UPDATE- Someone pointed me to the comments to the Scientific American article and this one from Ken Schafer makes some excellent points, so I hope he doesn't mind me cutting and pasting:
..............I have read the study. This study had nothing to do with cushioned shoes. They took experienced barefoot runners. And compared how much energy they used running barefoot and how much energy they used running in very light weight minimalist running shoes (little to no cushion).
The subjects used slightly more energy when running barefoot. It is important to understand that the subjects maintained the same "barefoot" running technique with and without shoes. So this was not a test of fore-footed running technique vs. heel striking running technique. Most of the evidence to date indicates that the technique used by barefoot runners is more efficient than the heel landing technique that most people (from sedentary shoe wearing populations) use when running.
Second point, barefoot runners have NOT dominated distance running for decades. The person, who wrote this, in the caption above, has no idea what he is talking about. The African runners, who many times have grown up barefoot, and who often run using a fore-footed landing, have dominated distance running for decades, but mostly while wearing shoes. Finally, this was just one study. So it is the results are far from conclusive.