One does not need to know to explain a phenomenon to be able to observe it. For example, I may not know what exactly drives the color of skin, but I can observe a correlation between the skin color and the geography.

As a matter of fact, throughout all history science has been largely driven by empirical observations that it could not explain and which prompted development of new theories.

The only reason folks like Pinker are trying to come with plausible explanations is because often time the other sides would not even listen to the empirical evidence unless they are offered a plausible explanation of what could explain the gender differences