Fifteen years ago, a strange-looking child suffering from severe physical maladies and acute retardation was brought into the office of Dr. Theodore Tarby.

The pediatric neurologist regularly deals with a wide range of serious childhood diseases as a doctor with the state-funded Children's Rehabilitative Services in Phoenix. Tarby says he quickly realized he was dealing with a very unusual condition that he could not diagnose.

He prepared urine samples and sent them to the University of Colorado Science Center's Dr. Steve Goodman, a professor of pediatrics who runs a laboratory that detects rare genetic diseases.

Goodman soon made a startling discovery: Tarby's young patient was afflicted with an extremely rare disease called fumarase deficiency.

"I had never seen a patient with it," Tarby says. "Right away I asked the parents if there were any other children with the same problem."

The parents said their daughter had cerebral palsy. Tarby asked them to bring the girl to him for an examination.

"As soon as I saw her, I knew she had the same thing as her brother," Tarby says.

The fact that fumarase deficiency had shown up in one child was startling enough -- there had only been a handful of cases reported worldwide. But now that it was appearing in two children in the same family was an indication it was being spread by a gene that was getting passed to the children by their parents.

Tarby and a team of doctors from Barrow Neurological Institute at St. Joseph's Hospital in Phoenix and the University of Arizona College of Medicine in Tucson began researching the disease and soon discovered that fumarase deficiency was occurring in at least two other families living in the same isolated community that practiced an unusual custom.

Nearly everyone in Colorado City, Arizona, and the adjacent town of Hildale, Utah, was a member of a fundamentalist Mormon sect that practices polygamy and had long encouraged multiple marriages between close relatives.

By the late 1990s, Tarby and his team had discovered fumarase deficiency was occurring in the greatest concentration in the world among the fundamentalist Mormon polygamists of northern Arizona and southern Utah.

Of even greater concern was the fact that the recessive gene that triggers the disease was rapidly spreading to thousands of individuals living in the community because of decades of inbreeding.

Fast-forward to the present: About half of the 8,000 people living in the towns are blood relatives of two of the founding families that settled in the 1930s on the desolate high desert plateau against the base of the Vermillion Cliffs.

Religious leaders control all marriages in the community, and many of these relatives have married or likely will marry in the future. Some of these marriages will include parents who both are carriers of the fumarase deficiency gene, making it certain that more children will be afflicted with the disease.

"We have and will have a continual output of children with this condition," Tarby says.

In this isolated religious society north of the Grand Canyon, few secrets have been more closely guarded than the presence of fumarase deficiency. Fundamentalist Church of Jesus Christ of Latter-day Saints elders, who control the community, have labored to keep the public from finding out why the disorder is manifesting. Many members of the fundamentalist community don't even know it's occurring.

The state of Arizona is contributing to the secrecy. The state Department of Health Services and the Department of Economic Security have been quietly providing services to assist the children and families of fumarase victims for more than 15 years. Both DHS and DES officials refused repeated requests from New Times to document the type and cost of services the state is providing to treat fumarase deficiency. The agencies claim that federal health laws prohibit them from releasing records or allowing their authorities to comment on the situation.

Doctors and family members interviewed by New Times say up to 20 children from families in the polygamist community are currently afflicted with the condition that requires full-time attention from caregivers. Victims suffer a range of symptoms, including severe epileptic seizures, inability to walk or even sit upright, severe speech impediments, failure to grow at a normal rate, and tragic physical deformities.

"They are in terrible shape," says Dr. Kirk A. Aleck, director of the Pediatric Neurogenetics Center at St. Joseph's Hospital. Aleck is a geneticist who participated along with Tarby and others in the groundbreaking study of several polygamous families with fumarase deficiency in the late 1990s.

There is no cure for the disease, which impedes the body's ability to process food at the cellular level.

"We can only treat the complications of the disorder," Aleck says. Once a baby is born with the condition, Aleck says, "You really can't treat the underlying disorder."

There is one documented case of a child dying from the malady since medical experts began studying it, but it is unknown how many others could have died in the fundamentalist community before the condition was diagnosed.

