It feels a bit creepy to be counting pictures in Richard Dawkins’ downstairs loo, but evidence is evidence. Most of the pictures are actually awards, but it’s the number that counts: 21 honorary doctorates and international prizes, framed and hung along with a certificate from the 2008 Crufts dog show.

The dogs are around somewhere; we can hear them yapping. The loo gives onto a generous hallway, from where Britain’s top atheist leads the way through his sitting room and an enormous kitchen onto a terrace partly occupied by a two-tonne limestone picnic table hewn specially for him from Dorset’s Jurassic Coast. It’s pitted with hundreds of tiny fossils. We haven’t been shown the indoor swimming pool, but it’s there behind us in a long, low outbuilding.

It’s easy to envy Dawkins, as long as you have a thick skin and don’t believe in an afterlife. His gentler critics include the former Chief Rabbi and Professor Peter Higgs, of Higgs boson fame, and he has plenty of enemies (he added a few hundred thousand earlier this month by tweeting that Trinity College, Cambridge, had more Nobel prizewinners than all the world’s Muslims). But he has a huge and devoted following, too. He’s written 12 books including two epoch-making bestsellers. He has his large North Oxford home. He is a leading evolutionary biologist, a decent electronic clarinettist and a public intellectual in demand from Tokyo to Tennessee.

He hasn’t won a Nobel prize himself, but, as we sit at the Jurassic slab in glorious sunshine, he generously argues that several of his peers deserve one for books on science far less widely read than his own.

This is important, because one scientist whom Dawkins commends to the Nobel committee is Steven Pinker of Harvard University. Pinker’s book, The Better Angels of Our Nature, explains the decline of violence in human society partly in terms of what Dawkins calls our “shifting moral zeitgeist”. Apparently, this means we’re less beastly than we used to be because we disapprove of beastliness more than we used to.

Dawkins is fascinated by the way today’s transgressions might have been viewed differently not long ago. For instance, as a junior academic he went to the University of California at Berkeley for two years in the late Sixties, which gave him a ringside seat at the Summer of Love. He relates one vivid memory in his new memoir, An Appetite for Wonder:

“I was walking along Telegraph Avenue, axis of Berkeley’s beads-incense-and-marijuana culture. A young man was walking ahead of me, dressed in the insignia of the flower-power generation. Every time a young woman passed him, walking in the opposite direction, he would reach out and tweak one of her breasts. Far from slapping him, or crying, ‘Harassment!’, she would simply walk on by as if nothing had happened… Today I find this almost impossible to believe.”

He says he’s pleased how things have changed on the harassment front in the past 40 years. But on other occasions when that shifting moral zeitgeist rears its head – as boys, including him, are molested or beaten at his various boarding schools, for instance – he fails to be outraged. One master at his public school, Oundle, he writes, “was prone to fall in love with the prettier boys. He never, as far as we knew, went any further than to put an arm around them in class and make suggestive remarks, but nowadays that would probably be enough to land him in terrible trouble with the police – and tabloid-inflamed vigilantes.”

Is he guilty of rationalising bad stuff just because it’s past? “I am very conscious that you can’t condemn people of an earlier era by the standards of ours. Just as we don’t look back at the 18th and 19th centuries and condemn people for racism in the same way as we would condemn a modern person for racism, I look back a few decades to my childhood and see things like caning, like mild paedophilia, and can’t find it in me to condemn it by the same standards as I or anyone would today.”

The mention of paedophilia inevitably brings us to the recent run of arrests of old white men accused of child sex abuse, starting with Jimmy Savile. Has the moral zeitgeist been shifting at their expense? “I think we should acknowledge it. That’s one point… But the other point is that because the most notorious cases of paedophilia involve rape and even murder, and because we attach the label ‘paedophilia’ to the same things when they’re just mild touching up, we must beware of lumping all paedophiles into the same bracket.”

So is there a risk of a metaphorical lynching of well-known people as soon as they’re accused? “I think there is a risk of that.”

What about the child sex abuse scandals that have led to anguished soul-searching and multibillion-dollar payouts in various outposts of Christianity? “Same thing,” he says. “Although I’m no friend of the Church, I think they have become victims of our shifting standards and we do need to apply the conventions of the good historian in dealing with cases which are many decades old.”

