I have an intern since two month or so, and although it is incredibly rewarding to see him grow and become more and more capable, I still fear that he does not learn "enough". Of course there are goals for his internship (we will soon submit a paper), but I don't know what he should retain from this internship, how should a "good researcher" behave.

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I think there is this issue with PhD studies where no one, except the student, can assess the quality of the work. If you have either a low self-esteem or high expectations, things can go spiraling down real quick. The student is the only one deciding on a day-to-day basis when they should stop working or what is to be considered "a good working day". There are no objective, outside metrics that helps to assert that, because almost every research activity is peer-based.

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