Nicholas Thompson tries to diagnose them:
Our ancestors may have run barefoot, but they didn’t do it on asphalt and concrete. They didn’t do it on roads caked with broken glass. They also didn’t have potato chips and soda, or bodies shaped by days spent in offices. Running is an extremely complex physical motion. Changing your shoes might help, but the way stress is distributed across your body depends a great deal, too, on how your hold your head, and even how you swing your arms. Ultimately, we don’t really know whether the movement spurred by "Born to Run" will make us more or less hurt.
The Dish 