Philosophy 249/349 – Evidence and Evolution

Spring 2009

 Joel Velasco



    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

Sober, The contest between parsimony and likelihood

Velasco, The prior probabilities of phylogenetic trees