Topics & Assignments 

Unit 1: Systematics & Tree Thinking

Week 1 (Jan. 13 & 15):  Introduction to Population & Tree Thinking

• Baum, DA, Smith SD, and Donovan, SSS (2005) “The Tree-Thinking Challenge.” Science 310(5750): 979-980.
• O’Hara, RJ (1997) “Population thinking and tree thinking in systematics.” Zoological Scripta 26(4): 323-329. 

• Mayr, E (1959) “Darwin and the Evolutionary Theory in Biology” in Evolution and Anthropology: A Centennial Appraisal (Meggers, BJ, ed.)p.  1-10.  Washington D.C.: The Anthropological Society of Washington. 
• Sober, E (1980) “Evolution, Population Thinking, and Essentialism.” Philosophy of Science 47(3): 350-383.
• De Queiroz (1988) “Systematics and the Darwinian Revolution.” Philosophy of Science 55(2): 238-259.
• Nee, Sean (2005) “The great chain of being.” Nature 435: 429.
• Tree Thinking Group
• PhyloCode Resource Page (pdf)
  

1. Sign up for the Phil Bio Cafe & Request Membership in the Utah PHIL 3370 Group*
2. Sign up for turnitin.com
3. In-Class Exercises

*Once you sign in to the Phil Bio Cafe, click on "User Control Panel" in the upper right.

Next, click on "Usergroups" at the bottom of the column on the left.

Then, select the button to the right of the "Utah PHIL 3370" group.

Select "Join selected" (which should be the default) and click the "submit" button.

Then, wait for me to approve your request.

Week 2 (Jan. 20 & 22): Logic & Critical Thinking

• Hacking, I (2001) An Introduction to Probability and Inductive Logic Cambridge: CUP (Chapter 1).
• Weston, A (2008) A Rulebook for Arguments Chapter 1, 7-9.
  

• Teller, P A Modern Logic Primer (Vol. I) (http://tellerprimer.ucdavis.edu/)
• My Logic Course Website (http://www.phylosophy.org/phil3200)
  

• Assignments:
  Hacking Chapter 1 Exercises
• Hacking Answer Key

Week 3 (Jan. 27 & 29):  Biological Similarity

• Mayr, Ernst (1981) “Biological Classification: Toward a Synthesis of Opposing Methodologies.” Science 214: 510-516.
• Ridley, M (1983) “Can classification do without evolution?” New Scientist 100: 647-651.

• Hull, DL (1970) “Contemporary Systematic Philosophies” Annual Review of Ecology and Systematics 1:19-54.
• Hennig, W (1975) "Cladistic Analysis or Cladistic Classification?: A Reply to Ernst Mayr." Systematic Zoology 24(2): 244-256.

 Week 4 (Feb 3 & 5): Biological Individuality: Ontology of Biology

• Ghiselin, M (1974) “A Radical Solution To The Species Problem.” Systematic Zoology 23: 536-544.
• Hull, DL (1976) “Are Species Really Individuals?” Systematic Zoology 25: 174-191.
  

• Ghiselin, M (1966) “On Psychologism in the logic of taxonomic controversies.” Systematic Zoology 15: 207-215.
• Hull, DL (1978) “A matter of individuality.” Philosophy of Science 45: 335-360.
• Kitts, D (1983) “Can Baptism Alone Save Species?” Systematic Zoology 32(1): 27-33.
• Hull, DL (1984) “Can Kripke Alone Save Essentialism? A Reply to Kitts.” Systematic Zoology 33(1): 110-112.
• Kitcher, P (1984) “Species” Philosophy of Science 51(2): 308-333.
• Boyd, R (1999) “Homeostasis, species and higher taxa.” In: Species: New Interdisciplinary Essays (Wilson RA, ed), 141-185. Cambridge: MIT Press.
• Griffiths, P (1999) “Squaring the Circle: Natural Kinds with Historical Essences.” In: Species: New Interdisciplinary Essays (Wilson RA, ed), 209-228. Cambridge: MIT Press.
• Brogaard, Berit (2004) “Species as Individuals.” Biology and Philosophy 19: 223-242.
• Ereshefsky, M (2007) “Foundational Issues Concerning Taxa and Taxon Names.” Systematic Biology 56(2): 295-301. 
• Hamilton, A, Smith NR, and Haber MH (2009) "Social Insects and the Individuality Thesis" in Organizations of Insect Societies (Gadau J, and Fewell J, eds.).
  

