Well, it's hard to pinpoint where "thought," (as in Original Thought) comes from because, as of now, there are different views on the fundamental nature of the universe.
I would suppose that from a materialistic view, all thought is born from your first taste of stimuli. Your first "observation" of that which is other than the perception of "I exist" (or possibly that very one) would be the birth of thought. This, in turn, grows with all other following stimuli, which builds your cache of Experiences, from which further thought can be structured.
This, then, brings into play schemas, which is a term I first heard was coined by LaBerge. They are the tiny, individual "files" of conceptual information that is stored in our minds. They are the broken down form of any singular concept - a chair, a bicycle, the color red, your mother, her shoe, her favorite earing.
Schemas operate as a sort of buffer of thought which changes, constantly, in respect to your ongoing experience of life. Anything that is somewhat associated to what you are experiencing, even if on a subconscious level, is grouped together much more perceptively in your conscious mind. For instance, you walk into school and the first thing you see is the girl you like. Inside your mind, the schemas related to that girl are going to come rushing up to the surface. You're instantly "aware" of all those things about her that makes her her in your mind - Her hair, her eye color, her voice, the way she wears her hair, etc. They all slip from your unconscious/subconscious mind and into your conscious mind because they are in a mental context with the situation.
Everything else that you might have been thinking of before (all the other schemas,) such as homework, the dream you had last night, how awful your toothpaste tastes, etc. are the schemas that are now pushed back into your subconscious/unconscious mind, because the girl you like is now right in front of your face.
The exchange of schemas continues to progress, rather fluidly, as one conscious experience blends in to another. Each new thing you see, taste, hear, etc will remind your subconscious mind of something that is "in Some way" related to what you're experiencing. Those schemas can then, more easily, slip from an undetectable area (the subconscious mind) into something that you're consciously aware of and seem, to you, as a completely new Thought, when, in reality, it was brought about by a schema that came closer to the surface of your awareness by way of relation to something you were previously experiencing. (I've actually come to believe that this is how dreams, themselves change from concept to concept, but appear to keep the same sort of fluidity.) As you learn and grow, these relations based on experiences define why every individual's logic is unique, because no two people follow the same paths of experience and are able to make the same conceptual relations, throughout a lifetime.
But that's only one interpretation. There are still the possibilities of a universal consciousness, which could imply that thought arises from connection with some other data bank of all existing information. Call it "God," "singular consciousness," "the Akashic Records," or whatever you want. If any of these exist, then an "original thought" could be the work of divine influence, karma, telepathy, etc.
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