[Frost1x]

Your body isn't 100% efficient, some energy will be lost so assuming you have a perfect measurement of intake and expenditure, you're not completely sure how much of the intake your body has consumed. There are some estimates of these things. One thing you can do though is if you understand how your body metabolizes certain foods, you can measure the upper bound of energy consumed. With accurate measurement you can say that your body couldn't possibly have gained more energy from this given food than this amount. You can then use that upper bound figure to try and guide your expenditure. If you make sure your expenditure meets that upper bound and still creates a deficit, you know the deficit is at least that amount, likely more since 100% energy conversion isn't feasible.

External factors certainly come into play like environment. You're not a completely closed system as you point out based solely on food. You may sit in a cold office shivering throughout the day or in a hot room sweating, these factors will effect your energy expenditure (and even intake) differently just to maintain your existence.