Actually, thermodynamics is absolute and adhering to the laws of thermodynamics is a certainty. You can estimate your daily caloric needs on your basal metabolic rate combined with a multiplication factor based on your daily activities. Then you can estimate how much you eat. Within a small error you will be consuming and expending known amounts of energy. Eat less than you use and you'll end up losing mass whether it's fat if you are more active or muscles and fat if you are inactive. It won't be reflected 1-to-1 in the scale measurements and your size but over the long run you'll lose weight.
Remember, though, that we only absorb a certain proportion of the calories available in our food. Our rules of thumb about estimating caloric needs based on basal metabolic rate are approximate and work for many people, but not all. Digestive and metabolic disturbances can result in some folks not absorbing calories and nutrition (classic presentation of celiac) or extracting calories much more efficiently. The preparation of food also influences this processing: the energy required to digest your food starts to become a non-trivial factor. If you're struggling with weight despite tracking your intake, it might be worth switching your intake to foods from which you absorb fewer calories and for which you expend more energy in digestion: nuts, raw vegetables, and less sugar etc.
None of this violates the laws of thermodynamics. These are all quantities that one could measure/estimate/calculate. Once you know the rough quantities then you'll have a more accurate estimate. Perhaps "net calories" of food could become a thing - how much is left after the initial input of energy. Absorption will be a different deal altogether - a factor that you'd need to get measured.
