I am an obesity researcher and I think that in some sense the idea that we are programmed to eat and to store fat for lean days is correct, and that our current environment of abundance combines with this innate tendency to increase the prevalence of obesity. But this general statement hides many unknowns. For example, why are some people more prone to weight gain than others (in the same environment)? Why is obesity heritable (20-80% heritable depending on how you calculate it and the population you use)? Taubes is absolutely correct in stating that the "low-fat diet" mantra was promoted without any evidence to back it up and the evidence we do have seems to favor low-carb diets, at least in the short run. Fructose (and its not just high fructose corn syrup...sucrose is 50% fructose, HFCS is 55% fructose) does indeed seem to be deleterious above and beyond just adding calories, but its not the whole story either. Toxins and endocrine disruptors may play a role, but we really dont know too much about that yet.
Bottom line: the notion that we know NOTHING about nutrition is false. But the notion that we know all we need to know about diets and obesity is also false. The notion that higher carb intake is responsible for most of our increased weight gain is plausible (supported by data about total carb intake in the population..its the only macronutrient that has actually increased in per capita consumption. Fat intake has declined in the last 30 years, yet weight gain has accelerated) but not the whole story either.
Its also worth keeping in mind that there is no one-to-one correlation between obesity and particular disease outcomes (diabetes, heart disease). On a public health level, there is an increased risk, but there are a very large number of "healthy obese" people; there is good evidence that modestly obese adults trying to lose weight have higher mortality than those whose weight remains static or slightly increases; there is very good evidence that most diets and other prescriptions dont work and lead to yo-yo weight change that may itself be unhealthier than the baseline moderate obesity; there is good evidence that lack of fitness is a far more significant risk factor for morbidity and mortality than BMI (in adults), and so on....the "moral panic" about obesity is not always grounded in sound science.
"Prevention of obesity" by focusing on weight gain in children may bypass some of these concerns, but we have to be careful to see if we are responding to a fashionable moral panic or focusing on truly evidence-based fears AND interventions (even if the fears are real, all responses are not automatically justified; some responses to the disease may be worse than the original disease, others may be ineffective and hence a waste of time and money)?