It was in that clinic, under Spack’s care, that Nicole and her family finally began to have hope for her future.

Founded in 2007 by endocrinologist Norman Spack and urologist David Diamond, the clinic - known as GeMS and modeled on a Dutch program - is the first pediatric academic program in the Western Hemisphere that evaluates and treats pubescent transgenders. A handful of other pediatric centers in the United States are developing similar programs, some started by former staffers at GeMS.

The Children’s Hospital Gender Management Services Clinic can, using hormone therapies, halt puberty in transgender children, blocking the development of secondary sexual characteristics - a beard, say, or breasts - that can make the eventual transition to the other gender more difficult, painful, and costly.

Until recently, there was little help for children in such situations. But now a groundbreaking clinic at Children’s Hospital in Boston - one of the few of its kind in the world - helps families deal with the issues, both emotional and medical, that arise from having a transgender child - one who doesn’t identify with the gender he or she was born into.

Wayne and Kelly Maines have struggled to know whether they are doing the right things for their children, especially for Wyatt, who now goes by the name Nicole. Was he merely expressing a softer side of his personality, or was he really what he kept saying: a girl in a boy’s body? Was he exhibiting early signs that he might be gay? Was it even possible, at such a young age, to determine what exactly was going on?

That early declaration marked, as much as any one moment could, the beginning of a journey that few have taken, one the Maineses themselves couldn’t have imagined until it was theirs. The process of remaking a family of identical twin boys into a family with one boy and one girl has been heartbreaking and harrowing and, in the end, inspiring - a lesson in the courage of a child, a child who led them, and in the transformational power of love.

“Dad, you might as well face it,’’ Wayne recalls Jonas saying. “You have a son and a daughter.’’

Once, when Wyatt appeared in a sequin shirt and his mother’s heels, his father said: “You don’t want to wear that.’’

Wyatt favored pink tutus and beads. At 4, he insisted on a Barbie birthday cake and had a thing for mermaids. On Halloween, Jonas was Buzz Lightyear. Wyatt wanted to be a princess; his mother compromised on a prince costume.

Jonas and Wyatt Maines were born identical twins, but from the start each had a distinct personality.

“Even when we did all the boy events to see if she would ‘conform,’ she would just put her shirt on her head as hair, strap on some heels and join in,’’ Kelly says. “It wasn’t really a matter of encouraging her to be a boy or a girl. That came about naturally.’’

To this day, she feels guilty about it. “I know she was totally confused and felt like she had done something wrong,’’ says Kelly, 50, who works in law enforcement.

Kelly whisked him off and made him put on pants. Though she and Wayne were accustomed to his girly antics, they were afraid of what others might think.

When the boys were 5, Kelly and Wayne threw a “get-to-know-me’’ party for classmates and parents. Wyatt appeared beaming at the top of the stairs in a princess gown, a gift from his grandmother.

His parents had no idea what was going on. They had barely heard the term “transgender.’’ Baffled, they tried to deflect Wyatt’s girlish impulses by buying him action figures like his brother’s and steering him toward Cub Scouts, soccer, and baseball.

When Wyatt was 4, he asked his mother: “When do I get to be a girl?’’ He told his father that he hated his penis and asked when he could be rid of it. Both father and son cried. When first grade started, Wyatt carried a pink backpack and a Kim Possible lunchbox.

They had no preparation for what would come next.

When Wyatt and Jonas were born, their father was thrilled. Wayne looked forward to the day when he could hunt deer with his boys in the Maine woods. The family lived in Orono, near the University of Maine campus, where Wayne is the director of safety and environmental management.

“I have always known I was a girl,’’ says Nicole, now 14. “I think what I’m aiming for is to undergo surgery to get a physical female body that matches up to my image of myself.’’

It has been a hard road, but nothing that compares with the physical transformation of Wyatt into Nicole.

They have good reason for caution. Their journey has included a lawsuit to protect their daughter’s rights, and a battle against bullying and insensitivity that led them to move to a new place and new schools.

“We told our kids you can’t create change if you don’t get involved,’’ says Wayne, 53, sitting in the living room of their comfortable home in a southern Maine community they do not want identified.

The Maineses decided to tell their story, they say, in order to help fight the deep stigma against transgender youth, and to ease the path for other such children who, without help, often suffer from depression, anxiety, and isolation.

To Kelly, it seemed the next logical step. Family discussions merely centered around what the name would be. In the end, Nicole chose it. “I believed in Nicole,’’ her mother says. “She always knew who she was.’’

