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At 50, Roy Berkowitz-Shelton was a caring, well-respected family doctor with a flourishing practice in Massachusetts. He was bald and had a beard. He and his wife, Allison, had a long and loving marriage and two nearly grown kids.

There was just one problem with his life. Ever since he could remember, Roy had been attracted to women's makeup and clothes. One day, on a trip to the grocery store, he blurted out: "Allison, I feel I'm a woman."

Today, 2½ years later, he has fulfilled his dream. He is now Dr. Deborah Bershel. Deborah dresses in dark skirts and teal tops and owns a dozen pairs of high heels. She loves to shop. Thanks to female hormones and facial surgery, which smoothed her forehead, reshaped her nose, softened her jaw line and shaved her Adam's apple, she resembles someone's kindly aunt. Now, she wants to take the final step: surgery that would amputate her penis and create a vagina.

"I feel like a whole person now," she says.

Deborah's journey was sympathetically recounted this month by the Boston Globe magazine. It is not so unusual any more. Transgendered people now share equal billing with gays, lesbians and bisexuals in the ever-expanding panoply of sexual minorities. The standard explanation is that they are the victims of a biological mistake, born into a body of the wrong sex. The vast majority of transgendered people are biological men who wish to become women.

In liberal Massachusetts, Deborah encountered very little social disapproval of her sex change. On the contrary. Her patients and co-workers have been immensely supportive. Her Conservative Jewish synagogue never wavered. Most people in our tolerant, open society believe people should be able to follow their own path to happiness and self-fulfilment. If anything, they think Deborah is courageous. "It takes a lot of soul-searching to sacrifice the things you have to be true to yourself," said Denise Leclair, executive director of the International Foundation for Gender Education.

But not everything has been smooth. Deborah was certain she would be able to maintain her marriage. She believed that after her transition, she and her family would begin a deeper and more honest life together. And indeed, her wife, Allison, tried to keep an open mind. She went with Roy to a cross-dressing convention. She took care of Deborah after her facial surgery. They went to marriage counselling together. In the end, it didn't work. Allison told Deborah there was a reason she had married a man, and asked her to move out.

Deborah's teenaged son is handling the adjustment well. But her 20 year-old daughter has become estranged and refuses to speak to her. Deborah's father seems resigned. "I'm heartbroken," he says, "but he's my son."

Deborah says she wasn't suicidal as a man - just restless and unfulfilled. She doesn't seem to have much remorse or guilt for the destruction of her family or the pain she's caused. She's exploring the singles scene and has posted her profile on a women-to-women dating site.

In the gay-rights movement and the academic world, nothing - but nothing - is more explosive than the science and politics of gender. And that includes the subject of transgendered women.

In the prevailing narrative, people like Roy are essentially women trapped in the bodies of men. But there is another theory, one that's deeply unpopular, to say the least. It holds that they are really men with an unusual psychological quirk: a male deviation called autogynephilia.

This theory is largely based on research studies conducted at Toronto's Clarke Institute during the 1980s and 90s. It found that some men who seek sex changes are driven mainly by an intense erotic fascination with dressing up as women. The researchers found that as they get older, these men (predominantly heterosexual) become increasingly eager to add more realism to their presentations through surgery. As women, they rhapsodize about being able to express their natural inclinations for shopping, makeup, domesticity and gentleness. But in other ways, they aren't womanly at all. They aren't interested in babies and children. And, like Deborah, they still find women sexually attractive. After their transition, they see themselves as lesbians.

One expert who supports this theory is psychologist J. Michael Bailey of Northwestern University. His 2003 book, The Man Who Would Be Queen, explains the biology of sexual orientation and gender. It has been called a compelling explanation of the science. But he has been bitterly denounced for his treatment of transgender issues. One prominent academic, a transgendered woman, compared his views to Nazi propaganda. Another well-known transgendered academic, Deirdre McCloskey, called his work "false, unscientific and politically damaging." He has been accused of gross violations of scientific standards, and his research associates were warned by others in the field to keep their distance. He told The New York Times that the two years after he published his book were the hardest of his life.

Some people believe the crusade against Dr. Bailey is political correctness run amok. Alice Dreger, an ethics scholar brought in to conduct a lengthy investigation, exonerated him of wrongdoing and said, "What happened to Bailey is important, because the harassment was so extraordinarily bad and because it could happen to any researcher in the field."

It's obvious why this theory is so inflammatory. It challenges the foundation of transgender identity politics. It implies that people like Deborah need therapy, not surgery. Paul McHugh, a psychiatrist at Johns Hopkins University, goes further. He believes that all the social, medical and psychiatric resources employed in turning men into women are "a misdirection of psychiatry." He is even more reviled than Dr. Bailey.

Deborah's transition will probably turn out okay, for her if not her family. When the Clarke Institute patients were tracked down a few years after their sex-change surgery, most said they were happy they'd done it. But their hopes of becoming more emotionally fulfilled were largely unrealized. They had much the same problems with relationships, work and emotions as before.

Partly at the urging of Dr. McHugh, Johns Hopkins no longer performs sex reassignment surgery. "I concluded," he wrote, "that to provide a surgical alteration to the body of these unfortunate people was to collaborate with a mental disorder rather than to treat it."

But Deborah isn't looking back. After a year of living as a woman, she's met a woman she likes, a lesbian. And she's working on her walk, to make it more feminine.