At a private Toronto gathering to honour psychologist Ken Zucker last December, days after he was dismissed from his job at Toronto's Centre for Addiction and Mental Health, colleagues stood to give warm tributes. Some of them had come with prepared speeches, expressing shock over the closing of the Gender Identity Clinic, which Dr. Zucker had run for more than 30 years.

The decision was made under a cloud; Dr. Zucker was called in, given the news by an HR staffer and escorted out the door. Officials at CAMH, one of Canada's leading mental-health hospitals, apologized publicly that the clinic's therapy was not "in step with the latest thinking" and released an external review that was critical of the way the clinic treated children and youth struggling with issues relating to their gender identity. By closing the clinic, CAMH also walked away from a $1-million grant that had been awarded to Dr. Zucker and his team to study the effect of hormone blockers on teenagers. Those grants, in a country stingy with research dollars, are not easy to get.

In the transgender community, Dr. Zucker's dismissal was celebrated – he had long been controversial for research suggesting children should be steered away from becoming transgender adults.

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But under his leadership, the Gender Identity Clinic built an international research reputation and became the largest of its kind in Canada, treating more than 650 children. The sentiment among the 60 people gathered in the Toronto living room on that December evening was that its closing was a deplorable end to a fine career, wrought by political correctness and a misguided, but vocal, band of protesters with a flawed understanding of science.

When it came his turn to speak, Dr. Zucker, 65, was composed, according to several people at the gathering. "There's no crying in baseball," the avid Blue Jays fan reportedly said, in his deep, gruff voice. He was quoting Tom Hanks from the movie A League of Their Own, which, as it happens, portrays a women's team temporarily gender-swapping the role of male baseball players during the Second World War.

Dr. Zucker went on to share a story about his Jewish father, a graduate student of history in New York City in the 1950s, who had found himself out of work and blacklisted for his socialist views. Dr. Zucker's family left New York, settling into a Chicago suburb, where his father was an editor for the Encyclopedia Britannica and his mother was the director of a nursery school. In a 2013 interview with the left-leaning magazine The American Prospect, Dr. Zucker explained his parents' decision to "disappear from the scene" and take up a mainstream middle-class existence. "For the sake of their children," he is quoted saying, "they needed to become conformist."

It's a telling anecdote, an obvious comparison to Dr. Zucker's current status, banished from the clinic he helped build. An external report that contributed to his dismissal has since been revealed to contain errors, including a false allegation that Dr. Zucker insulted a patient. CAMH yanked it from the hospital's website and apologized for the mistake, but its decision stands.

In a statement to The Globe and Mail, CAMH said the review was not the only factor behind the closing and that "We are moving forward to engage with the community to determine the future of our service."

Dr. Zucker and his lawyer declined comment and have filed an intent to sue, according to CAMH.

In the meantime, many researchers and clinicians have rallied to his defence, signing a petition now more 500 names long. Others contend the closing of the clinic was the right call. The Globe and Mail spoke with some two dozens people – supporters, detractors, families and past patients – to understand the nature of the debate.

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The story Dr. Zucker told at the party is revealing on another level: The notion that conformity brings safety and clarity, and that difference is a risk, is a regular theme in his research. If one can find a way to live happily inside the boy-girl boxes that biology and culture have designed, wouldn't that be better? Dr. Zucker believed this – he advised parents, for instance, to limit how much their sons played with dolls and dresses, and to hold off when their daughters wanted to change their names in elementary school.

Dr. Zucker's approach made him a polarizing figure in an emotional debate about how to best treat children and teenagers not so easily pushed back into one box or the other. It put him at odds with a society increasingly willing to allow children to take the lead on how they define their gender. The other side of therapy says: Who cares, in the end, if a boy wants to wear a princess dress, or Martha wants to be called Martin?

"Let science do the talking," Dr. Zucker would say, when friends urged him to address his critics more directly.

But science isn't immune to human bias, as any student of history knows. It can dawdle too long on old questions and move too slowly to tackle the new ones. It treats the pursuit of knowledge like a marathon and, sometimes, society sprints ahead. This isn't a simple fight pitting fringe activists in one corner and scientists in the other. It is a legitimate debate about how to treat a complicated issue when science doesn't yet know what works best, when culture's view of gender identity is shifting quickly, and when behind all the politicking, infighting and duelling scientific papers, parents are just trying to raise their children to be happy.

