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The method most commonly used to assess the number of calories in foods is flawed, overestimating the energy provided to the body by proteins, nuts and foods high in fiber by as much as 25 percent, some nutrition experts say.

“The amount of calories a person gets from protein and fiber are overstated,” said Geoffrey Livesey, the head of Independent Nutrition Logic, a nutrition consulting company in Britain, and a nutrition consultant to the United Nations. “This is especially misleading for those on a high-protein, high-fiber diet, or for diabetics” who must limit their intake of carbohydrates.

Well Quiz The New Logic of Calorie-Counting Can you determine which of these foods provide fewer calories than originally counted?

An adult aiming to take in 2,000 calories a day on a low-carbohydrate, high-protein diet may actually be consuming several hundred calories less, he and other experts said. Calorie estimates for junk foods, particularly processed carbohydrates, are more accurate.

The current calorie-counting system was created in the late 1800s by Wilbur Atwater, a scientist at the Department of Agriculture, and has been modified somewhat over the past 100 years. Researchers place a portion of food in a device called a calorimeter and burn it to see how much energy it contains. The heat is absorbed by water; one calorie is the amount of energy needed to raise the temperature of one gram of water by one degree Celsius.

When experts talk about calories, however, they usually mean kilocalories; one kilocalorie equals 1,000 calories. Those are the amounts you see on food labels.

The system is most accurate when the foods are easily digested and all of their energy is made available to the body — as they are when consuming highly processed carbohydrates. But in the past few decades, scientists have begun to understand that a substantial number of calories are lost in the effort to digest food. For example, meat and nuts are harder to break down, and so the body expends energy trying to digest them.

In the end, some foods are also not fully digested: significant portions are excreted, and so those calories should not be counted, either. Nuts are among the hardest to digest, and estimates of the calories they contain by the old method are the furthest off — the counts are about 25 percent too high, according to recent research by David Baer, a nutrition scientist at the Department of Agriculture.

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Almonds are routinely listed as having about 160 calories a serving, when the real figure is about 120 calories, said Karen Lapsley, the chief scientist at the California Almond Board. Some manufacturers are considering making the change on their labels.

While the case for almond overcounting is clear, she said, some nutritionists are concerned that lowering the calorie estimates across the board might send the wrong message — that consumers can eat more — at time when Americans should be eating less.

An alternate and more accurate system of counting calories has been devised by Mr. Livesey and has been presented to the United Nations Food and Agriculture Organization, which provides recommendations to member nations. The new method has been discussed but not officially adopted.

It counts not just how much energy (or calories) are available in a food, but what the body can actually use of that energy. Additional calculations are made to consider the energy expended by the body in digestion and the degree to which the food is processed.

“People ask me, ‘if we know what is wrong, why hasn’t it been changed?’ ” said Rachel Carmody, a postdoctoral researcher at the University of California, San Francisco. “Because the old system is in place in most developed countries, and it would be a massive administrative and political undertaking to coordinate changes.”

“What you do not want to do is cause a crisis of confidence for consumers,” she added. “Paying attention to the food label is far better than not paying attention to the food label, even if the label is not precise.”

It may not be necessary to change the calorie counts broadly, said David Klurfeld, program director for human nutrition at the Department of Agriculture. To give consumers a better idea of how much they are eating, it may be more effective to revise the counts on a few specific foods rather than scrap the older approach all at once.

“On average, the system is right, but on individual foods, it’s not right,” he said. “It’s not possible to test every single food, or combination of foods, but if you test individual foods, you could get more precise.”

Dr. David Ludwig, who runs an obesity clinic at Boston Children’s Hospital, said that although there may be scientific value in having more precise calorie counts for all foods, changes in the system may not make much practical difference in the real world.

The body resists weight loss by increasing hunger, he said. In his clinic, patients are not expected to count calories, but instead learn how to choose types and quantities of food that will reduce hunger and promote weight loss without calorie restriction.

The Food and Drug Administration is responsible for the calorie labeling on most foods, but the task of making the actual calculation is delegated to the manufacturers, Theresa Eisenman, an agency spokeswoman, said. The companies are responsible for the accuracy of the estimates. If changes come, she said, it will be because food companies have decided to revise their labels.

Related: The New Logic of Calorie-Counting: Can you determine which of these foods provide fewer calories than originally counted?

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