Hi Emily, did you begin the process with a whole grain flour such as whole wheat or whole rye? Black specks wouldn't be too worrisome with these types of flour, since oxidation often causes some darkening on the surface, and some of the bran or germ might look like black specks. I can't be completely sure, but as long as you're not seeing any pink or orange, I think you're safe to continue. Just scoop the specks off before feeding some of the healthier looking starter below. If you continue to see these specks when you switch to feeding with all-purpose flour then you might want to check in with us again. 

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