"...it sets up a health amount of skepticism towards the idea that our innate cravings are in fact harmful."
It's modern processed food that's harmful.
We evolved to cope with the amount of salt, sugar, carbohydrates etc. that was readily available to our ancestors on a hunter-gatherer diet (we would've reached an evolutionary dead end otherwise if our "innate cravings" were not useful to us in a survival sense) - you would have to do a lot of hunting and gathering to get the amount of salt, sugar, saturated fat etc that a single fast food meal provides - it was relatively rarer so we have cravings to ensure we got enough of them back when they were scarce.
Evolution is a very slow process. Adding syrup to carbonated water, advertising the crap out of it and selling it at huge markup (coca-cola) can happen over the course of a single human's lifespan.
There is a common belief that meat and especially fat are bad for you and cause heart disease, which is the particular idea that Fat Head makes fun of. He reduces his carb and sugar intake and lowers his cholesterol and loses weight.
I quit drinking soda and reduced my sugar intake because it made me feel bad. I sometimes crave sugar after running a lot or when I'm tired and I will occasionally drink a soda, but I usually regret it. Same with candy etc.
I can only speak for myself, but the idea that my natural cravings and the reaction of my body are good indicators of what is healthy has been very successful for me. I currently believe that fat and meat, plus vegetables are very health and I crave all these things. My body is very sugar sensitive and so I avoid it because of how I feel. The guide that my evolutionary tastes are not trying to kill me seems to be a pretty good guide towards finding a healthy diet, and I believe it will serve me better than the National Health Services recommendations have. If you believe that there is good reason that evolution may be guiding you towards something unhealthy, you may be right, but my default answer is the it is correct unless there is a better explanation.
I don't think there's any doubt about this. Compared to evolutionary rates, the typical diet in the west has changed at lightning pace from just a few decades ago, meaning our bodies and taste buds are behind the curve. We need willpower and common sense to have a healthy diet, rather than raw survival instincts.
Unfortunately what's driving change in our diet is the demand for companies to serve food with high profit margins and low cost raw materials (e.g. high-fructose corn syrup). Capitalism is great for providing us with cheaper clothes and ever-cheaper computing power, but providing cheaper food means providing crappier food. There's no Moore's Law for food.
I think it was here on HN I read about studies done in remote communities (possibly some remote whaling community) that had recently become westerised, and the diet quickly shifted to one more similar to a typical American diet. Within 5-10 years (or a relatively short time frame, can't remember exactly) obesity and type-II diabetes rates exploded.
Another interesting story was reports from surgeons who operated on injured Afghan fighters from the current conflict. Normally when operating on westerners, you expect a certain amount of yellowish fatty tissue surrounding the major internal organs. This wasn't present on Afghan locals, which surprised the surgeons who were so used to seeing it on western patients and pretty much assumed it was normal up till that point. The difference was down to diet.
There are other fun examples. One is that our breathing reflex is based on CO2 concentration being too high rather than O2 concentration being too low, even though O2 concentration is more important! Breathe into a closed system with a CO2 scrubber in it and you'll quickly get loopy and then pass out from lack of oxygen (and then die, if nobody disconnects you) all the while feeling fine. Another is that the iris of the eye responds to visible light but protects against more. Looking at the Sun is normally OK (uncomfortable, but tolerable) because the feedback is set up properly, but during the totality of a solar eclipse (which of course occurred back then, but not often enough to matter, apparently) your iris will crank open and let in tons of UV from the Sun's still-visible corona, frying your retina if you look at it.
It makes a great deal of sense that we'd evolve strong cravings for things which are good for us in small quantities but bad for us in large quantities when those things were scarce in the distant past, and death came early by other means for other people, well before a bad long-term diet could kill. That doesn't mean this must be what happened, but given how much humans love sugar, and how rare concentrated sugar would have been for our ancestors, it's no surprise if sugar turns out to be bad for us when consumed in the quantities we really want.