When the body takes in excess energy it is stored as lipids in white fat cells. When there are too many calories coming in, and not enough being burnt, adult stem cells in the body produce more white fat cells, which leads to a flabby physique.
Increasing levels of the molecule which the scientists identified, tells the body to make more brown cells, rather than white. Although Harvard has merely shown proof of a concept, it believes that a pill could be created to produce the same effects.
A drug called tofacitinib, which triggers the molecule, is already being marketed for rheumatoid arthritis, and could also be an effective treatment for obesity.
"It's the first step toward a pill that can replace the treadmill," said Chad Cowan, an associate professor in Harvard's Department of Stem Cell and Regenerative Biology unit, who co-authored the study.
"What we saw here was a stable conversion of the white fat cells to brown cells."
Prof Cowan has been working with fat stem cells for more than seven years, looking for ways to prevent disease and obesity. He is in discussions with several pharmaceutical companies about producing a drug, and clinical trials have already begun in Germany.
A quarter of adults in England are obese - a figure that is on course to climb to 60 per cent of men and 50 per cent of women by 2050.
As well as helping people to lose weight, a drug that turns white cells into brown cells would reduce the chance of developing Type 2 diabetes and protect against heart disease.
The findings were reported in Nature Cell Biology.