what's missing with weight loss

The way weight loss is sold, the basic principle, is that "calories in" must be less than "calories out".
The trouble is, for someone with a physics background, there is a step missing here - from a logical point of view. My main problem with it is: Calorie is not a measure of weight.
It is a measure of energy. Despite Einstein mass and energy are not equivalent - at least not at this scale. Hence the missing step in the logic.
Now I am quite aware that there MAY be a close dependency between the energy content of food and its weight. But skipping that point means that we are disregarding some of the consequences. Loss of body mass is related to the difference between the *weight* of input and the *weight* of the output.
If we assume that the weight of gas in and out is roughly equivalent (which is a big assumption but lets go with it) then the liquid and solid input needs to be less than the liquid and solid output. I have heard that the liquid part of this dominates the equation enormously - by far the biggest impact on day to day weight it the amount of water that passes through the body. However, this is transitory and any reasonable measure (NOT "Biggest Loser") does not consider day to day changes when looking at weight loss - week to week or month by month is much more useful.
So, if it is the actual quantity of food which matters what difference does that make to counting calories.
Well, you still want to take in the same nutrients. Your body still needs its fuel. If you want to this with less mass of food then you need to choose nutrient rich foods. Ones which have less empty calories and more of the key things that your body needs. Which, of course, brings us back to the point we started at - calories - but with a much better idea of why.