>By the time the food you eat gets to the bacteria, there are no sugar, fat or protein left
You realize those bacteria are living off the fat, sugar and protein you consume right? They are essential to our ability to utilize the chemicals we get from these macro nutrients.
>Refined/processed food should be eaten in minimal quantities because it spikes blood sugar and causes insulin fatigue, which in the long run causes Type II diabetes. True, but this also an increasingly old school and one dimensional way of thinking about how type II develops. There are a host of genetic and environmental factors that effect an individual's response and eventual tolerance to insulin.
Sadly, being in med school does not guarantee you "know what you're talking about", in fact, even after you get to wear that white coat you'll probably realize you know way less than you could ever imagine. The perception that kind of attitude creates only narrows our minds and hurts our patients.
I'm done with med school.. and I realize on a daily basis I still have no clue what I'm talking about :)