You may want to reconsider getting that double cheeseburger with fries.

A study released in the Proceedings of the National Academy of Sciences contains controversial claims about menu items served at McDonald's, Wendy's and Burger King.

Using a technique that identifies carbon and nitrogen isotopes in meat, co-authors A. Hope Jahren and Rebecca Kraft tried to determine the animals' diets and in what conditions they were raised. Based on the high levels of carbon and nitrogen isotopes found in the meat products, the authors claim that the cattle and poultry were predominantly fed corn, which makes them as fat as possible in as short a time as possible, and were raised in extreme confinement.

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In an interview, Jahren, who is a geobiologist and professor at the University of Hawaii, even suggested that the nitrogen isotopic signatures found in meat products were so high that they were consistent with environments where animals had consumed their own waste.

Burger King declined to comment on the study. A spokesman for Wendy's said the company has "very strict procedures in place" to protect animal welfare. McDonald's declined to comment.

Where's the beef?

Over a two-year period, the authors purchased 480 servings of hamburgers, chicken sandwiches and french fries at multiple chains in six cities across the countryand tested them for carbon 13 and nitrogen 15 isotopes, both of which have been used by scientists for decades to reveal clues about eating habits in both humans and animals.

Farmers use nitrogen-enriched fertilizer to rapidly maximize their output. This is particularly true of corn crops; in 1940 a farmer could expect 70 to 80 bushels of corn per acre. Today, that number has reached 200 bushels.

This corn, in turn, has been used to feed livestock and poultry for quick and efficient growth. In 2007, the U.S. produced 48.7 billion pounds of commercial red meat, 90.6 billion eggs, and 8.1 billion chickens, according to the USDA.

The authors also found widespread homogeneity of chicken samples across chains. The chickens used were predominantly corn-fed. While the chicken samples had lower nitrogen levels than beef, the authors argue that they remained high enough to demonstrate that the poultry had been raised in extreme confinement.

Samples of french fries revealed that the restaurant chains are using one frying oil or a combination of oils despite claims stating otherwise. Wendy's, for example, claims their fries may contain one or more of canola, soy, cottonseed or corn oil. In fact, the study's findings pointed to a nationwide "corn-oil based protocol" for fries.

"It would be too bad if this adds to public fears about corn," she says.

Dr. Frank Monahan, a scientist at University College Dublin, has used the same technique to compare the eating habits of grass-fed and conventionally raised beef in Ireland. While he called Jahren's approach scientifically sound, he questioned the conclusiveness of the study's findings.

'Because the food chain has become so long now, and it's a global industry, we want to know the origin of our food as consumers.'—Frank Monahan, University College Dublin

The levels of nitrogen, he says, may not be directly linked to confinement practices. Instead, they may reflect the fact that most conventionally raised beef and poultry are given feed that was grown with nitrogen-enriched fertilizer. And while the high levels of carbon 13 indicate a diet abundant with corn, Monahan says their values could have been much higher, which would provide convincing evidence that the animals had an exclusive corn diet.

This technique has been increasingly used in the past decade to analyze the eating patterns of animals that become consumer meat.

"Because the food chain has become so long now, and it's a global industry, we want to know the origin of our food as consumers," says Monahan. "Consumers nowadays want to know the story of their food."

Bob Goldin, executive vice president of the food industry consulting firm Technomic, says that's probably not the case with fast food customers.

Jahren and Kraft, a doctoral student in at Johns Hopkins University, conducted the research unpaid. Jahren says she is trying to shed light on a dearth of information about how a cow becomes a McDonald's quarter-pounder, for example.

"The information gap is really fascinating," says Jahren, who tried for two years without success to obtain information from Burger King, Wendy's and McDonald's about their suppliers and food production practices. While McDonald's does disclose its primary suppliers, Wendy's declines to do so, citing "competitive reasons."