The last book as Jonathan was Primer of Ecological Theory, 1997. In 1998, at the age of 52, Jonathan came out as transsexual.
"It became clear to me that I wasn't ever going to figure out how to do the guy thing. Imagine as a woman if you'd set out to be a man, to learn how to live as a man. Could you do it? I couldn't. It's like asking a fish to fly."She took a sabbatical and returned as Joan. She soon noticed how she was now much more frequently interrupted, ignored and condescended to by men. At a meeting of the Ecological Society of America in Minneapolis a prominent expert jumped up on the stage after her talk and started shouting at her. Once every month or two, she said, ''I will have some man shout at me, try to physically coerce me into stopping …When I was doing the marine ecology work, they did not try to physically intimidate me and say, 'You have not read all the literature.' “
Undeterred by this, she ran for San Francisco's District 6 Supervisor in 2000.
In 2003 gay neurobiologist Simon LeVay had a temporary position at Stanford, and invited both Roughgarden and North American Man Boy Love Association to address the same class under the title 'minority sexualities'. She declined in that "being transgendered was not an expression of sexuality". He rescheduled her but spoke for 45 minutes giving what she could only regard as "an appallingly incorrect account of presumed biological bases to gender differences".
Roughgarden was one of many trans academics who was appalled by Michael Bailey's The Man who Would be Queen, 2003, and wrote a critique of it:
"From a transgender perspective, Bailey's claim that all transgendered women match one of these two profiles is clearly counterfactual. Many transgendered women come out late in life and yet are sexually oriented to men, many come out early in life and yet are oriented to women, many who are oriented to women are attractive nonetheless, many have changed direction of sexual orientation when they transitioned, many are bisexual, and many are not sexually active. Transgendered women also encompass heterogeneity in occupation, presentation, temperament, sexual history, and ethnicity. Furthermore, transgendered people are not as fixated on sex as Bailey evidently is. The need to locate in the social and occupational space of one's gender identity, to live as a woman, is a stronger motivation for many transgendered women than is attaining sexual pleasure. … Bailey has no data, none at all. He offers no surveys, no data tables, no statistics, nothing. He doesn't give the sample size for the 'study' he refers to occasionally. No references are offered to primary literature either. Six transgendered people are mentioned by name (pseudonym). Bailey did not take detailed and rigorous notes when interviewing these subjects, and relies on his recollection of their meetings. This sample is highly non-representative because the women he interviewed he met while 'cruising' (p. 141) in 'the Baton, Chicago's premier female impersonator club,' (p. 186) leading to an occupational and socio-economic bias."Roughgarden's next book was to be published by Princeton University Press, but she found that they were using LeVay as a reviewer and that he wanted the critical material about the search for a gay gene removed and in fact that he wanted "to reduce my book into a David-Attenborough-like nature book about gay animals, related by a transgendered woman". She moved her book to the University of California Press where it came out in 2004 as Evolution’s Rainbow. It argues for a correction to Darwin’s theory of sexual selection taking into account the varieties of gay and trans behavior found in most species. It also puts transgender behavior in the context of traditional alternate gender roles in traditional societies, and evaluates the estimated statistics. It argues for social selection rather than the Darwinian sexual selection oriented on the selfish gene, competition and deception. She further developed this approach in The Genial Gene, 2009.
Roughgarden is also a Christian and has written on the relationship between Christianity and evolution.
She retired Emerita in 2011, and moved to Hawai'i where she became an adjunct professor at the Hawai'i Institute of Marine Biology.
- Carol Kaesuk Yoon. “A Theorist With Personal Experience of the Divide Between the Sexes” The New York Times, October 17, 2000. www.nytimes.com/2000/10/17/science/17ROUG.html.
- Joan Roughgarden. "Making connections re psychologist Simon LeVay". Email to Lynn Conway, 11 Jul 2003. http://ai.eecs.umich.edu/people/conway/TS/Bailey/Joan-re-LeVay.html.
- Joan Roughgarden. The Bailey Affair: Psychology Perverted. February 11, 2004. Online at: http://ai.eecs.umich.edu/people/conway/TS/Reviews/Psychology%20Perverted%20-%20by%20Joan%20Roughgarden.htm.
- Joan Roughgarden, Evolution's Rainbow: Diversity, Gender, and Sexuality in Nature and People. University of California Press, 2004. Awarded 2005 Stonewall Prize for nonfiction from American Library Association. Chapter 1 online at www.ucpress.edu/books/pages/10139/10139.ch07.html
- Steven Kotler. “Oh So Natural: Sexual selection, the Good Book and why gay is good”. LA Weekly: Art + Books. April 15. 2004.
- Antony Thomas (dir & scr). Middle Sexes: Redefining He and She. With Louis Gooren, Anne Fausto-Sterling, Milton Diamond, Alice Dreger, Joan Roughgarden, Calpernia Addams, Andrea James. USA/UK 74 mins 2005.
- Joan Roughgarden, Evolution and Christian Faith: Reflections of an Evolutionary Biologist. Island Press. 2006.
- Joan Roughgarden. The Genial Gene: Deconstructing Darwinian Selfishness. Berkeley: University of California Press, 2009.
- Shankar Vedantam. “How the sex bias prevails”. The Age, May 15, 2010.
Joan's website used to be http://joandistrict6.com. However that is now a site in Japanese.
The history/anthropology chapters of Evolution's Rainbow are perhaps not as good as the biology chapters. For example the section on ancient Greek/Roman sexuality is based on Kenneth Dover alone. This is a very large topic and Dover's major virtue is merely his early date.
For some reason LeVay is not mentioned in Evolution’s Rainbow.
In WorldCat Jonathan's books are listed as by Joan, but in Amazon they are treated as two different people.
Ben Barres, a physicist, also at Stanford, transitioned in the other direction at around the same time. He commented on how he was interrupted, ignored and condescended to by men less often. The contrast was explored in several newspaper articles.