On his 82nd birthday, Dr. Charles Ray Jones sat in his New Haven office at 111 Park St., surrounded by patient files and wearing a blue tracksuit.

Though it has been a long while since Jones could last run — in fact, he now uses a cane to get around — Jones finds himself in a number of races: a medical one with a debilitating disease, a legal one with the Connecticut Medical Board, and even an academic one with Yale.

Over the past four decades, Jones has treated roughly 10,000 children with severe chronic Lyme disease. Parents from all over the world bring their children to Jones, and many said they consider him their final hope. But despite his popularity with his patients, many in the medical field strongly disagree with his practices, which, they say, treat a form of Lyme disease that does not exist.

Most doctors believe that Lyme disease, a tick-borne illness, almost always presents with a rash, fever or arthritic pain. But Jones says that Lyme disease can have a much wider array of symptoms, such as mental impairment, that can last for years.

Jones has already been brought before the medical board twice, both times receiving fines of $10,000 for procedural violations, which he claims threatens his ability to practice. Jones claims the high fines he received were due to the controversial length of his treatments, rather than because they caused any harm to his patients through his violations. Jones has never been sued for medical malpractice.

“I’m not being disciplined, I’m being harassed,” Jones told the News.

Jones began treating the disease’s symptoms in the late 1960s, before it was officially recognized by most medical professionals. When Yale doctors, led by then-Yale professor Allen Steere, worked to find the source of the disease in 1975, Jones gave the research team evidence by detailing the experiences of his own patients, lending Yale’s academic doctors a clinician’s perspective.

But in the early 1980s, Jones and the Yale scientists split on the longevity of the disease and the academic race to define the disease began. While Jones said he believed that Lyme disease can become chronic if untreated, Steere and other doctors claimed that the disease could be cured with three to six weeks of antibiotics.

More recently, Jones has been in conflict with Dr. Eugene Shapiro, a pediatrician at the Yale School of Medicine, who said he believes there is not enough evidence to support Jones’ theory.

“There is no benefit [to Jones’ long-term treatment], and there are expenses to both the individual and to society,” Shapiro told the News. “As for chronic Lyme, there is no definition and I believe there is no such entity.”

The two have clashed publicly and Shapiro has testified against Jones in front of the Connecticut Medical Board. Neither Jones nor Shapiro would comment about the other personally.

Jones said that despite the criticism from the medical community, he still strongly believes in what he does.

“I became the evil one,” Jones said. “But my kids got better.”

THE PATIENTS

Jones’ patients and their families said their lives would not be the same without Jones’ long-term course of treatment. Many said they have seen their children misdiagnosed with arthritis, dyslexia, or even autism — a result, they said, of the medical community’s denial that chronic Lyme disease exists.

Jones said he recalls one child, Timmy, a 6-year-old who came into his office with his mother, unable to speak or comprehend others. Timmy had been diagnosed by previous doctors with autism, but his mother believed it could be Lyme disease. Jones agreed.

“I remember he was sitting in my lap. He couldn’t talk, but he made eye contact well, showing signs of intelligence,” Jones said. “I looked him in the eye, I touched his cheeks and said, ‘I hope that I have the key that can unlock your brain.’”

Timmy then wiggled out of Jones’ lap and ran around the office, Jones said. Following a positive test for Lyme disease, Jones began treatment.

After roughly five months of antibiotics — far more than the generally prescribed three to six weeks — Timmy saw Jones for a second time.

“He came back four or five months later,” Jones said. “He didn’t run in the door, he walked in the door. He put my hands on his cheeks, he looked me in the eye, and said, ‘Thank you for giving me the key to my brain.’”

The walls of Jones’ office are covered in pictures, cards, and paintings — small pieces of gratitude from his patients. One card has a familiar Y with a bulldog over it.

A current pre-med sophomore, who asked to remain anonymous because of the rift between Yale’s medical professors and Jones, credits her place at Yale in part to Jones. Lyme disease had affected her processing and auditory abilities, but after five years with Jones, she graduated valedictorian of her high school.

“I’m immensely grateful for Dr. Jones, and the role he’s had in my life,” she told the News. “But I do feel like I shouldn’t use my name because I’ve heard some of my professors speak against chronic Lyme and those who treat it.”

LEGAL TROUBLES

While it started in academia, the controversy surrounding Jones’ practice has spread into the legal system.

Jones has been disciplined twice for diagnosing a patient without examining him in person as well as for keeping faulty records. Both complaints were filed by fathers of Jones’ patients, who were in custody battles for their children, Jones’ attorney Elliot Pollack said. The fathers claimed that Jones’ treatment was supporting their ex-spouse’s Münchausen syndrome, a psychiatric disorder in which a patient feigns illness in order to receive treatment from doctors, Pollack said.

As for his record keeping, Jones claims that his staff of three nurses can only do so much in such a busy office.

But Shapiro said it is very dangerous to treat a patient without proper evaluation, especially over a long period of time with drugs that have significant side effects.

In addition to the fines he has received, Jones has to pay for a special investigator to review his files once a month for four years. Jones estimates this will cost him $2,000 to $10,000 per month.

“It makes you wonder, ‘When’s the last time this Board disciplined someone for successful patient outcomes?’” Pollack said.

Jones claims that he received such harsh punishment because his treatment contradicts the views of many in the medical community, originated by Steere and continued by others like Shapiro.

The legal race continues, but it may be the race against time that is most dire.

“I’m 82. They’re looking for bankruptcy or death or both,” Jones said.

“But I’m still practicing,” he added, smiling.

Correction: April 7, 2011

An earlier version of this article incorrectly suggested that Charles Ray Jones routinely prescribes patients antibiotics over the phone. In fact, Jones only once extended another physician’s prescription over the phone because of a child’s respiratory troubles.