The best response to this that I've read, at least in my opinion, was SSC's "Contra Grant On Exaggerated Differences"[0]. The key point is that differences between the genders do exist, though they tend to be differences in interest rather than capability. And even small differences in interest can cascade through the selection effects of our educational systems.

[0] http://slatestarcodex.com/2017/08/07/contra-grant-on-exagger...