Urania's lessons for Clio

Crisis in the humanities? What crisis? If there is one, it is not of the kind commonly supposed. The evidence proves that funding is collapsing, student recruitment wavering or plunging, and academic posts vanishing. But understandable concern over these problems masks deeper troubles, which are not the result of the economic travails that arts departments undergo, or matters of the prestige or popularity of the disciplines they teach, but intellectual challenges that arise from within the humanistic tradition and its encounters with science.

A sense of crisis erupted in arts departments in US universities last October when George M. Philip, president of the State University of New York, Albany, announced the closure of most of its degree courses in modern languages, literature, Classics and theatre. He made no serious attempt to justify the move on intellectual grounds, but presented it as a mildly regrettable adjustment to market conditions - the outcome of the need to "rebalance resources".

The university lost $32 million (£20 million) of state funding in a single year, with a further $12 million expected to go in 2011. What's left must be concentrated on useful and sought-after programmes, so the argument goes.

Evidence that has poured in from the press since then seems to support this argument. Last month, the American Historical Association reported a 46 per cent drop in the number of history-related jobs advertised with it, the lowest level in 25 years. The previous year, 15 per cent of the ads were withdrawn without appointments being made.

Since then, according to the association's latest survey, the job market has collapsed, while the longstanding pattern of increasing numbers of students opting for history programmes has faltered and fluctuated. The same pattern, in even more accentuated form, is discernible in literature and philosophy programmes.

Economics, business studies, computer studies and other courses popularly associated with job opportunities have, by contrast, begun to show signs of recovery from the austerity of recent years, attracting relatively more funding, more students and more posts. Now Republicans have proposed abolishing the National Endowment for the Humanities - the world's largest single source of arts research funding.

I should confess that I contemplate these alarms from a privileged perch. The University of Notre Dame has the advantage of backing from benefactors who love and value humane letters. Our history department, where I work, continues to grow prodigiously. Plenty of students want to study with us. They seem alert to the benefits - quantifiable and beyond calibration - of learning to read and understand evidence, appreciating the presence of the past in our minds and environments, and locating experience in the context of tradition. And universities facing cuts know that the humanities are cheap: we can eat peanuts and perform like great apes.

But it is not complacency that makes me look beyond the supposed crisis. It is, on the contrary, profound unease about how scholars in the humanities generally go about their work.

The humanities are most threatened by short-term thinking and crass priorities - as is pure science. Indeed, to speak of a "crisis in the humanities" without acknowledging that science is in equal trouble succumbs to the old myth of the "two cultures". The way we organise academic life in discrete departments is a remnant of bygone thinking. We prattle about interdisciplinarity, but do little.

The number of projects in teaching and research that transgress the traditional boundaries of the arts and science remains disappointingly small.

Literature was among the first fields in the humanities to deploy quantitative methods to disclose new insights, when imagery analysis began to capture critics' imaginations in the 1930s. When I was young, cliometrics was all the rage among historians, some of whom also took a fleeting interest in catastrophe and chaos theory. Environmental history has rapidly become a major field, demanding cross-pollination with biology and ecology. Historians' awareness of the diversity of evidence and the importance of material culture has made untenable the kind of unremittingly textual approach to the subject with which I grew up.

Yet we do not seem to have moved on from these beginnings to embrace the opportunities that scientific developments have opened up. On the contrary, culture wars waged against traditional historical thinking by sociobiologists and Dawkinsites, who want to displace humanistic approaches entirely in favour of biological determinism, have inspired ideological rejection of science among many historians.

In partial consequence, while scholars have initiated fruitful exchanges across adjacent disciplines - for instance, history with geography, archaeology and anthropology, or literature with linguistics - some rich opportunities are going begging. I have personal experience of how hard it is to interest fellow historians in collaborations with workers in genetics, palaeoanthropology and primatology - but these disciplines have a huge amount to teach us about how and why cultural changes happen. No historian's armoury is complete without knowledge of them.

Cognitive scientists are doing startling work on memory and imagination, which historians need to take on board if they want to think about their subject with the freedom that mastery of relevant knowledge confers. The deepest crisis in the humanities is self-inflicted. It will only be resolved when those of us who work in the field rethink the very nature of what we do and take the unity of learning seriously.