Higher reasoning isn't all that great. E.g., people have constructed consistent systems of reasoning that are entirely misanthropic or, if not actually misanthr

Higher reasoning isn't all that great. E.g., people have constructed consistent systems of reasoning that are entirely misanthropic or, if not actually misanthropic, they conclude that the extinction of the human species is good. And you're missing the point that the stratification of phenomena into "higher reasoning" <-> "base instinct" is a false hierarchy. Even when you're working within ethics, you eventually have to ground yourself in moral intuitions, which is fundamentally irrational (the underlying mechanism of moral intuition can't be examined through reason). I think maybe what the author is ultimately saying is that it's not wrong to think about these uniquely human qualities as being just as natural and basic as anything else.