HAS the First Minister blinked? Is Nicola Sturgeon thinking twice about calling a second independence referendum later this month as widely trailed? Some believe her remarks to the David Hume Institute this week on devolution betray cold feet on independence.

Instead of repeating her call for Scotland to be allowed to remain in the single market after Brexit, or else she would call another referendum, Ms Sturgeon issued a dramatic warning that devolution is at risk, that powers exercised by the Scottish Parliament since 1999 are about to be stripped away by a right-wing clique of Brexit centralists.

The change of tone took some by surprise, including it seems, her deputy, John Swinney. He had some difficulty on BBC’s Good Morning Scotland specifying exactly which responsibilities were going to be removed from Holyrood, given that the UK Government White Paper last month promised that none would be. He suggested that Theresa May’s reluctance (so far) to specify any extra powers for Holyrood post-Brexit is effectively the same as powers removed. He also referred to the failure of the Supreme Court to agree that Westminster was, as he put it, “statutorially” required to recognise the Sewel Convention and not cut across Holyrood’s powers without its consent.

The First Minister hasn’t withdrawn her threat to call an independence referendum. It’s still very much in the air, even though Mrs May is indicating she won’t agree to one until after 2019. But at the very least, the focus has shifted from an independence referendum to defending devolution. Ms Sturgeon is clearly trying to put pressure on the PM to show her Brexit hand when she addresses the Scottish Tory conference this weekend. The Conservatives have all along said there will be a Brexit bonus for Holyrood; the First Minister is convinced this is bogus.

Since the June referendum, some have been saying that as soon as powers are removed from Brussels, and repatriated to the UK, then Holyrood’s powers will automatically be enhanced in areas already devolved, like agriculture and fisheries, family law and the environment. But this is based on a misunderstanding of devolution and Scotland’s relationship to the EU.

Holyrood – as the UK White Paper states – only exercises devolved powers so long as they accord with European Law. After Brexit, Holyrood will exercise powers over agriculture and fisheries as it does at the moment, but it will do so, not in accordance with Brussels law, but with UK law. This is a fundamental change and the reason why the First Minister is warning Brexit may diminish the powers of the Scottish Parliament.

The UK Government will insist that on “day one” after Brexit, nothing will actually change because the PM has said all repatriated laws are to remain the same for the time being. Brussels directives and regulations will be “cut and pasted” and instantly transformed into UK statutes. But clearly that is not going to continue indefinitely. It would be absurd for the UK to go to all the trouble of leaving the EU only to retain all of its laws intact. In future, UK laws will be changed as the UK Government sifts through all the EU directives and regulations. It may decide to allow things like hormone-treated beef, EU regulations on which currently prevent many US agricultural exports being sold in UK markets.

The UK could argue that this doesn’t actually alter Holyrood’s powers as such because they are the same as they were before Brexit – the only difference is that overall regulation is coming form Westminster rather than Brussels. And under the Scotland Act, isn’t Westminster ultimately sovereign in all instances? The UK could argue that Holyrood’s constitutional rights are unaffected and there is no more requirement for legislative consent (a Sewel motion) than there was over Article 50. The Scottish Government will dispute this interpretation, needless to say.

The material change to Holyrood is pretty obvious. If nothing else, Brexit ends the situation in which Scotland is in a sense the servant of two masters: Europe on the one hand, with its regulations and directives; and Westminster on the other which rules on reserved matters like defence, economy, welfare and so on. Now the powers are collapsed into Westminster, Scotland will be much more visibly a creature of Westminster. Moreover, Scottish agricultural subsidies are set and financed by the EU under the Common Agricultural Policy. All this will change.

The Tories are of course aware of all this, though they’ve tended to sideline the implications for devolution since the UK Supreme Court ruled in January that Holyrood had no veto power over Article 50. It was noticeable that, following the ruling, Theresa May and her ministers stopped talking about new powers.

This weekend the PM will have to fill in the gaps. She’s being asked to give assurances she cannot deliver: namely that Holyrood’s powers will not in any sense be diminished by Brexit. She will try to argue that Holyrood’s powers are the same, indeed enhanced by a dusting of new powers in areas like the environment (as I explained earlier this week). But she cannot in all honesty say that nothing will change.

Who pays the piper plays the tune, and it is Westminster, not Holyrood, that will take future decisions on agricultural subsidies. According to the Financial Times nearly three-quarters of Scottish farmers’ incomes comes from such subsidies. The UK Government has only promised to keep this level of support until 2020, and Holyrood will not decide what replaces the CAP regime.

Nor can or will Scotland have control of regulatory issues like GM crops. If Westminster accepts forms of genetically modified agriculture currently outlawed by Europe, Scotland will have to comply, unless there is a specific exemption. And this is not just about agriculture – Westminster will assume nearly all the regulatory powers currently exercised by Brussels.

Ms Sturgeon has always made clear that she has been fighting Brexit on two fronts; trying to keep Scotland in the single market while ensuring that Scotland gets the best deal from Brexit. The two are not incompatible. This week she is trying to get voters’ heads around the complexities of Brexit, and dispel the notion that somehow, after A50, everything will remain the same. It won’t and it can’t.