The committee found the department was short on innovation
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MPs have said the 18-month-old Department for Innovation, Universities and Skills "has not yet found its feet" and may take decades to make an impact.
A select committee said its annual report showed signs of relying on jargon as a substitute for having a clear idea where it was going.
The aim is to make Britain a centre for science, research and innovation.
The department said it was at the forefront of the government's response to the economic downturn.
'Positive tone'
The committee responsible for scrutinising the Department for Innovation, Universities and Skills (Dius) described the annual report produced by the department last May as "written in an impenetrable style and... peppered with jargon, unsupported assumptions and claims designed to promote Dius".
As a result its report had been "unhelpful" and too reliant on promoting a positive tone rather than providing clear and comprehensive information.
The MPs said they suspected this had been in part because the results of Dius's work "may take years, if not decades, to realise".
And for a department with "innovation" in its title, its methods of operation had been disappointingly lacking in innovation.
The committee's report also raised concerns about the quality of statistics supplied by the department - suggesting they should be reviewed independently, for example by the UK Statistics Authority.
"We commend Dius for owning up to the error in three tables in the Departmental Report setting out country and regional data and for supplying corrected tables.
"But we must put on record our concern that significant errors in the three tables setting out the country and regional analyses were not noticed before publication."
Evidence
The chief scientific adviser, Prof John Beddington, is said to have adopted a lower media profile and "more collegiate approach" than his predecessor.
The MPs express concern that, when giving evidence to the committee about homeopathy, Prof Beddington had not stressed the importance of evidence-based science.
"Professor Beddington is the government chief scientific adviser and we are surprised that rather than champion evidence-based science within government he appears to see his role as defending government policy or, in the case of homeopathy, explaining why there is no clear government policy."
In response, a spokesman for the department said it had achieved a great deal since its creation.
"We have massively expanded apprenticeships, reached our target of 2.25 million people achieving basic skills two years early, increased the number of students entering higher education and continued the record investment in funding for science and research."
The committee had made a number of useful points on the annual report to which it would respond in due course, he said.
"But we are confident that Dius is well placed to meet the challenges of the future and our work remains at the forefront of the government's response to the economic downturn giving real help now to individuals and businesses."
A spokesman for the government's chief scientific adviser said it was Prof Beddington's job to ensure that a new policy was based on the best possible scientific evidence available at the time.
"There will of course be times when contradictions exist between scientific advice and other policy imperatives, but the chief scientist has and will continue to challenge policy on scientific grounds when he feels it is right to do so."
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