In fourth grade, Wyatt started using “Nicole’’ as a name, and many classmates were calling him “Nikki.’’ The next year, the family went to court and had the name legally changed to Nicole.

Emma Peterson of Orono, a close friend from the elementary years at the Asa Adams School, recalls playing dolls with Nicole’s giant dollhouse, and the two of them putting on makeup. “Before Nikki started growing her hair out, she looked exactly like Jonas,’’ Emma says.

In elementary school, Wyatt told classmates that he was a “girl-boy.’’ In the fourth grade, he grew his hair longer and started talking about a name change. That same year, he drew a self-portrait as a girl, and in a class essay, wrote: “Wyatt needs hair accessories, clothes, shoes . . . likes to wear bikinis, high heels, mini-skirts.’’

“He told us everything,’’ Wayne says, recalling that first meeting. “I didn’t understand it all, but I saw the weight lift off Kelly’s shoulders and a smile in Nicole’s eyes. That was it for me. There were tons of challenges for us after that, but I knew my daughter was going to be OK, medically.’’

When the twins were in the first grade, their parents found a therapist for Wyatt, who was starting to act out. In the third grade, before the GeMS Clinic was even open, Kelly heard about Dr. Spack and made an appointment with him.

Their elderly pediatrician, nearing retirement, did not want to discuss the matter with them. Finally, Kelly picked another pediatrician out of the phone book. “I told her how it was, and it turned out that she understood and was very supportive.’’

Even the family Christmas card became a challenge. They would write about Jonas’s affinity for sports and Wyatt’s “flair for the dramatic.’’

But as they grew older, his concern grew. “I feared the unknown,’’ he says.

“I felt it had nothing to do with how they would grow up,’’ he says.

During those early years, while Kelly was doing her research, Wayne was hoping that this was no big deal, that this was a stage Wyatt just had to go through.

After Wyatt began to openly object to being a boy, his mother started doing research on transgender children. There was little out there; it seemed they would have to find their way largely on their own.

“She really is a girl,’’ Kelly says, “a girl born with a birth defect. That’s how she looks at it.’’

Kelly and Wayne didn’t look at it as a choice their child was making.

Nicole and her parents filed a complaint with the Maine Humans Right Commission over her right to use the girls bathroom. The commission found that she had been discriminated against and, along with the Maines family, filed a lawsuit against the Orono School District. The suit is pending in Penobscot County Superior Court, and the Maines family is represented by lawyers from the Gay & Lesbian Advocates & Defenders (GLAD) in Boston and by Jodi Nofsinger, who serves on the Maine ACLU board.

“He’s taken on a lot,’’ Wayne says. “Middle school boys and sexuality, you know . . . boys can get picked on.’’

It was a burden that Jonas shouldered as well. The same boy who in fifth grade objected to her using the girls bathroom made the mistake of saying to Jonas in sixth grade that “freaking gay people’’ shouldn’t be allowed in the school. Jonas jumped on him and a scuffle ensued.

“Separate but equal does not work,’’ she says.

To protect her from bullying at school, Nicole was assigned an adult to watch her at all times between classes, following her to the cafeteria, to the bathroom. She found it intrusive and stressful. It made her feel like even more of an outsider.

According to a 2009 study by the Gay, Lesbian and Straight Education Network, 90 percent of transgender youth report being verbally harassed and more than half physically harassed. Two-thirds of them said they felt unsafe in school.

“It was like a switch had been turned on, saying it is now OK to question Nicole’s choice to be transgender and it was OK to pursue behavior that was not OK before,’’ Wayne says. “Every day she was reminded that she was different, and the other kids picked up on it.’’

But one day a boy called her a “faggot,’’ objected to her using the girls’ bathroom, and reported the matter to his grandfather, who is his legal guardian. The grandfather complained to the Orono School Committee, with the Christian Civic League of Maine backing him. The superintendent of schools then decided Nicole should use a staff bathroom.

“They said, ‘It was about time!’ ’’ Nicole says. She was elected vice president of her class and excelled academically.

When fifth grade started, Wyatt was gone. Nicole showed up for school, sometimes wearing a dress and sporting shoulder-length hair. She began using the girls’ bathroom. Nikki’s friends didn’t have a problem with the transformation; there were playdates and sleepovers.

