© Catherine Losing

This entire enterprise, from the Beltsville facility to the numbers on the packets of the food we buy, creates an aura of scientific precision around the business of counting calories. That precision is illusory.

The trouble begins at source, with the lists compiled by Atwater and others. Companies are allowed to incinerate freeze-dried pellets of product in a bomb calorimeter to arrive at calorie counts, though most avoid that hassle, says Marion Nestle. Some use the data developed by Atwater in the late 1800s. But the Food and Drug Administration (FDA) also allows companies to use a modified set of values, published by the Department of Agriculture in 1955, that take into account our ability to digest different foods in different ways.

Atwater’s numbers say that Tara Haelle can extract 8.9 calories per gram of fat in a plate of her favourite Tex-Mex refried beans; the modified table shows that, thanks to the indigestibility of some of the plant fibres in legumes, she only gets 8.3 calories per gram. Depending on the calorie-measuring method that a company chooses – the FDA allows two more variations on the theme, for a total of five – a given serving of spaghetti can contain from 200 to 210 calories. These uncertainties can add up. Haelle and Bo Nash might deny themselves a snack or sweat out another few floors on the StairMaster to make sure they don’t go 100 calories over their daily limit. If the data in their calorie counts is wrong, they can go over regardless.

There’s also the issue of serving size. After visiting over 40 US chain restaurants, including Olive Garden, Outback Steak House and PF Chang’s China Bistro, Susan Roberts of Tufts University’s nutrition research centre and colleagues discovered that a dish listed as having, say, 500 calories could contain 800 instead. The difference could easily have been caused, says Roberts, by local chefs heaping on extra french fries or pouring a dollop more sauce. It would be almost impossible for a calorie-counting dieter to accurately estimate their intake given this kind of variation.

Even if the calorie counts themselves were accurate, dieters like Haelle and Nash would have to contend with the significant variations between the total calories in the food and the amount our bodies extract. These variations, which scientists have only recently started to understand, go beyond the inaccuracies in the numbers on the back of food packaging. In fact, the new research calls into question the validity of nutrition science’s core belief that a calorie is a calorie.

Using the Beltsville facilities, for instance, Baer and his colleagues found that our bodies sometimes extract fewer calories than the number listed on the label. Participants in their studies absorbed around a third fewer calories from almonds than the modified Atwater values suggest. For walnuts, the difference was 21 per cent. This is good news for someone who is counting calories and likes to snack on almonds or walnuts: he or she is absorbing far fewer calories than expected. The difference, Baer suspects, is due to the nuts’ particular structure: “All the nutrients – the fat and the protein and things like that – they’re inside this plant cell wall.” Unless those walls are broken down – by processing, chewing or cooking – some of the calories remain off-limits to the body, and thus are excreted rather than absorbed.

Another striking insight came from an attempt to eat like a chimp. In the early 1970s, Richard Wrangham, an anthropologist at Harvard University and author of the book Catching Fire: How cooking made us human, observed wild chimps in Africa. Wrangham attempted to follow the entirely raw diet he saw the animals eating, snacking only on fruit, seeds, leaves, and insects such as termites and army ants. “I discovered that it left me incredibly hungry,” he says. “And then I realised that every human eats their food cooked.”

Wrangham and his colleagues have since shown that cooking unlaces microscopic structures that bind energy in foods, reducing the work our gut would otherwise have to do. It effectively outsources digestion to ovens and frying pans. Wrangham found that mice fed raw peanuts, for instance, lost significantly more weight than mice fed the equivalent amount of roasted peanut butter. The same effect holds true for meat: there are many more usable calories in a burger than in steak tartare. Different cooking methods matter, too. In 2015, Sri Lankan scientists discovered that they could more than halve the available calories in rice by adding coconut oil during cooking and then cooling the rice in the refrigerator.

Wrangham’s findings have significant consequences for dieters. If Nash likes his porterhouse steak bloody, for example, he will likely be consuming several hundred calories less than if he has it well-done. Yet the FDA’s methods for creating a nutrition label do not for the most part account for the differences between raw and cooked food, or pureed versus whole, let alone the structure of plant versus animal cells. A steak is a steak, as far as the FDA is concerned.

