That the participation rate of women in software is experiencing a sharp decline in recent decades, mostly in the US, (while, say, women participation in physics is on the rise) is an undisputed fact; that women working in software companies report abuse is a similarly undisputed facts. That is the problem we're trying to solve. That there may be contributing immutable biological factors is completely irrelevant. The main difference between this and the chemical plant analogy is that while there is no doubt that there are causes of cancer other than exposure to radioactive waste, the studies the author of the manifesto cites are very much controversial on purely scientific grounds, plus he clearly does not understand their context (e.g. that women in liberal countries prefer to work less etc. is no indication whatsoever of any innate factors).

But the main problem is this: Damore is no expert on the subject. His belief that the studies he cites are relevant is based on a layman's intuition, which is wrong in this case, as in many others. Explaining exactly the problems is much harder than bringing up ridiculous hypothesis by people unfamiliar with the subject like Damore. If you want to know exactly what the issue is (and I doubt Damore does, because he clearly read no research on marginalization of women), you should read actual scholarship on the subject, and not rants by some random guy.