Before the plethora of fumarase deficiency cases was discovered in Colorado City and Hildale, many victims among the handful of cases documented worldwide died in the first several years of life.

"If you look in the literature, you won't find another dozen cases in the world that have been reported," says Tarby.

Experts say the number of children afflicted in the FLDS community is expected to steadily increase as a result of decades of inbreeding between two of the polygamous sect's founding families -- the Barlows and the Jessops.

"If you cross a Barlow and Jessop, you stand a high risk of getting this condition," Tarby says.

The genetic defect has been traced back to one of the community's founding patriarchs, the late Joseph Smith Jessop, and the first of his plural wives, according to medical literature, the Mormon Church genealogy database and residents of the community familiar with Jessop and Barlow family histories.

Joseph Smith Jessop and his first wife, Martha Moore Yeates, had 14 children. One of their daughters married another of the community's founding patriarchs and religious leaders, John Yeates Barlow. By the time Joseph Smith Jessop died in September 1953, he already had 112 grandchildren, the majority of them directly descended from him and Yeates.

Fifty-two years later, more than half of the 8,000 people now living in Colorado City and Hildale are blood descendants of the Barlows and the Jessops, says Benjamin Bistline, a lifelong resident of the area who has published a book, Colorado City Polygamists, on the history of the fundamentalist community.

An unknown number -- but believed to be in the thousands -- of Barlow/Jessop descendants carry the recessive gene that causes fumarase deficiency. If both parents carry the gene, the likelihood that their offspring will be affected by the disease or become carriers of the gene greatly increases, medical experts say.

"It's like any inbred disorder," Tarby says. "If the community gets larger, the number of people with fumarase deficiency gets larger."

Aleck says the fact that so many people in the polygamist enclave are blood relatives of the founding Barlow and Jessop families "shows the magnitude of the problem."

The disease is not widely known about even in Colorado City, a place where even normally public events such as marriages are conducted in secret. But residents who are aware of fumarase deficiency fear that the number of children afflicted with the disease will indeed increase.

"This problem is going to get worse and worse and worse," predicts 40-year-old Isaac Wyler, another lifelong Colorado City resident who was excommunicated from the FLDS in January 2004. Wyler's ex-wife's sister has had two babies afflicted with fumarase deficiency. "Right now, we are just looking at the tip of the iceberg."

For more than 70 years, all marriages in the isolated towns have been arranged by the leader of the FLDS, a breakaway sect of the Salt Lake City-based Mormon Church.

Marriages among first and second cousins have been common for decades in the community, where religious doctrine requires men to have at least three wives to gain eternal salvation. Only the FLDS prophet can arrange and perform polygamous marriages, and those marriages are taking place in a community in which almost everybody is related.

The current FLDS prophet is 50-year-old Warren Jeffs, who has not been seen publicly since August 2003. Last June, Jeffs was charged with seven felonies by Mohave County, Arizona, in connection with his performance of "spiritual" marriages of three underage girls to already married men. He was placed on the FBI's most wanted list last August. Eight other Colorado City polygamists have been indicted by a Mohave County grand jury for having unlawful sex with underage girls who were their plural wives.

The indictments have come amid a three-year investigation by New Times of the FLDS community. That probe has uncovered widespread sexual abuse of young girls forced into polygamous marriages that, until recently, was downplayed by Arizona political leaders and law enforcement.

The state not only ignored the crimes for decades, it helped facilitate them by allowing the FLDS polygamists to set up a town government, a public school district and a police department that have received tens of millions of dollars in taxpayer funds despite the fact that polygamy violates Arizona's Constitution. The FLDS has had an iron grip on the local governments, because it has been impossible to get elected or hired to a taxpayer-funded post without the church's blessing.

The fundamentalist community has also benefited immensely from state health-care services for the poor and indigent by receiving more than $12 million a year in state assistance in Arizona to pay for health-insurance premiums.

It turns out that taxpayers also have been footing the bill for the fumarase deficiency children born to polygamists who insist that plural marriage involving close relatives is their divine right.

There is no doubt in the mind of any expert interviewed by New Times that the practice of polygamy combined with inbreeding has fostered the spread of fumarase deficiency.

