When is a Calorie not a Calorie?

When is a Calorie not a Calorie? When you use the Atwater general factor system to determine how many calories are in a food product.  This is the most common method of determining calories.  Scientists at the USDA theorized that this method of measurement might not be representative for certain food groups such as nuts. So how is Atwater factor flawed?  Well it ignores the fact that some of the calories in a food may pass through a human as waste.  DOH!!