Philosophy 6890:
Philosophy and Biology
Fall, 2010

Professors Joel Velasco and Richard Boyd
Guests include Brent Mishler, Integrative Biology at California-Berkeley and Maureen Kearney, Systematic Biology at the National Science Foundation

Class meets Tuesdays, 10:10-12:35 in Uris 204

This is a tentative schedule/reading list:

Week 1 (8/31) - Introduction

Required Reading
- None
Extra Reading - Good background for the course
- Kearney, M. (2007), Philosophy and Phylogenetics: Historical and Current Connections
- Ereshefsky, M. (2010), Species, Stanford Encyclopedia of Philosophy
- Bird, A. and Tobin, E. (2008), Natural Kinds, Stanford Encyclopedia of Philosophy
- Ereshefsky, M. (2009), Natural Kinds in Biology, Routledge Encyclopedia of Philosophy

Week 2 (9/7) - Species ontology

Required Readings
- Hull, D. (1978), A Matter of Individuality
- Kitcher, P. (1984), Species
Extra Readings
- Ghiselin, M. (1974), A Radical Solution to the Species Problem
- Sober, E. (1984), Sets, Species, and Evolution: Comments on Philip Kitcher's "Species"
- Kitcher, P. (1984), Against the Monism of the Moment: A Reply to Elliott Sober
- Kitcher, P. (1989), Some Puzzles about Species

Week 3 (9/14) - Classification and Higher Taxa

Required Reading
- Hennig, W (1975) Cladistic Analysis or Cladistic Classification?: A Reply to Ernst Mayr
- Mayr, E (1981) Biological Classification: Toward a Synthesis of Opposing Methodologies
- Ridley, M (1983) Can Classification Do Without Evolution?
Extra Reading
- Hull, DL (1970) Contemporary Systematic Philosophies
- Mayr, E (1974) Cladistic Analysis or Cladistic Classification?
- Velasco, J (2008) Philosophy and the Tree of Life (Chap 1 is on phylogenetic classification and higher taxa)

Week 4 (9/21) - The Species Problem

Required Readings
- Coyne, J. and Orr, H. A. (2004), Speciation (Chap 1 on BSC)
- Mishler, B. and Brandon, R (1987), Individuality, Pluralism, and the Phylogenetic Species Concept
- Baum, D. and Donoghue, M. (1995), Choosing Among Alternative Phylogenetic Species Concepts
- Velasco, J. (2008), Species Concepts Should Not Conflict with Evolutionary History, But Often Do
Extra Readings
- Link to Extra Readings and explanations here

Week 5 (9/28) - The Meta-Species Problem

Required Reading
- Ereshefsky, M. (1992) Eliminative Pluralism
- de Queiroz, K. (1998) The General Lineage Concept of Species, Species Criteria, and the Process of Speciation
- Dupré, J. (1999), On the Impossibility of a Monistic Account of Species
Extra Reading
- Link to Extra Readings here

Week 6 (10/5) - Taxa as Natural Kinds

Required Readings
- Boyd, R. (1999), Homeostasis, Species, and Higher Taxa (*printable version*)
- Griffiths, P. (1999), Squaring the Circle: Natural Kinds with Historical Essences
- Wilson, R. A., Barker, M. J., and Brigandt, I. (2007), When Traditional Essentialism Fails: Biological Natural Kinds
Extra Readings
- Link to Extra Readings here

Week 7 (10/12) - No Class - Fall Break

Week 8 (10/19) - Taxa and Kinds (continued)

Required Readings
- Dupré, J (1981), Natural Kinds and Biological Taxa
- Rieppel, O. (2005), Monophyly, Paraphyly, and Natural Kinds
- Boyd R. (2010), Homeostasis, Higher Taxa, and Monophyly
Extra Readings
- Ereshefsky, M. (2010) What's Wrong with the New Biological Essentialism

Week 9 (10/26) - Brent Mishler visits

Required Reading
- Mishler, B. (1999), Getting rid of species
- Mishler, B. (2010), Species are not Uniquely Real Biological Entities
- Mishler, B. (2009), Three centuries of paradigm changes in biological classification: Is the end in sight?
Extra Reading
- Cantino, P. and de Queiroz, K. (2010) Preface to the International Code of Phylogenetic Nomenclature (Version 4c)
- Claridge, M. (2010), Species are Uniquely Real Biological Entities (the counterpoint to Mishler's above piece)

Week 10 (11/2) - Characters and Homology

Required Readings
- Richards R. (2003), Character Individuation in Phylogenetic Inference
- Griffiths PE (2006), Function, Homology, and Character Individuation
- Love, A. (2007), Functional homology and homology of function: biological concepts and philosophical consequences
Extra Readings
- Lots of extra readings on homology and characters

Week 11 (11/9) - Maureen Kearney visits

Required Reading
- Kearney, M. (2007), Philosophy and Phylogenetics: Historical and Current Connections
- Kearney, M. and Rieppel, O. (2006), Rejecting "The Given" in Systematics
- Rieppel, O. and Kearney, M. (2007), The Poverty of Taxonomic Characters
Extra Reading
- Rieppel, O. and Kearney, M. (2002), Similarity

Week 12 (11/16) Behavior and Homology

Required Readings
- Wenzel, J. (1992), Behavioral Homology and Phylogeny
- Rendall D, and Di Fiore, A. (2007), Homoplasy, homology, and the perceived special status of behavior in evolution
- Ereshefsky, M. (2007), Psychological Categories as Homologies: Lessons from Ethology
Extra Readings

Week 13 (11/23) - What is an Organism?

Required Reading
- Janzen, DH (1977), What are Dandelions and Aphids?
- Wilson, RA (2005), What is an Organism? (Chap 3 from Genes and the agents of life)
- Pradue, T (2010) What is an Organism? An Immunological Answer
- Turner, S (2004) Extended Phenotypes and Extended Organisms
Extra Reading
- Van Dijk, et al., An Apomixis-Gene’s View on Dandelions
- O'Malley and Dupré, Size Doesn't Matter: Toward a More Inclusive Philosophy of Biology
- Dupré and O'Malley, Varieties of Living Things: Life at the Intersection of Lineage and Metabolism
- Szathmary and Maynard Smith, The Major Evolutionary Transitions
- Wilson, The Biological Notion of an Individual From the Stanford Encyclopedia of Philosophy
- Wilson and Sober, Reviving the Superorganism
- Hamilton et al. Social Insects and the Individuality Thesis: Cohesion and the Colony as a Selectable Individual
- Smith et al. The humungous fungus paper
- Xu and Gordon, Honor thy Symbionts

Week 14 (11/30) - The metaquestion - do we need the organism category?

Required Readings
- Lewontin, R. (1983) The Organism as the Subject and Object of Evolution
- Wilson, J. (2000) Ontological Butchery
- Pepper J. and Herron M. (2009) Does Biology Need an Organism Concept?
Extra Readings