At first, though, he couldn’t bring himself to use the new name. An Air Force veteran and former Republican, he realizes now he was grieving the loss of a son. “But once you get past that, I realize I never had a son,’’ he says.

Wayne was nervous. Could he call his son Nicole? As usual, he relied on his wife’s instincts. “I have to tell you, Kelly’s the leader in our family,’’ he says. “Both she and Nicole are extremely strong-willed, and I went with the flow.’’

He also questions the role the parents have played; have they simply followed the child’s lead? “Say a 5-year-old says repeatedly that he wants to be a girl,’’ Zucker says. “The parents deduce this must mean the child is transgender, so they socially transition him to living in the other gender.’’

“One controversy is, how low does one go in starting blockers?’’ Zucker says. “Should you start at 11? At 10? What if someone starts their period at 9?’’ Nicole started on the blockers at age 11.

Though GeMS treatment is now considered the standard of care by mainstream medical groups, some have their doubts. Dr. Kenneth Zucker, a psychologist and head of the gender-identity service at the Center for Addiction and Mental Health in Toronto, says he worries about putting youngsters on puberty blockers, drugs that suppress the release of testosterone in boys and estrogen in girls.

Not everyone agrees that they should, of course, and Spack has heard the arguments: Man should not interfere with what God has wrought. Early adolescents are too young for such huge decisions, much less life-altering treatment.

He adds: “We can do wonders if we can get them early.’’

“Most of us look pretty similar until we hit puberty,’’ he says. “I bet I could go to any fourth or fifth-grade class, cut the hair of the boys, put earrings on various kids, change their clothing, and we could send all those kids off to the opposite-gender bathrooms and nobody would say boo.’’

He believes it is crucial to intervene with such children before adolescent changes begin in earnest.

Spack’s experience runs deep; before the clinic was established, he had long worked with transgender youth, as well as with adults. “The most striking thing about these kids was the fact that they were just normal young people who had this incredibly unusual and problematic situation,’’ says Spack, 68.

But the more he watched his child struggle, the better he felt about going to Spack. And once he got there, he says, it was a huge relief. “Not only does he know what he’s doing, he’s extremely comforting. He’s got to deal with a ton of dads who are just freaking out, and he made me feel good.’’

“I wasn’t always on board,’’ Wayne says. “Kelly and I were not on the same page. My question was, what is this doctor doing? It scared me. I was grieving. I was losing my son.’’

Since that first visit to Spack when Nicole was 9, her parents discussed putting her into the GeMS Clinic when the right time came. They were glad there was time to adjust to the idea. “Baby steps,’’ Kelly calls their path toward treatment.

“What Nicole and Jonas both went through in school was unconscionable,’’ says Jennifer Levi, one of the GLAD lawyers on the case. “Their one huge stroke of luck was having Kelly and Wayne as parents.’’

There is no definitive answer to the question of what causes gender identity disorder, though studies suggest a genetic contribution. “It’s still a very open question,’’ Zucker says. And how could it affect just one of two identical twins? “There can be genetic changes during fetal development that maybe hit one twin but not the other.’’

“In puberty,’’’ Spack says, “when your body starts making a statement, you either have to accept it or reject it.’’

It is the next big step - taking sex hormones of the opposite gender - that creates permanent changes, such as breasts and broadened hips, that cannot be hormonally reversed.

Since the 1970s, the blockers have been used for the rare condition of precocious puberty, when children as young as 3 can hit puberty. They are kept on the blockers until they are of appropriate age. “The drugs have a great track record; we already know that these kids do fine,’’ says Spack. “There are no ill consequences.’’

The effects of the blockers - an injection given monthly to prevent the gonads from releasing the unwanted hormones - are reversible; patients can stop taking them and go through puberty as their biological sex. This is critical, Spack says, because a “very significant number of children who exhibit cross-gender behavior’’ before puberty “do not end up being transgender.’’

Nicole and Jonas are the first set of identical twins the program has seen, and they have provided critical comparative data, Spack says.

Each patient must have been in therapy with someone familiar with transgender issues and who writes a letter recommending the treatment. The child’s family also must undergo extensive psychological testing before and during treatment. And the patient must be in the early stage of puberty, before bodily changes are noticeable.

About a third of the patients have undergone puberty suppression.

The clinic, which includes geneticists, social workers, psychiatrists, psychologists, and nurses, has so far treated 95 patients for disorders that range from babies born with ambiguous genitalia to cases where normal sexual development does not occur.

