Bibliography
Published online by Cambridge University Press: 05 June 2012
Summary
A summary is not available for this content so a preview has been provided. Please use the Get access link above for information on how to access this content.
- Type
- Chapter
- Information
- Evidence and EvolutionThe Logic Behind the Science, pp. 368 - 384Publisher: Cambridge University PressPrint publication year: 2008
References
(1973) “Information Theory as an Extension of the Maximum Likelihood Principle,” in and (eds), Second International Symposium on Information Theory, Budapest: Akademiai Kiado, pp. 267–81.Google Scholar
, , , and (1998) “Parenting and Survival in Anthropoid Primates: Caretakers Live Longer,” Proceedings of the National Academy of Science USA 95: 6866–9.CrossRefGoogle ScholarPubMed
(1954) “Fixed-Sample-Size Analysis of Sequential Observations,” Biometrics 10: 90–100.CrossRefGoogle Scholar
and (1991) “Ontoecogenophyloconstraints? The Chaos of Constraint Terminology,” Trends in Ecology and Evolution 6: 166–8.CrossRefGoogle ScholarPubMed
(1710) “An Argument for Divine Providence, Taken from the Constant Regularity Observ'd in the Births of Both Sexes,” Philosophical Transactions of the Royal Society 27: 186–90.CrossRefGoogle Scholar
(1999) “The Likelihood Principle and the Reliability of Experiments,” Philosophy of Science 66: S354–61.CrossRefGoogle Scholar
and (1991) “Adaptation Reviewed: A Phylogenetic Methodology for Studying Character Coevolution,” Systematic Zoology 40: 1–18.CrossRefGoogle Scholar
(2001) “Reply to My Critics:” A Response to Reviews of Darwin's Black Box: The Biochemical Challenge to Evolution,”Biology of Philosophy, 16(5) 683–707.CrossRefGoogle Scholar
(2006) “Whether Intelligent Design Is Science: A Response to the Opinion of the Court in Kitzmiller vs Dover Area School District,” Special Report, Center for Science and Culture, Discovery Institute. Available online at http://www.discovery.org/scripts/viewDB/filesDB-download.php?command= download& id=697. (Accessed April 21, 2007.)
and (1996) “Genetic Constraints to Life-History Evolution in the Pitcher-Plant Mosquito, Wyeomyia smithii,” Evolution 50: 1176–81.CrossRefGoogle ScholarPubMed
(2003) “Darwin and Victorian Christianity,” in and (eds), The Cambridge Companion to Darwin, Cambridge: Cambridge University Press, pp. 192–213.Google Scholar
(1986) “The Evolution of Darwin's Theism,” Journal of the History of Biology 19: 1–45.Google Scholar
(1993) The Correspondence of Charles Darwin, Volume VIII: 1860, Cambridge: Cambridge University Press.Google Scholar
and (1998) Model Selection and Inference: A Practical Information-Theoretic Approach, New York: Springer.CrossRefGoogle Scholar
and (2002) Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach, 2nd edn, New York: Springer.Google Scholar
(1988) “Comparative Methods Using Phylogenetically Independent Contrasts,” Oxford Surveys in Evolutionary Biology, Oxford: Oxford University Press, pp. 33–53.Google Scholar
and (2004) “Phylogenetic Comparative Analysis: A Modeling Approach for Adaptive Evolution,” American Naturalist 164: 683–95.CrossRefGoogle ScholarPubMed
(1982) Genetic Takeover and the Mineral Origins of Life, Cambridge: Cambridge University Press.Google Scholar
(1950) Logical Foundations of Probability, Chicago, Ill.: University of Chicago Press.Google Scholar
(1994) Nature's Capacities and their Measurement, Oxford: Oxford University Press.CrossRefGoogle Scholar
(1996) “Inconsistency of Evolutionary Tree Topology Reconstruction Methods When Substitution Rates Vary Across Characters,” Mathematical Biosciences 134: 189–215.CrossRefGoogle ScholarPubMed
, , and (1985) “The Quantitative Assessment of Phylogenetic Constraints in Comparative Analyses: Sexual Dimorphism in Body Weight among Primates,” Evolution 39: 1335–51.CrossRefGoogle ScholarPubMed
(1999) “The Ethics of Belief,” in The Ethics of Belief and Other Essays, Amherst, NY: Prometheus Books. First published 1877.Google Scholar
(2003) Life's Solution: Inevitable Humans in a Lonely Universe, Cambridge: Cambridge University Press.CrossRefGoogle Scholar
and (1978) “Predator Ingestion Rate and its Bearing on Feeding Time and the Theory of Optimal Diets,” Journal of Animal Ecology 47: 529–47.CrossRefGoogle Scholar
(1968) “The Origin of the Genetic Code,” Journal of Molecular Biology 38: 367–79.CrossRefGoogle ScholarPubMed
