Nonsense on Stilts: How to Tell Science from Bunk (University of Chicago Press, 2010, ISBN 978-0-226-66786-7): This book presents a number of case studies on controversial topics in order to examine how science is conducted, how it is disseminated, how it is interpreted, and what it means to our society.
Making Sense of Evolution (with Jonathan Kaplan, University of Chicago Press, 2006, ISBN 978-0-226-66837-6): A philosophical examination of the fundamental concepts of evolutionary theory and practice.
Phenotypic Integration (Oxford University Press, 2003): A collection of technical essays on the evolution of complex biological organs.
Denying Evolution: Creationism, Scientism, and the Nature of Science. (Sinauer, 2002): This book covers the evolution-creation controversy, better science teaching, and why people have difficulties with critical thinking. ISBN 0-87893-659-9
Phenotypic Plasticity (Johns Hopkins University Press, 2001): A technical volume on research concerning nature-nurture questions.
Tales of the Rational (Freethought Press, 2000): A series of essays on atheism, straw-man arguments, creationism and the like.
Phenotypic Evolution (with Carl Schlichting, Sinauer, 1998): A technical volume on the current status and future prospects of evolutionary theory.