A few weeks ago, Professor Anthony Clifford Grayling gave three talks at the Hong Kong International Literary Festival. In Britain, his fame has been forged on three fronts: he's a philosopher; he's the founder and Master of the New College of the Humanities, in London, which is an independent educational establishment for undergraduates; and he's an atheist. The last tends to get the most publicity: Richard Dawkins, Christopher Hitchens and Grayling have been described by the British media as the unholy trinity of non-believers. (Hitchens died in 2011 and no word has yet filtered back suggesting a change of opinion.)

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Grayling is also a prolific writer. His latest book, The Challenge of Things: Thinking Through Troubled Times, contains a list, almost two pages long, of previous titles, which include: The Meaning of Things, The Reason of Things, The Mystery of Things, The Heart of Things and The Form of Things. When people refer to him as a "militant atheist", he always says, "How can you be a militant non-stamp-collector? You just don't collect stamps." The literary impression, however, is of an eager boy, entranced by the sheer thinginess of human existence, who loves to gather observations, tidy them into notes and put them in various albums.

The stamp-collector comment came up in one of the talks he gave at the University of Hong Kong, at which a woman had addressed him as a "die-hard atheist". After his usual non-philately comparison, Grayling said, "Humanism is a deep, rich view. It invites us to be our best selves in relation to others." Then he added, patiently, "But you can be a militant secularist, like my friend Richard Dawkins."

Grayling himself doesn't do militancy. He's exceptionally courteous in person - listen to him in debate with Rowan Williams, the former archbishop of Canterbury, and the after-you-no-after-you tone of both men is barely distinguishable - though slightly less so in print. ("There was, in recent years, an op-ed in The New York Times by the Dalai Lama, headlined 'Many Faiths, One Truth'," begins an essay in The Challenge of Things. "He is, of course, right; there are many faiths and there is one truth: viz. that all the faiths are bunkum.") At a panel discussion on how literature can find its place in our digital culture, also organised by the literary festival, he spoke beautifully, deferred to others and congratulated questioners on the excellence of their points.

That talk was at the Museum of Medical Sciences, where I happened to be sitting at the back, next to a display on artemisinin. While Grayling (author of Scepticism and The Possibility of Knowledge) talked of Socrates (died 399BC) and Plato (died 347BC), I could see, out of the corner of my eye, a drawing of Ge Hong, who had written the Handbook of Prescriptions for Emergencies, in AD341. In this tome, Ge had recommended Artemisia annua - sweet wormwood - for its anti-malarial properties.

Some readers of the Handbook had tended to pooh-pooh such advice. Or, as the display put it, "However, the West was extremely skeptical. How can a previously unknown natural herbal remedy be so effective?" But alongside Ge was a photo of Professor Tu Youyou, who, 1,600 years later, had decided to explore his faith in Artemisia; she was jointly awarded this year's Nobel Prize in Medicine.

This added a curious flavour to the talk. The fingers of dead men - from both East and West, but always men - still vigorously clutch at our 21st century shoulders.

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Grayling, who is now 66, first encountered Plato in an African library when he was 12. That was the moment when he discovered his life's work. "It was a fever that took hold early and never afterwards abated," he has written. Now he debunks Christianity (2,000 years old), Judaism (at least 3,000 years old), Islam (about 1,400 years old) and every belief in transcendent beings, including fairies, that lies in between.

He has said that contesting religion is "like engaging in a boxing match with jelly", but it has its sting. The weekend he arrived for the literary festival, he was tweeting about a primitive occurrence: a secular Bangladeshi publisher had just been hacked to death. At least four atheist Bangladeshi bloggers have been killed this year. Militant fundamentalists of any creed don't care about witty semantics. Against such a disease, who can say which ancient remedy will be the most effective?

One of Grayling's favourite quotes about his daily routine is a Chinese one: "I leap from my bed and hasten, swift as a thirsty cat, to my work."

The morning we meet at the Lan Kwai Fong Hotel, the feline admits to a little jet lag. Still, he's immaculately coiffed and he's also wearing a moustache and beard which, as it's only November 2, would suggest either a devotion to Movember verging on the miraculous or a recent desire for a new look. "The women in one's life …" he explains helplessly, later, of this facial innovation. "I have two daughters."

It's clear, within about five minutes, that he enjoys female company. He's interesting, interested, funny, gossipy, a mellifluous speaker, generous with time and opinions. He says, believably, that his life is about the Great Conversation - a reaching out to engage, which is what all humanists should do. But there's also anger. It stems from a certainty that the world's religions, concocted round various mythologies, imprison society. On this, he is implacable.

