I can recommend the book Burn by Herman Pontzer on this:

The human body can adjust the Basal Metabolic Resting Rate quite a lot in the face of exercise. Spending an extra 500 kcals on exercise can easily only lead to 200 kcals higher total energy expenditure. The body apparently will for instance reduce sex drive and immune functions when under regular exercise. So to achieve weight loss exercise alone is a very hard path unless diet is also modified.

On the other hand it has been shown that dieting alone without exercise also makes it very hard to maintain a lower weight because for instance exercise seems to curb feelings of hunger.

So yes: human bodies definitely are complex adaptable machines. CICO alone doesn't cut it.

Correct, and has to because the evolutionary time that we had at least 3 meals a day has been really short. The body is made for extreme conditions, conditions that it's no longer exposed to.

So it had to be smart with when to store energy and when to spend it.

Great question, because the latest science is pointing to that hormones determine the states of body. Example Insulin triggers storage in cells, and t3 from the thyroid has influence over the metabolism. Testerone has many influences and there many more For feeling full and feeling tired there are different hormones. And they are finding out how little we actually know. Turns out for example the out understanding of cholesterol was incorrect[0] and like calories the wrong focus. So research into the marvel that is human body is very basic at the moment.

thermodynamics is made for steam engines. Just like calories. Its science from 1800, a moment time where everything was powered by steam engines. So understanding how much we need of something to increase the heat of water by 1 Celsius is very important.

But cells are not like steam engines, they don't burn energy. They use atp, mitchondria create atp with the kreb cycle.

Our gut biome plays very important role in digesting food. Turns out that its different for every person even twins.

The gut biome is one the readons everone reacts a bit different to food.

Calories are still used as a proxy. Eat less Calories within a given dieet also means eat less food.

Then the question what should we do to lose weight. Many people have been helped by low carb dieet or intermittent fasting and even prolonged fasting. So in the end you could say that's still Calories. And to that I would have to agree. But it's how we get to same point.

There was actually a study that forced the participants to adhere to low calorie dieet. Hint it turned out really bad for them.

https://en.wikipedia.org/wiki/Minnesota_Starvation_Experimen...

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6082688/#:~:tex....

the physics of weightloss is straightforward (CICO), the chemistry isn't as much, the biology is mind-numbingly complex, and that's before we get to the psychology.