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Tracy
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Actually, at engineering school, by the end of my three years I came away with a deep conviction of my ignorance and a feeling that I'd only had the merest of introductions to engineering. My fellow students felt the same. So the phenomenon doesn't sound familiar.
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No, critical thinking is not a definite skill set, in and of itself. Or at least, cognitive sciences, and all the known world's collected wisdom of several thousand years (dating back to the Ancient Chinese, Indians and Eyptians) has failed to discover a general way of teaching critical thinking. The process of thinking critically is intertwined with what you are thinking about - domain knowledge. So for example you can tell a student that they should consider reasonable alternative explanations for an event, but they can't do it unless they know what's reasonable in that context. You can tell a student to look at an issue from multiple perspectives, but if they don't know much about an issue they can't think about it from multiple perspectives. See http://www.aft.org/pubs-reports/american_educator/issues/summer07/Crit_Thinking.pdf
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