So, for muscle memory, it’s actually your brain memory that is doing it.
You’ve practiced the behavior so many times that you’ve created a pathway in your brain of doing that behavior (also why you follow the same path down the stairs, even when you mean to go to a different area). Then, when you start playing, your brain remembers the pathway you’ve created and puts it into motion.
“Muscle memory” is a bit of a misnomer, since your muscles don’t actually remember anything at all. The memory is still entirely neurological, and isn’t really that different from other kinds of memories. You can think about a certain sight or smell, sound, or smell and call it to memory. Likewise, you can do so with skills.
When I think “throw a punch” my brain acts it out as if it is preparing to do it. And because I’ve got a little bit of boxing training, what it acts out incorporates that training and my experience throwing punches, making the punch I throw in my head a more skillful one than that of someone who has never practiced.
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