"Polygamy leads to sexual predation, and that leads to genetic problems," says Rehabilitative Services' Tarby. "If you stop the sexual predation, you stop the genetic problem as well. But [FLDS members] don't think of it as sexual predation. That's the big problem."

"This man has left nothing of his worldly worth, but he has left far more than most people of God's work. There isn't another man in the U.S. that can boast this man's posterity," Life magazine quoted Virgil Jessop as eulogizing at the September 1953 funeral of his 84-year-old father, Joseph Smith Jessop.

Five decades later, it appears that Joseph Smith Jessop and his first wife also passed on the rare genetic disorder fumarase deficiency.

The stage was set for the appearance of the rare disease when their 12th child, Martha Jessop, married her second cousin, John Yeates Barlow, in 1923, according to LDS genealogy data and Colorado City historian Ben Bistline.

Like his father-in-law, John Y. Barlow became one of the towering patriarchs of the fundamentalist Mormon community and served as FLDS prophet from 1935 until his death in 1949.

The Barlow-Jessop marriage brought forth some of the major political and religious leaders of the community, including former Colorado City mayor Dan Barlow, police officer Sam Barlow, public school superintendent Alvin Barlow, teacher Louis Barlow, and civic leader Truman Barlow. All of these men have or had multiple wives and scores of children.

Fumarase deficiency began to manifest in the community when three sets of Joseph Smith Jessop and Martha Moore Yeates' great-grandchildren married each other. The three marriages between second cousins have produced at least eight children afflicted with fumarase deficiency, according to a report in the May 2000 Annals of Neurology (based on the study conducted by the group led by Tarby and Aleck), interviews with doctors treating the disease and anecdotal evidence gathered from the community.

The children afflicted with fumarase deficiency from these three marriages include the grandchildren of Dan Barlow and his brother, the late Louis Barlow, and Merill Jessop, a top aide to fugitive prophet Warren Jeffs. It is Merill Jessop who is overseeing construction of a massive FLDS temple in Eldorado, Texas, where many believe Prophet Jeffs plans to move his faithful eventually.

Dan Barlow, who has been excommunicated from the FLDS, and Merill Jessop could not be reached for comment. But Isaac Wyler, a former FLDS member who was excommunicated from the church last year, says he has firsthand knowledge of multiple fumarase deficiency children in each of the three families.

"I know this off the top of my head," Wyler says. "I know these people personally."

Medical experts say the incidence of the disorder will increase because the FLDS community is refusing to accept recommendations to reduce the likelihood of producing babies with fumarase deficiency. Tarby says he discussed the disease and its causes during a town meeting on November 18, 2004, that was attended by more than 100 FLDS members.

Tarby says he explained to the gathering at Town Hall in Colorado City that the only way to stop fumarase deficiency in the community is to abort fetuses that test positive for the disease and for the community to stop intermarriages between Barlows and Jessops, Barlows and Barlows and Jessops and Jessops.

Tarby says members of the community made it clear that neither choice was acceptable. Tarby recounts a conversation he had with a member of the Barlow clan in which he tried to explain why so much fumarase deficiency was occurring among Mormon polygamists.

"I said, 'You're married to somebody you're related to. That leads to problems.'

"The man's response was, 'Up here, we are all related,'" Tarby says. "They just don't worry about the effects of intermarriage."

Tarby says the disease could begin to show up in children at Warren Jeffs' new FLDS headquarters under construction on a 1,600-acre ranch outside of Eldorado. The FLDS already has moved several hundred men, women and children to the compound, many of whom very likely carry the fumarase deficiency gene.

The only long-term solution to the health crisis is for Barlows and Jessops to have children with spouses from outside the polygamist community.

"They have to outbreed," Aleck says.

But this is a very unlikely scenario for FLDS faithful, who practice a religious doctrine that requires men to be strictly obedient to religious leaders and requires women to give birth to as many children as possible to increase the sect's numbers.

"Who [from outside the fundamentalist Mormon religion] would want to go in there and join their population?" Aleck asks. "It's probably hard to recruit into that environment."