In the book, Dawkins mentions one occasion when a teacher put a hand down his trousers at a prep school in Salisbury, and four others at Oundle, when he “had to fend off nocturnal visits to my bed from senior boys much larger and stronger than I was”. The Oundle incidents don’t seem to have bothered him. The prep school one did, but he still can’t bring himself to condemn it, partly because the kind of comparison his adult mind deploys is with the mass murders carried out by Genghis Khan in the 12th century. “Without condoning what was done, at least try to put on the goggles of the period and see it through those eyes,” he says. “I find it much harder to put on those goggles where we’re talking about the monstrous cruelty that went on in past times. It’s hard to think of that and to forgive using modern standards in the same way as it might be for the schoolmaster who touched me up but didn’t actually do me any physical violence.”

It was a rare dark moment in a rather special childhood. His earliest years were spent in rugged bliss in southern Africa, where his father was a colonial servant. The trauma of moving to England in a converted troop ship and living with grandparents who forced him to say, “Good morning,” at breakfast briefly gave him a stammer. At 13 he became “intensely religious” and was confirmed into the Church of England. At 17, having learnt about other religions, he became “militantly anti-religious”, and has been ever since.

He was shy but pretty. Hence the unwanted advances at Oundle. Hence, too, a long delay before properly discovering girls, but when that happened it happened in style. “I didn’t finally lose my virginity until much later [aged 22],” he writes, “to a sweet cellist in London, who removed her skirt in order to play to me in her bedsitter (you can’t play the cello in a tight skirt) – and then removed everything else.”

The book is charming, and full of careful translations of phrases such as “public school” for American readers. Is it, then, a charm offensive aimed at those he may have offended down the years? He admits the thought occurred to him, but only once he’d finished it. At this point another thought occurred to him: “Hey! Wait a minute! Maybe I’m not so strident and shrill as people thought I was.”

In his back garden, he isn’t strident or shrill at all, but then he doesn’t have to be. It wasn’t the same when he used to tour the world doing live public debates with creationists, whom he found had to be demolished without mercy if the audience was to be prevented from getting the impression they were witnessing a genuine argument. Nor can he seem to avoid stridency on Twitter (795,000 followers in three months) or in panel discussions. In one such talk, which has been viewed more than a quarter of a million times on YouTube, Neil deGrasse Tyson, a distinguished American astrophysicist, wondered if Dawkins’ “articulately barbed” attacks on superstition in all its forms was not sometimes counterproductive. Dawkins replied with an approving homage to a former editor of New Scientist who once told an interviewer, “Our philosophy is this: science is interesting, and if you don’t agree you can f*** off.”

The only time he gets remotely worked up with The Times is when asked for his response to a suggestion by Professor Higgs that he, Dawkins, is “almost a fundamentalist”. Higgs (who probably will get a Nobel now that CERN has discovered his boson) made the remark to a Spanish newspaper last December. Dawkins is naturally aware of this.

“[Higgs] is obviously a great physicist and I admire him very much,” he says. You sense a “but” coming. Instead he muses that “it’s very easy to be goaded into calling somebody a fundamentalist,” especially when you may not have read that person’s books. Not that there would be any reason for Higgs to have read any of his books; merely that “It’s almost part of the folklore that I’m an extremist fundamentalist, and people who’ve actually met me or read my books tend not to say that.”

Perhaps the criticism is more that Dawkins seems to feel a compulsion to change believers’ minds. Why not leave people to believe what they want to believe? “Well, of course they can believe what they want to believe! They just don’t have to read my books, that’s all.”

Dawkins’ beef with religion is well known; the degrees of contempt he feels for different creeds and religious ideas are less so. Nowadays, creationists elicit weary despair from him at best. He no longer holds debates with them, on the advice of the late Stephen Jay Gould, another mass-market evolutionary biologist. “The moment you accept their invitation, they’ve won,” he recalls Gould telling him, “because that’s what they want, the oxygen of respectability, to be seen on a platform with a real scientist.” He points out that for similar reasons a gynaecologist probably wouldn’t hold a debate with a believer in the stork theory of reproduction.

The Church of England gets off lightly. It was the C of E that embraced him during his adolescent religious crush; the C of E whose hymns he sang as a choirboy until his voice broke; and the C of E whose former senior primate, Archbishop Rowan Williams, he has met several times and cannot bring himself to diss. On the contrary, he says, “I think he’s a lovely man, extremely kind, intelligent and nice. I’m just baffled by his entire belief system.”

