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First, to what degree you should be critical with a paper should be highly context dependent. If you are just trying to get familiar with a topic, it may not be useful to be extremely active and critical; if you are responding to an objection for a paper, then you should be!

Second, for me, here is a simple way of increasing my engagement with a paper: try to mentally reconstruct the ideas and argument of the paper on my own. (For instance, try doing this on a walk, or while doing dishes.) If I can't do it, then I go back and re-read the paper trying to find the places where I got lost or confused and couldn't reconstruct it. Normally this process, for me, identifies the points that I think are weak, since those points are frequently where I struggle to reconstruct the author's reasoning. This technique is also a little less time consuming than going line-by-line or writing your own reconstruction of the paper.

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