I meet Philip Pullman 24 hours after he has got into trouble for idly musing on Twitter that he would like to hang Boris Johnson. “It was a silly joke,” he admits, looking slightly embarrassed as he enters his sitting room with a plate of biscuits for us, perching them on teetering stacks of books beneath which there is said to be a coffee table. He says his publishers were a bit miffed: threatening to murder the prime minister was clearly not how they had agreed to start the publicity campaign for his forthcoming children’s novel, The Secret Commonwealth, and Pullman had to publicly retract his words after there were complaints. “But,” the 72-year-old author adds, his tone brightening, while one of his dogs clambers on to his lap and the other maintains a vigil beside the biscuits, “the upshot was I gained 2,000 followers on Twitter!”

Pullman creates magical realms in his award-winning fiction, writing it in his 16th-century farmhouse in a village outside Oxford, where he lives with his wife and his ukuleles and cockapoos and overflowing shelves. But if I expected to meet someone otherworldly, I was wrong. Pullman, who has two sons and several grandchildren, is very much of this world, and can talk in detail about the shadowy machinations of Dominic Cummings as well as the designs of Victoria Beckham and the woodworking videos he sometimes gets hooked watching on YouTube. His observation of the government is not one-sided: he tells me that Michael Gove, as education secretary, once invited him to discuss literacy. Pullman told him that “the basics” weren’t grammar and spelling, as Gove believed, “because everybody who’s got a word processor knows you correct those at the last minute,” but rather nursery rhymes, songs, a love of language itself. Nothing came of it, “but I’ll give him credit: he was very courteous and he listened, and there was a civil servant making notes. And Gove cracked a joke about me being ‘at the heart of the Magisterium now’, so he had plainly read my books.”

It’s a decent joke, given that the Magisterium is the shadowy, authoritarian body that governs the country in Pullman’s two trilogies: His Dark Materials, which began in 1995, and now The Book of Dust, of which The Secret Commonwealth is the second part. His best-known character, Lyra, is the heroine of all of them. The first trilogy took her from age 11 to early teens. The second trilogy began with her as a baby, in a prequel, but now leaps forward to Lyra’s early 20s, when she is finally an undergraduate at Oxford, like Pullman was. Naturally, she is once again doing battle with power, sniffing out corruption and fighting it as David to the Magisterium’s Goliath.

It is set in an unreal, almost British past, yet this book feels more consciously pegged to our present than the others. There are references to refugees landing on Greek islands and a character named Nur Huda el-Wahabi, after a schoolgirl who died in Grenfell Tower. (Her teacher won a bid in the Authors for Grenfell Tower auction to name a character in his next book and Pullman was very keen). Halfway through the book, Lyra explains what “bullshitting” really is, and, shortly afterwards, a character from the Magisterium is heard elsewhere telling someone that, “We should delicately and subtly undermine the idea that truth and facts are possible in the first place. Once the people have become doubtful about the truth of anything, all kinds of things will be open to us.”

I wonder if people such as Gove, Johnson and Trump, with their “fake news”, “had enough of experts” and Brexiteering narratives were on his mind when he wrote it.

‘The prime minister doesn’t mind who he hurts. He doesn’t mind if he destroys the truth or not’: on Boris Johnson. Photograph: Reuters

“It’s not really for me to judge,” he says, preferring not to tell people what to take from his work, explicitly, though “it might be the case”. He nods. “Inevitably, I am affected by the political background of the times, because I’m a citizen as well as a writer, and I’m interested in political news.”

Pullman is more than happy to talk about politics in itself, though. He believes the EU referendum was “a terrible thing, a terrible mistake. Parliament is now not sovereign any more. It’s the will of the people that’s apparently sovereign, and this is terribly dangerous because the will of the people can easily be manipulated, as we saw in Germany. Dictators love referendums.”

