Why Do We Get Knots In Our Muscles?

I once went to a doctor who did manual therapy to try to get relief for neck and shoulder pain. He worked on it for a while, but I had a knot in my neck that just wouldn't go away.
"Muscles are stupid," he said, "all we need to do is inject it with numbing medication and the brain will think everything is okay and tell the muscle to relax." a few hours later when the numbing medication wore off, the knot was still there unchanged.
"If muscles are stupid," I thought, "then that doctor was just outsmarted by a muscle."
Have you ever wondered why you have "knots" in your muscles? These "knots" are usually tender, even if only tender to touch. 
Many people go to massage therapists, do stretching, get injections, do ultrasound therapy, and seek many other treatments to try and get rid of the knots in their muscles. 
Unfortunately, many of the therapies are minimally effective if they work at all. The reason for this is that most people do not understand why muscles develop "knots." 
An invalid theory that is prevalent today is that muscles develop knots because of muscle imbalances. Everyone is looking for the right exercise thinking that if they strengthen the correct muscle and restore balance, then their muscular pain will go away. If this was the case, then athletes should have far less pain than the rest of the population.
Most therapies are aimed at relieving the knots once they have developed but do not consider why those knots are there in the first place. 
How can we know how to get rid of a knot in a muscle if we don't understand where it came from? Based on my experience as an osteopathic physician who treats people for musculoskeletal issues, there is a reason why muscles develop knots. It's important to understand why it develops to undo knots in our muscles.
The first concept that is important to understand is that nothing that occurs in the body occurs randomly. If the muscle has a knot, that knot is there for a reason. 
It has always been my impression that many practitioners look at knots on muscles as random events or they believe the knots have no reason for being there. 
Sometimes the knots are attributed to muscle imbalances or other theories that aren't necessarily correct or complete. Injecting a muscle, for example, that is knotted up for a reason will not work unless the reason why that knot is there is addressed. So why would the body then cause muscles to knot up?
I believe muscles are quite smart. In general a muscle is attached at two different ends and has a joint in between. When a muscle contracts, it produces a particular movement at that corresponding joint or joints. 
If something goes wrong at the joint, even if it is slight, the muscle or muscles associated with that joint will contract to protect the joint. In these cases, the muscles become knotted to prevent further dysfunction at the joint. 
When this happens, the knot and the area around it also become hypersensitive. Therefore muscles don't just contract to produce motion in a joint but also to protect it. 
This is why trying to massage out a knot or injecting it may not work. It is not addressing the reason the muscle is contracted to begin with.
Muscles also contract over areas where there are problems besides joints. An example of this can be seen over the abdomen. 
When an organ is inflamed such as the appendix or gallbladder, the muscles over those organs become very tight and hypersensitive. These are extreme examples but highlight the protective role that muscles play. 
So the musculoskeletal system can play a great role in showing us where we may have problems, even if they are just slight. 
If we can restore normality to the structures the muscles are responding to, then the muscles instantly and automatically relax and the overlying area is no longer hypersensitive.
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