AIRFIELD, Iowa — In 1984, John B. Fagan, a molecular biologist at the National Institutes of Health, left a promising job as a cancer researcher in Washington to come to this sleepy farm town to practice transcendental meditation and begin a new life as a university professor.

He took a post at the Maharishi International University here and became a star researcher, attracting N.I.H. research grants. But in the early 1990's, he began to have second thoughts about gene therapy and the genetic engineering of crops.

In 1994 he turned down a $614,000 research grant from the N.I.H. to study gene therapy because of concerns about the "dangerous consequences" of manipulating human genes. And two years later, he founded a company that tests crops for genetic alterations, giving processed-food makers the option of steering clear of biotechnology ingredients.

In September, Dr. Fagan's company, Genetic ID, found that a batch of grocery store taco shells sold by Kraft Foods, a unit of Philip Morris, were made with a genetically engineered corn that had not been approved for human consumption. The findings forced Kraft to recall millions of taco shells and reignited a long-standing debate over the safety and labeling of genetically altered foods.

The discovery also led to renewed allegations from the biotechnology industry that Genetic ID, one of the nation's largest testing labs, was working closely with opponents of that technology.

Genetic ID executives acknowledged Dr. Fagan's activism, but said the company itself was neutral about genetically altered crops, and relied on a widely accepted DNA testing technique, known as polymerase chain reaction, or P.C.R. And, they note, the taco shell results were independently confirmed by Kraft and the Food and Drug Administration.

The biotechnology industry, which has invested billions of dollars to create genetically altered crops, says Genetic ID has secretly waged war on the industry under the cloak of doing impartial testing for food companies, many of which support biotechnology. Genetic ID, many in the industry say, is trying to create a biotech scare to increase demand for testing.

"They claim to be impartial but their principal scientist for the past several years has made a name going around and raising questions about the safety of biotechnology without any supporting scientific data," said Val Giddings, a top official at the Biotechnology Industry Organization.

The high-stakes debate over testing is certain to intensify as global food companies weigh the merits of marketing genetically altered foods to consumers, and companies exporting products to Europe and Asia move to comply with new restrictions and labeling requirements on genetically altered foods.

And like it or not, Dr. Fagan, the soft-spoken 52-year-old chairman of Genetic ID, is caught in the middle of the debate over biotechnology. The scientist-turned-activist-turned-corporate-officer is now trying to explain the intersection of those lives.

Dr. Fagan, who was born in Michigan and raised in northern Idaho, earned a bachelor's degree in chemistry from the University of Washington at Seattle, where a neighbor introduced him to transcendental meditation and the teachings of Maharishi Mahesh Yogi, an Indian seer. Maharishi teaches that meditation and a more organic approach to life can raise consciousness, reduce crime rates and improve the environment, among other things.

After earning a Ph.D. at Cornell University, Dr. Fagan established himself in the field seeking to find genetic links to cancer. But after leaving Washington for the cornfields of southeastern Iowa — where he could practice transcendental meditation with other adherents who had gathered around the Maharishi International University here — Dr. Fagan began to have doubts.

"I was seeing a lot of hype about gene therapy and how it could be used, and it was beginning to get to me," he said. "I started to wonder whether I was doing the right thing in my profession."

Dr. Fagan said he came to believe that scientists and biotechnology companies were moving too aggressively to alter the genetic code of the world's food supply, and that not enough testing had been done to assess the risks and consequences.

And so in 1995, at the request of the Maharishi, he wrote a book critical of genetic engineering, which he called a "grave threat." His solution? "Vedic engineering," following the holistic principles of the Maharishi that call for, among other things, organic farming and transcendental meditation.

A year later, as concern over the safety of genetically altered crops grew in Europe and Asia, Dr. Fagan and a group of local investors founded Genetic ID to help companies determine that their products were free of genetically altered ingredients.

Dr. Fagan served the company as scientific adviser even as he doubled as an outspoken critic of genetic engineering. He spoke at conferences, published articles and served as an informal adviser to the Natural Law Party, which sought a moratorium on the commercialization of genetically altered foods. He was even a plaintiff in a 1998 lawsuit challenging an F.D.A. determination that genetically altered foods were safe. The United States District Court for the District of Columbia recently dismissed the suit.

Genetic ID executives, however, say that when Dr. Fagan took over as chairman of the company and became a shareholder in 1998, he agreed to cease his public criticism of genetically modified foods lest the company be seen as taking sides.

Dr. Fagan said he now took a more moderate position. He is not opposed to genetic engineering, he now says in softer tones; he is simply troubled by its what he regards as its premature commercialization. He also said that his book, "Genetic Engineering: The Hazards; Vedic Engineering: The Solutions," might hint at a tougher stance than he actually holds because it was written for followers of the Maharishi, who largely accept organic or vegetarian diets.

