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The basic flaw with the peer review system in higher education, whereby your colleagues decide whether or not you should receive funds for your research from one of the leading charities or government-funded research councils, is that ultimately it hinges on subjective judgments that are not publicly accountable: witness a recent survey, published in Nature last May, where sexism and nepotism were shown to be rife in the Swedish Medical Research Council. But I would argue that it is in the implementation of the system as it stands that the less obvious and hence more insidious injustices lurk.

For example, there is the increasingly popular mind-set of "safe science". The very phrase is a paradox, since one of the points of performing an experiment is that the outcome is not assured in advance. And why should caution be so desirable? Because "risk" is minimised. This admirable brief can readily impress fellow committee members, as they watch you, alert to ensuring that public-sector funds are only spent on studies that will "work". "Speculative", in a referee's report for research councils or charities, is currently regarded as the kiss of death, whereas the private sector cannot afford not to invest in originality. The irony is that, whereas a committee for a profit-making organisation is in the business of just that - making money - such anxieties are not within the remit of their public-sector counterparts.

After all, a grant is not a means of making money, but rather an expression implying the contrary, that money is being given away. The "product" can only ever be the subsequent published papers. If these results have merely dotted a few more "i"s and crossed some "t"s, then what has really been gained? Already we scientists are mired down with publications that we have no time to read, and which can distract us in their minutiae from the main issue, the big questions. Perhaps, dare I nervously suggest, it is the money spent on safe science that is money wasted.

The worst that can happen with a "high-risk" experiment, is that it does not give the predicted outcome. But, as Karl Popper wrote so long ago, the whole idea of science is to generate falsifiable hypotheses. If something different or new happens, it is nature telling you something. What a shame that the current fashion for funding science is to deafen us to these revelations.

A further, operational inadequacy in the system as it stands is that judgement is allegedly based on the reports from expert referees. But since there is no obvious reason to spend large amounts of your own precious, Hefce-haunted time on a forensic examination of someone else's plans, the take-up is notoriously low, and, worse still, highly patchy from one applicant to the next. In any case the final decisions rest with a panel, appointed as cryptically as Tory party leaders were in the days of Macmillan: there are no overtly special qualifications that distinguish those who receive the call. Such opaque selection is clearly ideal for old-boy exploitation and virtually guarantees that the complexion of the panels will not be representative of the scientific community as a whole, that wonderful broad church of Visionaries, Nerds, Pedants, Green Fingereds and Mavericks as well as the Politicians.

The operations of these central soviets serve as an enticing loophole for seemingly strong referees' reports to be trumped by asides whispered in camera. A discrepancy between rave reviews from referees and a mystifying rejection can be readily fobbed off to the hapless applicant as a "low priority" project that was less competitive in comparison with other, unidentified applications.

Most apologists for the peer review system admit that it is far from ideal, but claim that, in an imperfect world, there is no more attractive alternative. But there are alternatives that at least merit serious consideration: circulation of the complete minutes of in-camera meetings of the parts of the discussion relevant to the applicant; a jury-service-like rota for serving on panels, for which all academics of a certain tenure are eligible; a system to ensure that all applications are based on the same number of reports.

More radical suggestions would include: a scheme whereby available money could be simply divvied up equally among an agreed constituency of scientists, or perhaps restricting panel members exclusively to those with no vested interest in insider dealing, for example the grey-beards with a lifetime experience of science behind them, who can take the wider view that imminent or recent retirement allows. And if it just comes down to too many worthy applications for little available money, then let's be honest about it and have a lottery. Whatever happens, the concept of peer review is too inherently pernicious to be compounded by injustices in its practice, and potentially wasteful of time and talent to be shrugged off as the best that can be done.

The writer is professor of pharmacology at the University of Oxford.