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A long-held belief is that calories are calories no matter if they hail from bacon or broccoli. Take in fewer calories than you burn; that’s your ticket to winning the battle of the bulge.

It’s true that any calorie from a food supplies a set amount of energy. But once eaten, things become more complicated. A newer era of research is making it clear that perhaps not all calories are created equal.

The thermic effect

The true calorie count of a food may very well be different than what’s labeled due to its “thermic effect” (i.e., the energy required to digest and process it).

The best example is protein, which has a higher thermic effect than carbs or fat, so a lower percentage of its calories (4 calories per gram) will be available for storage in the body.

In a study in the Journal of the American Medical Association, people who got 25 percent of their calories from protein burned 227 more calories a day than those who only ate 5 percent of their calories from protein.

So even though 3 ounces of chicken breast may have 92 calories on paper, up to 35 percent fewer of those calories will actually be absorbed by the body.

Furthermore, “calories from protein have also been shown to have a greater impact on satiety, and hunger is the enemy of weight loss,” said New York weight loss expert Samantha Cassetty, M.S., R.D.

The carb math

A study in the American Journal of Clinical Nutrition showed that when people ate the same diet except for whole grains versus refined grains, those consuming items like brown rice and whole wheat bread burned almost 100 more calories per day than those who ate the refined versions. This was likely due to both a metabolic boost as well as extra calorie excretion.

“Your body has to work harder to digest a meal containing less-processed carbs, so will burn off more calories to do so,” noted Cassetty. In other words, 100 calories from quinoa are not the same as 100 sugary calories from soda in the weight loss equation.

A report in Obesity Reviews noted that calories from sugary drinks play a unique role in health problems, and that disease risk increases even when the beverages are consumed within calorie-controlled diets that do not result in weight gain.

Processing matters

Any degree of external processing — including cooking, grinding and juicing — ruptures cell walls in a food, thereby lessening the energy needed for our bodies to digest it. As a result, we end up with more of its calories.

Raw or lightly cooked meat (e.g., sushi and rare steak) require extra internal processing to deal with more tightly wound muscle fibers. Therefore, they supply fewer usable calories than well-done meat.

A study in the journal Obesity fed people the same number of calories as either a liquid or solid, and noted that post-meal hunger was greater after liquid calories.

Overall, a solid meal leads to a greater drop in levels of the hunger-inducing hormone ghrelin, which could help trim overall calorie consumption.

That’s nuts

Fascinating research shows that the amount of energy (calories) derived from nuts — such as almonds, walnuts and pistachios — after we eat them is up to 30 percent less than previously thought.

Some of the calories in nuts are found within hard-to-digest cell walls, and microbes in your gut get access to a handful of the nut calories as well, so in the end we don’t absorb all their upfront calories. This is likely one reason why studies have failed to show that eating calorie-dense nuts leads to weight gain.

“Some calories just work a lot harder for us than others, so if we’re focusing solely on calories alone we’re missing the big picture,” Cassetty said. In other words, calories from candy are not the same as calories from cauliflower.

Watch the clock

Eating calories at certain times of day may also make them less caloric. Data shows that consuming calories earlier in the day can lead to better weight management.

“Our biological clocks impact how our bodies handle the calories it receives, and it seems we are primed to deal with the biggest meal of the day in the morning,” Cassetty said. So consider eating breakfast like a king and dinner like a pauper for a bigger calorie burn.