Most of nutritional "findings" are based on sketchy statistics run on inaccurate data obtained from really bad experiments. If anything, what little evidence there is suggests that there may not even be such a thing as "healthy" or "unhealthy" food, but food that may be more or less healthy for a specific individual. And what is more certain (from large scale statistics) is that the effect food has on our health (within a reasonable margin) is quite small in most healthy people without some genetic anomalies. What makes it seem large is simply magical thinking (or placebo, if the two are different).
Which raises the far more interesting question of why is it that otherwise scientifically minded people treat nutrition as a science rather than the "science" it really is? The psychologist and anthropologist Jonathan Haidt believes that this is a psychological manifestation of a drive for "purity" (one of several common moral drives he's classified in many societies) as it expresses itself among some people, especially liberals. He says conservatives channel purity to sex and liberals to food. He says people in all cultures believe that some behaviours contaminate us; conservatives tend to think those behaviors are sex related, and liberals think they're food related. Which is why accounts of people "feeling more energetic" after changing their diet read just like conversion stories -- they are simply two manifestations of the same phenomenon. And just like what religion people convert to doesn't matter, the accounts of being "more energetic" and "feeling better" are the same no matter what diet people switch to (of course, sometimes you read other accounts, but such is the nature of placebo -- it's complicated). As long as there is the slightest excuse to justify a particular choice of diet -- and in the case of science fans that can be a "science" paper -- psychology kicks in.
Second, there's a world of difference between saying something is related to nutrition in general, saying it relates to some global nutritional variable such as calorie intake, and saying something relates to a more specific nutritional variable such as intake of animal fat. While making each of these statements may be dubious due to the inherent difficulty of doing any sort of nutritional research (it must be observational and longitudinal, and there are too many confounding variables), at each of these three levels of nutritional explanation, there are so many more variables being added, so that to prove the third one you'll probably need many more samples than there are people on this planet. The dimensionality is just too big to tackle with statistics.
Imagine that the real explanation could be something like: amount of animal fat consumed between the ages 0 and 13, and unrelated to anything consumed later. Or it could also be that the same causes of diabetes also reduce the chance of, say, brain cancer, and so what we're seeing is actually a good thing. There are just too many variables, especially that we know food interacts in very complex ways with anything from hormones to gut flora.
What we can say with certainty is that life expectancy has been increasing steadily (not at a steady pace, of course) since the industrial revolution, and that it is very similar among all industrialized countries. The variations are hardly more than a couple of percentage points in spite of sometimes very different diets, different levels of pollution, different amounts of sunlight, different occupations, different leisure activities etc. So countries are so different, yet life expectancy is almost the same everywhere (in the industrial world, of course). Another thing we know for sure is that life expectancy in the developing world is much, much lower.
Of course, rather than clinical studies -- or "clinical", as nutritional studies are observational and wildly confounded -- one could try to study nutrition through biological metabolism, but we're probably decades away from having a really good grasp of human metabolism.
Yes, but the whole point of the article is that what we consider today to be whole, unprocessed, natural foods are in fact:
* Selectively bred for digestibility and taste
* Only affordable thanks to agriculture becoming a mass-production industry
Plus, even if we did, nutrition is not a simple thing that we have all figured out. So even assuming the best of intentions from everyone involved, it's still a big leap that chopping everything up into its constituent parts, then reformulating it to be as tasty as possible (while still meeting nutritional standards of course!) is going to result in a healthy diet.
In this light, eating whole foods is not about declaring the superiority of "natural" foods, it's just a hedge against the ignorance and mis-aligned incentives that exist in the industrial foods industry.