, , , , , , , , and (2000) “The Future of Forensic DNA Testing: Predictions of the Research and Development Working Group,” National Institute of Justice, NCJ 183697.Google Scholar
and (1970) An Introduction to Population Genetics Theory, Minneapolis, Minn.: Burgess.Google Scholar
, , and (1998) “Reconstructing Ancestral Character States: A Critical Appraisal,” Trends in Ecology and Evolution 13: 361–6.CrossRefGoogle Scholar
and (2003) Science and Partial Truth: A Unitary Account to Models and Scientific Reasoning, Oxford: Oxford University Press.CrossRefGoogle Scholar
(1876) The Variation of Animals and Plants under Domestication, 2nd edn, New York: D. Appleton. First published 1868.Google Scholar
(1958) The Autobiography of Charles Darwin, 1809–1882, with original omissions restored, ed. , London: Collins.Google Scholar
(1959) On the Origin of Species: A Variorum Edition, ed. , Philadelphia, Pa.: University of Pennsylvania Press.CrossRefGoogle Scholar
(1964) The Origin of Species, London: Murray; Cambridge, Mass.: Harvard University Press. First published 1859.Google Scholar
(1994) “Topology: Invariance of Dimension,” in (ed.), Companion Encyclopedia of the History and Philosophy of the Mathematical Sciences, London and New York: Routledge, pp. 939–49.Google Scholar
(2002) “Bayes' Theorem and Weighing Evidence by Juries,” in (ed.), Bayes's Theorem, Oxford: Oxford University Press, pp. 71–90.Google Scholar
(2004) The Design Revolution: Answering the Toughest Questions about Intelligent Design, Downers Grove, Ill.: InterVarsity Press.Google Scholar
(1978) Brainstorms: Philosophical Essays on Mind and Psychology, Cambridge, Mass.: MIT Press.Google Scholar
(1987a) “Intentional Systems in Cognitive Ethology: The ‘Panglossian Paradigm’ Defended,” in The Intentional Stance, Cambridge, Mass.: MIT Press, pp. 237–86.Google Scholar
(1987b) “True Believers,” in The Intentional Stance, Cambridge, Mass.: MIT Press, pp. 13–42.Google Scholar
(1985) The Philosophical Writings of Descartes, trans. , , and , 2 vols, Cambridge: Cambridge University Press.Google Scholar
and (1989) “Methods of Studying Coincidences,” Journal of the American Statistical Association 84: 853–61.CrossRefGoogle Scholar
and (1996) “Testing Hypotheses of Correlated Evolution Using Phylogenetically Independent Contrasts: Sensitivity to Deviations from Brownian Motion,” Systematic Biology 45: 27–47.CrossRefGoogle Scholar
(1996) The Biological Universe: The Twentieth-Century Extraterrestrial Life Debate and the Limits of Science, Cambridge: Cambridge University Press.Google Scholar
(2000) “The Nature of the Universal Ancestor and the Evolution of the Proteome,” Current Opinion in Structural Biology 10: 355–8.CrossRefGoogle ScholarPubMed
and (2007) “Pattern Pluralism and the Tree of Life Hypothesis,” Proceedings of the National Academy of Sciences USA 104: 2043–9.CrossRefGoogle ScholarPubMed
(1989) “Pain and Pleasure: An Evidential Problem for Theists,” Noûs 23: 331–50. Reprinted in D. Howard-Snyder (ed.), The Evidential Argument from Evil, Bloomington, Ind.: Indiana University Press, 1996, pp. 12–29.CrossRefGoogle Scholar
(1996) “The Skeptical Theist,” in (ed.), The Evidential Argument from Evil, Bloomington, Ind.: Indiana University Press, pp. 175–92.Google Scholar
(1954) The Aim and Structure of Physical Theory, Princeton, NJ: Princeton University Press. First published in French 1914.Google Scholar
(1988) “Supernatural Speech and Biological Books,” History of Philosophy Quarterly 3: 257–72.Google Scholar
(1992) Bayes or Bust: A Critical Examination of Bayesian Confirmation Theory, Cambridge, Mass.: MIT Press.Google Scholar
(2000) Hume's Abject Failure: The Miracles Argument, New York: Oxford University Press.CrossRefGoogle Scholar
(1960) “The Aquatic Origin of Tetrapods,” Transactions of the Kansas Academy of Science 63: 115–20.CrossRefGoogle Scholar
(1989) “Two Perspectives on the Evolution of the Tetrapod Limb,” American Zoologist 29: 235–54.CrossRefGoogle Scholar
(1985) “Problems of Old Evidence,” Pacific Philosophical Quarterly 66: 283–302.CrossRefGoogle Scholar
and (1980) Phylogenetic Patterns and the Evolutionary Process, New York: Columbia University Press.Google Scholar
(2004) “Philosophical Significance of Akaike's Theorem,” Unpublished.
