It was while growing up in Philadelphia that Ruth Harris first heard about the Dreyfus affair, the great cause c¨¦l¨¨bre of late 19th-century France - and it came with a clear moral attached.

Her school history teacher, she recalls in The Man on Devil's Island: Alfred Dreyfus and the Affair that Divided France, certainly told the poignant story of the Jewish captain who in 1894 was convicted of treason - on ludicrously inadequate evidence - and imprisoned in appalling conditions off the coast of French Guiana. Yet what the teacher really stressed was the good guys who took up the cause, the "righteous Dreyfusards battling against iniquitous right-wing nationalists and anti-Semites", as he encouraged his pupils "to draw parallels between the struggle to free Dreyfus and the civil rights movement of the 1960s".

So this is a story that was iconic in Harris' own childhood and that remains iconic - and therefore underexamined - in today's France. What happens if we strip away the mythology and melodrama of a simple battle between the righteous and the iniquitous and try to look again at what really happened? Harris' career to date makes her perfectly suited to this task.

She is now a lecturer in modern history at the University of Oxford. She arrived there on a scholarship at the age of 20, after completing a joint bachelor's and master's degree at the University of Pennsylvania. She soon developed an interest in French history and found it "incredibly exciting" to do research in Paris and to sit next to academic superstars such as Michel Foucault in the Biblioth¨¨que Nationale.

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A grant from the Wellcome Trust kept Harris in Oxford. By then, she was already working on the history of science and medicine, an interest that eventually led to her 1989 book, Murders and Madness: Medicine, Law, and Society in the Fin de Siecle. She secured a research fellowship at St John's College in 1983 for four years and was then shortlisted for a job at Christ Church, but she decided to withdraw when she realised there was only one other woman Fellow at the college.

When Harris returned to the US to take up a post at Smith College, however, she became "very unhappy, because I missed Britain and Europe, so I took leave without pay and was thinking of retraining as a psychoanalyst". In the event, a position came up at New College in Oxford, where she has now been for 20 years. She is currently sub-warden and second-in-command, although, she observes, "Oxford is a place where you always feel junior and someone else has a longer memory".

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It was medical history that eventually brought Harris back to Dreyfus' story. Many French doctors at the end of the 19th century were confident that the triumph of science would soon sweep religion away. Yet this was also the golden age of Lourdes, with thousands of invalids pouring into the Pyrenean shrine in search of a cure. The conflict and the links between these two strands of French life, between progress and reaction, are at the heart of Harris' remarkable 1999 book, Lourdes: Body and Spirit in the Secular Age.

Although she is Jewish, secular and highly educated, and so presumably not a believer in the miracles of Saint Bernadette, Harris steadfastly refuses to pronounce on this issue and offers the book as "neither a Catholic apologia nor an anti-clerical tirade". She did feel a certain degree of sympathy with the supplicants, as she explains in the preface, because she used to suffer from a condition "for which medicine had no diagnosis, and only hit-or-miss treatment. What, I asked, do ailing people do when science can offer nothing?" She even decided to go on a pilgrimage, "half expecting to be repelled by the whole experience", but soon found herself "taken up with the business at hand, directed to help a mother care for her adult son who was incontinent, paralysed, blind and deaf".

The result is a work of deep historical scholarship that also manages to present Lourdes as a place dominated by "intense physicality, backbreaking labour, and (the) centrality of pain and suffering". Historians are very skilled at analysing written documents, Harris suggests, yet they often shy away from visceral issues. Her own book attempts, she says, "to open up new ways of addressing aspects of historical experiences that seem beyond retrieval and hopeless of understanding".

No one interested in French debates on science and religion, not to mention race, modernity and national honour, can avoid the Dreyfus case. At its heart was a terrible miscarriage of justice that not only deeply affected one man, but polarised the nation as deeply as would the Vietnam War in the US.

Asked about British equivalents, Harris argues that "there is no parallel in British history, which is why I'm so interested in it. It's very French, and indicative of a political culture that operates on different lines. The Dreyfus affair is the moment when the term 'intellectual' is coined and they become opinion-makers, in a way they never have in Britain." Although there had obviously been modernisers and traditionalists beforehand, this was also the moment when they solidified, she says, into "two blocs and two Frances".

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A famous cartoon depicts a fight breaking out at a dinner party when someone was foolish enough to mention the matter. Salons were strictly demarcated as either Dreyfusard or anti-Dreyfusard.

In one corner were the defenders of "tradition" and "honour": the top military brass and much of the Catholic Church who fitted Dreyfus up and obstructed all efforts to find the person responsible for the spying he was wrongly accused of. (The culprit turned out to be a gambling, womanising officer who sold secrets to the Germans with the aim of clearing his debts.) Prominent anti-Dreyfusards would go on to exert a major influence during the Second World War on the Vichy government, which collaborated enthusiastically with the Nazis, not least in deporting Jews to death camps.

In the opposite camp were the believers in "justice" and "truth", who fought for republican values and freedom for an unjustly convicted man who would not be exonerated until 1906. It is now very obvious which side most of us would support, but that is no reason to turn the two sides into stock villains and plaster saints. Harris says she was determined to do justice to the complexity, mixed motives and emotional undercurrents that underpin all political movements. Her research on Lourdes had already taught her that "the most extreme anti-Semites and the most extreme anti-Dreyfusards" could also be "gentle organisers of pilgrimage for the sick".

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Just as the "baddies" need to be understood (although not excused), it is wrong to idealise the good guys. Many right-wingers assumed that Dreyfus was guilty because he was Jewish. Some of his supporters were equally convinced of his innocence, Harris notes, "simply because they believed the Jesuits were responsible for his conviction". What is truly admirable about them is not that they were always calmly rational but that they were "full of competing impulses and desires", some of them ugly, and still managed to rise above them as they came to the defence of an innocent man. Harris also wants us to face up to "the aspects of the republican tradition that are themselves intolerant".

"The vehemence of the assault against the Church in the aftermath of the affair was part of a tradition of anticlerical intolerance and the fanaticism of a civic religion," she suggests, "which we continue to see today with the burka.

"I personally find it very disturbing when I see a woman wearing a burka, but it is still interesting that 2,000 women (in a population of 65 million) can be seen as a threat to the Republic. I think it's extraordinary the amount of emotional, intellectual and political capital that has been mobilised for outlawing it."

At a time of militant atheism, led by Harris' New College colleague Richard Dawkins, the Dreyfus case continues to shed light on both religious and anti-religious myopia and intolerance.

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