When it comes to Sir Peter Housden, we have a problem What they do is exclude him from their inner counsels - as we can see in the strange case of Sir Peter Housden. Sir Peter, 61, is permanent secretary - top civil servant - to the Scottish government and his political boss is First Minister Alex Salmond. Officially, he is no different to the other permanent secretaries and regularly attends their Wednesday morning meetings in Whitehall. Unofficially, though, they regard him - there's no nice way to put this - as "Salmond's nark." He is not on the crucial committee that is bringing together Whitehall's campaign against Scottish independence. "Good God, no," said one insider in shocked tones. Housden would just report everything back to Salmond. The Treasury will of course fight attempts to transfer real economic power from Whitehall to the cities. It is also the Treasury, and its top official Sir Nicholas Macpherson - not Sir Jeremy Heywood, the Cabinet Secretary, as has been suggested - that is co-ordinating Whitehall's case against Scottish independence. A number of papers will be published next year putting forward a series of questions for Mr Salmond to answer. Some of them may be tricky, yet nobody should underestimate Mr Salmond. In the past he has beaten the pundits and the polls to come out on top. If he wins independence, or even if he comes close, all sorts of constitutional ghosts will come out of the attic. Independence will not happen overnight. If the Scots vote to leave the Union in 2014, negotiations on the details would continue for years and Scottish MPs could still give Labour a majority at Westminster in 2015. That would not only cause a constitutional crisis but would surely provoke the English into demanding changes of their own, with more power being pushed out of Whitehall. Meanwhile the traditional Whitehall system is under attack from senior politicians like Cabinet Office Minister Francis Maude, who wants ministers to have powers to appoint civil servants. The result would be top advisers who are more prepared to take on board their ministers" party political aims - which is exactly what Sir Peter has been accused of in Scotland. His conduct during the row over whether an independent Scotland could join the European Union has caused particular dismay among civil service colleagues south of the border. The furore started when Mr Salmond suggested that an independent Scotland would inherit membership of the European Union and that he had legal advice to that effect. The Scottish government then went to court to block attempts to force disclosure of the legal advice through freedom of information. It turned out that the legal advice did not exist. The question for Sir Peter is why, as accounting officer for the Scottish government, he did not stop his political masters wasting £12,000 of taxpayers" money trying to prevent disclosure of advice that did not exist. If he tried but was overruled by Mr Salmond, did he insist on the First Minister giving him a written order to spend the money? The right to demand a written direction from a minister who wants to do something improper is the nuclear weapon of Whitehall's mandarins. Did Sir Peter use it? If not, why not? Some colleagues are also asking why he did not insist on Mr Salmond taking legal advice about Europe before speaking about it. Such details may seem arcane. Yet the disarray that the Scottish debate is causing in Whitehall, which would once have been unthinkable, may be like the first tremors of an earthquake. Already there is building hostility in England to the Scots remaining part of the United Kingdom. That is set to grow and, as it does so, demands for change in England, currently the most centralised government in Europe, will become louder. The Highland fling that players are currently dancing could become a final fling for the power barons of Whitehall.