that calories are not calories
You're evidently trying to switch us to talking about a literal unit of energy which is not what we were actually talking about. We were talking about types of foods, i.e. carbs vs protein vs fat.
Your argument was that the type of food does not matter because they all get turned into calories equally across all people in the end, and therefore a simple math formula trumps all else. My argument was that the type of food does matter and what the body does with each type of food is based on more complicated things like endocrinology, metabolic syndrome, insulin sensitivity, genetic factors, biochemistry, cellular metabolism, and so on.
You're accidentally confusing energy with physical materials. If I search a cup of sugar, I get 773 calories. If I search a 14 ounce steak, I get 798 calories. Let's just say hypothetically they had come out exactly equal. I don't treat a cup of sugar equal to a 14 ounce steak, but you are treating them equally. That's essentially the difference in our thinking.
When I talk about CICO being wrong, when I talk about a calorie is a calorie is a calorie being wrong, I'm saying a human body will not do the same thing with 800 calories of beef that it will with 800 calories of sugar. Not only that, but different human bodies will not even do the same thing with 800 calories of sugar. Some people just pack it away into their fat cells. Diabetics are even weirder. A type-2 diabetic can eat the steak but not the sugar. A type-1 diabetic can't eat either (without an insulin shot) because of a process called gluconeogenesis, where protein is converted into a form of glucose. The type-1 could literally consume ZERO dietary glucose and their blood sugar still would shoot sky high.
And I think you're accidentally being literal to the point of absurdity here, which to me is another example of moving the goalposts as well as a straw man. If we're going to be that literal, we may as well start saying that a person can consume things like wood chips or grass, which we can't break down at all from but certainly has energy because it has mass, and E=mc2. I mean as long as we're talking literal physics, let's talk literal physics.
Here's another example. Some people have more AMY1A copies in their genome, and they therefore have more of an enzyme called amylase in their saliva. Those people can break down and use starches and glucose more efficiently than the rest of us. And the crazy thing is that amylase is only a small piece of the puzzle of starch and glucose metabolism. It's just a single gene. ONE.
Intuitively you might think someone who cannot break down starch would not have high blood blood sugar after consuming a lot of it, but just the reverse is what happens in experimentation. The point is, just one single gene in our DNA plays a role, but by no means is it intuitive to understand the way it works with our overall metabolism.
I know it makes me sound like I'm not listening, but nothing you've put forward has convinced me that our bodies can make fat while at a calorie deficit. I'm not convinced that calories are not calories, because that in and of itself is a nonsensical statement. You're saying that some people don't absorb different food the same way, but that changes nothing about the energy content of the food. I firmly believe that with calorie restriction, I would lose weight even after being induced with diabetes and such. At the very least it would be impossible to gain weight on a calorie restricted diet. To do so would imply that I have misjudged the calorie content of what I'm eating. Seriously, check out the show Secret Eaters. They show how people constantly misjudge the calorie content of their diets, thinking they are eating low and gaining fat, when in reality they are ignorant to their own actions and sometimes in denial.
I think there are a lot of accidental straw mans in your statement but actually that none of this is really your fault. I think the main problem is that the second law of thermo is one of the easiest things to understand in all of physics, and a lot of people stopped investigating further after they learned it. There is a lot more to physics, biochemistry, biology, etc. that takes really hard work to grasp and, frankly, a decent intelligence (and these were people working for the government, so...). Rather than put in the hard work of learning everything that goes on in the human body, these people stopped after they figured out possibly the easiest law to understand in all of science (not just physics). And I honestly think this misinformation and FUD was just spread from there. It could have even been the Dunning-Krueger effect, where they didn't see very simple flaws in their thinking due to sheer ineptitude.
This all reminds me of the 100 Authors Against Einstein scientists who simply did not understand relativity. Those guys were not successful at spreading their way of thinking, but the folks giving us nutrition and dietary advice were successful. And it's a damn shame they spread this way of thinking about this topic, because now it's just part of the zeitgeist, and once a bad way of thinking takes root it's very hard to get people to change.
As Max Planck said: Science advances one funeral at a time.