Research on the biochemistry of foodstuffs – the chemical composition of foods – is much easier than studying the physiology of nutrition. It is exceedingly difficult to map the digestive functions of humans and their gut flora. Further, the digestion and nutrition of each person are unique.
A small fraction of the nutritional value of food is absorbed into our bodies, which are essentially fed leftovers. Our gut flora turn the food we eat into bodily nutrition. The health and diversity of these microbial colonies is critical to supplying the body with nutrients.
Some intake is selective. The body takes what it needs. But often what is needed is not absorbed, even though it passes through the digestive system.
Absorption depends on enzymes. If digestive juices are not adequately secreted, foodstuff is not broken down or absorbed, and the nutritional value lost.
The digestive system acts as both a facilitator and a barrier that nutrients must traverse to reach cells of innumerable sorts, all of which are interconnected into a holistic being by energy pathways that are powerfully affected by the mind and emotions.
Biochemical analysis is test-tube science: a reductionist approach that misleads as often as it informs. A biochemist would tell you that milk, with a pH around 6.5, is not particularly acidic; but digestion of milk requires an acidic environment to break down constituent fat and protein, and so acidity is necessary to derive any nutritional value from milk. Biochemistry has much less to say about nutrition than it has already said.