Darwinian Populations and Natural Selection. Oxford University Press, 2009.
Theory and Reality: An Introduction to the Philosophy of Science. Chicago University Press, 2003.
"On the Theoretical Role of 'Genetic Coding,'" Philosophy of Science, 2000.
"Goodman's Problem and Scientific Methodology," Journal of Philosophy, 2004.
"The Strategy of Model-Based Science," Biology and Philosophy, 2006.
"Dewey and the Subject-Matter of Science," in Shook and Kurtz (eds.) Dewey's Enduring Impact. 2010.