Mark Rippetoe explains why doing squats is safer than the misinformed might tell you:
One of the most persistent myths in the entire panoply of conventional exercise wisdom is that squats below parallel are somehow bad for the knees. This old saw is mindlessly repeated by poorly-informed orthopedic surgeons, physical therapists, and chiropractors all over the world. Better-informed professionals such as productive strength coaches, weightlifters and powerlifters, and those willing to examine the anatomy of the knees and hips for more than just a minute or two, know better.
As an athlete, the most important thing you can do is to increase your strength. Being stronger will help in anything that you do. No one knows more about getting strong than Mark Rippetoe.
If you don't know Coach Rippetoe's book Starting Strength, you owe it to yourself to look it up. It will make for a great start to your 2014.
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