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But you see, choosing boys even though the female applicants are more qualified would be discriminating based on sex! There are two ways to look at this.
You are assuming women are more qualified than men. If you look at the gpa/mcat, guys on average have higher mcats but girls have higher gpas. Schools that skew gender are outliers, and on average men and women get in at around the same acceptance rate, so we can roughly guess that men and women are are equal footing.