One of the key reasons is their daughter, born four years ago. They were able to get 12 weeks' parental leave, and decided Carol would take it, meaning she missed important milestones.
"What start off as small disparities can grow exponentially and become self-perpetuating," the couple wrote.
"As one partner makes more money for virtually the same amount of work, his or her work tends to be prioritised accordingly. Success breeds success, and before you know it, the thankless service work gets diverted to the less productive partner, who also happens to have the gender-typical traits of organisation and meticulousness."
But Carol told news.com.au there's more to the difference than her simply being on "the mommy track."
"There are gendered expectations about who's going to do what," she said. "We took it upon ourselves to fight that expectation. Even with that, we found it hard."
John is about to publish a book about them: American Philosophy: A Love Story.
Carol was also working on a book, but when she became pregnant, she found herself "utterly unable to think."
While she firmly believes "there are no fundamental differences between the sexes", she says, "it really did affect the work I was able to do."
The mother of one knows she had it easier than many parents. She had long university holidays in addition to her official leave, and a partner who helped with childcare. She didn't breastfeed.
And still Carol has fallen behind her closely matched partner, who is now a professor to her associate professor.
This disparity between the sexes continues across the world. Figures released today by the Australian Taxation Office show women in top jobs in business and public service are out-earned by their male counterparts by an average of $65,000 a year.
Female politicians trails male colleagues by an average of $60,000 and women in middle- and second-tier public sector management roles are more than $20,000 worse off each year.
There are often short-term reasons to go along with a sexist status quo that will, in the long run, advantage men over women.
The couple often face sexist presumptions, they say. Colleagues assume John was hired first, despite Carol being older and having spent more time in graduate school. Others act as though her professional persona is an extension of his, and she will automatically agree with his views.
Carol is now working on her book, The Stories We Tell About Women, which explores these issues in depth, and has written on the subject for the New York Times.
There's reason to think her career trajectory could catch up to her husband's, although she admits they are privileged in not having had financial struggles, and have been in the unique position of being able to share career opportunities.
"This is not an issue of pity, but of fairness," they write. They make a point of forgetting entitlement and "leaning out" so the other can "lean in", but admit it they still sometimes "fail miserably".
"Gender equality is hard, even when both partners are committed to it," says Carol. "There are often short-term reasons to go along with a sexist status quo that will, in the long run, advantage men over women.
"Seemingly small decisions can have a snowball effect.
"Ultimately, the appropriate level of analysis is one that is macroscopic, taking into account oppressive social roles and expectations and political forces that structure the backdrop against which these personal decisions are made."
