Gaunt and nervous, with trembling hands, former head of the University of East Anglia’s Climate Research Unit (CRU) Phil Jones faced some uncomfortable questions from a parliamentary science committee yesterday. The Guardian seemed to think he got off more easily than he might have done, because the members felt sorry for him.

Jones did his best to persuade the Commons science and technology committee that all was well in the house of climate science. If they didn’t quite believe him, they didn’t have the heart to press the point. The man has had three months of hell, after all.

Jones’s general defence was that anything people didn’t like – the strong-arm tactics to silence critics, the cold-shouldering of freedom of information requests, the economy with data sharing – were all “standard practice” among climate scientists. “Maybe it should be, but it’s not.”

And he seemed to be right. The most startling observation came when he was asked how often scientists reviewing his papers for probity before publication asked to see details of his raw data, methodology and computer codes. “They’ve never asked,” he said.

He gave a little ground, and it was the only time the smile left the face of the vice-chancellor, Edward Acton: “I’ve written some awful emails,” Jones admitted. Nobody asked if, as claimed by British climate sceptic Doug Keenan, he had for two decades suppressed evidence of the unreliability of key temperature data from China.

But for the first time he did concede publicly that when he tried to repeat the 1990 study in 2008, he came up with radically different findings. Or, as he put it, “a slightly different conclusion”. Fully 40% of warming there in the past 60 years was due to urban influences. “It’s something we need to consider,” he said.

Nor did the MPs probe how conflicts of interest have become routine in Jones’s world of analysing and reconstructing past temperatures. How, as the emails reveal, Jones found himself intemperately reviewing papers that sought to criticise his own work. And then, should the papers somehow get into print, judging what place they should have in the reports of the Intergovernmental Panel on Climate Change (IPCC), where he and his fellow emails held senior positions.

But the committee will be hard pressed to ignore the issue after the intervention of no less a body than the Institute of Physics. In 13 coruscating paragraphs of written evidence to MPs, it spoke of “prima facie evidence of determined and coordinated refusals to comply with honourable scientific traditions and freedom of information law”, “manipulation of the publication and peer review system”, and “intolerance to challenge … which is vital to the integrity of the scientific process.” Ouch.