On probability and systematics: Possibility, probability, and phylogenetic inference

Systematic Biology

Volumn 54, Issue 5, 2005, Pages 831-841

  Haber, Matthew H ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION; METHODOLOGY; PHILOSOPHY; PHYLOGENY; PROBABILITY; REVIEW;

CLASSIFICATION; PHILOSOPHY; PHYLOGENY; PROBABILITY;

EID: 31344449850     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/106351591007444     Document Type: Review

References (43)

1. Baum, D. A. 1998. Individuality and the existence of species through time. Syst. Biol. 47:641-653.
2. 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.
3. de Queiroz, K., and S. Poe. 2003. Failed refutations: Further comments on parsimony and likelihood methods and their relationship to Popper's degree of corroboration. Syst. Biol. 52:322-330.
4. Farris, J. S. 1983. The logical basis of phylogenetic analysis. Pages 7-36 in Advances in cladistics, Volume 2: Proceedings of the Second Meeting of the Willi Hennig Society (N. I. Platnick and V. A. Funk, eds.). Columbia University Press, New York.
5. Ghiselin, M. T. 1974. A radical solution to the species problem. Syst. Zool. 23:536-544.
6. Ghiselin, M. T. 1997. Metaphysics and the Origin of Species. State University of New York Press, Albany, New York.
7. Giere, R. 1988. Explaining science: A cognitive approach. University of Chicago Press, Chicago.
8. Giere, R. 1997. Understanding scientific reasoning, 4th edition. Harcourt Brace College Publishers, Fort Worth, Texas.
9. Gillies, D. 1990. Bayesianism versus falsificationism. Ratio (New Series) III:82-98.
10. Gillies, D. 2000. Philosophical theories of probability. Routledge, London.
11. Griesemer, J. 2000. Development, culture, and the units of inheritance. Philosophy of Science Supplement. Proceedings of the 1998 Biennial Meetings of the Philosophy of Science Association. Part II: Symposia Papers. 67:S348-S368.
12. Grunbaum, A. 1976. Is the method of bold conjectures and attempted refutations Justifiably the method of science. Br. J. Phil. Sci. 27:105-136.
13. Hillis, D. M., J. P. Huelsenbeck, and C. W. Cunningham. 1994. Application and accuracy of molecular phylogenies. Science 264:671-677.
14. Howson, C., and P. Urbach. 1993. Scientific reasoning: The Bayesian approach, 2nd edition. Open Court, Chicago.
15. Huelsenbeck, J. P., B. Larget, R. E. Miller, and F. Ronquist. 2002. Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol. 51:673-688.
16. Hull, D. L. 1976. Are species really individuals? Syst. Zool. 25:174-191.
17. Hull, D. L. 1983. Karl Popper and Plato's metaphor. Pages 177-190 in Advances in cladistics, Volume 2: Proceedings of the Second Meeting of the Willi Hennig Society (N. I. Platnick and V. A. Funk, eds.). Columbia University Press, New York.
18. Hull, D. L. 1988. Science as a process: An evolutionary account of the social and conceptual development of science. University of Chicago Press, Chicago.
19. Hull, D. L. 1999. The use and abuse of Sir Karl Popper. Biol. Phil. 14:481-504.
20. Jubien, M. 1997. Contemporary metaphysics: An introduction. Blackwell Publishers, Malden, Massachusetts.
21. Kitcher, P. 1982. Abusing science: The case against creationism. MIT Press, Cambridge, Massachusetts.
22. Kitching, Ian J., P. L. Forey, C. J. Humphries, and D. M. Williams. 1998. Cladistics: The theory and practice of parsimony analysis, 2nd edition. Oxford University Press, Oxford, UK.
23. Kluge, A. G. 1997a. Sophisticated falsification and research cycles: Consequences for differential character weighting in phylogenetic systematics. Zool. Scripta 26:349-360.
24. Kluge, A. G. 1997b. Testability and the refutation and corroboration of cladistic hypotheses. Cladistics 13:81-96.
25. Kluge, A. G. 2001. Philosophical conjectures and their refutation. Syst. Biol. 50:322-330.
26. Kripke, S. A. 1980. Naming and necessity. Harvard University Press, Cambridge, Massachusetts.
27. Kuhn, T. S. 1970. Logic of discovery or psychology of research? Pages 1-23 in Criticism and the growth of knowledge (I. Lakatos and A. Musgrave, eds.). Cambridge University Press, Cambridge, UK.
28. Kuhn, T. S. 1996. The structure of scientific revolutions, 3rd edition. University of Chicago Press, Chicago.
29. Lakatos, I. 1970. 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 University Press, Cambridge, UK.
30. Larget, B., and D. Simon. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16:750-759.
31. Lewis, P. O., and D. L. Swofford. 2001. Back to the future: Bayesian inference arrives in phylogenetics. Trends Ecol. Evol. 16:600-601.
32. Popper, K. R. 1957. The propensity interpretation of the calculus of probability, and the quantum theory. Pages 65-70 in Observation and interpretation; a symposium of philosophers and physicists. Butterworths Scientific Publications, University of Bristol, Bristol, UK.
33. Popper, K. R. 1959a. The logic of scientific discovery. Basic Books, New York.
34. Popper, K. R. 1959b. The propensity interpretation of probability. Br. J. Phil. Sci. 10:25-42.
35. Popper, K. R. 1989. Conjectures and refutations, 5th edition. Routledge, London.
36. Salmon, W. C. 1998. Rational prediction. Pages 433-444 in Philosophy of science: The central issues (M. Curd and J. A. Cover, eds.). W. W. Norton and Company, New York.
37. Siddall, M. E., and A. G. Kluge. 1997. Probabilism and phylogenetic inference. Cladistics 13:313-336.
38. Sober, E. 1983. Parsimony methods in systematics. Pages 37-48 in Advances in cladistics, Volume 2: Proceedings of the Second Meeting of the Willi Hennig Society (N. I. Platnick and V. A. Funk, eds.). Columbia University Press, New York.
39. Sober, E. 1988. Reconstructing the past: Parsimony, evolution, and inference. MIT Press, Cambridge, Massachusetts.
40. Sober, E. 2000. Philosophy of biology, 2nd edition. Westview Press, Boulder, Colorado.
41. Sober, E. 2004. The contest between parsimony and likelihood. Syst. Biol. 53:644-653.
42. Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. Pages 407-514 in Molecular systematics (D. M. Hillis, C. Moritz, and B. Mable, eds.). Sinauer Associates, Sunderland, Massachusetts.
43. Urbach, P. 1991. Bayesian methodology: Some criticisms answered. Ratio (New Series) IV:170-184.