The key premise is that the safest and healthiest foods are those to which we have had the longest exposure and therefore the greatest opportunity to adapt. Adaptation means that our bodies have ways of either utilizing or defending itself against the substances in the foods.
Until agriculture was developed it was impractical to eat grains, since gathering them would have been extremely time-consuming, with relatively little nutritional payoff. The bran of grains tend to contain anti-nutrients such as phytic acid, which inhibits the absorption of calcium and other minerals, thus contributing to calcium depletion. This can be avoided if the grains are refined, disposing of the bran, but what is left is a carbohydrate relatively high in calories and low in nutrients: flour. By processing the grains, most of the nutrients are lost along with the anti-nutrients. Many grains also contain proteins, such as gliadin, that can cause difficulties with the human immune system, sometimes damaging the intestinal lining. Legumes, which contain similar anti-nutrients, might have been eaten in small quantities. It would not have been practical to rely on them as a main protein source.
In addition, for the body to utilize carbohydrates as fuel, it must have thiamin (vitamin B1) available as a catalyst, along with other B vitamins. If these substances are not available in adequate concentrations, the carbs cannot be burned and must therefore be stored as fat. The more carbs one eats, the more B vitamins, and especially thiamin, one needs. But processed carbohydrates have only minimal amounts of these vitamins. The vitamin depletion of processed foods may have another, even more insidious, effect, i.e., making us more susceptible to heart disease by allowing levels of homocysteine in the blood to rise. Homocysteine is a substance that some scientists believe causes particles to adhere to arterial walls, eventually becoming plaques. Although the proteins in meats cause the production of homocysteine as a by-product, this shouldn't be a problem if one is getting plenty of folic acid and B6 at the same time. But if the meat is overcooked or processed and one is not eating fresh fruits and vegetables, these substances are not present in quantities sufficient to control the homocysteine levels. The problem is not the meat we are eating but the fruits and vegetables that we are not eating. For more information on homocysteine, have a look at this Kilmer McCully interview.
The typical diet of the hunter/gatherer consists of balanced amounts of animal and plant foods, minimally processed and cooked --- often raw, in fact. Carbohydrates, which are converted to glucose by the body, are found only in plant foods. They provide quick energy by raising blood glucose levels, but those elevated glucose levels in turn stimulate the release of the hormone insulin, which triggers the storage of extra calories as fat. Protein has a modest effect on insulin, but also triggers the release of glucagon, a hormone that opposes insulin, stimulating the release of stored fat as fuel. To lose weight, you want to keep insulin levels fairly low and have enough glucagon around to get the fat burning. This is best achieved by eating generous amounts of protein and moderate amounts of carbohydrates, since carbohydrates cause little glucagon release. When we eat large amounts of carbohydrate-dense foods and little protein, we cause insulin levels to be more elevated, with resultant storage of fat. This is another reason why foods such as pasta, rice, and potatoes are to be avoided.
Of course, there is protein in plant foods, especially legumes. The problem with using these as a primary protein source is that in most cases there is a good deal more carbohydrate than there is protein. Many beans are quite starchy, in fact. The best source of protein is therefore meat and eggs. It is a fact that some people have a poor response to the saturated fats in meats, resulting in unfavorable cholesterol levels (Although there is still much controversy as to what is "unfavorable"; See The Cholesterol Myth). Ancient humans would have eaten meats that were relatively low in saturated fats, compared to modern feedlot corn-fattened cattle. Recent research suggests that it is not the amount of fat in the diet that matters, but the kind of fat. In particular, it is important to get a balance of the so-called omega-3 and omega-6 (n3 and n6) fats. The n3 fats are found in oily fish, such as tuna, sardines, salmon, and mackerel. They are also found in the fats of wild animals. They are not present in significant amounts in the fats of domesticated cattle. They are also not present in very appreciable amounts in most polyunsaturated vegetable oils, with the exception of flaxseed oil and canola oil. Furthermore, the polyunsaturated vegetable oils present other health problems, due to the fact that they are extremely oxidation-prone, and thus readily oxidized in the body. It appears to be oxidized fats that cause much of the arterial damage that leads to coronary heart disease (CHD). Monounsaturated fats, which are found in many nuts and in olive oil, appear to have a beneficial effect. Interestingly, ancient people were very fond of bone marrow, which is high in monounsaturates.
Before 1920 or so, heart attacks were uncommon; they are not uncommon anymore. We are often told that this is because we are eating too much saturated fat, but the facts suggest otherwise. Although total fat consumption has increased since 1920, most of that increase has been in the form of polyunsaturated vegetable oils, which were simply not available previously. Crisco was invented in 1911. The increased consumption of vegetable oils has led to an imbalanced ratio of n6 to n3 fats. This imbalance causes the body too overproduce chemicals that also contribute to heart disease, and to underproduce chemicals that can help to reverse it (the series 1 prostaglandins). Insulin also favors the production of the wrong prostaglandins.
The prostaglandins belong to a group of short-lived signal chemicals in the body called eicosanoids. Some of these chemicals, such as prostaglandin E-1 (PGE1) actually help to clear arteries and improve cardiovascular health as well as fighting inflammation. Others, such as PGE2, promote inflammation and vasoconstriction. Both are necessary, of course. The inflammation response is a necessary part of the body's ability to fight disease and injury. When a cave man was wounded, his survival depended on his body's ability to form clots to arrest bleeding, for example. What we don't want, however, is chronic clotting and inflammation, but this is what we tend to get if our insulin levels are chronically elevated.
So, by eating foods that are carbohydrate-dense and using refined vegetable oils we have moved far away from the foods that our bodies evolved to deal with, and we thereby move into dangerous dietary territory. We become inclined to inflammation and clotting activities, and over a lifetime this adds up to health problems. The solution is to attempt to reverse the trend, by going back to whole fruits and vegetables, lean meats, and nuts. It is a good idea to use oily fish as n3 fat sources, rather than flaxseed and canola oils, since the latter are so oxidation-prone. Nuts contain their own endogenous antioxidants that keep the nut oils from spoiling, so it is far better to eat nuts than to use nut oils. And it's better to eat them raw than roasted, if possible.
Dairy products are only available to people who have herds of domesticated animals, so this again means that they were not available to prehistoric humans. The exception, of course, is human breast milk, which is consumed for the first few years of life. Consequently, many people lose the ability to digest milk after childhood, and many more can digest milk only with some distress. Although we are often urged to use reduced-fat milk products, there is some evidence that the problematic ingredient in milk, as far as CHD is concerned, is the protein casein as well as the fat. Casein appears to inhibit the function of the LDL receptors in the liver, slowing the reuptake of LDL cholesterol.