Which foods make you fatter? Counting calories has settled into a default mental habit for generations of women, and some men. Knowing by rote the calorific content of every Cadbury's product in a typical corner shop is no simple feat, but it is a necessary one, we've been told, for anyone who wants to keep tabs on the flab. A pound of flesh contains 3,500 calories, so in order to lose one pound a week, you should cut back by about 500 calories per day. Yes, some people do seem to lose or gain weight more easily than others, but it is widely accepted that in order to lose weight one must expend more calories than one consumes. Now, at this extremely late stage in the 2,000-year history of the dieting industry, the whole concept of calorie-counting is being questioned. The calorie itself is not 2,000 years old. Nor was it invented to help us pursue our dreams of waif-like figures and wardrobes full of size zero clothes. On the contrary, the calorie system was developed to help us eat enough. Do you know how far can you cycle on an egg, for example? Working out how far a man could cycle on one egg was one of the tests carried out in the late 19th century by the American chemist Wilbur Atwater, who painstakingly worked out the calorie content of different foods. As well as the egg test, Atwater locked students in a chamber and measured the energy fluctuation while they ate and carried out various tasks. He also burnt foods and measured the heat they gave off to determine how much energy - how many calories - they contained. This formed the backbone of the calorie system, which has been recognised and accepted internationally as the most straightforward way to assess the energy in food ever since. More often than not we talk about calories in the context of weight loss, and the Government urges us to eat fewer calories to tackle obesity. In the early days, calories had the opposite political use, as big employers and the army wanted to discover the cheapest foodstuffs that would provide their men with sufficient energy to do a job, be that on an assembly line or at the frontline. The answer was carbohydrates, which is why bread, pasta, rice and any starchy vegetables are the bugbear of today's dieting industry. We've known since the 1920s that some calories are worth more than others nutritionally, because of the vitamins and minerals they present the body with. A banana beats a chocolate digestive hands down, hence the phrase "empty calories," which is sometimes applied to sugary foods. But in recent years and following new scientific developments, the whole calorie system and its accuracy has come under examination. One nutritionist has said that the calorie content of typical items may be as much as 25 per cent out. The idea that we must eat fewer calories than we burn to lose weight still holds, but the calorie content of individual foods does not provide the full picture. Atwater's findings were not completely wrong. What he did not account for was how much energy our bodies use up to digest and process different foods. We have to work much harder to digest dense, fibrous foods and those high in protein, right from the initial process of chewing, through to the reactions that go on in the stomach and colon. The true calorie content - the bit that remains stuck to our hips or is available for that bike ride - is the energy left in the body once we've digested the food. The dieting club WeightWatchers overhauled its 40-year-old system late last year to take this theory into account. "What we know from the new science," says Zoe Hellman, WeightWatchers' UK dietitian, "is that it takes calories to digest calories. Foods that are rich in protein and fibre actually take more calories to digest than fat and carbohydrates. Marks & Spencer's Simply Fuller Longer range follows a similar structure, promising "high protein and balanced carbs" from ready meals. The line was developed with nutritional scientists from the University of Aberdeen, and based on research showing high-protein diets result in better weight loss results. The Atkins and the Dukan diets are famously effective for the same reasons, but now we understand more about why protein is such a good diet food - because it fills us up, and because we have to work hard to digest it. In addition, the measurement kilojoule is gaining credence over the kilocalorie. The number of kilojoules appears more threatening than calories on a food wrapper because there are about four times as many in any product. But the kilojoule is preferred to the calorie by scientists, because it was devised in the 1950s and is a more accurate unit to measure energy with. The problem with all this, say detractors, is that it is confusing. It is too late for the average non-scientist - you and I - to switch from calories to kilojoules. If you look at any label in a supermarket, you will see that calories are still very much on the agenda, along with the fat, protein and carb content. There are plenty of diets that recommend good food choices and portion control over calorie counting, but unless you have a grasp on what the right foods and sensible helping sizes are, you're stuck. Calorie counts still act as shorthand for dieters. If they didn't, Cadbury's would never have created its slim 99-calorie bar of Dairy Milk for dieting snackers. "It is important to keep it simple," according to Dr Ian Campbell from the National Obesity Forum, who thinks that befuddling struggling dieters with new rules is not helpful. "Paying attention to the general context of your food is more important than going into the deep science, which the general public doesn't want to embrace," he says. Our tempestuous love affair with the calorie is far from over. WeightWatchers produced successful dieters when it relied on calories, and anyone restricting their calorie intake today should continue to lose weight, but we now know that the process will be easier with a diet high in protein and fibre. However, a better understanding of how our bodies process different types of foods could well, in the long term, be helpful rather than confusing. Stepping away from punishing numbers and towards a fuller understanding of food is a welcome development that might end our tiresome and stressful reliance on calorie-counting.