because an enormous part of the problem is the percentage of our food today that is processed, and the percentage that contains vast amounts of sugar (and particularly high fructose corn syrup).
Processing can't really add much to the energy content of a food. Modern stores have many significantly more energy dense foods at low cost though which may be part of the problem.
I realize that on Slashdot, where people tend to be highly math-oriented, it's a popular fallacy to believe that a calorie is a calorie is a calorie. However, studies like this one have been coming out for years now showing that that's simply not true.
If you're talking about this particular study. It wasn't calorie restricted so it doesn't make your point. Calories can still be calories and two people on different diets can have different results IF they get to eat different amounts of food. Like they did here. If you read the study. Which you didn't.
Some kinds of energy are easier for our bodies to extract from food than others.
Midly but not terribly significantly. If there was a large degree of variability you wouldn't be able to do things like construct BMR tables by age, weight. The larger your sample you feed your regression the larger your error would be.
Some kinds of food make our bodies feel more full than others.
This isn't about a calorie being a calorie. The calories are the same. I realize that you are a little math-challenged but do try to keep up.
healthy, unless the toppings on that pizza are very carefully selected to provide the nutrients that our bodies actually need.
You've now moved to goalposts far, far away from a "calorie is a calorie" to some vague idea about being healthy. I've personally 10 lbs almost exclusively eating Kit Kat's and Ice Cream bars.
It would be nice if nutrition were a simple formula, where you could just calculate calories in minus calories expended and come out with a nice, pleasing mathematical formula.
Evidence suggests that for the vast majority of people you can do this to a pretty high degree of precision. When I use high-precision means (scales for all food, highly regular diet, highly structured weigh-ins and exercise). I can predict my weight to a margin of 5-10% a week out. When I talk to people who have trouble losing weight and I ask them about their diets. Most of the time they lack enough rigor to easily include their results. I'm not suggesting that everyone needs to be this rigorous but to understand that their confusion comes from not understanding exactly how much energy they are taking in.