You weren't born with shoes on your feet. Running barefoot is the natural way to run. If there's a fad in running, it is that you need to air cushions at your heels when you already have a superior mechanism to cushion your strides.
http://en.wikipedia.org/wiki/Tarahumara_people The word for themselves, Rarámuri, means "runners on foot" or "those who run fast" in their native tongue according to some early ethnographers like Norwegian Carl Lumholtz, though this interpretation has not been fully agreed upon. With widely dispersed settlements, these people developed a tradition of long-distance running up to 120 miles (190 km) in one session, over a period of two days through their homeland of rough canyon country, for intervillage communication and transportation as well as to hunt.
They also have the tendency to eat when hungry, sleep when sleepy (as in, anytime / anywhere) which has threads to other "genius" discussions (lets call being able to run 100's of miles a type of "physical genius" for a thought experiment). I know when I do barefoot walking on a frequent basis my chronic lower back pain starts to dissipate.
Side note: We also aren't naturally meant to sit all day in an office chair, yet...
Note, I'm not necessarily advocating barefoot running. I do run on my forefeet, so I run in Newtons, for now.
Two things though: (1) Heel running is less efficient, results in higher impact forces and leads to more injuries than forefoot running. (2) The only reason most of us heel run is because we started running in sneakers from a young age.
Again, your second link, did you even read it?