When compared to thick cushioned running shoes, barefoot running was found to engage widespread mechanical improvements that did a better job at reducing net impact loads and mechanical demands on the hips that accounted for stark reductions in hip pain.
The tight, inflexible fit of most cushioned running shoes unfortuntely do nothing to make your feet and ankles functionally strong. This is because the narrow design is counter to the normal shape of the human foot, which was found to irritate and inflame the soft tissues and tendons, not just in the foot, but the ankle and shin as well.
The best way to maintain healthy knees when running is to avoid heel strike running because it always accompanies a hyper-extended knee, an overly long stride and unusually long braking with the ground, which CANNOT be improved with a cushioned, motion control stability running shoe. The only proven method to protect your knees long-term is to land with a forefoot strike because it prevents hyper-knee extension at landing, an over-stride and a low cadence, all of which were consistently found to literally cure running-related knee pain and injury.
Safe and efficient knee mechanics were found to be only engaged through the use of a forefoot strike landing when running, not a heel strike. This is because forefoot striking was found to make the knee better at flexing and bending at landing, which in turn, reduced opposing forces on the knee by making the knee-joint hold more firm, while reducing excessive bouncing. Furthermore, improved knee flexion engaged by forefoot striking reduced high brake forces which resulted in little to no impact at the knee, while engaging more efficient accelerations with less muscle force generation than heel strike running.
Unfortunately, many components of the conventional running shoe was found to literally tear away at the functional strength of the arch in ways that causes long-term damage, including collapsed arches and chronic plantar fasciitis as compared with running barefoot or in minimalist (barefoot-like) shoes. 
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