(1994) “The Logical Basis of Phylogenetic Analysis,” in (ed.), Conceptual Issues in Evolutionary Biology, Cambridge, Mass.: MIT Press. First published 1983 in N. Platnick and V. Funk (eds), Advances in Cladistics: Proceedings of the 2nd Annual Meeting of the Willi Hennig Society, New York: Columbia University Press, pp. 7–36.Google Scholar
(1973) “Maximum Likelihood and Minimum-Step Methods for Estimating Evolutionary Trees from Data on Discrete Characters,” Systematic Zoology 22: 240–9.CrossRefGoogle Scholar
(1978) “Cases in which Parsimony and Compatibility Methods Can Be Positively Misleading,” Systematic Zoology 27: 401–10.CrossRefGoogle Scholar
(1979) “Alternative Methods of Phylogenetic Inference and their Interrelationships,” Systematic Biology 28: 49–62.CrossRefGoogle Scholar
(1981) “A Likelihood Approach to Character Weighting and What It Tells Us About Parsimony and Compatibility,” Biological Journal of the Linnaean Society 16: 183–96.CrossRefGoogle Scholar
(1985) “Phylogenies and the Comparative Method,” American Naturalist 125: 1–15.CrossRefGoogle Scholar
(1974) Against Method: Outline of an Anarchistic Theory of Knowledge, Atlantic Highlands, NJ: Humanities Press.Google Scholar
(1922a) “On the Dominance Ratio,” Proceedings of the Royal Society of Edinburgh 42: 321–41.CrossRefGoogle Scholar
(1922b) “On the Mathematical Foundations of Theoretical Statistics,” Philosophical Transactions of the Royal Society A 222: 309–68.CrossRefGoogle Scholar
(1959) Statistical Methods and Scientific Inference, 2nd edn, Edinburgh: Oliver & Boyd.Google Scholar
(1999) “The Plurality of Bayesian Measures of Confirmation and the Problem of Measure Sensitivity,” Philosophy of Science 66: S362–78.CrossRefGoogle Scholar
(2007) “Likelihoodism, Bayesianism, and Relational Confirmation,” Synthese 156: 473–489.CrossRefGoogle Scholar
, , and (1999) “How Not to Detect Design: A Review of W. Dembski's The Design Inference,” Philosophy of Science 66: 472–88.CrossRefGoogle Scholar
(1986) “Statistical Covariance as a Measure of Phylogenetic Relationship,” Cladistics 2: 297–317.CrossRefGoogle Scholar
(1999) “Model Selection in Science: The Problem of Language Invariance,” British Journal for the Philosophy of Science 50: 83–102.CrossRefGoogle Scholar
(2000a) “Hard Problems in the Philosophy of Science: Idealisation and Commensurability,” in and (eds), After Popper, Kuhn, and Feyerabend, London: Kluwer, pp. 231–50.Google Scholar
(2000b) “Key Concepts in Model Selection: Performance and Generality,” Journal of Mathematical Psychology 44: 205–31.CrossRefGoogle Scholar
(2001) “The New Science of Simplicity,” in , , and (eds), Simplicity, Inference, and Modeling, Cambridge: Cambridge University Press, pp. 83–119.Google Scholar
(2006) “Counterexamples to the Likelihood Theory of Evidence,” Mind and Machines 16: 319–38.CrossRefGoogle Scholar
(in press) “A Philosopher's Guide to Empirical Success,” Philosophy of Science.
and (1994) “How to Tell When Simpler, More Unified, or Less Ad Hoc Theories Will Provide More Accurate Predictions,” British Journal for the Philosophy of Science 45: 1–36.CrossRefGoogle Scholar
and (in preparation) “AIC Scores as Evidence: A Bayesian Interpretation.”
, , , and (2000) “Early Fixation of an Optimal Genetic Code,” Molecular Biology and Evolution 17: 511–18.CrossRefGoogle ScholarPubMed
and (2006) “Models in Science,” in (ed.), The Stanford Encyclopedia of Philosophy. Available at http://plato. stanford. edu/archives/spr2006/entries/models-science. (Accessed May 5 2007.)
and (1995) “Success of Maximum Likelihood Phylogeny Inference in the Four Taxon Case,” Molecular Biology and Evolution 12: 152–62.CrossRefGoogle ScholarPubMed
(2002) “The Genetic Control of Eye Development and Its Implications for the Evolution of the Various Eye-Types,” The International Journal of Developmental Biology 46: 65–73.Google ScholarPubMed
(1986) “Natural Selection and the Molecular Clock,” Molecular Biology and Evolution 3: 138–55.Google ScholarPubMed
, , and (1985) “The Hot Hand in Basketball: On the Misperception of Random Sequences,” Cognitive Psychology 17: 295–314.CrossRefGoogle Scholar
(1990) “Maximum Likelihood Inference of Phylogenetic Trees, with Special Reference to a Poisson Process Model of DNA Substitution and to Parsimony Analyses,” Systematic Biology 39: 345–61.Google Scholar
(1967) “On the Principle of Total Evidence,” British Journal for the Philosophy of Science 17: 319–21.CrossRefGoogle Scholar
(1999) “Toward Evidence-Based Medical Statistics: 1. The P Value Fallacy,” Annals of Internal Medicine, 130: 995–1004.CrossRefGoogle ScholarPubMed
(1977) “The Misnamed, Mistreated, and Misunderstood Irish Elk,” in Ever Since Darwin, New York: Norton, pp. 79–90.Google Scholar
(1991) “The Ant and the Plant,” in Bully for Brontosaurus, New York: Norton, pp. 479–88.Google Scholar
and (1979) “The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Paradigm,” Proceedings of the Royal Society B 205: 581–98.CrossRefGoogle Scholar
and (1982) “Exaptation: A Missing Term in the Science of Form,” Paleobiology 8: 4–15.CrossRefGoogle Scholar
(2007) “Statistical Inference: From Data to Simple Hypotheses,” Unpublished.
