To judge from media reports last week, you would think that Harvard University's president Larry Summers had told everyone in a skirt to quit science, pack up their handbag and head home to the kids — clearly biologically incapable of rivalling men in this intellectually thorny field.

What Summers actually said has been harder to discern. There is no transcript of the speech he made at an academic meeting. But by most accounts, he talked about potential reasons why so few women reach top positions in science and engineering. And he at least raised the possibility that innate differences could play a part.

Whatever his actual words, the interpretation — that women suffer an inborn and insurmountable intellectual handicap in science — whipped up a firestorm of protest both on and off Harvard's (male-dominated) campus. Swamped by fuming letters and stinging media reports, Summers has released serial cringing apologies in which he emphasized his efforts to bump up the number of female scholars at Harvard — actions for which some staff, at least, give him credit.

His latest remarks are consistent with his reputation for making blunt and provocative comments. That hasn't gone down well at Harvard, where his radical plans for change have raised hackles since he took over in 2001 (see Nature 433, 190–193; 2005).

The latest debate about gender inequality has provided an opportunity to look afresh at the causes and potential solutions. Is there any evidence for innate differences in the sexes' cognitive abilities? Researchers say there is. One well-explored area is gender disparity in processing spatial problems: men and women have been shown to use different areas of the brain to weave their way out of a virtual-reality maze (G. Grön et al. Nature Neurosci. 3, 404–408; 2000).

Unfortunately, this doesn't resolve the question in hand. Men's and women's brains may work in slightly different ways, but researchers cannot say for sure whether these disparities underlie differences in their exam performance or ability to scoop top academic jobs. By the time adolescents take tests or women are applying for tenure, it is difficult to tease apart possible contributory biological differences from the complex cocktail of other factors that could be holding them back. These include society's sexual stereotyping, dismal family support and old-fashioned discrimination. Summers also mentioned some of these in his speech.

The Harvard president needs to think more carefully before he speaks, even when, as here, the occasion is off the record. But the hullabaloo should not deter academics from discussing important if disquieting questions, both on principle and also in the hope of pinpointing causes and finding solutions.

The faculty at Harvard and other institutions should view this furore as an opportunity to highlight shortfalls in the system that handicap women, and demand that they be improved. Female scientists, engineers and mathematicians at Harvard might find this a good moment to ask for a promotion — and those outside its hallowed walls should mail in an application. With some concerted action, the fallout could be a boost for female scientists everywhere.