An excellent example is flour. Most baked goods are made of white flour (either partially or entirely), which has had the germ removed from the wheat. The germ is actually the most nutritious part of the wheat grain. When I scattered some wheat behind our old house in Bellingham to see if it would grow there, slugs came and ate many of the seeds, but only part of each seed. Guess which part they ate? The part they left is the only part that we consume in white flour. Seems to me that the slugs are smarter than most humans when it comes to nutrition.
My take on this is that we don't need to study nutrition textbooks to eat well. We just need to eat whole, unprocessed foods. If people weren't eating something a few hundred years ago, we probably shouldn't be eating it now. Michael Pollan has a great rule as well: Don't eat anything you've ever seen advertised.
My interest in farming is driven by a number of factors, but nutrition is a big one. Growing much of our own food is quite time consuming, but I think it's worth it.