The basic problem with atheists and modern liberals is that they have no conception of nature or physis in the Aristotelian sense. The atheist is a materialist of the basest variety. For him, all the world is matter, and it is utterly immaterial (pun intended) how that matter is to be shaped and organized. Male? Female? Dog? Cat? Just as though biological lego-pieces, it's just a matter of how the basic stuff is put together.
All that matters, in the end, is our choice. If there's the stuff and we want to arrange that stuff in a certain way, that's all that matters.
In fact, there's more to the world than "stuff." Things are what they are. A dog is not simply an arrangement of stuff. It's such and such a kind of animal.
A man is not simply an arrangement of stuff. It's such and such a kind of animal.
Likewise, the difference between male and female is not simply an arrangement of "stuff." Just as even and odd are proper accidents or properties of all numbers, so too, male and female are proper accidents of all of those animals to which gender applies.
The moment we recognize that there is such a thing as nature (that is, what things are) is the moment that we also must recognize that we can't just arrange and rearrange the world however we like. It's not the case that everything is dependent on our choice.
We must see in the perceptible organization of things their underlying natures. Male and female have different physical organizations because men and women are naturally different. We must recognize that the world is a certain way, completely independent of our choice.