Philosophy 249/349 – Evidence and Evolution
Spring 2009
Joel Velasco
READING LIST
For full citations, see here
4/2: Week 1:Introduction to the class - probability intro:
Extra readings:
Eells, Probabilistic Causality Appendix 1 (Boolean Algebra)
Eells, Probabilistic Causality Appendix 2 (Probability Axioms)
Sober, An introduction to Bayesian Epistemology (problem with fonts?)
Strevens, Notes on Bayesian Confirmation Theory (esp. pgs 1-22)
Hajek, Interpretations of Probability (from the Stanford Encyclopedia of Philosophy)
Fitelson, A Decision Procedure for Probability Calculus with Applications
Hacking,Odd Questions + Bayes Rule (from Introduction to Probability and Inductive Logic)
4/7: Week 2: Bayesianism and Likelihoodism
Required readings:
E&E 1.1–1.3 (and look through 1.4 and 1.5 as well)
Fitelson, Likelihoodism, Bayesianism, and Relational Confirmation
D. Steel, Bayesian Confirmation Theory and the Likelihood Principle
Extra readings:
Sober, Bayesianism: its Scope and Limits
van Fraassen, Indifference: The symmetries of probability (from Laws and Symmetry)
Fitelson, The Plurality of Bayesian Measures of Confirmation and the Problem of Measure Sensitivity (on Bayesian confirmation)
Eells and Fitelson, Measuring Confirmation and Evidence (on Bayesian confirmation)
Royall, The First Principle (Chapter 1 of Statistical Evidence: A Likelihood Paradigm) (Likelihoodism - more technical treatment)
4/14: Week 3: Frequentism
Required readings:
E&E 1.4-1.6
S. Goodman and R. Royall, Evidence and Scientific Research
S. Goodman, Toward Evidence-Based Medical Statistics I – the P-value Fallacy
S. Goodman, Toward Evidence-Based Medical Statistics 2 – the Bayes Factor
Extra readings:
Royall, Neyman-Pearson theory (Chap 2 of Statistical Evidence)
Royall, Fisherian theory (Chap 3 of Statistical Evidence)
Neyman and Pearson, On the problem of the most efficient tests of statistical hypotheses (the original foundational paper)
The New Math of Clinical Trials (the Bayesian doctor)
Stopping Rules:
Steel, A Bayesian way to make stopping rules matter
Mayo Why you cannot be just a little bit Bayesian (Chap 10 of Error and the Growth of Experimental Knowledge)
Backe, The Likelihood Principle and the reliability of experiments
Kadane et al. When several bayesians agree that there will be no reasoning to a forgone conclusion (very technical facts about stopping rules)
4/21: Week 4: Models and Model Selection Theory:
Required readings:
E&E 1.7-1.9
Forster and Sober, How to Tell When Simpler, More Unified, or Less Ad Hoc Theories will Provide More Accurate Predictions
Extra readings:
Diaconis and Mosteller, Methods for studying coincidences
Kieseppa, Statistical model selection and Bayesianism
4/28: Week 5: Intelligent Design
Required readings:
E&E Chapter 2
Extra readings:
Paley, Natural Theology, (first chapter)
Gould, The Panda's Peculiar Thumb (without pictures)
Dembski, Detecting Design? A First Response to Elliott Sober (response to a book review of The Design Inference)
Hempel, Empiricist Criteria of Cognitive Significance: Problems and Changes
Sober, Testability
McGrew, Testability, Likelihoods, and Design
Weisberg, Firing Squads and Fine Tuning: Sober on the Design Argument
Behe, Molecular Machines
5/5: Week 6: What is Natural Selection
Required readings:
Selections from Darwin, The Origin of Species (Chapters 3,4,6)
Kitcher, Darwin’s Achievement
Hodge, Natural Selection as a Causal, Empirical, and Probabilistic Theory
Extra readings:
Beatty, Chance and Natural Selection
Millstein, Are Selection and Drift Conceptually Distinct
Millstein, Natural Selection as a Population-Level Causal Process
5/12: Week 7: Selection in a single lineage
Required readings:
E&E 3.1-3.6
Extra readings:
Waters, The arguments in the Origin of Species (Cambridge Companion to Darwin)
Sober, Metaphysical and epistemological issues in modern Darwinian theory (Cambridge Companion to Darwin)
Ruse, Darwinian Evolutionary Theory: Its structure and its mechanism (The Oxford Handbook of Philosophy of Biology)
Sober, Is drift a serious alternative to natural selection as an explanation of complex adaptive traits?
Sober and Orzack, Common Ancestry and Natural Selection
Sober, Reconstructing ancestral character states: A likelihood perspective on cladistic parsimony
5/19: Week 8: Comparisons between lineages
Required readings:
E&E 3.6-3.12
Extra readings:
Harvey and Pagel, The Comparative Method in Evolutionary Biology
Sober, Venetian sea levels, British bread prices, and the principle of the common cause
Lang et al., Are human beings part of the rest of nature?
5/26: Week 9: Similarity as evidence for common ancestry
Required readings:
E&E 4.1-4.7 part 1
Penny, L. Foulds, M. Hendy, Testing the theory of evolution by comparing phylogenetic tress constructed from five different protein sequences
D. Penny, M. Hendy, and A. Poole, Testing Fundamental Evolutionary Hypotheses
Extra readings:
Sober and Steel, Testing the hypothesis of common ancestry
Sober, Modus Darwin
Forster, Statistical covariance as a measure of phylogenetic relationship
6/2: Week 10: Other kinds of evidence for common ancestry
Required readings:
E&E 4.7, 4.8, conclusion
Steel and Penny, Parsimony, Likelihood and the Role of Models in Molecular Phylogenetics
Huelsenbeck, F. Ronquist, R., Nielsen, J. Bollback, Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology
Extra readings:
Sober, Absence of evidence and evidence of absence
Strevens, Objective evidence and absence: Comment on Sober