New Scientist has a great article explaining how our food labeling system is wrong and how this affects your calorie counts. In particular, cooked foods and softer foods have a higher calorie count, while raw and hard-to-chew foods have a lower (less digestible) calorie count. What's more:

...calorie estimates on food labels are based on flawed and outdated science, and provide misleading information on how much energy your body will actually get from a food. Some food labels may over or underestimate this figure by as much as 25 per cent, enough to foil any diet, and over time even lead to obesity. As the western world's waistlines expand at an alarming rate, they argue, it is time consumers were told the true value of their food...

...the brownie is made from refined sugar and flour, making it easier for our bodies to extract the available calories than it would be from the complex carbohydrates of the oatmeal in the cereal bar. And while the Atwater system assumes that the proportion of food that passes through the gut undigested is more or less constant, at around 10 per cent, we have known for more than 60 years that this is not the case. Thirty per cent or more of coarse-ground wheat flour may be excreted, while today's finely milled flours may be almost completely digested. As a result, foods made from these fine flours - like that brownie - are likely to channel practically all of the energy from carbohydrate into the body.

New labelling would entail a huge amount of research and studies, millions of dollars, and lots of man and animal power. And, would a new labelling system simply be too confusing for the average person? Are we better off keeping our old (flawed) system and take into consideration the impact of cooking, processing and softening has on digestion?