The ciliary/flagellar system is perhaps unique in biology in that not only are biochemical manipulations used to elucidate the function, but physical manipulations as well. Thus, there is a considerable need to have an integrated physical-biochemical model of a cilium and its function. The emphasis of this paper will be to firstly, provide a mechanistic picture of the cilium and its environment because the biological community is perhaps less aware of this type of model development, and second, to point the way towards future experiments that will elucidate the role of the cilium in organ and organism level signaling and regulation.