Still, in December 1999, when the F.D.A. was holding public hearings on the issue of genetically modified foods, Dr. Fagan identified himself as a Genetic ID official and raised questions about the safety of genetically engineered foods.

Such outspokenness bothers some in the food industry. Gene Grabowski, a spokesman for the Grocery Manufacturers of America, which represents the nation's largest food companies, said Genetic ID's decision to hold a news conference to publicize the Kraft test raised suspicions about the company, which had tested the taco shells for Genetically Engineered Food Alert, a coalition of anti-biotechnology organizations.

"The fact that the company has ties to Maharishi doesn't mean they can't do good research," Mr. Grabowski said. "But their tactics clearly indicate that they are not neutral on the issue of biotechnology."

At least one major food maker that in the past used Genetic ID for testing appears to be turning to other labs. General Mills now tests at the United States division of Hanse Analytik, a German company.

Genetic ID executives blame the biotechnology industry, which they say has tried to discredit the company and the transcendental meditation movement to deflect attention from the debate over the safety of biotechnology.

Indeed, when biotechnology industry executives were asked about Genetic ID, they supplied The New York Times with handouts and "backgrounders" on the company, including descriptions of Dr. Fagan's affiliation with practitioners of Transcedental Meditation, which the notes said had "some very peculiar quasi-religious beliefs about food and health."

Dr. Fagan denounced the effort as "slanderous and bigoted." Transcendental meditation, he said, is not a religion.

Despite such attacks, the privately held company said its business was booming, though it declined to disclose a list of clients, citing confidentiality agreements. Food and agriculture experts agreed that Genetic ID was clearly among the biggest companies in the newly emerging testing field, partly because it was an early entrant into the business, whose growth has been fueled by European and Japanese restrictions on genetically modified foods. It now competes with such companies as Qualicon, a subsidiary of DuPont, and Strategic Diagnostics, a Delaware company that sells test kits.

Business was not always so good, however. Dr. Fagan said a lack of business two years ago forced him to find new investors and bring in an old friend, an organic-fertilizer entrepreneur named Bill Witherspoon, to reorganize the company.

Mr. Witherspoon, another transcendental meditation practitioner, created a new kind of corporation, where decisions, he said, would be "agreed upon" by the employees. Company offices would be devoid of the "negative forces" often present in corporate America, he said.

"There are no Harvard M.B.A.'s, no biz school geniuses," he said. "There's a group of people comfortable responding to the environment rather than people who want to push the environment. We are not hierarchical, we're a network of intelligences."

Mr. Witherspoon, who once was fined by federal officials for carving geometric designs into an Oregon desert to "enliven human consciousness," said he joined Genetic ID on the condition that he could continue to work intuitively.

He personally hired nearly all of Genetic ID's employees, many of whom are followers of the Maharishi because so many of Fairfield's 10,000 residents are transplants who practice transcendental meditation.

Still, executives say the science behind the company's testing is divorced from the Maharishi's "vedic" principles, based on the sacred writings of the Hindus. At Genetic ID labs, biologists grind and homogenize samples of, say, corn, then extract the DNA and use the polymerase chain reaction process to detect and amplify the presence of genetically modified DNA. The company said it could detect genetically altered DNA content as low as one part in 10,000.

Industry experts say P.C.R. tests are not entirely reliable, and are susceptible to falsely indicating the presence of genetically modified material even when it is not actually present. But Genetic ID executives said it triple-tests each sample to narrow the chances of a false result. And, the company noted, the United Kingdom Accreditation Service has certified Genetic ID as qualified to find genetically modified DNA in food. It is seeking similar accreditation from a new F.D.A. program.

After Genetically Engineered Food Alert brought grocery store taco shell samples to the company for testing, scientists were able to detect the presence of StarLink, a strain of biotechnology corn that was approved only for animal feed. Kraft announced a recall four days later, saying it had confirmed the result.

Critics questioned Genetic ID's methods, citing a test of corn snacks for a consumer group in Japan this year in which the company said it found an unapproved variety of bioengineered corn in some samples. The Japanese Ministry of Agriculture said its own tests on a similar batch were negative.

Genetic ID executives countered that the ministry's failure to confirm the result did not mean the company was wrong.

"You cannot disprove one sample with another sample that may have not come from the same lot," said Jeffrey Smith, a spokesman at Genetic ID. "We still stand behind our methods."

The company, which licenses its methods to other labs in Europe and Asia, said that it was likely to face continued hostility from major biotechnology companies. Dr. Fagan said the campaign against Genetic ID might drive him out of the company he created.

"I don't know what's going to happen," he said, noting that he has tried to keep his own views separate from company policies. "Maybe they're going to have to get rid of me."