On the top floor of Random House's offices in London, the world's number one thinker – according to Prospect magazine's annual poll – walks in from the roof terrace and shakes my hand. Richard Dawkins is a trim 72-year-old with one of those faces that, no matter the accumulation of lines, will always draw the adjective "boyish".

There's a smoothness to the way he carries himself – a touch of the Nigel Havers – that could no doubt be construed as an arrogance befitting his intellectual status, but in conversation he is restrained, even hesitant, and faultlessly modest throughout our interview.

Perhaps the renowned evolutionary biologist and the world's most famous atheist was feeling especially cautious. The day before I met him he had become embroiled in a Twitterstorm, which grew into a broader media monsoon, after he had tweeted the following: "All the world's Muslims have fewer Nobel prizes than Trinity College, Cambridge. They did great things in the middle ages, though."

He defended himself in the ensuing furore by saying that he was merely stating a fact. And it's true, it was a fact. Many objected that it was a fact used to demonise Muslims, that it was racist (Dawkins responded by pointing out that Islam is not a race), and that, out of context, it was, at the very least, mischievous and misleading.

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I returned later to this dispute, but first of all we got down to discussing his memoir, An Appetite for Wonder, a sort of portrait of the scientist as a young man. The first of two volumes, it takes us from boyhood to the publication of his landmark bestseller, The Selfish Gene. The story begins with his colonial childhood in Kenya and Nyasaland (now Malawi), and is full of dusty anecdotes of our young hero rummaging without a care in the great African outdoors. Does he look back with nostalgia at that now largely disappeared way of life?

"Yes," he says slowly, as if watchful for hidden traps. "It's now unfashionable and in many ways it's something we British have to live down. But yes, there is a nostalgia for it and, although I was never in India, I get it reading novels of the Raj. It's a lost era that you can't help having a certain affection for, even if you disapprove politically."

His parents were hardy, practical types, unflustered by war or life in the bush or, it seems, anything else. His father was a botanist, working in the agricultural office in Nyasaland, so Dawkins grew up in a family that took a scientific interest in living organisms, though he insists he never inherited his parents' extensive knowledge of flora and fauna.

Dawkins in his first term at Oundle. Photograph: © Richard Dawkins

He moved to England when he was nine and went through a very typical public school experience for the era, except that he managed to fend off the sexual predations of older boys. Other than in relation to genetic research, sex doesn't raise its titillating head at all in the book – apart from one occasion. We learn that at the ripe age of 22 he lost his virginity to a cellist in London. She "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."

But that's all that Dawkins allows in terms of romance.

"Well that was a little token to say, 'This is all you're going to get,' " he says firmly. "I wanted to announce that this is not going to be that kind of autobiography."

Why not? "Fear of betraying confidences," he says, shifting in his chair. "These things are private. Some people let it all hang out but I prefer not to."

You can say that again. Dawkins may have an appetite for wonder, but he is positively anorexic when it comes to personal revelation. Perhaps the most confessional section – and it can hardly be called exposing – deals with his years teaching at Berkeley in the late 60s, when the campus was a hotbed of countercultural revolt. Dawkins took part in protests against the Vietnam war, of which he remains proud, but also got caught up in a local militant initiative to take over some university waste ground and turn it into a "people's park". "With hindsight," he writes, "it was a trumped-up excuse for radical activism for its own sake."

I suggest that radical movements invariably function on peer pressure and he agrees that he succumbed to the impulse to belong. "There was a sort of feeling of flower power and drugs," he says. "I never actually took drugs, oddly enough. I never had the opportunity. But the music of the time and the atmosphere – there was a feeling of loyalty to the protesters: these are my people. The same people who marched against the Vietnam war marched for the people's park and it was an automatic decision to join them. One should be more independent-minded than that."

