Principles of Phylogenetics: IB200A

Home

Reading List 1
The required readings are marked with two asterisks**. Highly recommended readings
are marked with one asterisk*; the rest are for background information and to allow
you an entrance into the literature.

Jan. 17 & 19: What is Systematic Biology? History and Philosophy

Bock, W. J. 1973. Philosophical foundations of classical evolutionary classification.

Syst. Zool. 22: 375-392 [part of a general symposium on "Contemporary Systematic

Philosophies" -- there are some other interesting papers here].

Brower, A. V. Z. 2000. Evolution Is Not a Necessary Assumption of Cladistics.

Cladistics 16: 143-154.

Dayrat, Benoit. Ancestor-descendant relationships and the reconstruction of the Tree of Life. Paleobiology 31 (3) : 347-353 SUM 2005

Donoghue, M.J. and J.W. Kadereit. 1992. Walter Zimmermann and the growth of

phylogenetic theory. Systematic Biology 41(1): 74-84.

Faith, D. P. and J. W. H. Trueman. 2001. Towards an inclusive philosophy for

phylogenetic inference. Systematic Biology 50: 331-350.

Gaffney, E. S. 1979. An introduction to the logic of phylogeny reconstruction. pp. 79-

111 in Cracraft, J. and N. Eldredge (eds.) Phylogenetic Analysis and Paleontology.

Columbia University Press, New York.

Gilmour, J. S. L. 1940. Taxonomy and philosophy. pp. 461-474 in J. Huxley (ed.). The

New Systematics. Oxford. [Reprinted in 1971 by the Systematics Association.]

Hull, D. L. 1978. A matter of individuality. Phil. of Science 45: 335-360. [Reprinted in

E. Sober (ed.) Conceptual Issues in Evolutionary Biology, 1984, MIT Press.]

Hull, D. L. 1981. The principles of biological classification: the use and abuse of

philosophy. PSA 1978. Vol. 2; 130-153.

Hull, D. L. 1984. Cladistic theory: hypotheses that blur and grow. pp. 5-23 in T.

Duncan and T. F. Stuessy (eds.). Cladistics: Perspectives on the Reconstruction of

Evolutionary History. Columbia University Press, New York.

*Hull, D. L. 1988. Science as a process: an evolutionary account of the social and

conceptual development of science. University of Chicago Press, Chicago. [an

already classic work on the recent, violent history of systematics; used as data for

Hull's general theories about scientific change].

Kitts, D. B. 1977. Karl Popper, verifiability, and systematic zoology. Syst. Zool. 26:

185-194.

Kluge, A. G. 1999. The Science of Phylogenetic Systematics: Explanation, Prediction,

and Test. Cladistics 15: 429-436.

Kluge, A. J. 2001. Philosophical conjectures and their refutation. Systematic Biology

50: 322.-330.

Mayr, E. 1982. The Growth of Biological Thought. Harvard University Press,

Cambridge, Mass.

McKelvey, B. 1982. Organizational Systematics. Univ. of California Press, Berkeley.

Mishler, B. D. 1989. [Untitled review of Hull, D.L. 1988. Science as a process.

Univ. Chicago Press, IL.]. Syst. Bot. 14:266-268.

O'Hara, R. J. 1992. Telling the tree: Narrative representation and the study of

evolutionary history. Biol. Philos. 7:135-160.

O'Keefe, F. R. and P. M. Sander. 1999. Paleontological paradigms and inferences of

phylogenetic pattern: a case study. Paleobiology 25: 518-533.

de Queiroz, K. 1987. Systematics and the Darwinian revolution. Philos. Sci. 55:238-

259.

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. Systematic Biology 50: 305-321.

**Sober, E. 1988. Reconstructing the past. MIT Press. [Chapter 1]

Stevens, P. F. 1994. The development of biological systematics. Columbia University

Press, New York.

Wiley, E. O. 1975. Karl R. Popper, systematics, and classification: a reply to Walter

Bock and other evolutionary taxonomists. Syst. Zool. 24: 233-243.

Wiley, E. O. 1981. Phylogenetics: The Theory and Practice of Phylogenetic

Systematics. John Wiley and Sons, New York.

Cleland, C. L. 2001. Historical science, experimental science, and the scientific method.

Geology 29: 987-990.

Hull, D. L. 1974 Philosophy of Biological Sciences. Prentice- Hall, Englewood Cliffs,

NJ.

Hull, D. L. 1999. The use and abuse of Sir Karl Popper. Biology and Philosophy 14:

481-504.

Kuhn, T. S. 1970. The Structure of Scientific Revolutions. Second edition. University

of Chicago Press. [A must-read for any scientist.]

Laudan, L. 1977. Progress and Its Problems. University of California Press, Berkley.

Losee, J. 1980. A Historical Introduction to the Philosophy of Science. Second edition.

Oxford University Press. [The best single-volume account of changes since Aristotle

in how science proceeds -- strongly recommended.]

Stamos, D. N. 1996. Popper, falsifiability, and evolutionary biology. Biology and

Philosophy 11: 161-191.