(1965) The Logic of Statistical Inference, Cambridge: Cambridge University Press.CrossRefGoogle Scholar
(1987) “The Inverse Gambler's Fallacy: The Argument from Design. The Anthropic Principle Applied to Wheeler Universes,” Mind 96: 331–40.CrossRefGoogle Scholar
(1997) “Stabilizing Selection and the Comparative Analysis of Adaptation,” Evolution 51: 1341–51.CrossRefGoogle ScholarPubMed
(1969) Perception and Discovery: An Introduction to Scientific Inquiry, San Francisco, Calif.: Freeman-Cooper.Google Scholar
and (2007) Reliable Reasoning: Induction and Statistical Learning Theory, Cambridge, Mass.: MIT Press.Google Scholar
and (1991) The Comparative Method in Evolutionary Biology, Oxford: Oxford University Press.Google Scholar
(1992) The Inexact and Separate Science of Economics, Cambridge: Cambridge University Press.CrossRefGoogle Scholar
(1951) “The Concept of Cognitive Significance: A Reconsideration,” Proceedings of the American Academy of Arts and Sciences 80: 61–77.CrossRefGoogle Scholar
(1965a) “Empiricist Criteria of Cognitive Significance: Problems and Changes,” in Aspects of Scientific Explanation and Other Essays in the Philosophy of Science, New York: Free Press, pp. 101–22.Google Scholar
(1965b) “Studies in the Logic of Confirmation,” in Aspects of Scientific Explanation and Other Essays in the Philosophy of Science, New York: Free Press, pp. 3–46.Google Scholar
, , and (2004) “Comparing Strengths of Directional Selection: How Strong Is Strong?” Evolution 58: 2133–43.CrossRefGoogle ScholarPubMed
(1966) Models and Analogies in Science, Notre Dame, Ind.: University of Notre Dame Press.Google Scholar
(2005) “The Application-Conditions of Design Inferences: Why the Design Argument Needs the Help of Other Arguments for God's Existence,” International Journal for the Philosophy of Religion 57: 1–33.CrossRefGoogle Scholar
(1987) “Natural Selection as a Causal, Empirical and Probabilistic Theory,” in , , and (eds), The Probabilistic Revolution, Vol. II, Cambridge, Mass.: MIT Press, pp. 233–70.Google Scholar
(1991) “The History of the Earth, Life, and Man: Whewell and Palaetiological Science,” in and (eds), William Whewell: A Composite Portrait, Oxford: Clarendon Press, pp. 255–89.Google Scholar
(2003) “Nonstationary Time Series, Cointegration, and the Principle of the Common Cause,” British Journal for the Philosophy of Science 54: 527–51.CrossRefGoogle Scholar
(ed.) (1996) The Evidential Argument from Evil, Bloomington, Ind.: Indiana University Press.
(2001) “The Logic of Bayesian Probability,” in and (eds), Foundations of Bayesianism, Dordrecht: Kluwer Academic.Google Scholar
, , and (2004) “Bayesian Phylogenetic Model Selection Using Reversible Jump Markov Chain Monte Carlo,” Molecular Biology and Evolution 21: 1123–33.CrossRefGoogle ScholarPubMed
, , , and (2001) “Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology,” Science 294: 2310–14.CrossRefGoogle ScholarPubMed
(2000) “Why Did Darwin Fail? The Case of John Stuart Mill,” in and (eds), Biology and Epistemology, Cambridge: Cambridge University Press, pp. 48–63.Google Scholar
(1990) Dialogues Concerning Natural Religion, London: Penguin. First published in 1779.Google Scholar
(1897) “The Will to Believe,” in The Will to Believe and Other Essays in Popular Philosophy, New York: Longmans Green & Co., pp. 1–31.Google Scholar
and (1961) “Estimation with Quadratic Loss,” in (ed.), Proceedings of the Fourth Berkeley Symposium on Mathematical Statistics and Probability, Vol. I, Berkeley, Calif.: University of California Press, pp. 361–79.Google Scholar
(1983) The Logic of Decision, 2nd edn, Chicago, Ill.: University of Chicago Press. First published 1965.Google Scholar
(1995) “Statistical Sirens: The Allure of Nonparametrics,” Ecology 76: 1998–2000.CrossRefGoogle Scholar
and (1969) “Evolution of Protein Molecules,” in (ed.), Mammalian Protein Metabolism, New York: Academic Press, pp. 21–132.Google Scholar
(2007) “The Search for a Formal Criterion of Empirical Significance: A Reconsideration,” Unpublished.
