The human body comprises chemical compounds such as water, amino acids (proteins), fatty acids (lipids), nucleic acids (DNA/RNA), and carbohydrates (e.g. sugars). These compounds in turn consist of elements such as carbon, hydrogen, oxygen, nitrogen, and phosphorus, and may or may not contain minerals such as calcium, iron, and zinc. Minerals ubiquitously occur in the form of salts and electrolytes. All of these chemical compounds and elements occur in various forms and combinations (e.g. hormones/vitamins, phospholipids, hydroxyapatite), both in the human body and in organisms (e.g. plants, animals) that humans eat.

     The human body necessarily comprises the elements that humans eat and absorb into the bloodstream. The digestive system, except in the unborn fetus, participates in the first step which makes the different chemical compounds and elements in food available for the trillions of cells of the body. In the digestive process of an average adult, about seven litres of liquid, known as digestive juices, exit the internal body and enter the lumen of the digestive tract. The digestive juices help break chemical bonds between ingested compounds as well as modulate the conformation and/or energetic state of the compounds/elements. However, many compounds/elements are absorbed into the bloodstream unchanged, though the digestive process helps to release them from the matrix of the foods where they occur. Any unabsorbed matter is excreted in the feces. But only a minimal amount of digestive juice is eliminated by this process; the intestines reabsorb most of it; otherwise the body would rapidly dehydrate; (hence the devastating effects of persistent diarrhea).

     Study in this field must take carefully into account the state of the body before ingestion and after digestion as well as the chemical composition of the food and the waste. Comparing the waste to the food can determine the specific types of compounds and elements absorbed by the body. The effect that the absorbed matter has on the body can be determined by finding the difference between the pre-ingestion state and the post-digestion state. The effect may only be discernible after an extended period of time in which all food and ingestion must be exactly regulated and all waste must be analyzed. The number of variables (e.g. 'confounding factors') involved in this type of experimentation is very high. This makes scientifically valid nutritional study very time-consuming and expensive, and explains why a proper science of human nutrition is rather new.

     In general, eating a variety of fresh, whole (unprocessed) foods has proven hormonally and metabolically favourable compared to eating a monotonous diet based on processed foods. In particular, fresh, whole foods provide higher amounts and a more favourable balance of essential and vital nutrients per unit of energy, resulting in better management of cell growth, maintenance, and mitosis (cell division) as well as of appetite and energy balance. A generally more regular eating pattern (e.g. eating medium-sized meals every 3 to 4 hours) has also proven more hormonally and metabolically favourable than infrequent, haphazard food intake.

"Artificial" interventions in food production and supply:

• Should genetic engineering be used in the production of food crops and animals?
• Are the use of pesticides, and fertilizers damaging to the foods produced by use of these methods (see also organic farming)?
• Are the use of antibiotics and hormones in animal farming ethical and/or safe?

Sociological issues:

• Is it possible to eat right on a low-income? Is proper nutrition economically skewed? How do we increase access to whole foods in impoverished neighborhoods?
• How do we minimise the current disparity in food availability between first and third world populations (see famine and poverty)?
• How can public advice agencies, policy making and food supply companies be coordinated to promote healthy eating and make wholesome foods more convenient and available?
• Do we need nutritional supplements in the form of pills, powders, liquids, etc.?
• How can the developed world promote good worldwide nutrition through minimising import tariffs and export subsidies on food transfers?

Research Issues:

• How do different nutrients affect appetite and metabolism, and what are the molecular mechanisms?
• What yet to be discovered important roles do vitamins, minerals, and other nutrients play in metabolism and health?
• Are the current recommendations for intake of vitamins and minerals appropriate?
• How and why do different cell types respond differently to chronically elevated circulating levels of insulin, leptin, and other hormones?
• What does it take for insulin resistance to develop?
• What other molecular mechanisms may explain the link between nutrition and lifestyle-related diseases?
• What role does the intestinal bacterial flora play in digestion and health?
• How essential to proper digestion are the enzymes contained in food itself, which are usually destroyed in cooking (see Living foods diet)?
• What more can we discover through what has been called the phytochemical revolution?