There has actually been research performed recently, touched on here[1] which tells us that the body does actually communicate with the brain quite a bit-- it's not so much pre-science any more.
That has little to do with chacras, alignment and other such stuff though -- the same way that the fact that we have an electrical field around our body doesn't validate Kirlian photography of "auras".
It's not just your brain that thinks, you know. Your body has a way of knowing, processing and remembering experiences.
Sure, it's a pre-scientific system, but there are insights to be gained from it.