At one level, the tale of Philip Rutman’s resignation is just another story of the falling-out of a politician and a civil servant.

It is scarcely unique – especially at the Home Office.  Consider the departure from it, during Theresa May’s term as Home Secretary, of Helen Ghosh.

But Sir Philip’s departure is about much, much more than two people who couldn’t get on, or a row about delivery, or even a rift about policy.

At its heart is a culture clash between Boris Johnson’s Government, set on changing the direction of the country post-Brexit – and now backed by a majority of 80 in the Commons…

…And a civil service that is profoundly unhappy, at least at the top, not only with the way in which the journey is being carried out, but with where it is going.

That said, there are some more humdrum points to make at the start.  Not the least of them being that ConservativeHome is in no place to judge Sir Philip’s claims about Priti Patel.  But we note the following.

First, the Home Office seems still to be “unfit for purpose”, to quote the words first used about it by John Reid after his own appointment to head the department.

He was following Charles Clarke, who himself had been forced to resign.  As have no fewer than three of the last ten Home Secretaries.

The department has been hit by a succession of scandals – not least the Windrush affair, which forced Amber Rudd to quit only two years ago after she “inadvertently misled” the Home Affairs Select Committe over it.

A report into the affair concluded that she has been let down by her officials.  Sir Philip was Permanent Secretary at the department at the time.

Second, Sir Philip complains that he has been “the target of a vicious and orchestrated briefing campaign” against him.

Perhaps – but the first shots in this battle were fired on his behalf – in the Sunday Times on February 20, which reported that Sir Philip’s relationship with Patel became toxic during an election row about tasers.

Finally, it is difficult to believe that Mark Sedwill’s predecessor, Jeremy Heywood, would not have found a way of smoothing-over the rupture.

It isn’t hard to see how this would have been done.  Sir Philip would have been quietly “moved on”, perhaps duly to be translated into Lord Rutnam, and Patel’s card would surreptitiously have been marked.

(For reference, Ghosh went on to first to be Director-General of the National Trust for Places of Historic Interest or Natural Beauty, and thence to Balliol College, of which she is now Master.)

But Sedwill isn’t Heywood.  The latter was from the heart of the system: a Treasury man to his fingertips – once Principal Private Secretary to three Chancellors of the Exchequer, no less.

Sedwill is essentially a former diplomat – at one point Britain’s Ambassador to Afghanistan; later National Security Adviser, a post he still holds.

Indeed, he is the first man both to serve in that post while also being Cabinet Secretary and Head of the Civil Service – a triple accumulation of power.

But for all that, he doesn’t have Heywood’s experience in negotiating the concealed mirrors, trapdoors, and false bookcases of Whitehall.

“The Cabinet Office offered me a financial settlement that would have avoided this outcome,” Rutnam said yesterday.  That he is now suing the Government is a failure of the system over which Sedwill presides.

Furthermore, the lack of grip has been evident for the nine days that has passed since that original Times report.  We urged that this nettle be seized on February 22.  Instead, the fumbling continued.

Sir Philip must now explain why today he complains of the Home Secretary’s “behaviours” while, less than a week ago, he joined her to dismiss these and other claims about her as “false”.

“I hope that my stand may help in maintaining the quality of government in our country”, he said yesterday.  Which returns us to the culture clash at the core of the matter.

As we’ve put it before, the civil service is impartial but not neutral.  This is how it must be.  It must not choose between parties but it must select between values, as we all do.

Post-war, these have included: liberal democracy; NATO; the mixed economy; nuclear deterrence and, not least, EU membership.

We like to cite three names by way of example.  Michael Quinlan, a theoretician of nuclear deterrence; Charles Farr, a security policy-driver and Michael Palliser, early in the long line of euro-enthusiasts at the Foreign Office.

Or take a look at Twitter – where Nicholas Macpherson, the former Treasury Permanent Secretary, likes the hashtag #soundmoney.  And Simon Fraser, a counterpart at the Foreign Office, is critical of the Brexit project.

The long and short of it is that Boris Johnson’s Vote Leave Downing Street sees leaving the EU as the start and not the end of national renewal.

In its view, we are not taking back control from the European Court of Justice only to see it accumulate in the European Court of Human Rights.

The Conservative Manifesto commits to ensuring that judicial review “is not abused to conduct politics by another means or to create needless delays”.

The Constitution, Democracy and Rights Commission that it proposes will also scrutinise the functioning of the Royal Prerogative.  Number Ten has not forgotten the Supreme Court’s progation judgement.

All this is a further offence, coming as it does on top of Brexit, to the worldview of what ConHome used to call Britain’s pro-EU ascendancy.

The Sir Humphreys know well that their system is propped up by this scaffolding of modern governance, and grasp that paring it bacl it is integral to Dominic Cummings’ aspirations of civil service reform.

We will discover during the next few weeks what policy issues, if any, helped to drive Sir Philip’s resignation and decision to sue.

Or implementation issues: on the one hand, Downing Street wants its new immigration system delivered as soon as possible – to help demonstrate to voters that “the People’s Government” will deliver.

On the other, the Home Office and parts of the civil service elsewhere will be resistant to the sheer pace of change, arguing that it is impracticable.

That beaten and battered Ascendancy will see in Sir Philip a standard to rally round.  He complained of Patel’s “behaviours”. It will hope for more of the same – more challenges; more resignations.

It will be claimed that Sir Philip was “speaking truth to power”.  But who truly holds power in Britain?  Is it the people we put into office?  Or is it those that never leave government at all?

Is it politicians who we can put in and later throw out?  Or is it the specially-trained caste who, at their best, are selfless public servants but who, at the system’s worst, are too seldom held accountable for their mistakes?

We are going to find out – at least if the Prime Minister sees through the logic of what he has started, and applies himself to unleashing Britain’s potential.