I haven't read Taubes' books, but I have read some of his blog posts and here's how I understand this position. I'm not very certain that my understanding is correct, but maybe this will help.
He agrees the "simple thermodynamic" calories in - calories out = weight gain model is (necessarily) true. But he thinks it's misleading and isn't helpful, because it focuses on the (high) calories in and (low) calories out as the causes of weight gain, as if they were solely and directly influenced by deliberate behavioral choice. He says they are proximate, not ultimate causes, and are mostly determined by various complex metabolic states. And these states are in turn influenced, among other things, by the makeup of the diet - rather than just by its caloric value.
So if not conscious behavior, what determines calories in and out? For instance, various metabolic and hormonal states determine the level of hunger, food cravings, etc.
What his epiphenomenal claim means, if true, is that the causal graph doesn't look like this:
Decide what and how much to eat => Eat as decided => Lose or gain weight
But like this:
Eat something => Metabolic state changes depending on diet => Hunger levels and specific cravings change in response to metabolic state => Eating behavior changes in response to hunger.
And in particular:
Eat refined carbs => hunger levels rise, more food cravings => end up eating more => weight gain, sometimes in a runaway positive feedback loop leading to obesity.
On his blog he goes into a lot of detail about the biochemistry of hormonal signals relating to hunger, and to fat storage and release; I can't really follow those discussions.
Eat something => Metabolic state changes depending on diet => Hunger levels and specific cravings change in response to metabolic state => Eating behavior changes in response to hunger.
Looks reasonable. Are you sure you're not steelmanning his position?
Previously: Mainstream Nutrition Science on Obesity
Edit: In retrospect, I think it maybe should have combined this post with part 3. Unfortunately, the problem of what to do with existing comments makes that hard to fix now.
Taubes first made a name for himself as a low-carb advocate in 2002 with a New York Times article titled "What if It's All Been a Big Fat Lie?" When I first read this article, I was getting extremely suspicious by the second paragraph (emphasis added):
It's one thing to claim that, all else equal, low-carb diets have advantages over low-fat diets. It's another thing to claim you can eat unlimited amounts of fatty foods without gaining weight.
I'd heard of Atkins before but didn't know much about him. I got curious to know more about the man Taubes was casting as the hero who just may have been "right all along," so I popped over to the Wikipedia article on the diet, which says:
The last sentence of this paragraph is helpfully marked "citation needed," leaving an unresolved conflict between whatever Wikipedia editor wrote the paragraph and what the Atkins folks (at least now) claim. I ordered a used copy of the original 1972 edition of Atkins' book through Amazon, and what I found supports the Wikipedia editor. The folks currently in charge of Atkins Nutritionals are white-washing.
The sensational "truly luxurious food without limit" quote in Taubes' article, for example, can be found on page 15 and comes with no context that would make it more reasonable. In fact, lest anyone misunderstand it, it's followed by a statement that "As long as you don't take in carbohydrates, you can eat any amount of this 'fattening' food and it won't put a single ounce of fat on you." (In the book, this is italicized for emphasis.)
Atkins acknowledged that most of the people who used his diet ended up eating less overall, but claimed that some of his patients had lost significant amounts of weight eating 3,000 calories per day or more. In one case, Atkins claimed, a man had lost fifty pounds on a diet of 5,000 calories per day. He attempted to explain this by invoking the fact that extremely low-carbohydrate diets will cause people to excrete ketones (which Atkins referred to as "incompletely burned calories") in their urine. However, as a statement on the Atkins diet put out by the American Medical Association explains:
As far as I can tell, nobody today defends Atkins' original "ketones in the urine" explanation for how his diet supposedly works. It's not entirely clear to me what was going on with the patients Atkins claimed lost weight on a high-calorie diet, but it wouldn't be surprising if a minority of his patients had simply misjudged their caloric intake. In spite of this, Taubes still appears to want to defend Atkins' most extreme claims about people being able to eat unlimited fat without gaining weight.
This isn't entirely obvious when you read his books Good Calories, Bad Calories or Why We Get Fat, which go for a slightly less sensational presentation than the Times article. Nevertheless, in the epilogue to Good Calories, Bad Calories, he claims that "Dietary fat, whether saturated or not, is not a cause of obesity, heart disease, or any other chronic disease of civilization." There's a sense in which that claim might be somewhat plausible, if he meant that it's total calories, not fat per se, that's the main culprit in all those problems. But Taubes also puts a lot of energy (no pun intended) into attacking the mainstream emphasis on calories.
Why We Get Fat, for example, contains claims such as:
No effect? That's a strong claim. And as we'll see in the next two posts, Taubes' evidence for this claim ends up consisting largely on a series of misrepresentations of mainstream nutrition science, which allow him to present his views as the only alternative once he's knocked down his straw men.