popper and likelihood versus "Popper*". Syst. Biol. 50:438-444.
6. FELSENSTEIN, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
7. FELSENSTEIN, J. 1981a. A likelihood approach to character weighting and what it tells us about parsimony and compatibility. Biol. J. Linn. Soc. 16:183-196.
8. FELSENSTEIN, J. 1981b. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:368-376.
9. FELSENSTEIN, J. 1982. Numerical methods for inferring evolutionary trees. Q. Rev. Biol. 57:379-404.
10. FELSENSTEIN, J. 1983. Methods for inferring phylogenies: A statistical view. Pages 315-334. In J. Felsenstein (ed.), Numerical taxonomy. Springer-Verlag, New York.
11. FELSENSTEIN, J. 1988a. The detection of phylogeny. Pages 112-127. In Prospects in systematics (D. L. Hawksworth, ed.). Systematics Assoc., Clarendon Press, Oxford.
12. FELSENSTEIN, J. 1988b. Phylogenies from molecular sequences: Inference and reliability. Annu. Rev. Genet. 22:521-565.
13. GOLDMAN, N. 1990. Maximum likelihood inference of phylogenetic trees, with special reference to a Poisson Process Model of DNA substitution and to parsimony analyses. Syst. Zool. 39:345-361.
14. HENNIG, W. 1966. Phylogenetic systematics. Univ. of Illinois Press, Chicago.
15. HUELSENBECK, J. P., AND K. A. CRANDALL. 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu. Rev. Ecol. Syst. 28:437-466.
16. HUELSENBECK, J. P., AND B. RANNALA. 1997. Phylogenetic methods come of age: Testing hypotheses in an evolutionary context. Science 276:227-232.
17. KIM, J. 1996. General inconsistency conditions for maximum parsimony: Effects of branch lengths and increasing numbers of taxa. Syst. Biol. 45:363-374.
18. KLUGE, A. G. 1997a. Testability and the refutation and corroboration of cladistic hypotheses. Cladistics 13:81-96.
19. KLUGE, A. G. 1997b. Sophisticated falsification and research cycles: Consequences for differential character weighting in phylogenetic systematics. Zool. Scr. 26:349-360.
20. KLUGE, A. G. 1999. The science of phylogenetic systematics: Explanation, prediction, and test. Cladistics 15:429-436.
21. LAKATOS, I. 1993. Falsification and the methodology of scientific research programmes. Pages 91-196. In Criticism and the growth of knowledge (I. Lakatos and A. Musgrave, eds.). Cambridge Univ. Press, London.
22. MILLER, D. 1999. Being an absolute skeptic. Science 284:1625-1626.
23. PAGEL, M. D. 1999. Inferring the historical patterns of biological evolution. Nature 401:877-884.
24. PENNY, D., M. D. HENDY, P. J. LOCKHART, AND M. A. STEEL. 1996. Corrected parsimony, minimum evolution, and Hadamard conjunctions. Syst. Biol. 45:596-606.
25. POPPER, K. 1934. Logik der Forschung. Springer Verlag, Vienna.
26. POPPER, K. 1957. The poverty of historicism. Routledge and Kegan Paul, London.
27. POPPER, K. 1959. The logic of scientific discovery. Harper and Row, New York.
28. POPPER, K. 1962. Conjectures and refutations: The growth of scientific knowledge. Routledge and Kegan Paul, London.
29. POPPER, K. 1983. Realism and the aim of science. Routledge, London. [1992 reprint]
30. SANDERSON, M. J. 1995. Objections to bootstrapping phylogenies: A critique. Syst. Biol. 44:299-320.
31. SIDDALL, M. E., AND A. G. KLUGE. 1997. Probabilism and phylogenetic inference. Cladistics 13:313-336.
32. SIDDALL, M. E., AND A. G. KLUGE. 1999. Letter to the editor [evidence and character independence]. Cladistics 15:439-440.
33. SIDDALL, M. E., and M. F. WHITING. 1999. Long branch abstractions. Cladistics 15:9-24.
34. SOBER, E. 1993. Philosophy of biology. Westview Press, San Francisco, California.
35. STEEL, M., and D. PENNY. 2000. Parsimony, likelihood, and the role of models in molecular phylogenetics. Mol. Biol. Evol. 17:839-850.
36. THOMPSON, E. A. 1975. Human evolutionary trees. Cambridge Univ. Press, Cambridge.
37. TUFFLEY, C., AND M. STEEL. 1997. Links between maximum likelihood and maximum parsimony under a simple model of site substitution. Bull. Math. Biol. 59:581-607.
38. WATKINS, J. 1984. Science and scepticism. Princeton Univ. Press, Princeton, New Jersey.