As for the criticisms about “playing God,’’ Spack quotes from the Old Testament: “Leviticus says, ‘If thy neighbor is bleeding by the side of the road, you shall not stand idly by the blood of thy neighbor.’ It’s a mandate. I think these kids have been bleeding.’’

Spack and others, however, say the issue is a medical one and that early intervention makes sense. “We’re talking about a population that has the highest rate of suicide attempts in the world, and it’s strongly linked to nontreatment, especially if they are rejected within their family for being who they think they are,’’ says Spack, who adds that nearly a quarter of his patients admitted to “serious self-harm’’ before coming to him.

The male hormone suppressors have done their job, and the next step is to add female hormones so that Nicole will undergo puberty as a girl and develop as a woman, with breasts and curvy hips. She is due to see Spack in January, and a date may then be set for adding estrogen, which she will take every day for the rest of her life. Though she will have a higher risk of breast cancer than if she were a male, she will have a lower risk of prostate cancer, Spack says. The treatment will leave her infertile.

She recently started telling some of her new friends her story. One girl replied: “Does this mean you’re going to start wearing boys’ clothes to school?’’

“It made me a lot more comfortable,’’ Nicole says. “I thought, this is OK. I can do this.’’

This fall the twins entered high school, transferring to a smaller, private school known for open-mindedness. Before they arrived, the school changed its bathrooms to unisex. And before classes started, the family met with members of the school’s Gay Straight Alliance - “so she’d have older kids watching her back,’’ says Wayne. After the meeting, the group changed its name to include transgender; it is now the Gay Straight Transgender Alliance.

For two years, in seventh and eighth grade, Nicole went “stealth,’’ as she calls it: passing as a girl. She did not tell anyone that she was biologically male. Though she made friends at school, she never brought them to the house. After that hard last year in Orono, the family was afraid to come out.

After that episode, Kelly and Wayne decided a new start would be good for the family. The summer after the sixth grade, they moved to a larger, more diverse community in southern Maine, and the twins enrolled in public school. Wayne still works at UMaine and stays in Orono during the week, spending weekends with his family.

A difficult family conversation followed. Jonas and Wayne went on the trip. Nicole stayed home.

Wayne thought he had a good relationship with the club leader. But then the man informed him that Nicole would not be allowed to sleep in the tent with the girls - the same girls who had slept over her house several times. She and her father could have a separate tent.

In the sixth grade, the twins joined the school’s Outing Club. All year they attended meetings to prepare for the crowning event: a whitewater rafting trip. Wayne went to several meetings, too, so he could serve as a chaperone.

After the family’s lawsuit against the Orono schools was publicized, the atmosphere in town changed. When they went to the movies, people pointed and whispered. There were fewer party invitations, fewer sleepovers.

In some respects, Jonas has had as tough a time as Nicole. For one thing, there’s the personality difference: Nicole is the dominant twin, talkative and tough, while Jonas is cautious and reserved.

“As a conventional dad, hunter, and former Republican, it took me longer to understand that I never had two sons,’’ he told them. “My children taught me who Nicole is and who she needed to be.’’

Surrounded by Kelly and the kids, Wayne told the audience that he and his wife have had top-notch guides as they confronted the unknown.

In October, the family was honored for its activism in helping defeat the transgender bathroom bill. The Maineses received the Roger Baldwin Award, named for a founder of the American Civil Liberties Union, from the Maine chapter of the ACLU.

“She knows how to work a room,’’ her father says proudly. “She even convinced a cosponsor to vote the other way.’’

Last spring Wayne and Nicole roamed the halls of the State House, button-holing legislators and testifying against the bill. “I’d be in more danger if I went into the boys bathroom,’’ Nicole told the lawmakers, who ultimately rejected the bill.

Last winter, Maine state representative Kenneth Fredette, a Republican from Penobscot County, sponsored a bill that would have repealed protections for transgender people in public restrooms, instead allowing schools and businesses to adopt their own policies. The bill was a response to the Maines’ 2009 lawsuit against the Orono School District.

“I remind her that she needs to always be aware of her surroundings, to stay close to friends and her brother if she feels uncomfortable, and to call me anytime she feels threatened,’’ he said.

Wayne spoke to the crowd, telling them that as much as Nicole is loved at home, her family cannot always protect her.

But as well as things are going, the Maines family still worries about Nicole’s safety. Last year Wayne and Nicole attended Transgender Day of Remembrance in Maine, which honors those who have been killed in hate crimes.