Gender neutral toys

When Carol's eldest son was four years old, he would dream he was a girl and sob when he woke up as a boy. Around the same time, two ten-year-old kids threw him off the monkey bars when they saw him playing with a Barbie. He was still bleeding when his mom picked him up. Carol, a Toronto woman who works in education, says she and her husband had always honoured his preferences, for stereotypically "girl" movies, toys and clothes. They had three sons, and they were all different. But the bullying worried them, and school was proving tricky.

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So, in late 2007, they went to see Dr. Zucker. After lengthy family interviews and tests, he laid out his recommended treatment. "It was not offensive or cruel to us," recalls Carol, who detailed the family's experience to The Globe and Mail, but asked their identity be protected "It seemed pretty flexible." As Dr. Zucker explained it to Carol, his theory was to help kids value the "body they have." In that case, it meant helping her son see that "you may want to be a girl, but it's okay to be a boy." Carol says she and her husband had only one agenda for their son: "It was 100 per cent about his happiness."

For the next year, they visited the clinic twice a week, and then roughly once a week for nearly three years after that. Their son would have play therapy while Carol and her husband would meet with Dr. Zucker. At home, they slowly took away the dolls and pink toys, with their son choosing which ones. "He would be upset," Carol admits, "and ask for them the next day." But his favourites remained, and the missing toys were replaced with "gender neutral" options, such as Lego and toy animals. "Her son," Carol insists, "never touched a truck unless he tripped over it."

Over time, says Carol, he found common ground with his brothers. He was diagnosed as gifted and received help for attention deficit hyperactivity disorder, after the clinic's assessment diagnosed it. His school situation improved and he made friends. But always, Dr. Zucker cautioned them to resist too much accommodation from his teachers: "Don't let the school make him a poster child," Carol recalls him saying. "Don't let them parade him around for pink assemblies. This is his personal journey and we don't know where he is going to end up."

As Carol saw it, no direction was being prescribed – if her son still wanted to be a girl as he got older, Dr. Zucker said, hormone therapy was an option. "The work we did was centred around the whole idea that they are kind of young to make a decision, and if they are going to want to transition, we will know."

Carol previously spoke about her son's experience for a story on National Public Radio in 2008. The documentary was part of the case submitted to CAMH in January, 2015, by Rainbow Health Ontario, a province-wide organization that advocates on behalf of the LGBT community. Back then, only a few months into therapy, Carol detailed her son's distress, how he tried to hide his toys and soberly drew pictures of girls for hours. "I think he was really lost …" she told the radio program.

Rainbow Health's package to CAMH also included grim suicide rates among transgender teenagers, though not much from patients themselves. In a statement, the group said it had been getting complaints about the clinic from parents and clinicians working in other settings since the organization was created in 2008.

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Much of this material later made it into the external review that officials at CAMH ordered in February. But, by then, CAMH had already started making changes. In June, 2014, the centre stopped adding names to the clinic's waiting list – officially because it was getting too long. A month later, Dr. Zucker stepped down as chief psychologist at the hospital – a position he'd held for 13 years. In a statement to The Globe, CAMH explained the decision was "to make way for new leadership."

The review criticized the clinic on several fronts: the use of a two-way mirror during patient interviews; lengthy and intrusive assessments and tests; and for being slow in referring teenaged patients to hormone therapy. According to the reviewers, two Canadian child and adolescent psychiatrists, the clinic's focus on "understanding why" a patient is "the way they are," and attempting "to make a child comfortable in their biological sex" was not following the most up-to-date practices.

Critics argued that by directing children off the transgender path, the clinic's approach was a form of conversion therapy, an argument strongly denied by former staff. In interviews with The Globe and Mail, they point out that Dr. Zucker would tell parents that research showed their children were most likely to be gay, and that therapy was not working to change sexual orientation but to create a more "fluid" understanding of gender. As well, they say, teenaged patients at the clinic were regularly referred to hormone therapy, pointing to the clinic's own research showing that by adolescence, gender identity is usually fixed. The external review reached a non-conclusion: "We cannot state that the clinic does not practice reparative approaches (if outright therapies) with respect to influencing gender identity development."

