The foot is complex; it has 33 joints and huge neurological potential. It is supposed to be able to maneuver and adapt to different terrains and communicate with the brain about whole-body balance and proprioception. Proprioception is the feedback loop between your body and brain that allows your brain to know where your body is in space.
The invention of the running shoe is "the worst crime ever committed against the human foot." To see the proof, one needn't look further than the mysterious Tarahumara Indians of Mexico for whom 300-mile runs were routine, and 60-mile runs a jaunt. They wear nothing but sandals, and suffer no injuries.