Reading his books can make you feel - if you've been brought up in one of those systems - simultaneously idiotic and bereft. As a feebly flickering Catholic, I understand what he means about "the totalising effect on the mind" - but what about the yearning we all have for something, a meaningful otherness out there? (He sometimes calls this desire "the lingering splinter", as if it needs to be tweezered out.)

"What it is is a psychological wanting to belong, to feel part of a place," he says. "You can have a cause, work. I, for example, feel very much a cosmopolitan. I live in London, I have a British passport but if anyone asks me do I really feel nationalistic or patriotic - the answer is no. I feel obligations to the human race at large. What really does matter is values. The ethical question is hardly at all what people think it is. We're taught by the church it's about who you sleep with, things you do in private, but to make it about adultery trivialises it. It's about violations of human rights, the arms race."

OK. But surely he allows that religion can achieve some good? Faith groups recently have put pressure on world leaders to come up with a new climate-change agreement at the Conference of the Parties, which begins in Paris tomorrow; senior Buddhists responsible for the spiritual welfare of about a billion people chimed in last month. Does that count for anything?

"It doesn't in the slightest surprise me about the Buddhists," he says, smoothly. "Buddhism - as a philosophy, not a religion - enjoins compassion for all things. But it's a very, very tough ask for Jewish or Christian believers. If you take Judeo-scriptures literally, you're told that nature is given for our exploitation and use so if our attitudes are shaped by attitudes more than 2,000 years ago, we're in trouble. There is a self-interested reason to worry about climate change and that's perfectly rational - like turning off the taps not to flood the bathroom."

His own belief includes moral concern for animals. Naturally, he's vegetarian. Why not vegan? "It would probably be more consistent but being vegan eats into time that could be better spent writing about moral matters." This is uttered with greater levity than can be conveyed on the page, and he goes on to add, amiably, "That argument about doing one's best - it's a tremendous fig-leaf, isn't it?"

He certainly thought he was doing his best in 2011, when he announced plans for his New College of the Humanities (NCH), with its emphasis on stellar teaching and one-on-one tutorials. But immediately there was an outcry about the fees - £18,000 (about HK$215,800) per annum - and accusations of elitism. He was smoke-bombed at a talk in Foyles bookshop in London. His co-founder, the geneticist Professor Steve Jones, was obliged to bow out.

Grayling had previously been professor of philosophy at Birkbeck, University of London, and 34 of Birkbeck's academics wrote to The Guardian newspaper condemning "this opportunistic venture" that would "hasten the decline of the reputation for excellence that British universities, as public institutions, have fought so hard to establish". They also accused him - and here's the kicker - of a "loss of faith". Boris Johnson, London's mayor, wrote a piece about NCH in The Daily Telegraph, which was, ostensibly, in hearty favour but not entirely helpful. (The headline set the general tone: "At last, an Oxbridge for those who can't get into Oxbridge".)

Obviously, being in Hong Kong presents a good opportunity for a little genteel salesmanship; the territory has a page all to itself on NCH's website. When asked, Grayling says he's visiting two schools during his trip: St Paul's and Chinese International. "[NCH] is expensive but no more expensive than any other UK university for overseas students," he insists. "All universities in the UK are private, they all charge fees."

For domestic students, however, these are capped at £9,000, half of what he's charging. Yes, he parries, but more than a third of NCH students pay less than they would at other universities because of various bursaries and scholarships; he's also set up a trust to raise endowment money. The model is, clearly, American. "When I've got US$35 million like Harvard, everyone can come for free."

At the time, he was hurt by the ad hominem nature of the attacks. Presumably, he just had to be philosophical about it but it can't have been easy. Now, he describes the fuss as a "flurry" and says, dismissively, "There's no more conservative an individual than a 1960s leftie." But when we talk, briefly, about the Johannes Chan Man-mun shenanigans at HKU, his first question - "Do you think it's political or personal?" - suggests he's a man familiar with the viper-pit of academia.

Grayling's strong interest in China goes back to the 80s, when he went to Beijing with his then-partner, the sinologist Susan Whitfield, who was at Renmin University. "I loved it, I really, really love things Chinese," he says. Whitfield and he jointly edited China: A Literary Companion ("a great pleasure"). He also taught at the Chinese Academy of Social Sciences, co-wrote a 1991 book titled The Long March to the Fourth of June with Xu Youyu (they used a pseudonym), and has twice served as director of the Sino-British Summer School in Philosophy - a programme established in 1988 by the Chinese Academy of Social Sciences, in Beijing, and the Royal Institute of Philosophy, in London (it's now called the Philosophy Summer School in China).

