I have seldom felt so alone. Confronted with crisis, most of the environmentalists I know have gone into denial. The emails hacked from the Climatic Research Unit (CRU) at the University of East Anglia, they say, are a storm in a tea cup, no big deal, exaggerated out of all recognition. It is true that climate change deniers have made wild claims which the material can't possibly support (the end of global warming, the death of climate science). But it is also true that the emails are very damaging.

The response of the greens and most of the scientists I know is profoundly ironic, as we spend so much of our time confronting other people's denial. Pretending that this isn't a real crisis isn't going to make it go away. Nor is an attempt to justify the emails with technicalities. We'll be able to get past this only by grasping reality, apologising where appropriate and demonstrating that it cannot happen again.

It is true that much of what has been revealed could be explained as the usual cut and thrust of the peer review process, exacerbated by the extraordinary pressure the scientists were facing from a denial industry determined to crush them. One of the most damaging emails was sent by the head of the climatic research unit, Phil Jones. He wrote "I can't see either of these papers being in the next IPCC report. Kevin and I will keep them out somehow - even if we have to redefine what the peer-review literature is!"

One of these papers which was published in the journal Climate Research turned out to be so badly flawed that the scandal resulted in the resignation of the editor-in-chief. Jones knew that any incorrect papers by sceptical scientists would be picked up and amplified by climate change deniers funded by the fossil fuel industry, who often – as I documented in my book Heat – use all sorts of dirty tricks to advance their cause.

Even so, his message looks awful. It gives the impression of confirming a potent meme circulated by those who campaign against taking action on climate change: that the IPCC process is biased. However good the detailed explanations may be, most people aren't going to follow or understand them. Jones's statement, on the other hand, is stark and easy to grasp.

In this case you could argue that technically he has done nothing wrong. But a fat lot of good that will do. Think of the MPs' expenses scandal: complaints about stolen data, denials and huffy responses achieved nothing at all. Most of the MPs could demonstrate that technically they were innocent: their expenses had been approved by the Commons office. It didn't change public perceptions one jot. The only responses that have helped to restore public trust in Parliament are humility, openness and promises of reform.

When it comes to his handling of Freedom of Information requests, Professor Jones might struggle even to use a technical defence. If you take the wording literally, in one case he appears to be suggesting that emails subject to a request be deleted, which means that he seems to be advocating potentially criminal activity. Even if no other message had been hacked, this would be sufficient to ensure his resignation as head of the unit.

I feel desperately sorry for him: he must be walking through hell. But there is no helping it; he has to go, and the longer he leaves it, the worse it will get. He has a few days left in which to make an honourable exit. Otherwise, like the former Speaker of the House of Commons, Michael Martin, he will linger on until his remaining credibility vanishes, inflicting continuing damage to climate science.

Some people say that I am romanticising science, that it is never as open and honest as the Popperian ideal. Perhaps. But I know that opaqueness and secrecy are the enemies of science. There is a word for the apparent repeated attempts to prevent disclosure revealed in these emails: unscientific.

The crisis has been exacerbated by the university's handling of it, which has been a total trainwreck: a textbook example of how not to respond. RealClimate reports that "We were made aware of the existence of this archive last Tuesday morning when the hackers attempted to upload it to RealClimate, and we notified CRU of their possible security breach later that day." In other words, the university knew what was coming three days before the story broke. As far as I can tell, it sat like a rabbit in the headlights, waiting for disaster to strike.

When the emails hit the news on Friday morning, the university appeared completely unprepared. There was no statement, no position, no one to interview. Reporters kept being fobbed off while CRU's opponents landed blow upon blow on it. When a journalist I know finally managed to track down Phil Jones, he snapped "no comment" and put down the phone. This response is generally taken by the media to mean "guilty as charged". When I got hold of him on Saturday, his answer was to send me a pdf called "WMO statement on the status of the global climate in 1999". Had I a couple of hours to spare I might have been able to work out what the heck this had to do with the current crisis, but he offered no explanation.

By then he should have been touring the TV studios for the past 36 hours, confronting his critics, making his case and apologising for his mistakes. Instead, he had disappeared off the face of the Earth. Now, far too late, he has given an interview to the Press Association, which has done nothing to change the story.

The handling of this crisis suggests that nothing has been learnt by climate scientists in this country from 20 years of assaults on their discipline. They appear to have no idea what they're up against or how to confront it. Their opponents might be scumbags, but their media strategy is exemplary.

The greatest tragedy here is that despite many years of outright fabrication, fraud and deceit on the part of the climate change denial industry, documented in James Hoggan and Richard Littlemore's brilliant new book Climate Cover-up, it is now the climate scientists who look bad. By comparison to his opponents, Phil Jones is pure as the driven snow. Hoggan and Littlemore have shown how fossil fuel industries have employed "experts" to lie, cheat and manipulate on their behalf. The revelations in their book (as well as in Heat and in Ross Gelbspan's book The Heat Is On) are 100 times graver than anything contained in these emails.

But the deniers' campaign of lies, grotesque as it is, does not justify secrecy and suppression on the part of climate scientists. Far from it: it means that they must distinguish themselves from their opponents in every way. No one has been as badly let down by the revelations in these emails as those of us who have championed the science. We should be the first to demand that it is unimpeachable, not the last.

monbiot.com