does a LOR from my PI count as a science LOR?

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Admires

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It depends on the school and most will specify on their websites. I have 2 LORs from science profs and 1 from a PI who is a science prof but did not teach me in traditional course. If schools asked for science professors or science faculty who have taught me, I played it safe and did not assume my PI letter would qualify. However, some schools say that any science professional or faculty member will do, in which case I would use my PI letter (given the choice, I would use my PI letter as he knows me better)
 
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+1 on above.

Some schools are specific about their meanings of "science professor", usually they are "someone who has given you a grade" and "has taught you in a classroom setting".

Contact the individual school to find out.
 
I'll share an example that I came across today. Drexel is one of my schools and they have a requirement of three letters from individuals who hold college level academic appointments. 2 must be science faculty, 1 must be non-science faculty. I chose to submit my PI letter for one of the science requirements, as it doesn't specify that they need to have taught me in a classroom.

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