There has been research around for a while about modern trainers; Sarah and I talked about it in "Feet First" because there was an interesting parallel with proprioception in horses.
Basically, modern trainers are very cushioned and have a tendency to fool the proprioceptive nerves into thinking that you are running on a soft surface even if, in fact, you are doing a marathon on tarmac.
The result is that your stride-length and landing doesn't compensate for the hard surface and your joints take the impact - the cushioning in the shoes confuses the proprioception but doesn't protect your joints.
By contrast, running barefoot gives you immediate proprioception about terrain - hard, soft, even, uneven - and the body instantly adjusts and compensates. This means that, although there are huge biomechanical differences between people and horses (!), like a horse, a human runner will land differently on soft surfaces than on hard surfaces.