, , and (1996), “Reasoning to a Foregone Conclusion,” Journal of the American Statistical Association 91: 1228–35.CrossRefGoogle Scholar
(1980) “A Simple Method for Estimating Evolutionary Rates of Base Substitutions through Comparative Studies of Nucleotide Sequences,” Journal of Molecular Evolution 16: 111–20.CrossRefGoogle ScholarPubMed
(1981) “Estimation of Evolutionary Distances Between Homologous Nucleotide Sequences,” Proceedings of the National Academy of Sciences USA 78: 454–8.CrossRefGoogle ScholarPubMed
(1983) The Neutral Theory of Molecular Evolution, Cambridge: Cambridge University Press.CrossRefGoogle Scholar
and (1985) “Aerodynamics, Thermoregulation, and the Evolution of Insect Wings: Differential Scaling and Evolutionary Change,” Evolution 39: 488–504.CrossRefGoogle ScholarPubMed
and (1990) “Converting Distance to Time: Application to Human Evolution,” Methods in Enzymology 183: 550–70.CrossRefGoogle ScholarPubMed
(1993) The Advancement of Science: Science Without Legend, Objectivity Without Illusions, New York: Oxford University Press.Google Scholar
(2001) “Real Realism: The Galilean Strategy,” Philosophical Review 110: 151–98.CrossRefGoogle Scholar
(2003) “Darwin's Achievement,” in In Mendel's Mirror, New York: Oxford University Press, pp. 45–93.Google Scholar
, , and (2001) “Rewiring the Keyboard: Evolvability of the Genetic Code,” Nature Reviews: Genetics 2: 49–58.CrossRefGoogle ScholarPubMed
, , , and (2006) “A Drosophila Model for Age-Associated Changes in Sleep:Wake Cycles,” Proceedings of the National Academy of Sciences USA 103: 13843–7.CrossRefGoogle ScholarPubMed
(2000) “How to Detect Selection in Populations with Applications to the Human,” Annual Review of Genomics and Human Genetics 1: 539–59.CrossRefGoogle ScholarPubMed
(1962) The Structure of Scientific Revolutions, Chicago, Ill.: Chicago University Press.Google Scholar
(1970) “Conjuctivitis” in (ed.) Induction, Acceptance, and Rational Belief, Dordrecht: Reidel, pp. 55–820.CrossRefGoogle Scholar
, , , and (1984) “A New Method for Calculating Evolutionary Substitution Rates,” Journal of Molecular Evolution 20: 86–93.CrossRefGoogle ScholarPubMed
(1984) “Molluscs,” in (ed.), Photoreception and Vision in Invertebrates, New York: Plenum, pp. 699–725.Google Scholar
(1976) “Natural Selection and Random Genetic Drift in Phenotypic Evolution,” Evolution 30: 314–34.CrossRefGoogle ScholarPubMed
(1985) “Expected Time for Random Genetic Drift of a Population between Stable Phenotypic States,” Proceedings of the National Academy of Science USA 82: 7641–5.CrossRefGoogle ScholarPubMed
, , and (2002) “Are Human Beings Part of the Rest of Nature?” Biology and Philosophy 17: 661–71.CrossRefGoogle Scholar
(1951) Philosophical Essay on Probabilities, New York: Dover. First published in French 1829.Google Scholar
(1996) “The Argument from Design,” in and (eds), Adaptation, New York: Academic Press, pp. 55–92.Google Scholar
, , and (1994) “What Does the Comparative Method Reveal About Adaptation?” The American Naturalist 143: 381–402.CrossRefGoogle Scholar
(1998) “Maximum Likelihood as an Alternative to Parsimony for Inferring Phylogeny Using Nucleotide Sequence Data,” in , , and (eds), Molecular Systematics of Plants II, Boston, Mass.: Kluwer, pp. 132–63.Google Scholar
(2001) “A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data,” Systematic Biology 50: 913–25.CrossRefGoogle ScholarPubMed
(1993) “So, What About the Molecular Clock Hypothesis?” Current Opinion in Genetics and Development 3: 896–901.CrossRefGoogle ScholarPubMed
and (1987) “The Molecular Clock Runs More Slowly in Man than in Apes and Monkeys,” Nature 326: 93–6.CrossRefGoogle ScholarPubMed
and (1976) “Inference for a Bernouilli Process (a Bayesian view),” The American Statistician 30: 112–19.Google Scholar
(1991) “Squared-Change Parsimony Reconstructions of Ancestral States for Continuous-Valued Characters on a Phylogenetic Tree,” Systematic Zoology 40: 304–14.CrossRefGoogle Scholar
Maynard (1978) “Optimization Theory in Evolution,” Annual Review of Ecology and Systematics 9: 31–56.CrossRefGoogle Scholar
(1996) Error and the Growth of Experimental Knowledge, Chicago, Ill.: University of Chicago Press.CrossRefGoogle Scholar
(1976) “Typological versus Population Thinking,” in Evolution and the Diversity of Life, Cambridge, Mass.: Harvard University Press, pp. 26–9. First published 1963.Google Scholar
(1988) Towards a New Philosophy of Biology, Cambridge, Mass.: Harvard University Press.Google Scholar
(2000) “The Biological Species Concept,” in and (eds), Species Concepts and Phylogenetic Theory, New York: Columbia University Press, pp. 17–29, 93–100, 161–6.Google Scholar
and (1991) “Adaptive Protein Evolution at the Adh Locus in Drosophila,” Nature 351: 652–4.CrossRefGoogle ScholarPubMed
