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Dr. Robert Califf, President Obama’s recent nominee to head the Food and Drug Administration, has been the target of serious criticism in recent weeks over his close ties to the pharmaceutical industry. He has received hundreds of thousands of dollars from Big Pharma.

The New York Times reports that Dr. Califf, a cardiologist, is a renowned clinical researcher who has deep respect for the system in which he works, and no one who knows him thinks he wants to weaken the regulatory agency he has been chosen to lead. But he has deeper ties to the pharmaceutical industry than any F.D.A. commissioner in recent memory, and some public health advocates question whether his background could tilt him in the direction of an industry he would be in charge of supervising.

While the previous commissioner, Dr. Margaret A. Hamburg, a former top health official in New York City, came from the field of public health, Dr. Califf ran a multimillion-dollar clinical research center at Duke University that received more than 60 percent of its funding from industry.

His financial disclosure form last year listed seven drug companies and a device maker that paid him for consulting and six others that partly supported his university salary, including Merck, Novartis and Eli Lilly. A conflict-of-interest section at the end of an article he wrote in the European Heart Journal last year declared financial support from more than 20 companies.

“In a sense, he’s the ultimate industry insider,” said Daniel Carpenter, a Harvard political science professor who has written extensively about the F.D.A.

But , Dr. Califf’s supporters note that a résumé studded with industry funding is not unusual in academic medicine. Doctors are paid consulting fees all the time, and universities routinely conduct clinical trials on behalf of companies. Those contracts help support university researchers’ salaries, a standard practice. Many emphasize that it does not imply an inherent conflict. His supporters contend that Dr. Califf’s vast experience in the clinical science world could be a major asset in his new post.