An endocrinologist in Maine now administers the blockers Nicole needs, but Spack still sees her in Boston every four to six months. The Maines family has grown close to him and others in the clinic. “I love going to see him,’’ says Wayne, who has thanked Spack for “saving my daughter’s life.’’ The Maines family declined to talk about the cost of the treatment but said insurance has covered much of it.

“In my experience, the patients just blossom physically and mentally when they get the hormones of the gender they affirm,’’ Spack says. “It’s quite amazing. I feel good about Nicole and who she is and where she’s going.’’

But before the estrogen is administered, the GeMS clinic will reevaluate Nicole to make sure that she still identifies as a female and wants to continue.

“If this had been Jonas, I would have had to home school him,’’ his mother says.

The twins have always been close. During an interview, Nicole sits next to her brother on the couch and occasionally lays her head on his shoulder. At one point, when Jonas goes silent as the twins talk of their lives, she whispers words of encouragement into his ear.

But the next minute, like typical teenage siblings, they’re teasing and tussling. Jonas displays a faint scar on his arm where Nicole jabbed him with a pencil. Both have black belts in tae kwon do, which they started at age 5.

They often hang out in Jonas’s spacious basement room, where they watch TV and play video games.

“I love having a sister,’’ says Jonas, who acknowledges being protective of her. “We have a very strong relationship.’’

Nicole calls Jonas her closest friend.

“I would say my brother got lucky with me. Because we grew up with only boy neighbors, I developed a liking to shoot-’em-up and military video games,’’ she says. “I could have come out a lot girlier.’’

At 14, Jonas is handsome, Nicole pretty. Jonas is midway through puberty. His shoulders have broadened, his voice has deepened, and there’s a shadow on his upper lip. He’s 5 feet 6 and weighs 115 pounds, with a size 11 shoe.

Nicole is petite: 5 feet 1, 100 pounds. She’s got long, dark hair and she wears girls’ size 14-16. Her closet contains nice shirts and jeans, party dresses, glittery shoes, and a pair of footy pajamas.

“The thought of being a boy makes me cringe,’’ she says. “I just couldn’t do it.’’

Excited, worried about surgery

Nicole’s final step on her journey to womanhood would be gender reassignment surgery. Doctors generally won’t perform it until the age of consent, which is 18. No hospitals in New England perform such surgery, says Spack. The nearest that do are in Montreal and Philadelphia.

Nicole says she’s excited about the idea of surgery, though a bit worried about the results - “and maybe the pain, too.’’

While she’s interested in boys, she has expressed fear that “nobody is ever going to love me.’’

She has gone on weekend retreats sponsored by the Trans Youth Equality Foundation and to summer camp for transgender children, where she developed her first crush on a boy.

Over the years, the family has become close to several adult transsexuals, and Nicole has seen that some have found happy marriages. “She says she does feel better about it,’’ Kelly says, “but still wonders if she ever met a boy who falls for her, and then found out that she was trans, if he would still like her, or say awful things as he skedaddled out the door.’’

Nicole knows there is a long road ahead, but she feels she’s on the right path.

“Obviously my life is not going to be as easy as being gender-conforming, but there are perks like being able to get out there and do things that will benefit the [transgender] community,’’ she says. “I think everything’s going to turn out pretty well for me.’’

For now, at least, life feels more normal to the Maines family.

Wayne recently spoke at GLAD’s Spirit of Justice dinner in Boston and was introduced by Nicole. She kept her composure in her brief remarks and thanked GLAD for giving them a rare chance to “safely speak out.’’

Wayne choked up when thanking the group for its support. He recounted young Wyatt asking him, sadly, “Daddy, why can’t boys wear dresses?’’ Wayne hated to tell his son that society wouldn’t accept that.

But today, when Nicole asks her father what he thinks of a certain dress she’s wearing, his typical response, he told the audience, is: “That dress is too short. Go change your clothes.’’

In conversation later, Wayne tells another story of how things have changed, for good and forever. He and the twins were getting out of the car recently, and he grabbed their hands to walk with them.

Jonas, being a teenage boy, shook his father off, while Nicole was happy to walk hand-in-hand, swinging arms.

“She’ll do that the rest of her life,’’ Wayne says with a wide grin. “It was an epiphany for me.’’

Bella English can be reached at english@globe.com.

© Copyright 2011 Globe Newspaper Company.