• Calories are calculated based on either how much a certain amount of food heats up a certain amount of water when burned or just guessed based on how many of each macro the food has.
• This is NOT how your body converts food to energy
• Food calories are calculated via macronutrient amount.  So if a food has 100 grams of carbohydrates, it has 400 calories.  
• They do not differentiate between forms of carbs so if you adjust serving sizes 25 grams of carbs from sugar equals approximately the same as 25 grams of carbs from sweet potatoes.
• It is very hard to know how many calories you burn.  Not everyone that is the same gender, age, height, and weight have the same metabolic rate.
• The foods you eat affect how many calories you burn
• Processing food actually takes some energy, and certain foods take more. 
• Protein uses about 20% of the calories just to convert to a usable source of energy so 100 “calories” of protein is more like 80
• Hormone levels control exactly where nutrients and energy go within the body

I have a few personal experience that seems to support the fact that health and weight is way more than just calories.

• I generally do not eat breakfast.  More of a laziness in the morning than any type of specific health choice – though in the past I have experimented with intermittent fasting with some success.  I’ll leave that topic for another time.   Last year I went a few months where I had overnight oats every morning but did not change anything else in my diet.   These were approximately 250 to 300 calories.  They were lower sugar and higher in protein and fiber.  Over the course of a few months, if calories were all that mattered I should have gained a few pounds, but I did not.  
• A few months ago, I started using more natural honey for sweetening things instead of always using a zero calorie sweetener like stevia.  I don’t really measure how much I use, but most days I probably have an extra 100 to 300 calories.  This change coincides with some other food additions such as fermented foods though, so it is a bit harder to judge.  Overall, I lost a few pounds.

Calories were originally calculated using a “bomb calorimeter” and was essentially a process of burning food and measuring how much it heated water.  These days, they are mostly calculated by something called the “Atwater system” which as developed over a hundred years ago.  It assigns a certain number of calories to each gram of carbs, protein, and fat.  4 for carbs and protein and 9 for fat.  It does not ake into account how our bodies process food though.  Our bodies use a different checmical reaction to convert food to energy that is likely not going to treat all carbs the same.  Also, certain types of carbs, such as fiber, aren’t fully digested but are still counting as calories.  Protein takes energy to convert to a usable energy source.  This does not even take into account the protein that is used to build muscle, bone, or repair other tissues.  Fat can be turned into ketones which act different as well.  One way people on a keto diet measure if they are in ketosis is checking for the presence of ketones in their urine, which means that at least some of the calories they eat from fat are not being burned OR stored as fat, but being eliminated. 

How do you know how many calories to eat?  Guidelines will give you a number based on your height and weight, and your age and activity level if you are lucky.  There are way more factors than that, though.  I have a bit more muscle than average and if I plug my numbers into a system, I would be classified as as borderline obese.  While I’m not ripped with zero body fat I think most people would not say I am overweight, let alone obest.  Regarding my calorie needs, most systems do not take into account the muscle mass.  Everyone hopefully knows that muscle burns more calories than fat, so my base metabolic rate should be higher than the calorie needs calculator tells me.

Even two people with the same body size and activity level will not burn the same amount of calories though.  There are so many more factors such as hormones and even the temperature.  A large amount of our energy is simply burning to keep our mody temperature higher.  It may be a small amount, but a colder temperature makes your body burn more to keep the normal body temperature.  

Your body is processing food as you eat it and depending on your current needs, but all the calorie recommendations are per day.  If I eat 2500 calories in one meal and then 200 the next, according to the calculator I am within my range.  However, you are likely going to put on fat if you eat that much in one meal, especially if you are not eating the right type of food.

Some people might say, during the rest of the day your body will burn enough fat to offset that gain and that the calories in vs out model will still work, but I doubt it is that simple.  If I eat the wrong foods both times, I could be sending the hormonal signals to store fat even though I am not eating much the second meal, or the hormonal changes can take longer to change so the first meal is still affecting the fat burning vs. fat storage equation during my small second meal.