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Maybe we are indeed born to run barefoot.
Maybe we're not born to run barefoot on cement and asphalt.
Maybe you're born to run barefoot, but I'm not.
I dunno. All I want is to be able to get back out there, put some miles on, feel that glorious abandon.
Everyone who is born with bare functional feet and legs, is born to run (barefoot or otherwise). However, we are not born knowing precisely how to run (barefoot or otherwise).
The advantage of having an early childhood mostly, if not all, barefoot, is that your bare soles can take plenty of time to teach you to first take baby steps, then walk and run (usually running comes first, as baby falls toward parent or adult).
Hard surfaces are not newer than our feet. Our ancestors contended with every surface imaginable; from granite bedrock, to razor-sharp gravel-littered trails in the mountains. Actually, the hard surfaces we have today, are, for the most part, less littered than what our ancestors dealt with. Today we have street and sidewalk sweepers cleaning these hard surfaces on a regular (if not frequent) basis.
Our ancestors also may have suffered broken metatarsals occasionally as well. I had one a couple years ago. Keep in mind, not all natural terrain is perfectly safe. In fact, LIFE is not perfectly safe. None of us were made bio-mechanically perfect (if we were, we certainly wouldn't be designed so that we can choke our our food!). Unlike a stress fracture (repetitive stress injury), my injury was traumatic (single stress incident). I twisted my ankle on uneven terrain and that torqued my small metatarsal. This is apparently a common injury (as are stress fractures) even among those wearing shoes.
Basically if you think your shoes or a soft terrain are going to protect you from injury, then you're probably not going to run the way anyone who is born without shoes is built to run or walk naturally! We get cocky when we think we are invulnerable. Put a helmet or bullet proof vest on a child, and first things they'll want to do is hit themselves in the head and shoot themselves in the chest!
That said, how to learn to run barefoot?
Best way is to start at the beginning, preferably, before you learn how to walk.
That ship, having sailed, I strongly recommend taking a short-cut by studying the experiences of those who have spent a great deal of their life (say 5 or more decades) figuring out, not just how to run safely (at least reasonably safely), but analyze what they are doing so they can share what they learn.
From there, it is very important to FEEL what you are doing. The most important aspect (often overlooked, especially by shoemakers) of barefoot running and walking is the sensory feedback from our soles - the sometimes very painful and always immediate sensations we feel as our sole interact with terrain. This feedback, when painful, helps us figure out how to constantly improve our techniques by walking and running more and more gently.
So, I strongly recommend not entirely avoiding any uncomfortable terrain, and in fact at the beginning use such to terrain to remind you not only to not do too much too soon, but also to focus more on learning more gentle technique and less on trying to increase distance.
With gentle and efficient (wasted energy also causes immediate pain in the soles, especially on hard and rough terrain) technique, distance (and maybe speed too - depending on your natural abilities, age, and other factors) will come much faster.
It's like building a house, without a foundation, you'll waste a lot of time building and rebuilding and rebuilding again, because the house keeps falling down, again and again.
Likewise, without a sound foundation (which we SHOULD naturally acquire over years of learning to walk and run while barefoot as a young child) we tend to run with technique that is likely to cause injury, over and over again.
I know this is a long drawn out message, but that's a lot like the process of learning to walk and run should be - long and drawn out, focusing first and foremost on the learning (foundation).
Anyway, if you're still interested in following my thoughts and learning to run more gently, gracefully, and efficiently, check out my website, especially the How page:
http://How.BarefootRunning.com
and/or BUY MY BOOK!
Barefoot Running Step by Step
http://amzn.to/1ZCcJ9a