When Dr Shalizi writes the rhetorical question "why it is so important to you that IQ be heritable and unchangeable?" in the context of "'human equality' and 'genetic identity'" his tone is not that of scientific skepticism of an unproven claim but rather an apologetic defense of an embattled creed. Really, why is it so important to you what the truth is?
I read Shalizi differently, as asking something like, "Really, is it because you care about the truth qua truth that you find this particular alleged truth so important?" Far from apologetic, he is — cautiously, because there is a counterfactual gun to his head — going on the offensive, hinting that the people insistently disagreeing with him are motivated by more than unalloyed curiosity. It is not, of course, dispassionate scientific scepticism, but nor is it a defensive crouch.
My interpretation could be wrong. Shalizi isn't spelling things out in explicit, objective detail there. But my interpretation rings truer to my gut, and fits better with the fact that his peroration rounds off ten thousand words of blunt and occasionally snarky statistical critique.
A long blog post explains why the author, a feminist, is not comfortable with the rationalist community despite thinking it is "super cool and interesting". It's directed specifically at Yvain, but it's probably general enough to be of some interest here.
http://apophemi.wordpress.com/2014/01/04/why-im-not-on-the-rationalist-masterlist/
I'm not sure if I can summarize this fairly but the main thrust seems to be that we are overly willing to entertain offensive/taboo/hurtful ideas and this drives off many types of people. Here's a quote:
The author perceives a link between LW type open discourse and danger to minority groups. I'm not sure whether that's true or not. Take race. Many LWers are willing to entertain ideas about the existence and possible importance of average group differences in psychological traits. So, maybe LWers are racists. But they're racists who continually obsess over optimizing their philanthropic contributions to African charities. So, maybe not racists in a dangerous way?
An overly rosy view, perhaps, and I don't want to deny the reality of the blogger's experience. Clearly, the person is intelligent and attracted to some aspects of LW discourse while turned off by other aspects.