Many researchers believe that what we think of as knots are myofacial trigger points that occur when specific muscle fibers are continuously misused. For instance - bad posture or poor body mechanics in a task that is constantly repeated. This causes the muscles to contract in certain areas and also restricts blood flow.
I have often compared this to an old school telephone cord. As we stretched out the coils, released them back, twisted them around our fingers and tangled them up within themselves they would eventually become misshapen. The knots and tangles of the telephone cord are independent of any outside source. If the myofacial trigger point theory is correct then this is true of our muscles. We stretch them, bend them, overuse them and then the fibers tangle up on themselves.
Even if that is the case, breaking up those neural transmissions so they can reform correctly is still the appropriate way to solve that problem. So while we don't know for certain what a knot is we do know that relief can often be found in the form of a well performed massage.