Let me attempt to distill the argument down to its essentials. It has both a negative and a positive aspect. The negative is its criticism of current nutritional science. The positive is its construction of a causal arrow to explain the explosion in obesity and its associated diseases. I'll lay out the positive first. (I will simplify but will take care to say nothing flatly false.)
Let us consider the so-called SAD - the Standard American Diet. It is a diet rich in sugars and starches. The root cause of obesity in those who eat the SAD, Taubes argues, is the quality of the calories ingested. When we eat carbohydrate-rich foods such as sugar, wheat, rice and potatoes, this leads to a spike in insulin. This spike in insulin results both in an increase in fat stores and in an too-early onset of hunger. This hunger is again sated through ingestion of sugar and starch, and thus we circle back again to fat storage and resurgent hunger.
If this is so - if, as Taubes argues, the root cause of obesity (and its attendant diseases) is the quality of the food we eat - then to attack the root of the problem, we must change not the amount but the kind of foods we eat. We must, in a word, cut out the carbs. The sugars must go; the starches must go. They must be replaced by an increase in fat and protein. (Just how much of each? This is not the place to answer, but I will say that we must lose our fear of fat. Fat does a body good.) If this is so, the body will no longer find itself in fat-storage mode. Fat stores will be released; pounds will be shed. Moreover, the body will seek out its proper weight, and the maintenance of that weight will be just as much a matter of homeostatic equilibrium as is body temperature. If we give the body the proper sort of food, then the body will adjust to fluctuations in caloric intake so that it might maintain an ideal weight. Less than is necessary and it will raid its own fat and protein stores; more than is necessary and it will "turn up the thermostat" and simply burn the excess calories off.
Now let's consider the negative aspect of Taubes' argument. This is his brilliant critique of the diet and nutrition and status quo. That status quo would have us believe that the body does not seek out an ideal weight, that it will always put on extra weight if fed an excess of calories. It will not adjust. It will burn calories at the same rate no matter what we eat or how much. If this were so, then to attack the root cause of obesity, we must simply convince the obese to eat less, and indeed this would be the only way to attack the obesity epidemic. Obesity is, on this view, a matter of behavior and behavior alone. The obese choose to overeat, and as a result they grow fat.
Taubes' objection to this is that it gets the direction of the causal arrow wrong. Of course the obese eat more than they use; if they did not, they could never have gained weight. But that this is so does not imply that their overindulgence is the cause of their obesity. Indeed another hypothesis has much stronger empirical support. The other hypothesis flips the direction of causation. On it, we aren't fat because we overeat. Instead it would be much closer to the truth to say that we overeat because we are fat. The same mechanism that drives fat accumulation - spikes in insulin production - is the very same mechanism that drives us to overeat. This mechanism is the product of the quality of the food we eat. It comes about because we eat too little fat and protein and too much carbohydrate.
Here's a little suggestion. Give a low-carb diet a try for two weeks. Cut out all sugar (except for the minimal amounts contained in low-carb vegetables). Cut out all grains and potatoes. Eat meat and fat to satiety, and make certain that those fats are of the "old" sort - tallow, lard, butter, olive oil and nut oils. Observe your weight. Compare your new energy levels to those from before. (You might feel unwell in the first few days. Some do, some don't. The body has to undergo a basic metabolic transformation. It has to transform from a machine that burns carbs to one that burns fat.) I do believe that you will find that Taubes' arrow of causality is the right one. You won't be hungry, but you will begin to burn off your fat stores and lose weight; and if you're anything like me (or the thousands of other folks who've done the same) you'll feel great.