This is great article on our natural ability to run and why we have so many problems with it today.We evolved to run because of the evolutionary advantages it gave us,both after prey and away from predators. Shoes wear in our feet rather than our feet wearing in our shoes. When we think of how distorted our feet can become, as in the bound feet of the Chinese or the bunioned feet of the high heeled, it is no surprise that we suffer the sores of the slingbacks and the agony of the arrow toed.
Have you ever seen the foot of someone who has never worn shoes? Not the same creature as ours at all.
http://www.boston.com/bostonglobe/magazine/articles/2009/04/19/what_ruins_running/