To further complicate matters, the review contained a glaring error. It cited a specific report from one patient, saying that Dr. Zucker had told him to strip to his waist in front of other staff, and called him a "hairy little vermin." But the reviewers had not bothered to confirm this account; the patient has since said he made a mistake and CAMH has acknowledged it didn't happen.

The reviewers called for changes to the clinic's practice, not its outright closing. A month after receiving their findings, however, CAMH announced the clinic "would be winding down," and Dr. Zucker was no longer an employee.

Many supporters

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Dr. Zucker has many supporters – more than a dozen who talked to The Globe on the record extensively about his work and termination – who describe him as a top-notch scientist, a demanding but supportive mentor and a compassionate psychologist who answered phone calls from his patients late at night, and worked at the clinic six days a week. He has written more than a hundred papers, and has been editor of the academic journal Archives of Sexual Behaviour for 15 years. His friends describe his "encyclopedic knowledge" of research. At conferences, he would often sit in the back row, wearing his trademark ball cap and sunglasses, raising his hand at the end of presentations to make an illuminating – or challenging – comment.

His stature placed him centre stage of a shift happening in the treatment of transgender children. Two other approaches had gained ground: a "wait-and-see" approach developed by respected gender identity researchers in the Netherlands that doesn't try to direct cross-gender expression, but also doesn't encourage early transitioning in most cases; and the "affirming" approach, which prioritizes a child's right to define his or her own gender identity.

Dr. Zucker argued in published research and previous interviews that his therapy should be guided by the age of the patient and based on best evidence, particularly longitudinal studies that showed that gender identity is "malleable" in young children, and that the majority will outgrow their cross-gender identity by the time they are teenagers, and most often grow up to be gay adults. "If a five-year-old black kid came into the clinic and said he wanted to be white, would we endorse that?" Dr. Zucker said in 2008 interview in Atlantic Monthly. "I don't think so. What we want to do is say, 'What's going on with this kid that's making him feel that it would be better to be white?'"

In the case of their patients with "gender identity dysphoria," the clinic's staff might uncover mental health or family issues. Parents, as Dr. Zucker's research suggested, often contributed to the problem. But they also had a role in deciding the goal of the therapy – including, as a 2012 paper on the clinic's therapy noted, wanting to "reduce their child's desire to be of the other gender." This is a reasonable goal, Dr. Zucker would often point out in his research, given society's attitudes and the difficulty of hormone therapy and surgery. (On the other hand, one mom who first brought her child to the clinic, having already socially transitioned to a boy at age 5, described Dr. Zucker as "non-judgmental and supportive." )

As part of the therapy, children were directed to more gender-typical activities and toys, even haircuts. Sometimes, that meant taking a toy away: One mother interviewed for the story described burying a favourite Barbie in a shoebox in the backyard, while her son watched. But clinicians who worked at the Gender Identity Clinic in the past 10 years insist it was not all or nothing. "It was never do this, do that, play with this, play with that," says Devita Singh, a psychologist at the Children's Hospital of Western Ontario in London, Ont., and a former student of Dr. Zucker's. It wasn't that kids were told not to play with their friends, she says, but it might be suggested parents look for same-sex peers with similar interests. Patients would say, "If I like Barbies and I don't like rough-and-tumble play, than I must be a girl," Dr. Singh says. "Our approach was to increase flexibility" around how children viewed their gender.

Carol believes that Dr. Zucker's advice worked for her son, who is now a popular gay 13-year-old. He doesn't talk about wanting to be a girl any more, though Carol says they are careful not assume his path is set. "The biggest and most important thing I hold on to as a mother, was that when he was young, he would never talk about his future, never talk about himself as an adult." Now, she says, he is making plans. "This was a healthy outcome for us." She gives Dr. Zucker the credit: "I know the positive impact his therapy had on the culture of our family."

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Not every family feels the same way about this approach.

