There are some extremely important facts untouched in the other answers. Forecasts as far as 50 years in the future are almost always wrong. But anyway, supposing that the depletion of natural resources doesn’t become too critical, that no catastrophic planetary event or world war happen, that civilization doesn’t collapse, let’s hope that these facts will be commonly known and that this knowledge will result in a drastic change of the society.
Cooked food
Particularly important and generalized but still essentially ignored, heating and cooking food generate millions of different new chemical compounds. Organic molecules are extremely complex and precisely shaped three-dimensional structures. It is essential that their exact layout and that of their atoms between themselves remain intact to function properly in the metabolism of living organisms. Any disorder in such a delicate arrangement triggers an anomaly, thus potentially an illness.
Structure of β-galactosidase at 3.2-Å resolution obtained by cryo-electron microscopy
To be biologically active and specific, a protein must be composed of the proper amino-acids sequence and each of its atoms must be correctly positioned in space. Enzymes intervene to foster a precise biochemical reaction exclusively between clearly defined and individualized molecules. The specificity of a protein composed of several thousand atoms may depend of the position of a single carbon atom, for example its location on the right or left on a plane of symmetry.
This is the simplest model to represent how an enzyme works. The substrate simply fits into the active site to form a reaction intermediate.
As a molecule goes through the metabolism, each of its facets has to correspond exactly to the successive enzymes met on the way. It is obvious that a real danger rather comes from molecules slightly damaged but still looking sufficiently normal to defeat the body’s vigilance. They might go deep into the metabolism and remain jammed somewhere along the way, blocking it to others and causing a big jam.
Chemistry for Biologists: Enzymes
As the temperature rises, reacting molecules have more and more kinetic energy. This increases the chances of a successful (violent and damaging F.D.) collision and so their rate increases. There is a certain temperature at which an enzyme's catalytic activity is at its greatest. This optimal temperature is usually around human body temperature (37.5° C / 100° F) for the enzymes in human cells.
Above this temperature the enzyme structure begins to break down (denature) since at higher temperatures intra- and intermolecular bonds are broken as the enzyme molecules gain even more kinetic energy.
Past and present research has already found noxious compounds generated by cooking at high temperature such as Maillard reaction products: acrylamide, heterocyclic amines, (HCAs) and advanced glycation end-product (AGEs). But a lot of other abnormal compounds form from temperatures just over 40° C / 105° F. If only slightly damaged, an organic molecule can be proceeded in the metabolism after the immune system failed to recognize it as antigens - while a totally wrecked molecule won’t be taken up by the first enzymes in charge of starting digestion and will be discarded.
Risk assessment of chemical substances of safety concern generated in processed meats
Cooking processes generating major amounts of HAA (Heterocyclic aromatic amines) are frying, roasting, barbecue and grilling due to the high temperatures reached (30,36). However, they are slowly generated during baking and cooking at low temperatures (37).
White blood cells, for instance, can produce antibodies specific for millions of different proteins that can thus be neutralized. A cell can identify a particular molecule, take it up or discard it, depending on its usefulness or lack of it. In borderline cases, if for instance a molecule has been partly broken down, the cell will be in a difficult situation: it might let the molecule in, mistaking it for a normal molecule and subsequently being unable to metabolize it owing to a flaw which hadn’t been identified at first.
(Cooked) “Natural” Foods Contain Lots of Carcinogens
"Humans also ingest large numbers of natural chemicals from cooking food. Over a thousand chemicals have been reported in roasted coffee: more than half of those tested (19/28) are rodent carcinogens. There are more rodent carcinogens in a single cup of coffee than potentially carcinogenic pesticide residues in the average American diet in a year, and there are still a thousand chemicals left to test in roasted coffee." - Bruce Ames
Maillard reaction was first described in 1912 by French chemist Louis-Camille Maillard. Most of the above is basic biochemistry found even in textbooks more than 50 years old. The logical conclusion is that heating food over 40°C / 105° F is harmful and should be avoided. The implications of that fact are so tremendously disturbing that still almost nobody dares to draw the obvious conclusion. In 50 years maybe?
Dairy products and cereal grains
No animal other then modern humans drinks the milk of other animal species and no grown up wild animal drinks milk (extremely few exceptions infirm that rule). Dairy consumption dates back to about 8,000 years only. That’s most probably a much too short period for a satisfactory adaptation. Some populations (mostly Northern) are somewhat habituated to lactose and some individuals may be better habituated than others, being able to consume dairy products without short term apparent harmful effects. But it doesn’t mean that dairy presents no long term hazards for these people as well.
Large scale consumption of wheat and other cereals could only happen with the invention of pottery and generalized cooking at the beginning of Neolithic, about 10,000 years ago. Agriculture was formerly seen as a progress, but it’s now clear that it brought its lot of evils - described in several papers. Farming is seen by Jared Diamond as The Worst Mistake in the History of the Human Race.
The global pattern of varying prevalence of diseases of affluence, such as obesity, cardiovascular disease and diabetes, suggests that some environmental factor specific to agrarian societies could initiate these diseases.
We propose that a cereal-based diet could be such an environmental factor. Through previous studies in archaeology and molecular evolution we conclude that humans and the human leptin system are not specifically adapted to a cereal-based diet, and that leptin resistance associated with diseases of affluence could be a sign of insufficient adaptation to such a diet.
The Relatively Peaceful Societies of Simple Hunter-Gatherers
According to modern anthropology, and contrary to popular thought, simple hunter-gatherer societies are relatively peaceful. According to modern archeology, the simple hunter-gatherer type of societies have been demonstrated to be the main type of society to produce some relatively peaceful societies free from warfare so far. Simple hunter-gatherer societies are mostly nomadic, they typically promote co-operation, sharing, egalitarianism, female-male equality.They had lots of free time to do things they want and they were/are generally healthy.
More about that:
The Consequences of Domestication and Sedentism
Opioid peptides derived from food proteins. The exorphins.
Human societies are defined by their food
Viruses
Common cold virus strain could be a breakthrough in bladder cancer treatment
Oncolytic Immunotherapy for Bladder Cancer Using Coxsackie A21 Virus
As a clinical setting in which local live biological therapy is already well established, non-muscle invasive bladder cancer (NMIBC) presents intriguing opportunities for oncolytic virotherapy. Coxsackievirus A21 (CVA21) is a novel intercellular adhesion molecule-1 (ICAM-1)-targeted immunotherapeutic virus.
So, some viruses would be therapeutic! Current medical theories about viruses and bacteria will probably have to be revised, modified or even totally discarded and replaced. Previous centuries ones have been proved wrong and thus it would not be surprising that the current ones are flawed as well.
Conclusion
Will the above points be widely known and recognized in the future? In 2069, 50 years from now? Let’s hope so!