Indeed, even if an outsider wanted to join the FLDS community, such a person would not be welcome.

"They are discouraging any new blood," historian Bistline says. "They've got this idea that their blood is pure and that they want to keep it pure."

With no other options available, more FLDS families will be faced with the difficult burden of caring for children suffering with fumarase deficiency. Rather than take steps to avoid the problem, the FLDS loyalists may believe it is their duty to accept their fate.

"They think it is a test from God," says Wyler, who was born and raised in the FLDS before he was booted out.

And a terrible test it is.

Fumarase deficiency is caused by a lack of the fumarase enzyme, an essential component in a biological process called the Krebs cycle, which converts food into energy within each cell. Not enough of the fumarase enzyme can lead to severe mental retardation and physical deformities.

"The kids that I have seen have terrible seizure disorders and developmental delays," says Dr. Aleck. "They are functioning way below their chronological age."

Yet, Aleck says, some children are more seriously affected by the disorder than others. "Some are very debilitated and some aren't," he says.

Some fumarase deficiency children, he says, develop a small degree of motor skills over time: "They don't remain infantile their entire life. They do develop to some degree, but it's way behind their peers."

Dr. Tarby, who routinely treats fumarase deficiency children at a state-funded clinic in Flagstaff, says, "They are funny-looking kids [with] biggish heads and coarse, thick features."

Their brains, he says, "are strangely shaped" and are frequently missing large areas of brain matter that has been replaced by water. An MRI of the brain of one fumarase deficiency child showed that more than half the brain was missing.

Tarby says most of the children "can say at least a word or two," but that all of them "have severe mental retardation" with IQs of less than 25.

Some of the kids can walk, but others have a difficult time even sitting. The children who can't walk, the medical experts say, have most likely suffered strokes during severe seizures.

Despite the secrecy in the community over fumarase deficiency children, Wyler says he has observed his ex-wife's sister's children and others on several occasions.

"People don't like to talk about their fumarase babies for obvious reasons," Wyler says. "I don't know how many who die within the first two or three years that we don't even ever know about."

Wyler says he has seen some fumarase deficiency children who can walk, but others can barely move and spend their entire lives prone.

Children of the latter variety, he says, "can't crawl. They can't sit up. They are lucky if they can even move their head and eyes a little bit."

All of the fumarase deficiency children Wyler has seen remain dependent on the parents or caregivers.

"They are totally helpless," he says.

Frequent and powerful seizures are among the most disturbing characteristics of the disease. Wyler says he once saw a fumarase deficiency child suffer a seizure while she was sitting with her mother and two other children also suffering from the disorder.

"All of a sudden [with] this one little baby, everything tightened up and she arched her back so hard her head was almost touching her toes," Wyler says.

"The mother," he says, "was just sitting there rubbing her hands on [the child's] back trying to get her to relax."

Families with fumarase children receive in-home help from the Division of Developmental Disabilities, a unit of the state Department of Economic Security. Much of the state care is simply helping parents with hygiene, feeding and mobility of the child.

"One lady I know, she just cannot physically pick [her son] up anymore to get him into the bathtub," Wyler says. "A lady comes in and helps her. And it takes two of them to get him into the bathtub just to wash him down and clean him up."

One advantage of polygamous families, Wyler says, is that the mother of a fumarase child will likely have other women in the household to lend a hand.

"A sister wife would be a godsend just to be able to help out," he says. "Not only to help physically, but to be somebody to talk to."

Arizona used to send doctors from Children's Rehabilitative Services, which is a division of the state health department, to Colorado City on a regular basis to examine fumarase deficiency children.

But doctors stopped going to Colorado City after the state and press stepped up scrutiny of the community in 2004. Doctors feared that the media would photograph fumarase deficiency children as they were entering a medical clinic in Colorado City.

"We had no desire to encounter ABC News at the clinic entrance," Tarby says.

The doctors only agreed to talk to New Times after Tarby was approached with a copy of the fumarase deficiency study.

Families now must drive fumarase children to Flagstaff for regular evaluations. Despite the frustrations doctors have with dealing with a community that refuses their recommendations on how to prevent the condition in the future, there is no question that treatment will continue.