The will of the people can easily be manipulated

He lives in a Tory stronghold, where he has to vote Lib Dem, because a vote for Labour would be wasted, so he strongly believes in electoral reform. In any case, the thing that raises our current politics “from farce to tragedy is the lack of opposition from the Labour party. People say they elected the wrong Miliband. I think they elected the wrong Ed actually. Ed Balls would have been a marvellous leader. So that was a big mistake, and then saddling themselves with an electoral system that weighs it so much in favour of the trade unions. That’s populism again. If party leaders were elected simply and solely by MPs, we’d get a much better choice of leaders. But it’s also open to corruption of the Tory sort, where they’ve managed to franchise the choice of their leadership out to elderly members of bowls clubs. That’s all right, they deserve a vote too – but all of the vote?”

Did he ever believe in Corbyn?

“Corbyn is most at home on the back of a lorry with a microphone in his hand. He’s one of nature’s backbench rebels. He’s not at home in committee rooms making deals, agreeing with, making compromises. He’s not formed, by nature, to be the leader of a party, let alone a prime minister, and it’s an absolute tragedy that he’s now locked into it.”

I’ll take that as a no, then. As for the prime minister: “Well, he’s a psychopath. Or he’s a sociopath. He’s born without the normal human reactions of shame, embarrassment, you know, all those things… He’s without them. He doesn’t mind who he hurts. He doesn’t mind whether he destroys the truth or not. In those respects, of course, he’s learned a lot from Trump; that you can go into a high office of state and throw your weight around and break things, and nobody minds, or nobody manages to stop you. And the opposition is so helpless, so useless.”

If Johnson does hold an election, Pullman suspects he will pitch it as “people versus parliament – and he’ll be on the side of the people. I mean, it’s just a joke – but he could do it and he could win and it’s terribly dangerous.”

‘To regard the basics as being spelling properly, and not ending a sentence with a preposition, is a monstrous perversion’. Pictured: Michael Gove. Photograph: Vudi Xhymshiti/AP

I mention that the first trilogy of Lyra books, in which children are taken away into camps and mistreated, stripped of their daemons (their animal souls), also feels prescient now, looking at the American border with Mexico.

“I hadn’t thought of that,” Pullman says. “Gosh, I’m a prophet and I don’t know it. We’re living in very interesting times and there’s going to be a big crisis of some sort, isn’t there?”

A TV production of His Dark Materials is coming soon to the BBC and HBO, starring James McAvoy, Ruth Wilson and Lin-Manuel Miranda. Pullman seems reasonably interested when I bring it up, but points out that it’s hardly the first production of it. There were the stage plays at the National Theatre in 2003, then the audiobook, which he found “a bit disconcerting” because so many of the cast were from The Archers. Then the Hollywood film of the trilogy, which got cancelled after the first one, which was sad, because he loves Nicole Kidman and wanted to see her reach the stage of her character’s trajectory where she is “being overpowered by the love for Lyra that she couldn’t help feeling”. (He had written to Kidman himself to ask her to be in it. “But if the letter hadn’t worked, I was going to cross out her name and write ‘Dear Cate Blanchett’ instead.”)

Disconcertingly, the new show’s American executive producer has issued a statement denying that Pullman’s stories are anti-religion, which is hardly accurate, but clearly something deemed necessary to assuage the Bible Belt, which raged about the movie and its anti-Christian devilry. I bring this up and Pullman sighs, gutturally.

“America is an entirely different place,” he says. “We kind of fooled ourselves into thinking we can understand them.”

Interestingly, though, the new book finds Lyra losing her way with magic and becoming something of a down-hearted rationalist. This takes us to the heart of Pullman’s paradox: that his books seek to undo the institution of Christianity while he remains steeped in its liturgical beauty; and that he respects science so deeply that he uses it to furnish his impossible, imaginary worlds. The Secret Commonwealth ends, after 687 pages, with the words “To be continued.”

