On Tuesday afternoon, Gillian Beer will climb into a sumptuous Georgina von Etzdorf gown, take a taxi to London's ancient Guildhall, meet the four co-judges who, like her, have spent the last month re-considering the merits of six short-listed books and, over tea and biscuits, decide on which one will make its author a millionaire. Flushed with largesse, the quintet will mingle with the metropolitan literati, swilling Sauvignon and fending off pre-emptive enquiries. In the dining room, fenced off at a Judges' Table far from earwigging hacks, they will eat their supper under the hot lights of Channel Four's patrolling cameramen and, amid the debris of coffee, stickies and cigars, Ms Beer will make a speech about the state of the nation's literature.

"I have got to make one, haven't I?" she says with fake alarm. "I haven't even thought about it yet. Unlike one of my predecessors, George Walden, the former MP, who apparently started writing his Booker speech at the beginning of the summer..." The organisers need not gnaw their nails with worry, however, about Professor Beer's ability to string some literary- critical words together. One of a smallish group of transcontinental, multi-disciplinary uber-academics, she was born to lecture. Her natural habitat is behind a lectern or podium. Her discourse is naturally magisterial, judicious, ex cathedra.

Among her many titles is "King Edward VII Professor of English Literature at Cambridge University" - a Crown appointment without applicants or shortlist, the gift of Buckingham Palace. "No, I've never been to tea there," she says regretfully, "nor met the Queen. The Appointments Secretary makes the decision about the professorship. He handles it like an American executive search programme, asking dozens of people privately about who should get it." But the regal connotations of the job remain, aptly embodied by the striking queenliness of Prof Beer herself. She is a handsome woman in her late fifties, with merry eyes, silver hair and the kind of face you might find on the stamps of a returned monarchy in Eastern Europe. Built on generous lines, she glides around with serene energy, though nobody I talked to can agree which kind of sea-craft she most resembles. "A vessel in full sail". "A galleon". "A quinquereme"... Personally, she puts me in mind of the royal yacht Britannia, as well as that other Britannia on our 50p pieces. Professor Beer, valiant for intellectual truth, would look quite at home with a lion and trident by her side.

The business of reading over a hundred novels in a few months is enough to give any working don (she's also President of Clare Hall, Cambridge) palpitations. To Ms Beer, whose second Booker stint this is, it's meat, drink, pudding and double espresso. "I enjoy reading fiction inordinately," she breathes. "I've enjoyed the discussions because they were very wide- ranging and intense. But now we've reached the meagre end of it, because out of all this wonderful welter, you choose six books and that's all the outside world sees. But for the judges, we still have the long shortlist in our minds, all the arguments... And every judge has on the shortlist a book they didn't like."

Among the final sextet - Jim Crace's Quarantine, Mick Jackson's The Underground Man, Bernard Mac Laverty's Grace Notes, Tim Parks's Europa, Arundhati Roy's The God of Small Things, and Madeleine St John's The Essence of the Thing - the last-named has been selected by disobliging commentators as a ghastly aberration. It's a slender, novelettish tale of a marital bust-up in Notting Hill, fuelled by listless conversations and fake epiphanies in a succession of tiny chapterettes. To the jaundiced eye, it appears to have the emotional depth of a Pringle crisp. Can it have been the Professor's choice? "It's a book that's very spare, limited in its social range, but it works from beginning to the surprise ending. We kept finding books that just collapsed halfway through. And people who liked it also thought that to choose a book which wasn't filled with learning and the usual virtues would be a good thing to the Booker Prize itself."

The last time she was a judge was in 1993, the year the prize went to Roddy Doyle's Paddy Clarke Ha Ha Ha. It was a popular choice (achieving the biggest volume sales of any Booker winner, ever) but seemed a rather odd choice for the classically-minded Beer to have supported. Now she's presiding over another choice of the light-toned and accomplished, rather than the sturdy and earnest. "People remember these Golden Ages of the Booker Prize," she says dismissively. "And they're always wrong. They remember 1993 as the only year when there wasn't a row - but there was one, because we hadn't chosen Vikram Seth's A Suitable Boy for the shortlist. We were abused by James Wood in the Guardian, and by that head of the Suitable Boy publishers, whoever he was [Anthony Cheetham] who described us very rudely and said we were all wankers."

One is frankly taken aback to hear such a football-terrace locution on Professor Beer's delicate lips. Her conversation is enthusiastically salted with academic words and phrasings, like "analect", "sequestered", and the "costive idiolect" of Europa. When listing some favourite books that failed to make the shortlist, she moves between expressions of delight and Lit Crit formulations without any change of gear. "If I'd been a dictator, a number of other books would have got on the list. Caryll Phillips's The Nature of Blood, which I liked very much, and John Banville's The Untouchable. It meanders in the middle and goes very dry and thin, but he's trying to describe the condition of dryness and thinness and the queasy instability of treachery. I thought it was terrific. And Jeanette Winterson's Gut Symmetries - people said of the science bits, 'Oh it's not real physics', but it's also about Paracelsus, of course, and how the human body is framed by the Universal."

