Last Monday, a group of 18 volunteers on the outskirts of Washington, D.C., began the second phase of a multi-week feeding experiment that will govern every morsel of food going into their bodies and analyze almost everything that comes out. The study, led by Department of Agriculture (USDA) scientists, is part of an ongoing effort to re-evaluate the number of calories eaters derive from popular foods. This particular experiment is focused on how the human body digests lentils and chickpeas, but it builds on prior ones conducted on almonds, walnuts, pistachios, and cashews. Taken together, the various studies make up a growing area of research that’s making calorie estimates more accurate regarding how our bodies interact with food.

That’s right: The calorie count—a common measure used to estimate nutritional needs, as well as shame many of our dietary choices—might not be as accurate as we’ve been led to believe. The origin of the calorie as we know it dates back to the late 19th century, when a chemist named Wilbur Atwater popularized a method of energy calculation that assigned a fixed number of calories to every gram of protein, carbohydrate, and fat in a given food. These numbers—“Atwater factors,” as they’re known—were derived from a series of ethically questionable experiments that his team conducted. In them, Atwater and other scientists sequestered people in air-tight chambers for extended periods of time to calculate their metabolic rates based on diet and different physical activities. Today, Atwater factors are the basis of how most manufacturers calculate calories in accordance with the Food and Drug Administration’s (FDA) food labeling regulations.

However, it turns out that some foods are more difficult for our bodies to digest than Atwater predicted. In particular, researchers have found that nuts have lower “bioavailability”—a term that refers to the proportion of a food’s nutrients that our bodies can absorb and use—compared to other foods, because of their tough, crunchy structure. That hardness is due to their rigid cell walls, which contain a lot of fiber.

“The thing about fiber is: Mammals can’t digest it. But until we disrupt that plant cell wall, we can’t get what’s inside the plant cells. That’s where the protein, the fat, the carbohydrates are located,” says David Baer, a supervisory research physiologist at USDA involved with the ongoing research on calorie recalculations.

And because nuts contain so much fat—about 9 calories per gram per Atwater factors—a lot of energy from whole nuts ends up passing through our digestive systems unused, Baer explains. 

In 2012, a team of USDA scientists including Baer found that eaters absorb 5 percent fewer calories from eating pistachios than indicated by conventional estimates. These findings came from an experiment funded by USDA and Paramount Farms, a nut company owned by California’s notorious billionaire farmer, Stewart Resnick. In the study, scientists controlled every meal eaten by participants over 18 days, and collected and analyzed every ounce of their feces and urine for nine. The results were derived from measuring the caloric content of the feces.

The first-of-its-kind study sparked interest in the nut industry, which rushed to fund more research. Later that year, the same team published results from an experiment on almond consumption, finding that Atwater factors overestimated the caloric value that eaters could digest by 32 percent. That work was funded by USDA and the Almond Board of California. In a 2015 study funded by USDA and the California Walnut Commission, researchers found that eaters could access just 80 percent of the calories in walnuts. Last January, they determined that cashews fared only slightly better—eaters could digest 84 percent of their caloric worth. The study was funded by USDA and the Global Cashew Council arm of the International Nut and Dried Fruit Council.

The methodology for all these experiments, including the ongoing research on lentils and chickpeas, is fairly similar: At first, participants are fed a strictly monitored diet without the ingredient under investigation. This is the control phase that gives their bodies a chance to acclimate to set menus, and they’re not supposed to eat outside the experiment. During the subsequent phase, participants eat the same meals slightly adjusted to accommodate for the introduction of nuts (or chickpeas or lentils) into their diets. On the first and last day of this stretch, scientists give participants a pill to dye their poop blue, marking the beginning and end of the corresponding feces collection period. But not just any old blue—Brilliant Blue. (“It’s actually more green in the feces than blue,” Baer notes.) Typically, about a week’s worth of feces is amassed, and then it gets analyzed for unused fat and energy content. Ta-da!

These findings are specific to whole nuts. Processed products like cashew butter and almond milk will likely interact with our digestive system differently, Baer says. Still, experts argue that the discrepancy between caloric content in whole nuts and what people really absorb from them is worth noting and will likely have practical consequences for eaters.

“That’s useful information to have and important to indicate on food labels,” says Bradley Bolling, an assistant professor of food science at the University of Wisconsin-Madison, who wasn’t involved in USDA’s nut research. “Nuts kind of have a stigma of being too high in calories, that maybe they should be consumed in very limited quantities because of that reason. ….[But] when you account for when there’s a proper counting of calories, they’re not necessarily leading to increased weight gain.”

Now that sounds like music to the nut industry’s ears. The Almond Board of California has eagerly marketed the findings they funded, as has the Global Cashew Council. This week, popular nut bar company Kind announced it would be updating calorie counts in the upcoming months, a move that its in-house dietician Stephanie Csaszar estimates will affect 95 percent of their products. FDA allows manufacturers to calculate calorie counts based on research regarding particular foods.

USDA researcher David Baer tells me the issue of caloric bioavailability is fairly unique to nuts, but could also apply to a number of other foods, particularly seeds. The ongoing lentil and chickpea study—partially funded by the American Pulse Association—is one instance where the team has begun experimenting on non-nut foods. Baer hypothesizes that the team will find a gap between the calories that pulses contain and what eaters can actually digest, though perhaps not to the extent of nuts. Those results will likely be published at the end of 2020.

This research push isn’t the first time the scientific community has tried to correct inaccurate calorie measurements. Numerous studies have found that energy and nutrient estimates on product labels have been, at instances, overstated. But maybe miscalculation isn’t the real issue; maybe our faith in the calorie is.

“[There’s a] persistent promise of the calorie—this idea that we can take food, which is complicated, and reduce it to something where we can just say, ‘This is how much you can eat and everyone should just act rationally,’” says Deborah Levine, an associate professor of health policy at Providence College, who has written extensively about the history of the calorie in American food policy.

The idea that calorie counts can guide people towards “better” eating choices has long been tempting. It’s the thinking behind everything from our web of food and menu labeling laws to America’s pervasive, ever-mutating diet culture. Atwater, Levine tells me, even went so far as to argue that employers could be justified in lowering wages if workers maximized calorie intake per dollar.

Today, calories continue to play a central role in federal dietary guidelines, and are often an important parameter in nutrition programs everywhere, from schools to prisons to nursing homes. For individuals, it’s often a key measure we consider when grocery shopping, we monitor when dining out, and we track on our apps. Perhaps the takeaway from the emerging body of caloric research isn’t just that some foods are lower in energy than we think, but that these measures can guide our choices only so far.

“My hunch is that it’s not because we don’t have accurate enough measurements, and it’s not because we don’t have sufficient education,” Levine says. “It’s because food is more than simple fuel.”