I'm not an expert at all, but I have read and watched a fair bit on this recently. I tried to explain a little bit of "why we get fat" to you in the post you quoted.
But here's a pretty good animation taken from the anti-Super Size Me documentary "Fat Head" that might help clear up the concept.
The short of it is that not all calories are equal, which is the fatal mistake we make when we merely talk about calories. It is the reason why the "calories in calories out" idea doesn't make sense and definitely doesnt help people that want to lose weight. The fact is the body responds to different kinds of calories in different ways. It is not controversial that there are "good" carbohydrates and "bad" carbohydrates. The bad carbs being things like sugar, better carbs being things like oats. Oats are said to be a lower GI food, and sugar is a high GI food. The gycemic index is to do with how fast the carbohydrates will covert to glucose in the gut. Sugar converts quickly and for that reason can provide a quick burst of energy, while something like oats converts much slower and so the rate of energy provided by the glucose is at a more sustained period of time.
It is well understood that consuming a high GI substance like sugar may give you a burst of energy but you use it up quickly, and so you get hungry again faster. This is why its uncontroversial to say that you should significantly reduce sugar intake if you want significant change in reducing body fat, that you should eat low GI carbohydrates to provide longer lasting energy "so you feel full for longer." We know that the hormone
insulin drives fat storage and stimulates fat cells to take in glucose. Insulin is released prominently when we eat carbs, because carbs convert to glucose and that needs to be dealt with. If we eat too many foods that spike our insulin too much for too long our body can't cope and we can become insulin resistant, which can lead to diabetes. All that insulin can lead to obesity/weight gain because insulin causes the fat cells to become greedy and not release their energy easily when you need it like it's meant to. Meanwhile, your body thinks it's starving and it tells your brain to eat more despite having all this stored fat.
So now you've now got a metabolic disorder, and are much more inefficient at fat regulation. Someone that doesn't have this problem can eat much more than you, while you can still put on weight eating less. If someone with a metabolic disorder follows the typical guidelines for a healthy diet, the very diet that may have got them into the situation in the first place, they will continue to base their diet on carbohydrates. Even if they reduce simple sugars, they may consume foods that can have the same or even higher GI than sugar has. We even have the Heart Association saying foods are "heart healthy" that are high GI and significantly spike your insulin levels. They might have some success but only because there's less energy for the insulin to push into the fat cells. They keep their fat levels low since that's what they are told to do, so their body is crying out for energy which is why so many rebound and can't keep the diet up. When it comes to exercise, exercise itself doesn't burn many calories. What it will do is increase the appetite, which will then cause them to want to eat more. So they'll eat the same foods that was causing them to get fatter, except they'll eat more of it. Since they are still eating a high carb diet they will still crave sugar and so also be more prone to cheating. The reduction in appetite alone on a low carb diet is a non-trivial aspect of weight control, even if it really did come down to "calories in calories out" the recommend high carb low fat diet is still a very bad idea.
In regards to losing weight because you're in a calorie deficit diet, I'm going to quote from someone on another forum: 'Taubes often used the example of a growing child. A child grows because of growth hormone, and then eats more to compensate. We could retard this growth by caloric restriction, however it would not stop growth hormone itself. The growth will still be driven by GH, we'd only restrict the materials needed for this growth to be realized. In a similar fashion, we could reduce obesity by caloric restriction, but it wouldn't stop the cause of obesity, we'd simply restrict the materials needed to sustain obesity. On the other hand, if we stopped the cause of obesity directly, the materials needed to sustain obesity would not be needed anymore, and caloric reduction would spontaneously occur.'
I recommend you give him more of a shot than this. The person immediately misrepresents him, ironically while also talking about strawmen.
Here is the first few obvious failures on the part of the writer you linked me to:
1. He implies Taubes is saying the laws of physics don't have anything to do with weight gain. That is not what Taubes is saying. He is saying that it is not as simple as "calories in calories out" and the "law of thermodynamics" is not being applied correctly to the human body when people argue against what he is saying. It reminds me of evolution being said to break the law of thermodynamics, which it does, so long as you make false assumptions as to how the earth/universe works.
2. He says Taubes believes reducing calorie intake cannot work. This is also not accurate. As should should be clear from the example I gave earlier, it is not that reducing your calories won't necessarily cause weight loss it's just that it isn't getting to the root cause of why you are putting on weight. When we are growing we have growth hormone flowing through us and we eat more food to compensate for that. We can stunt our growth by reducing our caloric intake, but that doesnt mean eating was the reason for us growing, it was the growth hormone. We ate more because the growth hormone needed us to eat more.
3. He talks about how some people are more efficient at storing calories than others, and even says Taubes is right when he says people get fat due to the way their fat is regulated, but then says that it's all still about how many calories you consume anyway. If you took two people with very similar body types and gave them the same food and they did the same exercise then the assumption of "calories in calories out" means we would have to assume they both get fat, or both lose weight, at more or less the same rate. Why? Because they would both be consuming more or less than the calories they were burning. Yet as this person already recognises some people have bodies that are very efficient at storing calories and handling fat regulation, and some are not. If an obese persons body is inefficient at storing fat and has a metabolic disorder, then telling them they are just eating too much completely misses the point of why it is happening. They may well be eating more, which could be due to their metabolic disorder making them eat more (the same way a growing child filled with growth hormone is driven to eat), or they could be eating the same thing a sedentary slim person eats who has a body that has a healthy metabolism. If it is the former, then just like with a growing child,
maybe eating more is the symptom not the cause of their obesity. This is why its absurdity to reduce obesity and gaining fat merely to terms of "calories in calories out", which ends up being practically meaningless and hardly tells you anything.
4. Skipping ahead he seems to be unaware of just how debunked the idea that fat's cause heart disease, especially in recent years.
This article does not seem like it is written by someone who has more than a superficial understanding of what Taubes is saying, or there is some intentional or subconscious tendency to misunderstand him.
I know, its a bad typo habbit.