The key of any healthy eating system is to get your body working as efficiently as possible. Low fat, low carb, low calorie, exercise-rich, etc. - all of them aim to get the proper mix of nutrients into you, enough protein for your muscles, enough fats for your brain, enough carbs for your energy, etc. They all require you to have exercise on a regular basis to keep your body healthy. Pretty much all diets have something to say about uppers, amphetamines and caffeine and tobacco. These are not things that are good for your body.
So why in particular do things like uppers and caffeine get nixed? Your aim in a healthy eating system is to have your body running smoothly. You want slow, even infusions of energy. You don't want your blood sugar to spike. So the same is true for caffeine. Caffeine causes spikes in blood pressure - not good for your body. It is a diuretic, which interferes with your water levels. It leads to insulin resistance.
Here's more details on exactly what caffeine does -
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