The reason for this is simple. For 99.9% of human existence, our species lived on foods that were either raw or minimally processed. The technology needed to increase food processing did not exist until very recently. It is therefore reasonable to assume that our bodies are best adapted at utilizing and dealing with the raw or minimally processed foods which sustained us, and our predecessors, for millions of years: fruits, vegetables, meats, nuts and seeds.
Often, the more recent the food is, the more likely it is to be less beneficial or even directly harmful - possibly due to lack of full adaptation to such foods. For example, it is estimated that food cooking started about 500 000 - 250 000 years ago (depending on the source, the range may vary). During this time frame, it is likely that human species have at least adapted in some way to very simply cooked animal and vegetable foods. On the other hand, the beginnings of grain consumption are much more recent. Evidence of earliest known, systematical collecting of grains for food goes back to about 23 000 years ago - giving less time for adaptation to grain based foods.
Now, let's fast forward to recent times and consider all the new, human invented, highly processed foods so common today: fast foods, pizza, sweets, chips, convenience foods, canned foods, etc. along with the dramatic rise in heart attacks, high blood pressure, stroke, cancers, diabetes, liver and kidney problems (and all the complications that arose from these conditions) during the past 100 years or so.
Considering the declining health of most western nations as opposed to good health of the ethnical groups described above, it seems reasonable that the most recent food inventions are directly harmful to human health. Further, it has been repeatedly observed that as ethnical groups around the world adopt the modern western diet, their health dramatically declines and they develop the same diseases that are so common to westerners. Not to mention the fact that the above listed diseases were far less common among westerners themselves barely 100 years ago.
The more food is processed - through excessive cooking, pasteurization, homogenization, high heat, mechanical processing, etc, - the less natural and nutritious it becomes to a point of becoming a harmful burden to the body, rather than a useful and health promoting food. Some industrial processing practices deprive food of their nutrients to such high degree that the food has to be "enriched" by artificially adding some nutrients back into the food. This is especially true of flours where some vitamins are added back after the processing is done.
A good diet is based on natural, whole or minimally processed foods. A large portion of it should consist of foods that can be eaten raw, such as fruits and vegetables. Fermented or cultured, unpasteurized foods such as kefir, yogurt, cheeses, miso, sauerkraut and pickles are considered highly beneficial in many cultures. Cooking should be minimal and only applied to foods that must be cooked in order to be edible. Ancestral heritage also plays an important role as certain foods may need to be excluded or emphasized.
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