It's important to have balance. I think as humans it is difficult to be completely objective in our decisions, and often what we believe to be true is actually false. This makes science a beautiful thing when it comes to making appropriate decisions. In theory, it provides an objective look what kind of foods can promote health and which tend to be harmful.
But science is not perfect, and it is not always a good idea to assume that the findings of a study will necessarily be true for us. It's important to remember that research is conducted on a sample of the population, and the results are completely dependent on the characteristics of that sample. Many nutrition experiments are done on rats in very artificial situations that do not reflect our environment. Does this mean they are not applicable to humans? No, they may very well be. But I really think that each study needs to be taken within the context of our own experience. We are not always aware of every single variable that is involved, which makes certain findings dangerous to accept as unquestionable truth.
On the other hand, our personal experience can often be misleading. When my digestive health deteriorated, I began to be fearful of eating certain foods. I thought that everything was making my stomach problems worse, so I cut out more and more. I was "listening to my body", thinking that it was telling me that it couldn't handle these foods very well. This just caused me to become weak and anorexic-looking. But only when I allowed myself to eat normally again regardless of my stomach, did it start to get better. The problem still comes and goes but is more manageable now. In this case I needed to move beyond what I was experiencing, and change my perspective. Often new information is what is needed to do so.
Knowledge and experience complement each other, we need not rely on either one alone.