(1985) “Galilean Idealization,” Studies in the History and Philosophy of Science 16: 247–73.CrossRefGoogle Scholar
and (eds) (1999) Models as Mediators: Perspectives on Natural and Social Science, Cambridge: Cambridge University Press.CrossRef
(1960) “The Realist-Instrumentalist Controversy,” in , , and (eds), Philosophy, Science, and Method, New York: Harcourt, Brace, and World, pp. 106–22.Google Scholar
(1996) “The Role of Theology in Current Evolutionary Reasoning,” Biology and Philosophy 11: 493–517.CrossRefGoogle Scholar
and (1933) “On the Problem of the Most Efficient Tests of Statistical Hypotheses,” Philosophical Transactions of the Royal Society, Series A 231: 289–333.CrossRefGoogle Scholar
(2005) “Molecular Signatures of Natural Selection,” Annual Review of Genetics 39: 197–218.CrossRefGoogle ScholarPubMed
and (1994) “A Pessimistic Estimate of the Time Required for an Eye to Evolve,” Proceedings of the Royal Society London, Series B, Biological Sciences 256: 53–8.CrossRefGoogle ScholarPubMed
(2003) “Science Without God: Natural Law and Christian Beliefs: An Essay on Methodological Naturalism,” in and (eds), When Science and Christianity Meet, Chicago, Ill.: University of Chicago Press, pp. 265–86.Google Scholar
(1988) “Homage to Clio, or, Towards an Historical Philosophy for Evolutionary Biology,” Systematic Zoology 37: 142–55.CrossRefGoogle Scholar
(1998) “Population Thinking and Tree Thinking in Systematics,” Zoological Scripta 26: 323–9.CrossRefGoogle Scholar
(1996) “Darwin v. Intelligent Design (Again),”Boston Review of Books, Dec/June: 28–31.Google Scholar
and (1993) “A Critical Examination of Richard Levins' ‘The Strategy of Model Building in Population Biology’,” Quarterly Review of Biology 68: 533–46.CrossRefGoogle Scholar
and (2001) “Adaptation, Phylogenetic Inertia, and the Method of Controlled Comparisons,” in Adaptationism and Optimality, Cambridge: Cambridge University Press, pp. 45–63.CrossRefGoogle Scholar
(1981) The Development of Darwin's Theory: Natural History, Natural Theology, and Natural Selection 1838–1859, Cambridge: Cambridge University Press.Google Scholar
(1809) Natural Theology, or, Evidences of the Existence and Attributes of the Deity, Collected from the Appearances of Nature, 12th edn, London: Rivington. First published 1802. Available online at http://darwin-online.org.uk/content/frameset?itemID=A142 & viewtype=text & pageseq=1.Google Scholar
(1978) “Searching for Mates,” in and (eds), Behavioral Ecology: An Evolutionary Approach, Oxford: Blackwell, pp. 214–44.Google Scholar
and (1976) “Animal Behavior as a Strategy Optimizer: Evolution of Resource Assessment Strategies and Optimal Emigration Thresholds,” American Naturalist 110: 1055–76.CrossRefGoogle Scholar
(1981) “Significance of Fossils in Determining Evolutionary Relationships,” Annual Review of Ecology and Systematics 12: 195–223.CrossRefGoogle Scholar
(1934) “The Fixation of Belief,” in , , and (eds), The Collected Papers of Charles Sanders Peirce, Cambridge, Mass.: Harvard University Press, Volume V, pp. 223–47. First published 1877.Google Scholar
(1999) Tower of Babel: The Evidence Against the New Creationism, Cambridge, Mass.: MIT Press.Google Scholar
, and (1982) “Testing the Theory of Evolution by Comparing Phylogenetic Trees Constructed from Five Different Protein Sequences,” Nature 297: 197–200.CrossRefGoogle ScholarPubMed
and (2004) “Model Selection in Phylogenetics: Advantages of the AIC and Bayesian Approaches,” Systematic Biology 53: 793–808.CrossRefGoogle ScholarPubMed
and (2001) “Selecting the Best-Fit Model of Nucleotide Substitution,” Systematic Biology 50: 580–601.CrossRefGoogle ScholarPubMed
(1989) “Progress in Evolution and Meaning in Life,” in (ed.), Evolutionary Progress, Chicago, Ill.: University of Chicago Press.Google Scholar
(1953) “Two Dogmas of Empiricism,” in From a Logical Point of View, Cambridge, Mass.: Harvard University Press, pp. 20–46.Google Scholar
(2005) “Deviance, Darwinian-Style: A Review of A. Lustig, R. Richards, and M. Ruse's Darwinian Heresies (Cambridge: CUP, 2004),” Metascience 14: 453–7.CrossRefGoogle Scholar
, and (1996) “Probability Distribution of Molecular Evolutionary Trees: a New Method of Phylogenetic Inference,” Journal of Molecular Evolution 43: 304–11.CrossRefGoogle ScholarPubMed
(1970) “Statistical Methods Related to the Law of the Iterated Logarithm,” Annals of Mathematical Statistics 41: 1397–1409.CrossRefGoogle Scholar
, , , and , (1990) “The General Stochastic Model of Nucleotide Substitution,” Journal of Theoretical Biology 142: 485–501.CrossRefGoogle ScholarPubMed
(1979) “The Problem of Evil and Some Varieties of Atheism,” American Philosophical Quarterly 16: 335–341.Google Scholar
(1997) Statistical Evidence: A Likelihood Paradigm, Boca Raton, Fla.: Chapman and Hall.Google Scholar
