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There seem to be at least two kinds of confusion regarding novel concepts.

In one, the brain simply can't form an abstract model from whatever information is being presented. It's where you can't "wrap your head around" something.

In another, the brain perceives a cognitive dissonance, where something doesn't "add up", but further information provides a unifying model that can explain everything being presented.

They seem to be related.

The brain is somehow able to evaluate the fidelity of an abstract model that it's trying to construct. How does this happen?

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Welcome to cogsci.SE. This seems like an interesting question, but I don't think I understand. Cognitive psychology isn't my specialty, so maybe that's on me, but I wonder if an example of each kind of confusion would clarify things. Also, I'm not sure what you want to know in response to "How does this happen?" Would it be insufficient to say something like, "The brain tries to apply the model (schema, probably) to explain/predict observations, and when it fails, it changes the schema ('accommodation learning')?" –  Nick Stauner Mar 27 at 20:38
    
An example for the first idea might be a student first learning about differential calculus. The idea of instantaneous change and the differential takes some getting used to, and the first time the idea is encountered, the student might lack an "intuitive grasp" of it. Perhaps you're right, that the inability to apply the concept is what raises the flag of confusion. But the raising of that flag seems to happen well before the student actually tries to apply the concept. It seems to happen when the student somehow predicts whether or not she can apply it. –  MackTuesday Mar 27 at 20:47
    
Maybe another way of phrasing it is, how does the brain decide that it's certain about something? Hm, maybe different theories compete subconsciously, and certainty comes when there's a clear winner? –  MackTuesday Mar 27 at 20:54

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