The discovery of vitamins led to Wonder Bread, when we thought that we could make highly processed white flour healthy by adding vitamins. We now know that Wonder Bread, despite the vitamins, is one of the least healthy things you can put into your body since it basically converts directly to sugar. And that's just one example, the middle of a supermarket is replete with boxes of processed foods which claims to have added healthy stuff that have consistently made the people who consume them less healthy than the people who get their food from the produce and deli aisles, where there's no added vitamins and no such health claims.
If we've learned one immutable truth from recent health studies, it's that we're really bad at constructing foods that are healthier than what nature has already constructed. That's not to say that we shouldn't continue to try to learn about what's in the foods we eat, but that information should be used to constitute a diet of natural foods rather than foods engineered to be healthy.
Research, especially when it's reported without understanding like the media typically does, leads to fads that almost always turn out to be wrong. It's how we spent 4 decades trying to eat low fat which led to the highest obesity and diabetes rates ever. Meanwhile, those eating traditional diets based on the foods that their ancestors have eaten for generations are consistently healthier. Given that we know so much more about vitamins and minerals than they do, how is that they're so much healthier than us? If our understanding of vitamins hasn't made us healthier, is it really a big step forward?
[1] https://metasteve.wordpress.com/2010/02/14/in-defense-of-foo...
Nixtamalization is an easy example of a process that enhances nutrition. Perhaps the world would be better if people were not constrained to eating so much corn that it mattered, but that isn't the world we have. The list of beneficial processes goes on and on and on, but I like that one because it involves adding caustic chemicals to a starchy grain. Another good one is pickling. Controlled rotting with those hip probiotics!
The issue with modern food science isn't that it is over reductionist nonsense, it's that it is used to decrease satiation and increase palatability. It turns out that when huge resources are devoted to figuring out how to get people to eat more, you get results. I cringe every time I see Sabra Hummus advertise their great new idea, a fourth meal where you and your family cram Sabra Hummus in your mouth.
I certainly hope we can take our medical understanding of diet and nutrition to a place where it is easier to help people lead healthy lives, but I'm not going to sit here and look at the elimination of deficiency diseases as the start of some sort of modern disaster.
[1] http://www.newyorker.com/magazine/2014/05/12/the-end-of-food
The average American meal is not a healthy, fulfilling group activity. Soylent is there to replace those meals and free up time and money to more frequently enjoy the other type of meal (or whatever else you might want to do with your time).
"How does changing the raw materials going into this mind-bogglingly complex collection of biochemical processes we call a body affect the whole?" is a rather difficult question to answer.
I love this website for health science news and wish there were more like it: http://www.nhs.uk/news/Pages/NewsIndex.aspx
In each article they break down what the actual study was, how robust the evidence is and what it says in the context of other research which you never see in mainstream press.
For example, this article traces a flurry of headlines in the mainstream press about the importance of breakfast back to the original research and critically looks at the evidence in depth: http://www.nhs.uk/news/2014/08August/Pages/Breakfast-not%20t... It nearly always end in "needs further study" but it's sad there's no incentive for news outlets to have more accurate science reporting.