THIS WEEK's decision on biotechnology patenting in the European Parliament is of more than passing interest to Britain's science community. Redrafting the European Biotechnology Patent Directive, defeated two years ago, saw both greens and industry adopting predictable positions.

For some it is a recipe for profit for industry and a means of stifling research - an attempt to patent life per se. Others argue vociferously that the new directive is essential to safeguard Europe's flourishing biotechnology research and to maintain research jobs. The vote on Wednesday in favour of the directive was decisive. But the implications were far from clear this week and confusion continued.

The directive aims to provide consistent patenting guidelines across Europe, enabling the biotechnology industry to remain competitive with the United States. It attempts to tell businesses and public and private sector researchers what is patentable and will go some way to reducing uncertainties in biotechnology that have persisted for a decade.

The directive appears to allow companies and researchers to patent naturally occurring genes and cells, including human genes, providing some science is done on them and an industrial application defined for them. Identifying and sequencing a gene will in itself be insufficient for a patent, but isolation, manipulation or copying could constitute a patentable invention. The proposed industrial application of an invention has to be included in a patent application. So, for example, identifying a gene for a particular disease and sequencing it is not sufficient for a patent. But isolating it from the human body, even if the structure of the gene remains unchanged, and describing a novel use, such as a new diagnostic test, could warrant a patent and secure exclusive rights to benefit financially.

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This is the murky water between discovery and invention. For some it is a nonsense to allow patenting of human genes because they exist in nature and can therefore, they say, not be invented. But although they exist in nature, they are not in a form that can be used directly to combat disease without processing. What is clear is that strict process and application criteria must be maintained if the new directive is not to permit the patenting of discovery, as opposed to invention.

Proponents of the directive argue that companies involved in gene research deserve the exclusivity gained through patents if they have spent many millions on research. Typically it takes ten years and Pounds 300 million to bring a treatment to market. Unless biotech companies can make profits and maintain their advantage when they make a breakthrough, who will invest in research and openly announce success? No patent, they say, no cure.

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But things are seldom so clear cut. What if a company picks up the results of others' years of publicly funded research, adds the finishing touches and applies for a patent? Should they be able to charge academic researchers for using the gene?

There are real fears that these patents could end up in the hands of just a few big players, killing research elsewhere. A survey last year showed that most of the 1,175 patents for human DNA sequences were held privately, with most of the 213 companies involved being US and Japanese. Only 17 per cent were granted to public institutions. Such patents could drive up the cost of public research and diagnostic tests for genetic diseases, limiting universities' ability to work in these areas. But without patent protection a culture of secrecy can develop that also inhibits research. Patents, by making work public, allow others to use and extend it.

It is a confused situation with all kinds of moral objections to genetic manipulation entangled with commercial considerations. The exact effects of the directive appeared this week still to be far from clear. The water remains murky.