I think it 100% depends upon the gap between the two.
I've always heard if you have a pretty good GPA, but all your science classes caused your GPA to drop and they were upper level, it looks poorly upon you because it shows that you struggle in more difficult classes (which lets be honest, I never had a non-science class that challenged me in the slightest).
If your GPA started dropping once you hit your upper level sciences, bad sign, shows you can't handle those difficult classes.
So if it's a small gap, no problem; big gap, bigger problem.
and after saying this, my science GPA is slightly lower (only because of organic, evil evil organic)