Will it put me at a disadvantage for college applications if I don't have 3 lab sciences?
I am wanting to graduate at the end of this year (my 3rd year of high school) but if I do this I will have 3 sciences, but only 2 of those will be lab sciences. Would this put me at a disadvantage for applying to more selective colleges such as MIT, Michigan, and Case Western?
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You will not be put at any explicit disadvantage, so long as you have taken challenging courses throughout your high school years. However, you should know that these schools are STEM intensive, so there will be a lot of science in it. The lab classes in high school were meant to prepare you for the lab classes in university.
What I think is this: you should apply. Not having STEM lab classes will not disqualify you from being admitted.
You would be okay at Michigan or Case Western unless you are an Engineering student.
Not so much at MIT since they recommend a full year of Biology, Chemistry, and Physics.