The emails stolen from the University of East Anglia in November have cast an uncomfortable light on the behind-the-scenes actions of some of the most senior and respected climate scientists in the world. The affair raises serious questions about access to data and the way scientific peer review can be used to stifle dissent. But is the science of climate change fatally flawed by the climategate revelations? Absolutely not. Nothing uncovered in the emails destroys the argument that humans are warming the planet.

None of the 1,073 emails plus 3,587 files containing documents, raw data and computer code upsets the 200-year-old science behind the "greenhouse effect" of gases like carbon dioxide, which traps solar heat and warm the atmosphere. Nothing changes the fact that carbon dioxide is accumulating in the atmosphere thanks to human emissions from burning carbon-based fuels like coal and oil. Nor the calculations of physicists that for every square metre of the earth's surface, 1.6 watts more energy now enters the atmosphere than leaves it.

And we know the world is warming as a result. Thousands of thermometers in areas remote from any conceivable local urban influences tell us that. The oceans are warming too. And we have the evidence of our own eyes. The great majority of the world's glaciers are retreating, Arctic sea ice is disappearing, sea levels are rising ever faster, trees are climbing up hillsides and permafrost is melting. These are not statistical artefacts or the result of scientists cherry-picking their data.

Equally, many of the most widely publicised claims from sceptics about what is in the emails are demonstrably unfounded. There is no conspiracy to "hide the decline" in temperatures. Nor that a lack of warming in the data is a "travesty" – still less of attempts to fix the data.

But, within the narrower confines of assembling a reliable history of global temperature, the emails have done significant damage to the credibility of scientists. They show that in their desire to give the world a clear message that humans are heating the planet here and now, a group of scientists cut corners and down-play uncertainties in their calculations. Their opponents charge that they then covered their tracks by being secretive with their data and suppressing dissent.

Taken with the recent revelations about shortcomings in reports of the Intergovernmental Panel on Climate Change (IPCC), this suggests a wider problem of scientific sloppiness, but not of outright fraud. Many scientists believe their community has to own up to that, and put its house in order.

Part of the problem is secrecy in science. Climatologist Judy Curry of the Georgia Institute of Technology, who has been trying to make peace between her colleagues and the sceptics, says the various data sets connected to the famous "hockey stick" temperature graph and Phil Jones's thermometer data sets "stand out as lacking transparency". Science is too much of a closed shop, she says. Outsiders need to be let into the ivory towers for the good of science itself. "Einstein didn't start his career at Princeton, but rather at a patent office." Bring on the bloggers. Maybe there's an Einstein among them.

The doors of the labs are being opened whether scientists like it or not. The Information Commissioner's office last week released a statement saying that the University of East Anglia had "not dealt with [FoI requests] as they should have been under the legislation". There is evidence in the emails that some scientists at the Climatic Research Unit wanted to delete files rather than hand them over – although it is not clear whether any deliberate deletions actually happened.

Probably nobody anticipated that a law intended to unwrap state secrets might end up freeing data from scientists' computers. But the science community now urgently needs to figure out how to respond to this altered landscape – or scientists will end up in court before long.

The need to open up science is made all the greater by the question raised in the emails about the "gold standard", the peer review system. In many fields of research, peer review creates serious conflicts of interest in which, as the emails have revealed, senior researchers can act in a way that could have the effect of blackballing the research papers of their critics. The dangers are all the greater when, again as the emails show, the conventions of anonymity in peer review are not rigorously upheld.

Finally, "climategate" raises questions about the IPCC report-writing process, in which many of the emailers have been involved. Governments set up the IPCC 20 years ago to get scientists to speak with one voice on climate change. But often there is no clear consensus. Scientists are trained to disagree. That's how science advances. The tensions created by the pressure to agree are clear in dozens of the emails.

One of Jones's colleagues at the University of East Anglia, climatologist Mike Hulme, says: "Climate scientists will have to work harder to earn the warranted trust of the public – and maybe that is no bad thing." And he thinks the IPCC may have run its course.

While science gets its house in order, we need some perspective. In the midst of a cold winter it may be hard to convince ourselves, but the world is still warming. Humanity is still to blame. And we still, urgently, need to do something about it.

• This article was amended on 11 February 2010. A quote in the original referred to Einstein working in a post office. This has been corrected.