Assignments :

• Short Paper #1: Individuality
• Janzen, DH (1977) "What Are Dandelions and Aphids?" The American Naturalist 111(979): 586-589.
  

Week 5 (Feb. 10 & 12): The Species Problem: What Kinds of Biological Individuals Are Species?

• Ereshesfsky, M (1992) “Eliminative Pluralism” Philosophy of Science 59(4): 671-690.
• De Queiroz, K (1998) “The General Lineage Concept of Species, Species Criteria, and the Process of Speciation.” In: Endless Forms: Species and Speciation (Howard D, Berlocher S, eds), 57-75.  New York: OUP.

• Coyne, JA & Orr HA (2004) “Appendix A (& other excerpts).” in Speciation p. 25-54 & 447-472.  Sinauer Associates.
• Mishler, BD and Donoghue, MJ (1982)  “Species concepts: a case for pluralism. “ Syst. Zool. 31: 491-503.
• Mishler, BD (1999) “Getting Rid of Species” in Species: New Interdisciplinary Essays (Wilson, R, ed.) p. 307-315.  Cambridge: MIT Press.
• Baum, DA (1992) “Phylogenetic Species Concepts” TREE 7(1): 1-2.
• Baum, DA & Shaw, KL (1995) “Genealogical perspectives on the species problem.” in Experimental and Molecular Approaches to Plant Biosystematics (Hoch, PC and Stephenon, AG, eds.) p. 289-303.  St. Louis, MO: Missouri Botanical Garden.

• Short Paper #2: Species 

Week 6 (Feb. 17 & 19): Taxonomy & Nomenclature: What & How Should We Name Taxa?

• PhyloCode (Preface)
• De Queiroz & Gauthier (1994) “Toward a phylogenetic system of biological nomenclature.” TREE 9(1): 27-30.
• Nixon & Carpenter (2000) “On the Other ‘Phylogenetic Systematics’.” Cladistics 16: 298-318.
  

• Bertrand, Y, Pleijel F, & Rouse GW (2006) “Taxonomic surrogacy in biodiversity assessments, and the meaning of Linnaean ranks.” Systematics and Biodiversity 4(2): 149-159.
• Ereshefsky, M (2007) “Foundational Issues Concerning Taxa and Taxon Names.” Systematic Biology 56(2): 295-301.
• Pennisi, E (2001) “Linnaeus’s Last Stand?” Science 291(5512): 2304-2305+2307.
• PhyloCode Resource Page (pdf)

Week 7 (Feb. 24 & 26): Biological Simplicity: Phylogenetic Inference

Change in Syllabus! Human Evolution will be covered instead.  Primary Reading will be S. Downes "Evolutionary Psychology" Stanford Encyclopedia of Philosophy

• Haber, MH (2008) "Phylogenetic Inference"

• Felsenstein, J (2001) “The Troubled Growth of Statistical Phylogenetics.” Systematic Biology 50(4): 465-467.
• Hull and Farris exchange (1983) in Advances in Cladistics: Proceedings of the Second Meeting of the Willi Hennig Society (Volume 2) (N. Platnick & V. Funk, eds.).
• Farris, J, Kluge A, and Carpenter J (2001) “Popper and Likelihood versus ‘Popper’.” Systematic Biology 50(3): 438-444.
• De Queiroz K, and Poe, S (2001) “Philosophy and Phylogenetic Inference.” Systematic Biology 50(3): 305-321.
• Haber, MH (2005) “On Probability and Systematics: Possibility, Probability and Phylogenetic Inference.” Systematic Biology 54(5): 831-841.
• Alfaro, M and Holder, M (2006) “The Posterior and the Prior in Bayesian Phylogenetics.” Annual Review of Ecology, Evolution, and Systematics 37: 19-42.
  