"Here's a difficulty," he begins, thoughtfully. "I wrote a piece in The Observer about the Beijing Olympics …" - he wasn't in favour - "… and ever since I haven't been able to get a visa. They must have a long list of not-very-important people. I was thinking of appealing … Then about a month ago, one of my books, I don't know which one, was translated into Chinese and I was asked by the publisher if I'd agree to have three chapters deleted. I refused."

So he's a man cast out; and the excommunicated tone contains discernible splinters of yearning. For years, I tell him, when people in Ireland have asked me about China and how its - secretive, male, geriatric, family-planning-obsessed - authority operates, I've suggested that they simply substitute the word "Vatican" for "Communist Party". That tends to do the trick. Grayling likes the analogy. It presses his buttons, you can see them delightedly lighting up in his head as he works out the overlaps. Perhaps China needs someone along the lines of Pope Francis? Grayling, however, prefers the Nelson Mandela mould.

IN THE BEGINNING WAS THE WORD, and the Word was in Luanshya's public library in what used to be Northern Rhodesia and is now Zambia. Grayling grew up the youngest of three children and "a mistake", as his mother told him - one that she had hoped would at least result in a daughter. When he writes about his childhood love of books, he attributes it to the long "drowsy afternoons" of expat life; but as famous philosophers have been rather thin on the equivalent Hong Kong ground, it can't just be that.

His father worked for Standard Chartered Bank. His mother was frightened of Africa, he says, but liked having servants. One of them, Johnnie Penza, slept on the floor by the child Grayling's bed. "I used to suffer from night terrors," he says. "Overstimulated by the universe." His parents were completely non-religious, but did Johnnie talk about God? "He told me stories. One was about how God decided that all the people of the world who were black could become white - like him."

And Grayling retells a missionary myth: three animals are told to summon all humankind to whiten themselves in a cleansing lake. The cheetah swiftly brings the people of the north, who emerge snow-pale; the more tardy hare gathers the people of the east to the now churned-up waters; and the chameleon tells the people of the south but so late that when they arrive they can only press the palms of their hands and the soles of their feet into the faint dampness of sand left behind by the others. In a tone of outrage, he says, "I was stricken by that story."

When he was 19, and studying at Sussex University, in England, his sister, Jennifer, was stabbed to death in Johannesburg, South Africa, her body left in a river. His parents had to identify it; his mother had a heart attack and died a few weeks later. After the funerals, he returned to England - December, the bleak midwinter - and found he couldn't sleep for months, and for many years he couldn't eat tropical fruit. "The taste was so evocative," he says. "It was too difficult, too painful."

Work was his solace. "I used to think about my father's suffering, that if I could take it on, I could bear it because I'd just get on with my work."

Earlier, I'd asked him if he'd like to write a novel. In 2003, he'd been one of the Booker Prize judges - can it be a coincidence that that year's winning title was Vernon God Little? - and he was chairman of last year's panel. He'd said there were too many distractions (although, in 2006, he co-wrote a play called Grace). Now, suddenly, he remarks, "I've been asked by my publisher to write a memoir of my childhood in Africa."

He hesitates. "I love writing. My world is fashioning words. But the one thing I find difficult to write is memoir, to think of the tone, to get it right, to get behind the lens. So many aspects of that experience are uncomfortable. I don't want to write - what's it called … ?"

A misery memoir?

"I'm conscious of plucking the same strings others have."

Unexpectedly, he leans back in his chair and begins to talk about Africa: "I'd like to write about the contrast between the high plateau of Zambia and the extraordinary beauty of Nyasaland, Malawi. We lived on a high hill, looking east towards Mozambique and Mount Chiperone, and there was the river …"

As it happens, the river is named Shire, an echo of Tolkien's Middle-earth. In 2011, he wrote The Good Book, his secular alternative to the Bible. (It begins with the fall of Isaac Newton's apple.) Ever since, he likes to joke that, having created scripture, he's a divinity, too.

When I tell him that his own history - the fruit, the unexpected pregnancy, the loss of innocence, the suffering - sounds like mythology, he says, "As you know, I'm going to be a god."

And he adds, smiling, deadly serious, "But the bar hasn't been set high."