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I'm interested in studying economic geology for Fall 2017. I have decent grades, GRE scores and letters of recommendation. I also have a strong background in teaching/research and should be published in Economic Geology soon. However, my primary drawback is that the economic geology professor at our school is a brutal grader and even though I was very passionate about the class, I received a C+ in his course. I want to continue my studies in economic geology, but I suspect that this will be a big warning flag to admissions committees

Should I address this problem in my letter of interest? How can I best explain this negative grade?

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Saying that a professor is a known tough grader in your SOP will not do you any favors because it'll make you look unprofessional at best and immature at worst. The better approach, if this really is a thing, is to have one of your recommenders address the course's grading in their rec letter. This of course presumes that the view of this prof's grading is as widespread as you think it is. Otherwise, you'll want to show through research experience, other coursework, and assignments that you are committed to and capable of excelling in graduate work in economic geology.

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