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Last year, Lawrence Summers was forced to resign as president of Harvard University after he suggested that underrepresentation of women in some fields of science could be explained partly by differences in the innate abilities and preferences of men and women. His comments were delivered at a private seminar at the National Bureau of Economics and were initially fed to the press by Nancy Hopkins, a biologist at the Massachusetts Institute of Technology, who said that if she had not walked out of Summers's talk, she "would have either blacked out or thrown up".

In something of a public relations disaster, the full transcript of his speech was not made available for more than a month, in which time Summers drew fire from his Harvard colleagues, international media, female scientists and others. By the time the transcript was released and it became clear that the press had widely misrepresented his remarks, his presidency was irreparably dented and Summers subsequently stepped down.

Rather than claiming that "women can't do science", as was frequently reported, Summers offered three reasons, in order of decreasing importance, for why there are very few women working in some fields. "My best guess, to provoke you, of what's behind all of this is that the largest phenomenon, by far, is the general clash between people's legitimate family desires and employers' current desire for high power and high intensity; that in the special case of science and engineering, there are issues of intrinsic aptitude, and particularly of the variability of aptitude; and that those considerations are reinforced by what are in fact lesser factors involving socialisation and continuing discrimination," he said, according to the transcript.

Summers qualified his remarks by saying "to provoke you" on several occasions; he stressed that his suggestions could be wrong, and he challenged researchers to examine them.

Now Polly Matzinger, section head at the US National Institute of Allergy and Infectious Diseases, has given robust support to the idea that sex can influence how a person does science. In a seminar on "Male and female scientists", given at the Oxford Univerity society for Females in Engineering, Science and Technology (Fest) in June, she claimed that, far from being offended by the suggestion that there may be differences between men and women, her female perspective has played a crucial role in her success as a scientist.

Matzinger's route into science was unorthodox, to say the least. After dropping in and out of college and taking a succession of jobs, including spells as a Playboy bunny, jazz musician, carpenter and dog trainer, she ended up working as a cocktail waitress in a bar popular with academics from the University of California, Davis. After noting her knack for asking sharp questions, one professor, Robert "Swampy" Schwab, encouraged her to become a scientist. After nine months of persuasion, she applied to graduate school in 1973, got a belated bachelor's degree in biology in 1976 and a PhD in 1979. She went on to revolutionise the field of immunology with her so-called danger model.

Matzinger believes that bringing a female point of view to a field dominated by men since its inception has helped her uncover inadequacies in conventional theories. "At college I was taught the 'self/non-self' model of the immune system," she says. "I had some problems with the model and started asking questions."

The self/non-self hypothesis is based on the idea that, after a "training" period in infancy in which the immune system learns the concept of "self", our immune cells attack anything they perceive as foreign, that is, "non-self". But Matzinger felt that the model didn't square with her day-to-day experience of how the body behaves and concluded that it must be incomplete.

One of the biggest flaws was the model's prediction that the immune system of a pregnant woman should reject the foetus given that it clearly expresses characters inherited from the father, which are not part of the mother's make up. Because this prediction is patently wrong, Matzinger felt there was a strong case for revising a model that had prevailed since the 1950s. But her desire for change did not always meet with approval. "What can happen in science is that people get stuck in a paradigm," she says. "In this case, the people who were stuck happened to be male."

Rather than scrapping the self/non-self model, many immunologists took a "Mohammed and the mountain" stance, revising their view of everyday biology to make it comply with their views. Matzinger describes how one of her colleagues "in his Oxford-educated male arrogance" could not imagine that his model might be wrong and suggested instead that there was something wrong with female physiology. He wrote that foetuses immunosuppress their mothers and that is why they are not rejected. As Matzinger pointed out: "This is dumb. Didn't he notice that pregnant women don't have to walk around in bubbles? They're not sick like Aids patients!"

After being silenced temporarily by her professors as a student, Matzinger revisited the problem some years later and came up with the danger model. This argues that, rather than responding to anything that is "non-self", the immune system responds to things that are "dangerous". The danger model has provided new explanations for maternal/foetal immunity, autoimmunity and the ways the immune system adapts to changes such as organ transplants and the hormones released during puberty.

Matzinger is comfortable with the notion that there could be aggregate differences in the abilities and, even more, the interests of men and women. She was unperturbed by Summers's speech. "Afterwards, the transcript was going round, and I really didn't have a problem with what he said."

"There was a time in my life when you couldn't have brought me to admit there were differences between men and women. We lived in a man's world and admitting differences was quasi-admitting that we are not as good." Now speaking from a position of academic authority, Matzinger has long since proved she can hold her own.

Her words are reminiscent of the shift in feminist philosophy over the past few decades. In the 1970s, there was a popular theory that gender identities were mere social constructs and that any differences between the sexes should be attributed to nurture alone. Today, new brain-scanning techniques show average differences in the structure of male and female brains.

Neuroscientists such as Steven Pinker believe that these findings translate into differences in behaviour and ability. "There are as many instances in which women do slightly better than men as ones in which men do slightly better than women. For example, men are better at throwing, but women are more dexterous. Men are better at mentally rotating shapes; women are better at visual memory," Pinker said in a debate on "gender disparities in science" held at Harvard shortly after Summers's speech.

Although Matzinger is open to the idea of gender differences, she does not suggest that science is a level playing field. "Things haven't changed enough," she says. "When I was a grad student, 50 per cent of my class was female. But now when I look around, there are hardly any women at my level or above, which makes me so angry." While it may prove to be the case that part of the reason that there are fewer women in, say, astrophysics comes down to intrinsic differences between the sexes, the huge under-representation of women in senior jobs cannot easily be explained by these alone.

In a professional context where men and women have equal prospects of promotion, it is not taboo to discuss differences in approaches between the sexes. It is hard to avoid articles about, say, the advantages of "female management style". Yet in science, where women fill a mere eight per cent of senior academic roles, it is clear from the Summers controversy that talking about differences is still seen as covert sexism. Until women have equal chances of success in science, this is likely to remain the case.

Hannah Devlin is a PhD student at Oxford University.