There's nothing wrong with a professor not being in your department or your phd program. I assumed all of your other professors were in Material engineering so it would be "more" relevant. That was the only real reason I chose the rest over C. If he can write about your potential then by all means! If I was faced with a similar situation that being whether or not I should get a rec from someone in bioinformatics or from computer science even though I did good in a cs grad class, I would probably choose the guy from bioinformatics. One, there might be an off chance that a person from the adcom will know the guy from bioinformatics rather than computer science (in my case it's a very small group of people who do this stuff). Two, the bioinformatics guy can talk about much more relevant things in the rec letter than a cs person. I actually did this now that you reminded me. I could've gotten a rec from an algorithms professor, database professor, or my biodatabase systems prof. I did well in all the classes, all grad level but I chose the biodatabase systems prof. You're right, chemistry is definitely a big player in material engineering - I didn't even consider that actually. I'm not sure really sure about how disjoint or connected the two are honestly. In my case CS is close..but not close enough to bioinformatics. Couple of questions: Does professor C remember who you are? Can he write a recommendation that takes into consideration something other than the fact that you can do graduate work and something that might focus on the type of program you want to get into? If you're applying to top program they'll know you can handle graduate work. This fall I'll be attending Stanford actually.
Applied to: Duke, WUSTL, Stanford, Columbia, University of Pennsylvania, MIT/Harvard