Industrial food processing, which subjects foods to extremely high temperatures and pressures, might be freeing up even more calories. The food industry, says Wrangham, has been “increasingly turning our food to mush, to the maximum calories you can get out of it. Which, of course, is all very ironic, because in the West there’s tremendous pressure to reduce the number of calories you’re getting out of your food.” He expects to find examples of structural differences that affect caloric availability in many more foods. “I think there is work here for hundreds and probably thousands of nutritionists for years,” he says.

There’s also the problem that no two people are identical. Differences in height, body fat, liver size, levels of the stress hormone cortisol, and other factors influence the energy required to maintain the body’s basic functions. Between two people of the same sex, weight and age, this number may differ by up to 600 calories a day – over a quarter of the recommended intake for a moderately active woman. Even something as seemingly insignificant as the time at which we eat may affect how we process energy. In one recent study, researchers found that mice fed a high-fat diet between 9am and 5pm gained 28 per cent less weight than mice fed the exact same food across a 24-hour period. The researchers suggested that irregular feedings affect the circadian cycle of the liver and the way it metabolises food, thus influencing overall energy balance. Such differences would not emerge under the feeding schedules in the Beltsville experiments.

Until recently, the idea that genetics plays a significant role in obesity had some traction: researchers hypothesised that evolutionary pressures may have favoured genes that predisposed some people to hold on to more calories in the form of added fat. Today, however, most scientists believe we can’t blame DNA for making us overweight. “The prevalence of obesity started to rise quite sharply in the 1980s,” says Nestle. “Genetics did not change in that ten- or twenty-year period. So genetics can only account for part of it.”

Instead, researchers are beginning to attribute much of the variation to the trillions of tiny creatures that line the coiled tubes inside our midriffs. The microbes in our intestines digest some of the tough or fibrous matter that our stomachs cannot break down, releasing a flow of additional calories in the process. But different species and strains of microbes vary in how effective they are at releasing those extra calories, as well as how generously they share them with their host human.

In 2013, researchers in Jeffrey Gordon’s lab at Washington University tracked down pairs of twins of whom one was obese and one lean. He took gut microbes from each, and inserted them into the intestines of microbe-free mice. Mice that got microbes from an obese twin gained weight; the others remained lean, despite eating the exact same diet. “That was really striking,” said Peter Turnbaugh, who used to work with Gordon and now heads his own lab at the University of California, San Francisco. “It suggested for the first time that these microbes might actually be contributing to the energy that we gain from our diet.”

The diversity of microbes that each of us hosts is as individual as a fingerprint and yet easily transformed by diet and our environment. And though it is poorly understood, new findings about how our gut microbes affect our overall energy balance are emerging almost daily. For example, it seems that medications that are known to cause weight gain might be doing so by modifying the populations of microbes in our gut. In November 2015, researchers showed that risperidone, an antipsychotic drug, altered the gut microbes of mice who received it. The microbial changes slowed the animals’ resting metabolisms, causing them to increase their body mass by 10 per cent in two months. The authors liken the effects to a 30-lb weight gain over one year for an average human, which they say would be the equivalent of an extra cheeseburger every day.

Other evidence suggests that gut microbes might affect weight gain in humans as they do in lab animals. Take the case of the woman who gained more than 40 lbs after receiving a transplant of gut microbes from her overweight teenage daughter. The transplant successfully treated the mother’s intestinal infection of Clostridium difficile, which had resisted antibiotics. But, as of the study’s publication last year, she hadn’t been able to shed the excess weight through diet or exercise. The only aspect of her physiology that had changed was her gut microbes.

All of these factors introduce a disturbingly large margin of error for an individual who is trying, like Nash, Haelle and millions of others, to count calories. The discrepancies between the number on the label and the calories that are actually available in our food, combined with individual variations in how we metabolise that food, can add up to much more than the 200 calories a day that nutritionists often advise cutting in order to lose weight. Nash and Haelle can do everything right and still not lose weight.

None of this means that the calorie is a useless concept. Inaccurate as they are, calorie counts remain a helpful guide to relative energy values: standing burns more calories than sitting; cookies contain more calories than spinach. But the calorie is broken in many ways, and there’s a strong case to be made for moving our food accounting system away from that one particular number. It’s time to take a more holistic look at what we eat.