(1979) The Darwinian Revolution: Science Red in Tooth and Claw, Chicago, Ill.: University of Chicago Press.Google Scholar
(1919) Introduction to Mathematical Philosophy, New York: The Macmillan Company; London: George Allen & Unwin, Ltd.Google Scholar
(1984) Scientific Explanation and the Causal Structure of the World, Princeton, NJ: Princeton University Press.Google Scholar
and (1977) “On the Evolution of Photoreceptors and Eyes,” in , , and (eds), Evolutionary Biology, Vol. X, New York: Plenum, pp. 207–63.Google Scholar
and (1998) Phenotypic Evolution: A Reaction Norm Perspective, Sunderland, Mass.: Sinauer.Google Scholar
(2004) God, the Devil, and Darwin: A Critique of Intelligent Design Theory, Oxford: Oxford University Press.CrossRefGoogle Scholar
and (2007) “Epiphenomenalism: The Do's and Don'ts,” in and (eds), Studies in Causality: Historical and Contemporary, Pittsburgh, Pa.: University of Pittsburgh Press.Google Scholar
(1987) “The Continental Controversy over Arbuthnot's Argument for Divine Providence,” Historia Mathematica 14: 133–46.CrossRefGoogle Scholar
(1981) “The Architecture of Complexity,” in The Sciences of the Artificial, Cambridge, Mass.: MIT Press, pp. 193–229.Google Scholar
(1996) The Evolution of the Social Contract, Cambridge: Cambridge University Press.CrossRefGoogle Scholar
(2006) Reforming Philosophy: A Victorian Debate on Science and Society, Chicago, Ill.: University of Chicago Press.CrossRefGoogle Scholar
(1980) “Evolution, Population Thinking, and Essentialism,” Philosophy of Science 47: 350–83.CrossRefGoogle Scholar
(1984) The Nature of Selection, Cambridge, Mass.: MIT Press. Second edition published 1993 Chicago, Ill.: University of Chicago Press.Google Scholar
(1988) Reconstructing the Past: Parsimony, Evolution, and Inference, Cambridge, Mass.: MIT Press.Google Scholar
(1989) “Independent Evidence About a Common Cause,” Philosophy of Science 56: 275–87.CrossRefGoogle Scholar
(1994) “Progress and Directionality in Evolutionary Theory,” in (ed.), Creative Evolution?!Boston, Mass.: Jones and Bartlett, pp. 19–33.Google Scholar
(1998) “Three Differences Between Evolution and Deliberation,” in (ed.), Modeling Rationality, Morality, and Evolution, Oxford: Oxford University Press, pp. 408–22.Google Scholar
(1999b) “Testability,” Proceedings and Addresses of the American Philosophical Association 73: 47–76.CrossRefGoogle Scholar
(2000a) “Evolution and the Problem of Other Minds,” Journal of Philosophy 97: 365–86.CrossRefGoogle Scholar
(2000b) “Quine's Two Dogmas,” Proceedings of the Aristotelian Society, Supplementary Volume 74: 237–80.CrossRefGoogle Scholar
(2001) “Venetian Sea Levels, British Bread Prices, and the Principle of the Common Cause,” British Journal for the Philosophy of Science 52: 1–16.CrossRefGoogle Scholar
(2002a) “Intelligent Design and Probability Reasoning,” International Journal of Philosophy of Religion 52: 65–80.CrossRefGoogle Scholar
(2002b) “Instrumentalism, Parsimony, and the Akaike Framework,” Philosophy of Science 69: S112–23.CrossRefGoogle Scholar
(2002c) “Reconstructing Ancestral Character States: A Likelihood Perspective on Cladistic Parsimony,” The Monist 85: 156–76.CrossRefGoogle Scholar
(2003a) “It Had to Happen: A Review of Simon Conway Morris' Life's Solution in a Lonely Universe,” New York Times, November 30, Book Review Section, p. 18.Google Scholar
(2003b) “Two Uses of Unification,” in (ed.), The Vienna Circle and Logical Empiricism: Vienna Circle Institute Yearbook 2002, Dordrecht: Kluwer, pp. 205–16.Google Scholar
(2004a) “The Contest Between Likelihood and Parsimony,” Systematic Zoology 53: 6–16.Google ScholarPubMed
(2004b) “The Design Argument,” in (ed.), The Blackwell Guide to the Philosophy of Religion, Oxford: Blackwell, pp. 117–47.Google Scholar
(2004c) “Likelihood, Model Selection, and the Duhem–Quine Problem,” Journal of Philosophy 101: 1–22.CrossRefGoogle Scholar
(2004d) “A Modest Proposal: A Review of John Earman's Hume's Abject Failure: The Miracles Argument,” Philosophy and Phenomenological Research 118: 487–94.CrossRefGoogle Scholar
(2005) “Parsimony and its Presuppositions,” in (ed.), Parsimony, Phylogeny, and Genomics, Oxford: Oxford University Press.Google Scholar
(2007a) “Intelligent Design Theory and the Supernatural: The ‘God or Extra-Terrestrials’ Reply,” Faith and Philosophy 24: 72–82.CrossRefGoogle Scholar
(2007b) “Sex Ratio Theory, Ancient and Modern: An 18th Century Debate about Intelligent Design and the Development of Models in Evolutionary Biology,” in (ed.), Genesis Redux: Essays on the History and Philosophy of Artificial Life, Chicago, Ill.: University of Chicago Press, pp. 131–62.Google Scholar
(2008a) “Empiricism,” in and (eds), The Routledge Companion to the Philosophy of Science, London: Routledge.Google Scholar