The Old Testament, to Dawkins, is just as baffling, only worse, and herein lies a problem for Dawkins’ relations with those who hold it dear. Chapter Two of The God Delusion, his biggest volume of religion-bashing, begins: “The God of the Old Testament is arguably the most unpleasant character in all of fiction: jealous and proud of it; a petty, unjust, unforgiving control freak; a vindictive, bloodthirsty ethnic cleanser,” and goes on in that vein. Last year Lord Sacks, still Chief Rabbi at the time, called the passage “profoundly anti-Semitic”. Dawkins stood by it but said it was basically a joke. Lord Sacks still didn’t get it.

Now Dawkins says of Sacks: “He’s such a nice man that I don’t want to hurl brickbats at him, but he seemed to say that because I had attacked God, that was anti-Semitic, as though God’s a Jew. And I’ve had that from other Jews as well.” To the complaint that Dawkins singles out the God of the Old Testament for harsher treatment than the God of the New Testament, he replies brightly: “That’s right, and the God of the Old Testament is nastier than the God of the New Testament. It’s one of the things that Christians never tire of telling us.”

Isn’t this therefore a “Christian atheist” as opposed to a “Jewish atheist” view, as Sacks complained? “There’s probably something in that, yes… My C of E upbringing probably does show through.”

And that, dear reader, is a rare concession from Oxford’s former Professor for the Public Understanding of Science. He then comes close to making another on the subject of Mormons, whose scripture he says at first is “recent nonsense and therefore somehow more reprehensible than that which has a certain amount of age”. But what does the age of nonsense have to do with its reprehensibility? That sounds rum. “It does, doesn’t it?” he mutters, but it doesn’t make much difference.

Soon he’s off again, repeating an argument that he made often during last year’s White House run by the Mormon Mitt Romney, that the founder of Mormonism was a “19th-century charlatan” and that anyone who believed him was a fool. As for Dawkins on Islam, the tweet on Nobel prizes gives you the flavour of his more printable views.

He is friendly with that other big-tweeting humanist, Stephen Fry, and was close to Christopher Hitchens, speaking through tears at his funeral. He has recently been called “the worst kind of zealot” by the American Muslim academic Reza Aslan; and a case study in how not to talk about religion, by Daniel Trilling, the editor of New Humanist.

You wouldn’t know any of this from his autobiography; nor does he seem like a zealot across the corner of his picnic table. Maybe this is because he’s not being goaded. He’s patient and, on the whole, obliging. Does he have any advice for Prince George? “Think for yourself. Reach your own conclusions by looking at the evidence.” He adds: “If you end up being an atheist, that would be very interesting for the Church of England.”

Would he care to explain how he came to be married three times? He would not. He will reveal that his one daughter, Juliet, is a doctor in Cambridge, but he won’t talk about his first wife, Marian Stamp, who went with him to Berkeley and is Professor of Animal Behaviour at Oxford; nor his second, Eve Barham, Juliet’s mother, from whom he divorced acrimoniously in 1999; nor his third, the writer and actress Lalla Ward, formerly married to Tom “Dr Who” Baker, whom he met through their mutual friend Douglas Adams, cult hero and creator ofThe Hitchhiker’s Guide to the Galaxy.

Last year he took an expensive trip to the Antarctic, but otherwise he can’t remember taking a holiday at all. He has been a publishing phenomenon ever since producing The Selfish Gene in 1976, aged 35, popularising the idea that our bodies are mere “survival machines” for our genes.

Since then the honorary doctorates have been piling up, and, with them, one recurring regret: “I wasted my time at school,” he says. “I envy my teenage self the opportunities he had and didn’t take advantage of, and sort of think, ‘You little idiot, why didn’t you pay more attention and join the astronomy club?’”

What could he have done that he hasn’t?

“I could know a lot more mathematics than I do. I could be a lot better linguist than I am. I could have read a lot more books than I have.”

The author of The Selfish Gene has been called a selfish genius, and even a source of theoretical underpinning for Thatcherism. That idea is nonsense – it’s genes that are quintessentially selfish, as he has shown, not humans. Even so, it may be significant that if there is an inner void, he wishes he had filled it with self-improvement rather than good works.