That's Dawkins at his most self-reflective. He avoids any details of interest about his first marriage – to the ethologist Marian Stamp. And according to him, he is unlikely to be any more forthcoming in the second volume about his second marriage to Eve Barham, or his third to the actress Lalla Ward, a former assistant to Dr Who, who was introduced to him by his late friend Douglas Adams.

The couple live in Oxford, where Dawkins has resided almost all of his adult life, and where he spent 13 years until his retirement in 2008 as the professor for public understanding of science. As he was free in that role to pursue his own interests, he says his "nominal retirement" has made no difference at all.

The memoir is strong on the professional excitement of his early years as an academic, but it assiduously sidesteps the rivalries and disputes that mark even the most unremarkable scientific careers, let alone one as distinguished as Dawkins's. He didn't want any score settling, he says, or to "appear hostile".

So although he notes that the biologists Richard Lewontin and Steven Rose were two of the rare voices who criticised The Selfish Gene on its widely acclaimed publication in 1976, he fails to discuss their arguments or his thoughts on them, other than to say that both came from the "political left". Did he think their case against him was political rather than scientific?

"Yes, I think politics," he says after another anxious pause. "I actually wrote a fairly savage review of the joint book they produced later [Not in Our Genes] which I suppose I'll probably mention in volume two." He weighs his words again and then adds, "It was sarcastic rather than savage."

Dawkins seems determined in both the memoir and our interview to present a calm, conciliatory side to his character that has not always been associated with his public image. Later the photographer, Andy Hall, will tell me that Dawkins requested to look at the screen on Hall's camera to see what he had captured during the shoot. "You've made me look too harsh," complained the biologist.

Hall told him he was merely giving him appropriate gravitas.

"I don't want fucking gravitas," Dawkins snapped. "I want humanity."

One senses that for all the recognition he's garnered – the world's leading intellectual, the bestselling books, the rapt audiences etc – Dawkins would like to be a little more loved. I ask him if he thinks he's misunderstood by the media and the general public.

"Yes," he says without hesitation. "I seem to be perceived as aggressive and strident and I don't actually think I am strident and aggressive. What I think is that we have all become so accustomed to seeing religion ring-fenced by a wall of special protection that when someone delivers even a mild criticism of religion, it's heard as aggressive when it isn't. I like to think I'm more thoughtful and reflective."

Although he has only written one book specifically about religion – The God Delusion – it's the subject that has increasingly come to define Dawkins. He may have spread the message of evolution to millions, and he may have helped revolutionise our understanding of genetic biology, but it's his pronouncements on the irrationality and absurdity of religion that stick most prominently in the public's imagination. He's that bloke.

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Dawkins has long maintained that there is no real difference between his work on evolution and his anti-religion position as an atheist. To some extent, he has a point. As he puts it: "I suppose my particular branch of biology is kind of in the front-line trench where religion is fighting evolution. So in a way even my science books are forced to take a stance, not against posh theologians who accept evolution but surely the absolute majority of religious people in the world who literally believe that every species was separately created and even, in the case of the Abrahamic religions, believe that Adam and Eve were created 6,000 years ago. Chemists and other scientists don't have to battle with that."

While this may be true, no other evolutionary biologist has been quite as outspoken as Dawkins in his denunciation of religion and, indeed, the religious. As a consequence, he's the go-to guy for a scathing quote on dissembling theologies and their gullible believers. He was led into attacking Peter Kay (although he later said he was unaware of who Kay was) when the comedian said that he found religion comforting; savaged the historian Paul Johnson for the "ignominious, contemptible, retarded" basis on which he held his religious beliefs; and described the British Airways employee who was suspended for wearing a gold cross at work as having "one of the most stupid faces I have ever seen".

His comments about religion grew noticeably less restrained after the 9/11 attacks in America. It was those religiously inspired acts of terrorism that prompted Dawkins to write The God Delusion. He had wanted to write the book immediately after the twin towers were destroyed but was dissuaded by his agent, who told him that America would never buy a book that was so avowedly critical of religion. He waited several years and the book was eventually published in 2006. But as many observers have since noted, the people who flew planes into the World Trade Centre were motivated by a powerful belief in Islam, while The God Delusion was a sustained critique of Christianity.