Years of pain

When Trish's son was seven years old, he declared that God had made a mistake and he was meant to be a girl. He had always liked to dress up like his sisters in princess costumes and not shown much interest in traditional boy activities. "God doesn't make mistakes," his mom told him. "You are perfect."

But his parents, who lived in Toronto, were worried about him, and after doing some research, they were referred to Dr. Zucker. They met with him four times, but never brought their son. They felt it wouldn't be a good match, but they were reassured by what Dr. Zucker was telling them: Their son would likely grow up to be gay. Trish, who asked that her family not be identified, says Dr. Zucker told them "it was important to encourage our child to feel more comfortable with the gender matching their biology." At the same time, Trish recalls, "we wanted our son to be a boy. So we jumped at any suggestion. … When we heard he is probably gay, you can't imagine the relief we felt."

By age 10, however, he was still struggling, so they returned to CAMH; this time, they didn't see Dr. Zucker at the clinic, but went to see another clinician about their son's anxiety. That clinician, they recall, consulted with Dr. Zucker. The advice they received was to normalize male behaviour and reduce female diversions. So they went home and removed the princess costumes and his father tried to interest him in karate.

Their son didn't say much – he didn't forcefully insist he was a girl – and his parents didn't talk to him about it. Based on how they'd interpreted the advice at CAMH, they were worried about putting the idea in his head. But Trish would continue to find clothes hidden away. At night, her son would pull his hair out while he slept. Trish and her husband knew this couldn't go on. At 13, when their son came out as gay, they thought, thankfully, that Dr. Zucker had been right.

A year later, their child told them what she had been feeling for years: She was transgender. This time, her parents took her to Toronto's Hospital for Sick Children, where the truth spilled out and she was given hormone blockers to slow puberty.

She finally told them: "Every birthday, every time I blew out the candles, I wished to be a girl." She admitted to hiding costumes and wigs so she wouldn't get in "trouble," and expressed anger that her parents had not asked her more about how she was feeling, and that they had waited so long to start the hormone treatment.

When at 15, she wanted to start taking estrogen, her mother sat her down. "I said, 'How can I give a 15-year-old, who is not responsible, who doesn't clean their room, who doesn't always tell the truth – how can we give you this power to change your body in an irreversible way for the rest of your life?"

She recalls her daughter answering back: "This is my entire existence. I can't live this way any more."

Her parents deeply regret that they didn't see this sooner; if they had gone to a psychologist who encouraged them to accept their daughter as she was and follow her lead, Trish believes they could have spared her years of pain.

Her husband agrees: "Every step we make that affirms her femininity, it just gets better and better."

This is what advocates of the "affirming" approach argue: Children who insist they don't fit a stereotypical gender role already know that they are being judged. While most may grow up to identify with a gender that matches their biological sex, getting the message, even indirectly, from the adults they trust, that their behaviour is wrong and needs fixing, only creates stress and despair along the way – and doesn't change the child's path.

Today, when Trish's daughter looks back on her childhood, she says: "I just feel angry. I feel like why didn't they ask me sooner, why didn't they protect me? But they are loving parents and they are really working on being supportive. They were just really confused for a lot of years."

Science doesn't know

The problem is this: Science simply doesn't know which method produces the best outcome – and scientists can't say which children who experiment with gender expression will grow up to be transgendered. Neuroscience is just starting to weigh in, but the nature-nurture debate about gender identity continues.

Still, plenty has changed since a young Ken Zucker first arrived at what was then the Clarke Institute as a curious grad student in 1975. One year later, Bruce Jenner – now trans icon Caitlyn Jenner – would be celebrated as a male hero for winning the decathlon at the Olympic Games in Montreal. And it was only two years before that homosexuality had been removed as a mental illness from the DSM, the diagnostic manual for psychiatrists. "Gender dysphoria," previously called "gender identity disorder," is expected to make it way out of the DSM as well. Indeed, one of the issues for CAMH has been whether there should even be a gender identity clinic at a mental-health hospital.

If, in the future, more children grow up to be transgender, will that be because a too-accommodating society pushed them in that direction? Or because a less-judging society allowed those already destined for that path the freedom to choose?