Unit 2:  Creationism, Intelligent Design(ism), Darwinism, and Evolutionary Theory

Week 8 (Mar. 3 & 5): The New Creationist Challenge & A Naturalistic Account of Science

• Doubting Darwin: Ch. 1: Introduction
• Meyer, S (Feb. 9, 2006) “Intelligent Design is not Creationism.” The Daily Telegraph (London) Feb. 9. 

• Dobzhansky, T (1973) “Nothing in Biology Makes Sense Except in Light of Evolution.” The American Biology Teacher 35: 125-129.
• Institute of Creation Research Tenets
  

Week 9 (Mar. 10 & 12):Historical and Contemporary Evolutionary Theory (Not Darwinism)

• Doubting Darwin: Ch. 2 & 4
  

• Downes, S (2008) “Evolutionary Psychology” Stanford Encycolopedia of Philosophy
  
• Gould, SJ (1997) “Darwinian Fundamentalism” The New York Review of Books June 12, 44(10).
• Kalant, H, Pinker, S, Kalow, & Gould SJ (1997) “Evolutionary Psychology: An Exchange” The New York Review of Books Oct. 9, 44(15).
• Elmendorf Evolution Tree

Week 10 (Mar. 24 & 26): Evolutionary vs. Human Design; Justifying Historical Inference

• Doubting Darwin: Ch. 3
• Dembski, W “Science & Design” First Things

• Paley, W (1805) Natural Theology (excerpt).
• Hume, D (1779) Dialogues Concerning Natural Religion (From Parts 2 & 5).
• Nilsson DE & Pelger S (1994) “A pessimistic estimate of the time required for an eye to evolve.” Proceedings of the Royal Society (London), Biological Sciences 256: 53-8.

Week 11 (Mar. 31 & Apr. 2): Irreducible Complexity & The Complicated Matter of Biological Complexity: Science is Hard

• Doubting Darwin: Ch. 6
• Behe, MJ (1996) “Darwin Under the Microscope” New York Times, October 29, p. A25.
• Orr, HA (2005) “Devolution: Why Intelligent Design Isn’t.” The New Yorker, May 30.

• Discovery Institute
• Coyne, JA (2007) “The Great Mutator” The New Republic, June 18, 38-44.

Week 12 (Apr. 7 & 9): The State of Evolutionary Theory & Naturalism Revisited: The Double Reverse Wedge Strategy

(Apr. 9: Pacific APA)

• Doubting Darwin: Ch. 9 & 10

• Jones (2005) Kitzmiller vs. Dover Area School District, p. 64-89

Unit 3:  Normative & Ethical Implications of Evolutionary Thinking

Week 13 (Apr. 14 & 16): Introduction to Ethical Theory; Using Animals in Research

• Bioethics and the New Embryology: Ch. 15
• Singer, P (1975) “All Animals Are Equal” from Animal Liberation
• Cohen, C “The Case For the Use of Animals in Biomedical Research.” New England Journal of Medicine 315(14): 865-870.

• Bekoff, M (2006) “Animals are rich with public pleasure” TREE 21(11): 601-602.
• Gawande, A (2002) “The Learning Curve: Like everyone else, surgeons need practice. That’s where you come in.” The New Yorker Jan. 28, p. 52-?.

Week 14 (Apr. 21 & 23): The (Lack of) Normativity of the Biological Normal

• Bioethics and the New Embryology: Ch. 13
• Hull, DL (1986) “On Human Nature” PSA: Proceedings of the Biennial Meeting of the Philosophy of Science Association, Vol. II: Symposia and Invited Papers. 3-13.

•  Downes, S (2008) “Evolutionary Psychology” Stanford Encycolopedia of Philosophy

Week 15 (Apr. 28): Part-Human Embryonic Research: Biological Individuals and the Ethics of Crossing Species Boundaries.

• Bioethics and the New Embryology: Ch. 14
• Haber, Benham, & Piotrowska (draft)

• Robert, JS & Baylis F (2003) “Crossing Species Boundaries” American Journal of Bioethics 3(3): 1-12.
• Baylis, F & Robert JS (2007) “Part-Human Chimeras: Worrying the Facts, Probing the Ethics.” American Journal of Bioethics 7(5): 41-45.