"It concentrates on Christianity," he says, "because it's the religion I know a lot about, having been brought up in Christian schools."

All the same, it seemed a little perverse to be galvanised by the acts of followers of one religion to set about debunking the presumptions of another, especially as Christianity, particularly in Europe, and specifically in Britain, had become largely a toothless affair which had almost reformed itself out of existence. Did he really think that Christianity matters very much nowadays?

"Ayaan Hirsi Ali has at times suggested that Christianity might [in relative terms] be a good thing, like the Hilaire Belloc line: 'Always keep a-hold of nurse for fear of finding something worse'. I'm occasionally tempted by that view that maybe it would be a shame if Christianity died." But then he goes on to insist that a more muscular and sinister version of Christianity is flourishing in many parts of the world.

Douglas Murray, an outspoken critic of many aspects of Islam, recently lambasted Dawkins for taking the easy target of Christianity and ignoring the more problematic question of the Islamic world. "He can't have read anything I've actually written," Dawkins says. "Just this week I'm assailed mightily for going after Islam and had been for a very long time before that."

This "going after Islam" refers to his Twitter contribution on the number of Muslim Nobel laureates. But there's a distinction to be made between "going after Islam" – ie criticising the Koran and the Islamic prophet, Muhammad – and going after Muslims. The latter is likely to lead to accusations of racism and bigotry, which Dawkins duly received, while the former can bring far more threatening consequences He insists that he wasn't speaking of Muslims as an undifferentiated mass. He merely wanted to highlight how Islam, which produced algebra and kept safe the Greek philosophers of antiquity in the middle ages, had lost its way scientifically by focusing too much on the study of religion.

"The point I wished to make is that something about the Muslim cultural tradition seems to be inimical to doing science. I mean an Egyptian Muslim, a Pakistani Muslim and an Indonesian Muslim, they are not all the same, clearly. One thing they have in common is their religion. And one could make the case that the Islamic religion is not friendly to science. That's not saying anything about all Muslims."

He sounds genuinely offended that anyone could think otherwise. He does regret, he says, the comparison with Trinity College. He wishes he had set contemporary Muslim academic achievement against that of the Jews. "Something like between 20% and 25% of all Nobel prizes have gone to Jews, who are less than 1% of the world's population. That's a very embarrassing comparison."

I suggest that this may not have been wise. Leaving aside the sensitivities surrounding the Arab-Israeli conflict, you can also argue that Jews are a race. "No you can't!" he replies. "It's just total nonsense to talk about Jews being a race. That's precisely where Hitler went wrong."

By now my controversy seismometer is going off the Richter scale: Muslims, Jews, Hitler – it's like a mass invitation to every irate commentator in the blogosphere. For while Dawkins's arguments tend to be studiously rational, they are not always couched in the language of provisos, exceptions and disclaimers that is necessary to avoid the minefield of cultural sensitivities. Instead he places a high premium on clarity, which his critics often see as simplicity or a lack of intellectual sophistication.

In a sort of half-compliment towards his demystifying style of writing on evolutionary biology, Fay Weldon once called him a "poetic reductionist". Sometimes in his commentary on religion, the poetry can go missing. The Spectator rather cruelly called him "the Mary Whitehouse of our day", as if the religious debate had turned him into a busybody bore.

When I ask him if he's not tempted to back away from public pronouncements on religion, given all the grief it generates, not least for himself, he says, a little wearily: "No, I don't think so. It is important. I think it is worthwhile."

But it seems apparent that some air has gone out of the New Atheist balloon, particularly with the death of Christopher Hitchens. Dawkins agrees. "He was irreplaceable, probably the greatest orator I've ever heard. Such articulate cogency and a splendid voice like Richard Burton."

