The message from this year's World Humanist Congress is clear: the earth has never been in more urgent need of secularism

I never thought secular society would be something that would, in my lifetime, need defending. Yet, without having become any more religious, en masse, we find that state education has been handed over to any have-a-go Harry that feels up to it, which in a quarter of cases means religious people, and in a handful of cases, people like the advocates of Rudolf Steiner.

We have a new minister of state for faith and communities who talks about "militant atheism". That doesn't exist – if militant means anything at all distinct from "argumentative", it means advocating violence, and when did you last hear an atheist advocating violence in the name of his or her belief?

I was unpersuaded, anyway, of the case for such a minister, particularly the way it conflates faith and community as though those concepts were indivisible. But now filled by Eric Pickles, the role really becomes a slap in the face to secularism.

Some really fundamental principles have been breached, I was thinking to myself, on the way to Oxford for the World Humanist Congress.

That was before I heard the video address from Wole Soyinka, Nobel prize-winning Nigerian writer, accepting his international humanist of the year award. "It's considered virtuous by some to abduct 200 girl pupils from a sanctuary of learning in the name of a religion.

"The lesson of Boko Haram is not for any one nation. It is not for the African continent alone. The whole world should wake up to the fact that the menace is borderless, aggressive and unconscionable."

It was before I met Gulalai Ismail, who founded Aware Girls when she was 16 years old to forge somewhere that "young women can come together and they can speak for their rights. If we can't speak for ourselves, nothing will change".

She's only 26 now, and the organisation has achieved monumental things – Malala Yousafzai is one of their activists. Ismail herself has had threats against her, and her family, from the start.

It was before I met Leo Igwe, a Nigerian campaigner fighting on two fronts – the Christian witch hunters on one side, the Boko Haram kidnappers on another – who has been physically attacked many times for his work. "Many people said, 'Are you getting into witchcraft issues? You don't want to live long.'

"It is taken to be a dangerous occupation. It is a minefield." But if the vicious, perilous conditions under which many humanists are living make the irritation of Eric Pickles seem like small potatoes, then remember that it's not a game of whist in which the person in the worst situation wins.

"When you are living in this situation," Igwe says, "you need allies, you need supporters. You need people to say to you, 'I love what you're doing'."

The atmosphere, in consequence, is sort of thrilling, for an atheist. There is one stall, a guy called David Bonney, 35, making beautiful atheist shoes, with "Ich Bin Atheist"imprinted on the sole. They look a bit like Campers.

He says the shoes started out as an absurdist footwear statement, but now: "We've got a lot of customers in America who find a lot of utility in the idea. They can use them to come out [as atheist] to their parents. Or you can wear them in a bar to attract other atheists. It's like Grindr for the godless."

Mainly, though, it is about conversations, a hugely broad sweep of territories – literal and mental – across the world where secularism is urgently needed.

Tom Holland, the historian, said of the situation in Gaza: "If you think about what Palestinian radicals looked like in the 70s, and you think about kibbutzim, there was potential in the shared language of socialism to find some common ground. If both sides think that God's given them the land, there's not a huge scope for dialogue."

His interlocutor, Professor Francesca Stavrakopoulou, moves on to self-censorship, and notes that the only time she has had to censor herself is in her own lectures, because of her own radical students.

"Very quickly, when they arrive, if they're even vaguely Protestant, they'll be enveloped by the evangelical Christian unions on campus, most of whom are funded by the US."

"Can't you tell them to pipe down?" I ask. "Well, I've got modules to get through. I just don't have time for a lecture to be derailed about whether angels exist."

There is a lot of optimism, not all of which I share. Ian Dunbar, 61, a physicist, said: "Actually, I think humanism is on the verge of a breakthrough. It only feels as though it's under threat because faiths are hurting, and lashing out."

Ultimately, though, I saw it much more as a call to arms than a reason to be cheerful. There has never been a more important time, if you are secular, to say so. Call to arms I mean metaphorically, by the way. Nobody take up any arms, OK?