"Running in a minimalist and lightweight shoe is not the same as running barefoot: a biomechanical study"

Yep. Now it's official!

"Experimental conditions
"The protocol involved four experimental conditions: (1) barefoot; (2) a minimalist shoe (NIKE Free 3.0); (3) a lightweight racing flat (NIKE LunaRacer2) and (4) the shoe in which they were currently completing the most training mileage (herein called regular shoe)....

"Conclusions
"Barefoot running was different to all shod conditions. Barefoot running changes the amount of work done at the knee and ankle joints and this may have therapeutic and performance implications for runners."

Full-text at the link.