Not that he’s done yet. A blood pressure cuff and pill dispenser in his office indicate that he takes seriously the maintenance of his genes’ survival machine. He has volume two of the autobiography to write, and may get round to writing a letter to those Nobel people on behalf of those he most admires.

But you know how that would be reported, I say. “Britain’s greatest living science writer in desperate bid…” That sort of thing.

“Ah, well.” He sighs. “I am actually more humble than I’m sometimes given credit for.” And a bit less worldly, too.

Times+ members can attend a Q&A with Richard Dawkins on September 11 at Cadogan Hall, London. Buy tickets for £10 atmytimesplus.co.uk

‘I didn’t lift a finger to stop the grotesque bullying’

Exclusive extract from Richard Dawkins’ new memoir

Much of the apparent bullying [at Chafyn Grove prep school] was pure braggadocio, futile threats whose emptiness was attested by their invocation of an indefinite future: ‘“Right! That does it. I’m putting you on my beating-up list” was about as nebulous a threat as “You’ll go to hell when you die” (though, alas, not everybody treats the latter threat as nebulous).

But there was real bullying too, the especially unkind form of bullying where gangs of sycophantic henchmen rally around a bullying leader, courting his approval. [The victim] was a precociously brilliant scholar, large, clumsy and ungainly, with an unharmonious, prematurely breaking voice and few friends. He was an unfortunate misfit, an ugly duckling doubtless destined for swanhood, who should have aroused compassion, and would have done in any decent environment – but not in the Goldingesque jungle of the playground. There was even a gang bearing his name, the “anti- –––– gang”, the sole purpose of which was to make his life a misery. Yet his only crime was to be awkward and gangling, too uncoordinated to catch a ball, unable to run except with a graceless staggering gait – and very, very clever.

I cannot even begin to imagine how human beings could be so cruel, but to a greater or lesser extent we were, if only through failing to stop it. How could we be so devoid of empathy? I didn’t lift a finger to stop the grotesque bullying. I think this was partly due to a desire to remain popular with dominant and popular individuals. It is a hallmark of the successful bully to have a posse of loyal lieutenants, and again we see this brutally manifested in the verbal cruelty and bullying that has become epidemic on internet forums, where the abusers have the additional protection of anonymity. But I don’t recall feeling even secret pity for the victim of the bullying at Chafyn Grove.

How is that possible? These contradictions trouble me to this day, together with a strong feeling of retrospective guilt. I am struggling to reconcile the child with the adult that he became; and the same struggle, I suspect, arises with most people. This is no place for a philosophical disquisition, so I will content myself with the observation that continuity of memory makes me feel as though my identity has remained continuous during my whole life, while I simultaneously feel incredulous that I am the same person as the young empathy-failure.

I was also a games-failure, but the school had a squash court and I became obsessed with squash. I didn’t really enjoy trying to win against an opponent. I just liked knocking the ball against the wall by myself, seeing how long I could keep going. I had squash withdrawal symptoms during the school holidays – missed the echoing sound as ball hit wall, and the smell of black rubber – and I kept dreaming of ways in which I might improvise a squash court somewhere on the farm, perhaps in a deserted pig sty.

Back at Chafyn Grove I would watch games of squash from the gallery, waiting for the game to end so I could slip down and practise by myself. One day – I must have been about 11 – there was a master in the gallery with me. He pulled me onto his knee and put his hand inside my shorts. He did no more than have a little feel, but it was extremely disagreeable (the cremasteric reflex is not painful, but in a skin-crawling, creepy way it is almost worse than painful) as well as embarrassing. As soon as I could wriggle off his lap, I ran to tell my friends, many of whom had had the same experience with him. I don’t think he did any of us any lasting damage, but some years later he killed himself. The atmosphere at morning prayers told us that something was up even before [the headmaster] Gallows made his grim announcement, and one of the woman teachers was crying. Many years later in Oxford, a large bishop sat next to me at high table in New College. I recognised his name. He had been the (ah me, much smaller then) curate at St Mark’s church, to which Chafyn Grove marched in crocodile for matins every Sunday, and he was evidently in touch with the gossip. He told me that the same woman teacher had been hopelessly in love with the paedophile master who had killed himself. None of us had ever guessed.

© Richard Dawkins 2013. Extracted from An Appetite for Wonder, published by Bantam Press on September 12 and available from theTimes Bookshop for £15.95 (RRP £20), free p&p, on 0845 2712134;thetimes.co.uk/bookshop