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Does belief always come before understanding? Should it?
I don't think that belief necessarily comes before understanding (although it will likely come before full understanding). However, it often will because of the way we are taught and learn (and there is nothing necessarily wrong with this).
In the case of an adult engaging in serious self-education on a subject I would expect belief and understanding to develop together, although they may well start with a basic belief.
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How large is the role of confirmation bias in our learning process?
That is hard to say. I think that it may play a limited but useful role, especially in children.
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Are we doing the same thing to Intelligent Design that they obviously are to the Theory of Evolution?
If anything it seems that they do it to Intelligent Design - and frequently to anything. My impression is that it is less the subject matter than a general attitude.
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Are any of us really beating up anything other than strawmen?
As I say, it is a difference in attitude. Those of us who are prepared to do at least basic research, consider objections to our arguments and consider the implications of our arguments are far more likely to accurately represent our opponents than those who prefer to simply assume that they must be right.
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What does this mean for science education? Surely our professors (are ourselves, for those who are professors) have their "own theories": won't this color their lectures?
At degree level, this does happen to an extent (although I have no reason to believe that it reaches the level of being a serious problem in any but a tiny handful of cases - although it may be more of a problem outside of science).
Of course, the more advanced the education, the more the students should be able to go out and do their own research. And the more basic the education, the more it can be performed well by sticking to the accepted mainstream views.
So, I would argue that we should be far more concerned about High School teachers - dealing with a less-well informed and more impressionable audience - teaching fringe ideas, than we should be about university professors occasionally dropping their own ideas and preferences into a lecture.