First, let me try (my changes presumably answer some of your questions implicitly): Comparing the opposing sides , the author problematizes the relationship of scientific analyses to genre texts and tries to examine the position of academic critique in unjustifiably neglecting contextual quality in the popular domain . No, I cannot think offhand of a word to replace 'problematize'; it seems awkward, but it is a word, and I think it works well enough. a problem', then you could use that.
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