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Roughgarden received a Bachelor of Science in biology and a Bachelor of Arts in Philosophy from University of Rochester in 1968 and a Ph.D. in biology from Harvard University in 1971. She is the author of 5 books and over 120 articles.
Roughgarden has taught at Stanford University since 1972. She founded and directed the Earth Systems Program at Stanford and has received awards for service to undergraduate education. Roughgarden's current research links ecology with economic theory.
In addition to a seminal ecology textbook written with Paul R. Ehrlich, Roughgarden published a 2004 challenge to certain tenets of sexual selection titled Evolution's Rainbow (2004): this is not an attack on the central idea of natural selection; it is a proposed correction to Darwin's explanation of the mechanism of selection. Roughgarden rejects Darwin's sexual selection theory based on instances in which animals do not follow traditional sex roles where the male attempts to impress the female, and the female chooses her mate. This work also contains a literature survey on unexpected sexual behavior in many species of animals: homosexual behavior; several genders and two sexes in a species (in which a gender that never participates directly in reproduction still participates indirectly, thus affecting natural selection.) The book is noted for its outspoken negative attitude towards Darwin's theory of sexual selection.
An article published by her lab on these ideas received criticism in the pages of the journal Science. Forty scientists produced ten critical letters; one of the critical scientists said that the paper was "completely shoddy science and poor scholarship." However, Roughgarden, quoted as being "not altogether surprised" by the volume of dissent, argued that her team had replied to most of the criticisms.
Roughgarden is also a Christian who has written on the relationship between Christianity and science. In her book Evolution and Christian Faith: Reflections of an Evolutionary Biologist, she reinterprets scripture passages commonly used to oppose evolution in order to emphasize her belief that the Bible does not conflict with evolutionary biology. The book further relates Christianity and evolution by saying that all life is interconnected, as members of a faith community are connected. Roughgarden opposes the theories of creationism and intelligent design, but asserts her belief in God's involvement in evolution. She attended and was a speaker at the Beyond Belief symposium in November 2006.
- Roughgarden, Joan. Evolution and Christian Faith: Reflections of an Evolutionary Biologist. Hardcover ed. Washington, D.C.: Island Pr., 2006.
- Roughgarden, Joan. Evolution's Rainbow: Diversity, Gender and Sexuality in Nature and People. Paperback ed. Los Angeles: Univ. of California Pr., 2004.
- Roughgarden, Joan. Theory of Population Genetics and Evolutionary Ecology: an Introduction. 1st ed. Prentice Hall, 1998.
- Roughgarden, Joan. Primer of Ecological Theory. 1st ed. Prentice Hall, 1997.
- Roughgarden, Jonathan. Anolis Lizards of the Caribbean: Ecology, Evolution and Plate Tectonics. Hardcover ed. Oxford Univ. Pr., 1995.
- Roughgarden, Jonathan, May, Robert M., and Levin, Simon A. (eds.). Perspectives in Ecological Theory. Oxford Univ. Pr., 1995.
- Ehrlich, Paul R., and Roughgarden, Jonathan. Science of Ecology. Hardcover ed. Prentice Hall, 1987.
- Stonewall Book Award, 2005
- Joan Roughgarden profile: A plea for diversity. Retrieved on 2006-09-19.
- Sexual selection alternative slammed. Retrieved on 2007-05-15.
- First Congregational Church of Berkeley: Event Details. Retrieved on 2006-09-19.
- Roughgarden, Joan. Evolution and Christian Faith: Reflections of an Evolutionary Biologist. Washington D.C.: Island Press, 2006.