If James Lovelock is right, our maltreatment of the planet will come to haunt us. Hugh Aldersey-Williams listens to the 'planetary physician'

How should a scientist live? Specifically, how should a scientist handle matters when feelings get mixed up with findings? For most, the question seldom arises. The laboratory routine and the rules of scientific publishing see to that. But those who do find themselves asking the question face some uncomfortable choices.

The chemist James Lovelock faced his choices in 1964, when, after more than 20 years in medical research and working for Nasa, he struck out to establish himself as that rarest of intellectual beasts, an independent scientist. He prospers now by doing the experiments that involve too much health and safety paperwork for institutional laboratories. By 1964, he had built a solid reputation based on his invention of the device that later detected pesticides and CFCs (chlorofluorocarbons) in the atmosphere.

In the 1970s, however, he developed the Gaia hypothesis that the Earth automatically maintains the conditions for life. His scientific papers were rejected by the major journals and attacked by his peers when they did appear. Lovelock turned increasingly to putting forward his ideas in popular books.

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The Revenge of Gaia is his latest and by far his most unsparing - and gloomy - work. Originally, Lovelock believed that Gaia's self-regulation would adapt the Earth painlessly to humankind's contamination of it.

Indeed, other scientists felt he was merely offering industry, in the words of one of them, "an elaborate excuse to pollute".

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But now Lovelock adjudges that our bad habits have pushed Gaia too far. She is striking back at humankind, which might be reduced to a "few breeding pairs" pushed back by rising sea levels to live in savagery on high ground in the temperate Arctic.

Having initially held that our adding carbon dioxide to the atmosphere was not contributing to the greenhouse effect, Lovelock now believes the worst-case scenarios for global warming and throws in some neglected factors that could make things worse. As a "planetary physician", he prescribes some uncomfortable remedies for what may have to be civilisation's "sustainable retreat", including drastically reducing energy use and increasing nuclear power.

As with the original Gaia announcement, his language is likely to inflame his peers. The Revenge of Gaia is about the way science works as much as it is about the state of the planet. He distinguishes "whistle-blowers" from the "lumpen middle management of science" who have little to say or who cannot say it clearly. "Hardly any laboratory scientist anywhere is as free as a good writer can be," Lovelock writes in the most personally telling sentence of the book.

Lovelock's freedom with language has always made him controversial. He announced the Gaia hypothesis in 1972 in a relatively minor journal as follows: "The purpose of this letter is to suggest that life at an early stage of its evolution acquired the capacity to control the global environment to suit its needs and that this capacity has persisted and is still in active use... Such a large creature, even if only hypothetical, with a powerful capacity to homeostat the planetary environment needs a name; I am indebted to Mr William Golding for suggesting the use of the Greek personification of mother Earth, 'Gaia'."

Gaia seemed to touch on many of the scientific themes of the moment. The suggestion that the Earth exerted a mysterious control, not only over life on its surface but also over the fine-tuned systems that permit its existence, enveloped biodiversity, population biology, chaos theory and complex systems of environmental chemistry, as well as the broader context of the first exploration of other, barren, planets. Gaia here is no metaphor. Though hypothetical, she is, so far as we can tell, meant to be imagined as a real, minded being, "a large creature", no less.

Lovelock immediately realised that he had overstated the idea of a knowing control of the Earth's systems and launched a barrage of papers in an attempt to undo the damage. These were written with a new collaborator, Lynn Margulis, a biologist at Boston University, "to be comprehensible to a wide scientific audience" and were characterised by greater interdisciplinary understanding and more careful phrasing.

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It is curious that Margulis and Lovelock again chose a relatively obscure journal of the atmospheric sciences, Icarus, if, as they claimed, they wished to reach "a wide scientific audience". But Lovelock's unorthodox papers were beginning to be rejected by Nature and Science . The editor of Icarus was Margulis's husband, the atmospheric physicist Carl Sagan.

In this paper, Lovelock noted that what made the Earth unique was "the ubiquitous scum of the planet... namely the biota". He marvelled that the Earth had for 3.5 billion years "followed the straight and narrow path optimal for surface life". These are biblical references such as any literary writer might employ. They serve rhetorically to set a moral framework around the Gaia hypothesis. But they grate in a scientific paper.

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Lovelock recalls now that as a child he was "marinated in Christian belief, and still it unconsciously guides my thinking and behaviour".

Other metaphors were unhelpfully anthropomorphic, such as one that likened the planet's control mechanisms to human sweating and shivering. More seriously, Lovelock seemed to employ a circular logic. His presupposition that life is what makes the Earth different is used to help make the case that Gaia exists on Earth. "Presumably it is this living system that is responsible for the phenomenon we are calling Gaia."

Lovelock is not unique in his difficulties. In Findings: Hidden Stories in First-Hand Accounts of Scientific Discovery , I examine the literature of the environmental sciences that were emerging during the 1970s, including Lovelock's Gaia papers and reports by Paul Crutzen, Sherwood Rowland and Mario Molina, who later won a Nobel prize for their work on the depletion of ozone in the stratosphere by CFCs from man-made sources. These scientists find themselves - to their own manifest consternation - struggling to balance dispassionate reporting of new data with campaigning advocacy. Their data have implications that must be communicated, but the formal constraints of the scientific literature offer them no help.

In 2006, Lovelock strives to call Gaia "it" rather than "she". "It has never been more than a metaphor," he insists, "an aide pens¨¦e , no more serious than the thought of a sailor who refers to his ship as 'she'." The trouble is that scientists do not really do metaphor. Nor, within their journal pages, ought they to advise, recommend, caution or warn. And yet these scientists at this time are briefly emboldened to extrapolate from their findings to advocate policy not only on pollution controls but also on everything from supersonic air travel to strategic arms limitation.

Lovelock portrays himself as a whistle-blower, but in the context of warnings by other environmental scientists he is merely returning to the fold. Crutzen was one of the first scientists prepared to discuss Gaia on Lovelock's terms. In 1995, he stated as the crucial question "not whether Gaia-type systems are active, but whether humanity's actions can drive the Earth system beyond not only any short-term repair capabilities directed by humans, but also beyond any hypothetical Gaia repair capability".

Lovelock is now amplifying this thought. The regret is that, once stated, it should need amplifying at all. Lovelock wishes he had done in the 1970s what he finally thought to do in the 1990s - talk to his scientific opponents face to face, where he was better able to persuade. But he also wishes to find a way for science to speak. "Science is supposed to be objective, so why has it failed to warn us sooner of these dangers?" he demands. "If the middle management of science had been less reactionary about Gaia, we might have had 20 more years in which to resolve the much more difficult human and political decisions about our future."

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Hugh Aldersey-Williams is a science writer. James Lovelock's The Revenge of Gaia is published this week by Allen Lane, ?16.99.