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Not that this book has anything to do with pickup, but it does describe what you feel is instinct. It's called Blink: The art of thinking without thinking. Basically, what happens is that you do pick up on are visual cues that only happen in a split second. Although you don't consciously realize what has happened, your subconscious is well aware of it because of past experiences. At some point, if you pay attention, you'll actually realize what the actual visual cue is and at that point it is knowledge and not instinct.
It's a good book put it's core tenet is that your instincts become more honed the more you practice.
That guy who shot down the missile was fucking unbelievable. They even ran it as a simulation telling the guys doing it that one of the incomings was a missile and they still didn't spot it!