(2008b) “Evolutionary Theory and the Reality of Macro-Probabilities,” in and (eds), Probability in Science, Chicago, Ill.: Open Court.Google Scholar
and (2003) “Common Ancestry and Natural Selection,” British Journal for the Philosophy of Science 54: 423–37.CrossRefGoogle Scholar
and (2002) “Testing the Hypothesis of Common Ancestry,” Journal of Theoretical Biology 218: 395–408.CrossRefGoogle ScholarPubMed
and (1998) Unto Others: The Evolution and Psychology of Unselfish Behavior, Cambridge, Mass.: Harvard University Press.Google Scholar
(2001) Vagueness and Contradiction, Oxford: Clarendon Press; New York: Oxford University Press.Google Scholar
(2000) “Cytology and Cytogenetics as a Fundamental Taxonomic Resource for the 20th and 21st Centuries,” Taxon 49: 451–77.CrossRefGoogle Scholar
(2006) Science, History, and the Problem of Unconceived Alternatives, Oxford: Oxford University Press.Google Scholar
and (2000) “Parsimony, Likelihood, and the Role of Models in Molecular Phylogenetics,” Molecular Biology and Evolution 17: 839–50.CrossRefGoogle ScholarPubMed
and (2004) “Two Further Links between MP and ML under the Poisson Model,” Applied Mathematics Letters 17: 785–90.CrossRefGoogle Scholar
and (1999) Sex and Death: An Introduction to the Philosophy of Biology, Chicago, Ill.: University of Chicago Press.Google Scholar
(1977) “An Asymptotic Equivalence of Choice of Model by Cross-Validation and Akaike's Criterion,” Journal of the Royal Statistical Society B 39: 44–7.Google Scholar
(1978) “Further Analysis of the Data by Akaike's Information Criterion and the Finite Corrections,” Communications in Statistics, Theory and Methods A7: 13–26.CrossRefGoogle Scholar
(1990) “The Limits of Explanation,” in (ed.), Explanation and Its Limits, Cambridge: Cambridge University Press, pp. 177–93.Google Scholar
, , , and (1996) “Phylogenetic Inference,” in , , and (eds), Molecular Systematics, 2nd edn, Sunderland, Mass.: Sinauer, pp. 407–514.Google Scholar
(1976) “Distribution of Informational Statistics and a Criterion of Model Fitting,” (in Japanese), Suri-Kapaku (Mathematical Sciences) 153: 12–18.Google Scholar
(1986) “Some Probabilistic and Statistical Problems on the Analysis of DNA Sequences,” Lectures on Mathematics in the Life Sciences 17: 57–86.Google Scholar
and (1997) “Links Between Maximum Likelihood and Maximum Parsimony under a Simple Model of Site Substitution,” Bulletin of Mathematical Biology 59: 581–607.CrossRefGoogle Scholar
(1988) “Population Genetic Models for Polygenic Variation and Evolution,” in , , , and (eds), Proceedings of the Second International Conference on Quantitative Genetics, Sunderland, Mass.: Sinauer, pp. 601–18.Google Scholar
(1982) “The Charybdis of Realism: Epistemological Implications of Bell's Inequality,” Synthese 52: 25–38.CrossRefGoogle Scholar
(2004) “Modus Tollens Probabilized,” British Journal for the Philosophy of Science 55: 747–53.CrossRefGoogle Scholar
, , and (1983) “On the Problem of Stasis in Organismal Evolution,” Journal of Theoretical Biology 101: 211–24.CrossRefGoogle Scholar
, , and (2002) “The Trials of Life: Natural Selection and Random Drift,” Philosophy of Science 69: 452–73.CrossRefGoogle Scholar
(1999) “Statistical Tests for the Hot-Hand in Basketball in a Controlled Setting,” Technical Report, Department of Statistics, University of Wisconsin, Madison. Available online at http://hot-hand. behaviouralfinance. net/Ward99. pdf. (Accessed 4 February 2007.)
(1833) Astronomy and General Physics Considered with Reference to Natural Theology, Philadelphia, Pa.: Carey, Lea and Blanchard.Google Scholar
(1847) The Philosophy of the Inductive Sciences, Founded Upon Their History, Vol. I, London: J. Parker.Google Scholar
(1981) Phylogenetics: The Theory and Practice of Phylogenetic Systematics, New York: Wiley.Google Scholar
(1975) Sociobiology: The New Synthesis, Cambridge, Mass.: Belknap Press of Harvard University Press.Google Scholar
(1998) “The Universal Ancestor,” Proceedings of the National Academy of Sciences USA 95: 6854–9.CrossRefGoogle ScholarPubMed
(1984) “The Humean Obstacle to Evidential Arguments from Suffering: On Avoiding the Evils of ‘Appearance’,” International Journal for Philosophy of Religion 16: 73–93.CrossRefGoogle Scholar
(1991) “The Use, Overuse, and Misuse of Significance Tests in Evolutionary Biology and Ecology,” Bulletin of the Ecological Society of America 32: 106–11.Google Scholar
(1985) Darwin's Metaphor: Nature's Place in Victorian Culture, Cambridge: Cambridge University Press.Google Scholar
(1926) “Why Do We Sometimes Get Nonsensical Relations Between Time Series? A Study of Sampling and the Nature of Time Series,” Journal of the Royal Statistical Society 89: 1–64.CrossRefGoogle Scholar
and (1965) “Evolutionary Divergence and Convergence in Proteins,” in and (eds), Evolving Genes and Proteins, New York: Academic Press, pp. 97–166.Google Scholar