“If I am spared to write the third book, all will be made clear, I hope,” he says, half joking, half not. After years of prostate trouble and surgery, and his wife’s own medical issues, he says that, “Neither of us is in very good health, and travelling anywhere or going out for long evenings are not really possible any more. But I don’t mind that a bit. I don’t want to travel anywhere.” Indeed, he researched some of the faraway locations in his new book, such as Istanbul, by strolling down the roads on Google Street View. I don’t know if he’s summoning all his strength to put on a brave face for the interview, but he does seem on excellent form today, making the tea, showing me round, giving me a lift in their car back to Oxford station.

And, of course, there’s always Twitter, where he remains as lively as ever. “I got into terrible trouble a year or two ago because I said, in all innocence, ‘Look what is this quarrel between feminists and trans people? What’s the argument about?’”

The prime minister is without the normal human reactions of shame and embarrassment

He claims, rather mischievously, that he still doesn’t understand the debate about whether gender can be overthrown biologically or socially, but I suggest it’s a relevant topic to his books, in which almost all children are born with a daemon of the opposite sex, who represents the other part of them, perhaps their soul. The daemon changes animal until puberty, when it takes a fixed form and the child finds out who they really are. It does make me think about the question of trans children and blocking puberty. He turns very thoughtful about this.

“If I had a child, boy or girl, who felt passionately from an early age, manifestly that they were in the wrong body, I hope I would be understanding and as kind as possible,” he says. “What I don’t think I’d do is hasten them away to an endocrinologist. I know that if you want to transition, it is physically more plausible, or persuasive, if you do it before puberty, but is a child before puberty capable of… I mean the answer is, we don’t know, do we? We don’t know. The only thing we can do is to be as kind as possible.”

A former teacher, Pullman is hugely interested in what we tell children and how we raise them. He is a fan of Michael Rosen, and believes that Kate Clanchy’s book Some Kids I Taught and What They Taught Me “should be in every single staff room”.

He stopped teaching before the national curriculum even came in, “so I’m really speaking like Disgusted of Tunbridge Wells when I talk about education now.” As for the literacy regime in primary schools today: “To regard the basics as being spelling properly, and not ending a sentence with a preposition, is a monstrous perversion of everything that’s right and true. Fronted adverbials? Nonsense. It drives me mad to think about them teaching that.”

‘We’re living in very interesting times and there’s going to be a big crisis of some sort’: Philip Pullman. Photograph: Emma Hardy/The Observer

He has seen SATs tests where they say, “Spend 15 minutes making your plan and 45 minutes writing the story.” “When I used to speak to classes, I would say yes you must make a plan when you write the story, but write the story first and make the plan afterwards, because that way the plan will be exactly like the story and you’ll get more marks.”

He’s not joking – this is how he does it himself. “It’s not doing it backwards. I call it doing it the right way.”

We discuss the growing obsession in academy schools with strictness. He says that when he was at school, his teachers had been in the war, so weren’t going to be scared by a bunch of kids. “The French teacher had been on the Arctic convoys; the geography teacher had driven tanks in the desert. The physics teacher, he was a brute, he’d flown Catalina seaplanes across the Atlantic.” When Pullman himself came to teach, he lacked their sense of authority, “so the only thing I could do to keep them in order was to tell them stories.” He also observed that every class already had a king and a queen who the other children looked up to, so if you sussed out who they were, and focussed on them for the first few weeks, the rest of the class would follow.

We go outside to look at the decorative boxes he’s been making in his carpentry workshop, only to discover that the two cockapoos, Coco and Mixie, who look like designer doggies, but behave like feral beasts, have escaped. Some minutes later, after Pullman has set off down his acres of land to look for them, I find them in the next-door neighbours’ garden, having the time of their lives. We haul them back into the house and discover that they have also eaten the biscuits, leaving a trail of fallen books behind them.

The Secret Commonwealth: The Book of Dust Volume Two by Philip Pullman is published on 3 October by Penguin at £20. Order it for £17.60 at guardianbookshop.com