Tom Hughes wants to change the way you think about obesity. As the chief executive officer of Zafgen, a company developing a weight-loss medicine that went public in June, he has reason to. But he argues the evidence just doesn't stack up to support the idea that diet and exercise can effectively reverse obesity. "Treating obesity with dietary prevention and exercise is like putting sunscreen on melanoma. It's too late," Hughes told CNBC. "People who have established obesity, they will need treatments, they will need care to get out of that, and unless we wake up to that fact and understand and research what is at the heart of that problem, we're not going to have an answer." Hughes noted that diet and exercise have shown in dozens of studies to help people lose about 3 to 5 percent of their body weight in the course of a year. Read MoreObesity game-changer? Why this time it's different

"That's about it," he said. "For somebody who needs to lose 100 pounds, that's more like 30 percent weight loss, and we know that diet and exercise are really out of that reach."

Steven Puetzer | Photodisc | Getty Images

Last year, the American Medical Association, the largest physician group in the U.S., officially recognized obesity as a disease "requiring a range of medical interventions to advance obesity treatment and prevention." And it's a large problem; more than a third of U.S. adults, or 79 million people, are obese, according to the Centers for Disease Control and Prevention. Obesity is linked to higher rates of heart disease, diabetes, stroke and some types of cancer, "some of the leading causes of preventable death," according to the CDC. Read MorePharma CEOs: Tax system flaws help overseas rivals

Yet it's been an uphill battle for developers of obesity treatments. Two years ago, Arena Pharmaceuticals and Vivus got approval for the first new obesity drugs to market in the U.S. in 13 years, and a third new drug, from Orexigen Therapeutics, is now under review at the Food and Drug Administration. The area had been plagued by safety concerns, including the withdrawal of some drugs like fen-phen, a combination of drugs that was pulled from the market in 1997 after it was linked to heart-valve problems, and Abbott Laboratories' Meridia, which was taken off U.S. shelves in 2010 after it was tied to heart attacks and strokes.