When it comes to calories, the argument over calories has done a great disservice to the health and nutrition industry. They are simple and really easy to understand. People can intuitively pick up a package and look at the calorie count on the label. However, the calorie count is not the most effective metric for determining if that food is good for you or not. Calories were designed to understand how quickly different fuels burn in a steam engine and determine how effective the fuel is at heating water. They really fall short when you try to place a calorie in a really complex system like the body. So when it comes to thinking about if something is healthy or is it not healthy, calories are an outdated metric that does not apply anymore.
When it comes to thinking about the equation, it is much more complicated than just a simple calorie count.
Even I used to say “calories in should equal calories out”, based on the law of thermodynamics. However, the law of thermodynamics (energy cannot be destroyed) gets lost in the complicated world of cellular biology and hormone interactions in the body. It is important to think about more than just how much energy a food gives off, but to also think about how that food effects your hormones and inflammation in the body. A food can be very high calorie, which we would currently think as not good for us – but can also be something that effects insulin or leptin (insulin effects fat storage and leptin effects appetite) in very positive ways. A food that is low in calories can cause high inflammation, and in turn be very bad for you. The effect of the food on your hormones and the effect on your inflammation levels is far more important in the way that people store fat (which is what more people REALLY care about).
Eating a high calorie, low inflammation, low toxin diet is much better for you, as it can still allow you to lose weight and even put on muscle at the same time. Even the timing of when we eat that food plays important roles in how we use it in our body (look up intermittent fasting).
If you want to read more on the the best nutritional practices today I would suggest reading books such as “Wheat Belly” and “Rich Food, Poor Food”.