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I have seen in many places explanations of hypertrophy and how our muscles become stronger under load, but why do people become flexible when they practice exericses like yoga and such?

tryst with freedom
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You are training your stretch receptors and muscles. Every muscle/tendon complex has stretch receptors that protect your body from injury by limiting your range of motion (ROM). Your ROM when you are asleep or comatose is much greater than when awake.

What stretching, yoga and similar activities do is train your nervous system that being at or past a certain point is normal and to not limit the motion.

JohnP
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