After months of controversy, the University of East Anglia climate unit was exonerated last week over the leaked emails affair. Science editor Robin McKie says there are lessons to be learned – but those who call themselves sceptics must address their own intellectual dishonesty

It was, by many accounts, the worst academic outrage of modern times. A host of emails, illegally obtained from the climate research unit at the University of East Anglia, "revealed" that researchers were manipulating data about global warming and were guilty of perpetrating "the worst scientific scandal of a generation". At least that is how many writers reacted to the news of the leaking of emails between unit leader Phil Jones and fellow researchers.

Last week, however, they adopted a different approach after a report, written by a team of experts recommended by the Royal Society and led by Lord Oxburgh, vindicated the work of the climate research unit, completely exonerated Jones and pronounced that his research was robust and solid. Those hostile writers were largely silent. Given all the hot air they have vented over the affair, this is perhaps not surprising.

Nor am I complaining. A bit of silence from climate-change deniers is always welcome. However, it would be wrong to let last week's revelations pass without comment. Climate science, and science in general, has undoubtedly been harmed by the affair. It is important that lessons are learnt from it.

For a start, it is obvious that scientists need to face the simple matter of dealing with requests for access to data. The small-scale nature of Jones's operations made him a target for critics who bombarded him with requests under freedom of information legislation. Jones struggled to meet those demands. Hence the testy nature of his email responses on occasions, a feature that was seized on by deniers.

Bureaucratic help is now needed when dealing with the deluge of data requests that scientists face. Questions must also be asked if freedom of information legislation should cover access to raw scientific data.

So far, so good. However, there are deeper issues to emerge from this affair, and these will be harder to address. Most fundamental of all is understanding how science itself proceeds, a point made by Tim Palmer, professor of climate physics at Oxford. As he says, scientists operate by trying to disprove ideas put up by fellow researchers. Those ideas that survive this critical analysis are then accepted. Newtonian physics, relativity, continental drift and a thousand other theories are only believed today because they have survived such trials by academic fire.

Thus science is simply organised scepticism. "In truth, we are all climate sceptics," says Palmer – a key point that should be borne in mind when you examine those who claimed that Jones's emails revealed that he and his colleagues were involved in a vast conspiracy to suppress the "fact" that carbon dioxide emissions are not really heating the planet and that they were fraudulently trying to get grants to keep them in work.

In reality, few groups of people would submit themselves to that kind of degradation. Yet somehow we are supposed to believe that scientists, the most sceptical of all professions, were doing that. As Palmer says: "People who believe they are involved in a global conspiracy simply don't understand the process of science and the mindset of its practitioners."

And that leads us to a second key issue: that of terminology – for if the scientist is the true sceptic, then what name do we give to those individuals who dispute the validity of their work and who deny global warming is happening. The latter like to flatter themselves by claiming they are sceptics, but lack the intellectual integrity which goes with the term.

Hence the term denier, which neatly encapsulates their flat refusal to face facts. Some complain that the term has echoes of Holocaust denial. I find such emotional sensitivities hard to stomach, however, given the vitriol that so many deniers pour out in blogs and emails.

The issue that divides the sceptical scientist and the denier is a simple one, says Professor Alan Thorpe, director of the Natural Environment Research Council, one of the bodies that funds the climate research unit at East Anglia.

"We know that carbon dioxide is a molecule that heats up the atmosphere," he says. "We also know we are pumping more and more of it into the atmosphere. Theory then says we should be observing a rise in global temperatures, and that indeed is what we see – thanks to research units like the CRU."

And here the story of the CRU and Phil Jones is illuminating in another way. Jones had been working for decades on the collection of data – from instrument measurements, tree rings (which reveal ancient weather variations) and other sources – that have provided clear evidence that global temperatures are higher now than they have been for several thousand years.

It should be noted that this work was begun long before climate change was considered a mainstream science and was carried out by Jones, a man working virtually on his own – scarcely a sign that he was part of a grand conspiracy involving thousands of others.

The other key issue raised by the CRU affair is the perennial problem of explaining uncertainty. Scientists have uncovered compelling evidence that the world is warming, but cannot say by how much. Rises of between 1C and 6C this century are put forward. This lack of specificity puzzles many people and suggests, to deniers, that scientists are unsure of their facts. Such a claim confuses caution with ignorance. Nor is it an excuse for inaction.

You may be confident that your house will not burn down this year, but you would be considered a fool by many people if you failed to take out insurance. And so it is with climate change. The detailed nature of global warming's impact on the planet is not yet agreed by scientists. It could be dreadful; it could be limited. It might destroy vast stretches of the planet's farmlands and send deserts spreading round the globe. Or it might merely result in sea level rises that inundate parts of Bangladesh and Florida and not much else.

"There might be a 50% risk of widespread problems or possibly only 1%," says Palmer. "Frankly, I would have said a risk of 1% was sufficient for us to take the problem seriously enough to start thinking about reducing emissions."

Most observers now agree that the risk of the world undergoing serious temperature rises by 2100 is certainly greater than one in a hundred. The implication is therefore clear. It's time to stop talking about conspiracies and think seriously about fire insurance.