The perceptions that many of the people talk about in the articles (the implications that the parent-to-be should stop the program, the sideways glances from dissertation committees that suggest a loss of hope, the apprehension when going on the job market) seem disproportionately to come from pregnant women.
Consider these quotes:
"It honestly never occurred to me that there might be a prejudice against hiring a woman so visibly in the throes of motherhood." ("Giving Birth in Graduate School")
"When I met with my co-chairs, they offered heartfelt congratulations, but I know that they wondered, as I did, if I would actually finish. My waistline was growing faster than the stack of pages on my desk." ("Giving Birth to Two Babies")
And then consider this one:
"Forty-six percent of the female graduate students we surveyed said they began their careers with an eye toward obtaining a faculty position at a research university. Babies changed that; only 11 percent of the students who were new mothers said they wanted to continue on that career path. Fatherhood for men similarly situated appears to have far less of an impact on their career choices—59 percent of men began their programs planning to pursue a research-intensive academic career, and 45 percent who were new fathers still planned to do so." ("Why So Few")
Now, I know that some of this is the age-old issue of women being seen (and seeing themselves) as primary caregivers while the men have more freedom (socially) to pursue their careers, but I really don't think that's all that's going on here.
I know several men in graduate school who are the fathers of young children. A lot of them are the primary caregivers while their wives/partners work outside the home. As far as I can tell, these are not men who shy away from stereotypically un-masculine roles, and they seem genuinely devoted to their children and their children's care. (And the three-part Chronicle article is written by a father who seems to fall into this camp.)
The mothers I know in graduate school are equally devoted, and many of them have shared caregiving responsibilities.
The problem, then, seems not to be the way that men and women fashion themselves into parents, but how certain figures in academia seem to view them. And these articles seem to suggest that the most harsh light often falls upon women who are visibly pregnant.
Does this mean that these same committee members and job interviewers who view pregnant women skeptically have their fears relieved when they see a parent actually making it work with a child? If so, why the discrepancy between women who go on to tenure-track career paths as parents and men?
Does this mean that the mothers and fathers who are on job talks and meeting with their dissertation committee are actively hiding (or at least downplaying) their parenting status when around these people? If so, that would explain why pregnancy--such a visual, undeniable sign of parent status--would be more of a hindrance.
Does this mean that the pregnant women who see and sense these reactions are imagining them? Maybe their own misgivings about balancing their careers, educations, and children coupled with the vulnerability of pregnancy make them more sensitive. If so, why do so many women report this happening during pregnancy?