Science and Ms Beer have had a long and fulfilling relationship. Since she began to study Darwin, and the ways in which he introduced evolutionary theory to the world (his style, Beer argued, was heavily influenced by George Eliot), she has found herself entering arenas mostly denied to literary academics. Her book, Darwin's Plots (1983), was praised by critics in the rival disciplines of anthropology, history and philosophy. She's probably best known in academic circles as a synthesiser of arts and sciences. For this interview, we met at the Wellcome Trust in London's Euston Road, where she was attending a "Sci-Art" conference, in which the extreme wings of design technology collaborate in medical and surgical projects. "I don't claim in any way to be a scientist," she says modestly. "I'm interested in the ideas that scientists can generate but can't control." On 19 October, she will appear on stage at the Cheltenham Festival of Literature, discussing (with Melvyn Bragg, Robert Winder, Philip Kerr and Lewis Wolpert) whether science and literature can ever understand each other. "I can't see why people who like the arts should have any incapacity - but science has become so extraordinarily specialised, and outsiders can't grasp it without a great deal of work." Did she feel perfectly up to speed about Heisenberg's Uncertainty Principle and Schroedinger's Cat? "No, no, of course I've a cut-off point of understanding. That's why I work predominantly with 19th-century scientific writing."

A strange Victorian-sepia tinge sits like a filter over the early life of Professor Beer. She was born Gillian Thomas "in the middle of a heath - not exposed to the elements, exactly, but in a cottage" in a place called, presciently, Little Bookham, Surrey. Her parents split up when she was three. "I have no idea what my father did," she says shortly. "He was just not part of my life. It was wartime and he joined up, but that was the occasion of their break-up, not its cause. But everyone else's father was away at the war, so it didn't have anything like the traumatic effect it might've had." She and her mother relocated to Somerset, where they occupied two rooms of a bricklayer's home. They lived on her mother's salary as a primary school teacher. "We were not poverty stricken," she says defensively. "I never had a sense of being poor. There were just no luxuries. I spent a lot of time outdoors, because there were hardly any cars on the road. You could bicycle everywhere." Wasn't she warned against strangers? She considered. "I remember being told that, when the gypsies came along, I shouldn't really go off for the day with them. But that was all."

The rustic cyclist lived with her mother and the bricklaying family till she was 11 and went to boarding school in Bruton, north Somerset. Though it was an unusual and enlightened place ("All the houses were named after early feminists"), she didn't like it. "The lack of competition was an expression of its low expectations of everybody there. But I had a wonderful French teacher and a geography mistress who was very good at putting on drama, and that was where the richness lay, being in a whole succession of plays." At 14, she had an accident, hurt her spine and, in her year off school, began to read seriously - Ibsen, Wilde, Shakespeare - and to write. "I managed a complete novel when I was 14, and never have again. It was about a girl who dressed up as a boy and became a player in Shakespeare's company. I sent it to a publisher who wrote back and said, 'You should write about what you know'. I remember thinking at the time, but that's the hardest thing in the world."

She was never a teenager, she says. "I was very sequestered. And I just never felt right in my body then. My best times have always been the fives, for some reason - 25, 35, 45. I won't go on." The first romantic interlude in her life seems to have been in Austria, where she went to live at 19. "I was interested in the language, having heard these strange Germanic barks on the radio. I decided I wanted to learn it, so I went to live with a family, had lessons, helped in the house and had a wonderful time. I hardly read a thing. We swam, we walked about, I fell in love..." Was he Austrian? "Yes." Blond? "Dark." Did he break her heart? "No, it was all right, but he was 10 years older than I, so..." At this point, the Prof silently stabs her forefinger at the tape machine, as if reluctant to divulge any more in front of a spy.

She read English at St Anne's, Oxford where, according to her old tutor, Patricia Ingham, she radiated cleverness but giggled a lot. "That's because she scared the wits out of me," says Beer. She got a first and made it her career. "I began to think that this was what I should be doing, being paid to sit around reading George Herbert." Her first job was at Bedford College, London, where she narrowly pipped a UCL graduate, and young aspirant novelist, to the post. "I remember sitting in a room at Bedford, waiting to be interviewed, and feeling pretty confident," says David Lodge today. "Then this strapping blonde strode in, and I knew I was sunk." The rest of her life has been a succession of postings, chairs, research fellowships and other more esoteric "-ships". She married John Beer, a fellow academic and a prolific writer on Coleridge and the Romantic movement. They had three boys, and moved to university posts in Liverpool and Cambridge. Ms Beer loyally followed her husband, but never thought of relinquishing her ambitions. "I felt very stuck for a long time," she says crossly. "All my male contemporaries were already professors, and I'd become this wholesome figure doing far too many hours of teaching. It was only when I brought out Darwin's Plots that my life changed, and people wanted to publish what I wrote."

Her new book is a typically poly-disciplinary affair. "It's going to be called Experimental Islands. I'm going to ask a question - why did the island site become the domain for experiment in evolutionary theory, in colonialism, in boys' books like Treasure Island - and when I've got the answer, I'll have finished the book. Are islands seen as autonomous zones, like laboratories, as with Bikini atoll and in The Voyage of the Beagle. Or is an island a place where the ego can expand to fit it?". (As with Richard Branson?) She talks with delight about the ramifications of her current thinking, which turns out to be a little too unfeasibly broad. "I've been writing it for too long," she says, laughing. "I thought I was writing this nice little Isle of Wight. And it's turned into Australia"