The first is our reverence for animal protein. Our society believes so passionately in the health value of milk and meat that it is hard for us to conceive that we might be wrong - that these foods might in fact be very unhealthy. It is too far outside of what we have been taught for decades for us to believe it easily, no matter how true it may be.This is a golden opportunity for Google with their new health venture Calico. Since they won't (as they claim) be driven by profit, they will be free to ask non-reductionist research questions and to back broad-effect studies. They will be uniquely situated to break us out of the reductionist paradigm that, as a result, has us focusing on secondary and tertiary prevention instead of primary prevention.
Second is the reductionism paradigm that leads us to focus on parts of things separate from, and to the exclusion of, the whole. The body is a wholistic, interconnected system, but we are accustomed to thinking of it instead as a collection of individual parts and systems, in which solitary chemicals do solitary, unrelated things. Through the lens of reductionism, we see nutrition as a matter of individual nutrients rather than a comprehensive diet, and as an isolated field of study rather than the most influential determinate of our health as a whole.
Third is the profit-oriented system that discourages us from behaving in non-reductionist ways. There's much greater profit in reductionism, with its quick and easy fixes, each targeted to one of thousands of different potential problems, than in wholism. And so long as industry is a driving force in determining what research questions get asked, what studies get funded, and what results are published and publicized and turned into official policy, breaking out of the reductionist paradigm will be an uphill battle.
These three types of prevention - primary, secondary, and tertiary - are useful in categorizing interventions. My field, public health, refers to them often. This site offers a good description of what they are. In a nutshell, primary prevention keeps someone from getting sick in the first place, secondary keeps them from getting sicker once they're sick, and tertiary focuses on quality-of-life when there's no good intervention left.
I liked this analogy for prevention:
"Imagine you're standing beside a river and see someone drowning as he floats by. You jump in and pull him ashore. A moment later, another person floats past you going downstream, and then another and another. Soon you're so exhausted, you know you won't be able to save even one more victim. So you decide to travel upstream to see what the problem is. You find that people are falling into the river because they are stepping through a hole in a bridge. Once this is fixed, people stop falling into the water. When it comes to health, prevention means “going upstream” and fixing a problem at the source instead of saving victims one by one."