- Ever Since Darwin: Reflections in Natural History — 1977
- Ontogeny and Phylogeny — 1977
- The Panda's Thumb: More Reflections in Natural History — 1980
- The Mismeasure of Man — 1981
- Hen's Teeth and Horse's Toes: Further Reflections in Natural History — 1983
- The Flamingo's Smile: Reflections in Natural History — 1985
- An Urchin in the Storm: Essays About Books and Ideas — 1987
- Time's Arrow, Time's Cycle: Myth and Metaphor in the Discovery of Geological Time — 1987
- Wonderful Life: The Burgess Shale and the Nature of History — 1989
- Bully for Brontosaurus: Reflections in Natural History — 1991
- Finders, Keepers: Eight Collectors — 1992
- Eight Little Piggies: Reflections in Natural History — 1993
- Dinosaur in a Haystack: Reflections in Natural History — 1995
- Full House: The Spread of Excellence from Plato to Darwin — 1996
- Questioning the Millennium: A Rationalist's Guide to a Precisely Arbitrary Countdown — 1997
- Leonardo's Mountain of Clams and the Diet of Worms — 1998
- Rocks of Ages: Science and Religion in the Fullness of Life — 1999
- Crossing Over: Where Art and Science Meet — 2000
- The Lying Stones of Marrakech: Penultimate Reflections in Natural History — 2000
- I Have Landed: The End of a Beginning in Natural History — 2002
- The Structure of Evolutionary Theory — 2002
- The Hedgehog, the Fox, and the Magister's Pox: Mending the Gap Between Science and the Humanities — 2003
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