"We do not deny medical care to people because of religious beliefs," Tarby says.

In fact, the state's willingness to provide medical assistance to afflicted children may be allowing Utah families to receive treatment paid for by Arizona taxpayers. "I don't know if all the patients I treat are technically eligible for my services [because they may live out of state]," Tarby says.

Researchers have identified a gene on the first chromosome that causes fumarase deficiency, but no test has been developed that could be used to identify individuals carrying the malady. If such a test were developed, a community-wide screening program could be instituted that would identify those carrying the fumarase gene.

Dr. Vinodh Narayanan, a pediatric neurologist at St. Joseph's Hospital, says he is seeking funding to develop a test that would allow public health officials to collect voluntary blood samples from as many FLDS members as possible. The samples could be tested for the gene at the Translational Genomics Research Institute in Phoenix.

He estimates the test would cost about $50 per sample and would provide crucial information to community members of who is carrying the recessive gene that causes fumarase deficiency.

Until the test is available, Tarby says, the best prevention measure remains refraining from crossing Barlows, Jessops and their relations -- who make up half the population of the polygamist enclave.

It's unlikely the polygamous community will heed the doctor's advice.

Even the few highly educated people there, including a medical doctor who practices at the Hildale Health Center, refuse to accept advice from any outsider, including doctors such as Tarby, who has treated their children for years.

"They don't believe anything written about Colorado City [by outsiders, even medical experts] carries much truth," Tarby says.

For Colorado City and Hildale to avoid more fumarase, polygamist leaders must use their authority to make sure that those potentially carrying the fumarase gene are not allowed to marry, says geneticist Aleck.

The leaders must also understand the ethical considerations of continuing behavior, he says, that is bringing children into the world who suffer tragic deformities.

"They have the authoritarian structure necessary to keep this from happening, but I don't think they have the advanced thinking," Aleck says.

"I try in my own, quiet way and tell them to outbreed. But that's like spitting in the ocean."

The ultimate decision on marriages rests with FLDS Prophet Warren Jeffs. And Jeffs so far has shown no indication that he is concerned about the increasing prevalence of fumarase deficiency children in the community, former FLDS member Isaac Wyler says.

Even if a genetic screening test were available, Wyler says, Jeffs would have to be cautious about how he allowed it to be implemented. If the FLDS faithful believed that Jeffs was relying on science to determine marriages rather than divine revelation from God, he could lose control of the church.

"Warren has to be really careful that he doesn't lose his position as a god to these people," Wyler says.

FLDS marriages, Wyler and other community experts say, are an extension of a breeding program that began with Mormon Church founder Joseph Smith in the 1830s. The early Mormon Church practiced polygamy until 1890, when leaders abandoned the practice as a condition for Utah to gain statehood. The FLDS was formed by Mormons who refused to give up polygamy.

Warren Jeffs, like Joseph Smith before him, has emphasized the importance of obedience among members of the church. Jeffs is following a long-established practice -- started by Smith 170 years ago -- of excommunicating those who do not strictly adhere to church leaders' commands.

"The 'gene' that Warren is really selecting for," Wyler says, "is the 'obedience gene.'

"Joseph Smith was also selecting for the 'obedience gene.' He was kicking people out, too, who weren't obedient.

"I hate to talk like this about my own genealogy," Wyler says, "but, literally, they are keeping all the breeding stock -- the women, the [strictly faithful] men -- and weeding out the disobedient men."

The ultimate goal of the breeding program, Wyler says, is to create the perfect race.

"Remember how Hitler was trying to breed a perfect race?" he says. "Warren Jeffs is also trying to breed a perfect race."

The widespread presence of the fumarase deficiency gene in the bloodlines of the founding families of Colorado City is going to make reaching any such goal extremely difficult.

The few dissenters in the community say the serious genetic problems that are beginning to surface are an indication that the closed FLDS society could eventually collapse.

"Maybe it will just self-destruct," historian Bistline says of the fundamentalist church he quit 20 years ago because of a dispute over religious doctrine and property ownership. "In the meantime, the taxpayers have to pay the bills."