The final research assessment exercise was always going to be controversial. Things were a little more tense than they had been in previous exercises, with £1.5 billion in funding on offer and the expectation that it would be distributed more widely - rewarding excellence wherever it was found at the expense of traditionally research-intensive universities.
The results vindicated the decision to invest significant additional resources in higher education over the past decade. But the euphoria of success had hardly been savoured before the arguments began. Complaints about lack of transparency and the work of the subject review panels are hardly new, but the failure of institutions to include all research staff in the RAE is unacceptable. Not being able to set research output against total departmental research efforts make the results at best questionable and at worst meaningless.
The Higher Education Funding Council for England's failure to insist on full disclosure of research-active staff to counterbalance the drafted-in "stars" who may contribute little to departmental research teams appears to undermine the very essence of the research ethic.
It is obvious why some universities were selective - a high RAE rating raises institutional reputation and traditionally has boosted research funding. But it's time to change how both these elements of research success are evaluated.
I question whether our systems are fit for purpose as the UK comes under increased global pressure to raise its game on basic research, knowledge transfer and wealth creation, and to educate an ever-growing proportion of the population to graduate level.
Finding acceptable alternatives, particularly in an economic downturn, is not easy. Nevertheless, the current review of higher education presents the opportunity for a more open debate.
Central to this is how best to maintain world-class research. Although it was rewarding to see so much 4* research in so many institutions, we must co-ordinate our research efforts more effectively to avoid, on the one hand, a retreat to research-only institutions and, on the other, the "poaching" of bright stars that strips smaller institutions of their capacity.
This challenge is particularly acute in science, medicine and engineering, where it is essential to maintain costly world-class facilities and academic capacity.
The Universities Secretary, John Denham, is aware of the problem. In his grant letter to Hefce, he instructs it to "safeguard the share of mainstream QR (quality-related) funding for science, engineering, medicine and maths". He recognises that to do so will mean fewer resources for arts and humanities, but he offers few incentives to resolve the issue of research-intensive capacity.
There are many examples of institutional, departmental and individual group collaborations operating formally and informally. Great Western Research, which promotes collaborations between the top research groups in the South West, has 20 research fellowships and 130 PhD studentships.
In my own region, the universities of Leeds, Sheffield and York have created the White Rose University Consortium. Uniting their efforts in science and technology has resulted in a research power that ranks alongside Oxbridge and accounts for 86 per cent of the region's research spend.
Combining the power of elite universities is both desirable and essential - they have complementary strengths and do not threaten each other. The challenge is to find a way to link smaller, less research-intensive institutions into a framework while protecting their academics and intellectual property.
As part of the post-RAE exercise, Hefce must provide a structure, incentives and safeguards to promote co-operation on a contract-specific basis between university teams where quality research is central to their mission.
By offering semi-formal support structures, we can allow small pockets of excellence such as Alison Bruce's physics team at the University of Brighton to flourish, while gaining access and support from research-intensive institutions. Hefce might not relish this challenge, but it seems it has little choice but to become more proactive in this area.