Of course, while there are endless ways to describe an omnipotent god, and his various moral commands, there are a limited number of ways to state his non-existence. For Hitchens, says Dawkins, the argument was political. "He saw god as a kind of divine North Korea." But Dawkins maintains that his own beef has always been scientific. "I'm passionately interested in the truth about the universe and I've always thought of the existence of an intelligent creator as a scientific hypothesis. A universe with a creator would be a totally different kind of universe scientifically speaking than one without."

But he also has an aesthetic opposition. "Yes," he agrees, "because I do think that the scientific worldview is so wonderful and poetically uplifting that the children who don't get it and are being fed a second-rate alternative are being short-changed."

It's not the most profound psychological insight to suggest that Dawkins's intolerance of religion may stem from his own brief period of "religious frenzy" as a teenager at Oundle school. His belief in a supreme creator was only deepened by his love of Elvis Presley, a fellow believer. What saved him was a schoolfriend who persuaded him of the brilliance of Darwin's idea.

Everything comes back to the science with Dawkins, and sooner or later everything comes back to evolution. I ask him if Darwinism informs his everyday apprehension of life.

"Well, in one way it does. My eyes are constantly wide open to the extraordinary fact of existence. Not just human existence but the existence of life and how this breathtakingly powerful process, which is natural selection, has managed to take the very simple facts of physics and chemistry and build them up to redwood trees and humans. That's never far from my thoughts, that sense of amazement. On the other hand I certainly don't allow Darwinism to influence my feelings about human social life."

Apart from anything else, that last sentence is a necessary defence against the accusation that Dawkins sees humans simply as the "survival machines" he described in The Selfish Gene, organisms whose only purpose is gene reproduction. Dawkins argues that we as individuals can opt out of Darwinism. For while we may be compelled by biology, we are freed by consciousness.

This sets up a fascinating battle between, as it were, the mind and the body, the conscious self and the survival machine. Dawkins agrees and says that it's a question that requires much more research. But he cites pain as one of the potential battlefields that ought to be examined.

"From a Darwinian perspective it is clear what pain is doing. It's a warning: don't do that again. If you burn yourself you're never going to pick up a live coal again. But you might think a little red flag in the brain would be enough to do that. Why does pain have to be so damned painful?"

His answer is that our brains have evolved to treat certain things as rewards and others as punishments. "And those can run away so that you can become hedonistic to the extent that you neglect your Darwinian responsibilities, and we do all the time. So it could be that this tussle between the genetic imperative and the brain leads to pain becoming so painful that, as it were, the hedonistic brain can't overrule."

But clearly hedonistic consciousness is capable of overcoming our biological programming. The more materially successful a society becomes, the better educated and more physically comfortable, the less inclined its members are to reproduce. If we, like Dawkins, view the evolutionary determinant as the survival of the gene rather than the species, then is that not a problem for genes whose survival machines are reluctant to reproduce?

"Well this worried my dear colleague Bill Hamilton," he answers, "and he got a lot of stick for it. It is an unfashionable point of view and one of the reasons it has become unfashionable is Hitler. In pre-Hitler times eugenics was very much a cause of the left, and Hitler did for all that. It's not a view I go out of my way to espouse but it possibly is a worry. R A Fisher, probably the greatest Darwinian of the first half of the 20th century, deliberately had lots of children because he knew he was bright."

This is not an accusation that could be levelled at Dawkins. He has one child, a 29-year-old daughter from his second marriage. But just in case I walk away with the wrong idea, in spite of his own example, he adds: "So while it's probably true that there is something a bit dysgenic about what you've just identified, I would absolutely hate to see any kind of draconian attempts to reduce the reproduction of some people at the expense of others."

That's a relief. Twitter would probably have crashed under the strain of that backlash and who knows what would have happened to the Guardian website. Instead we part company on a benign note, without controversy or dispute, the great humanist having succeeded in showing his humanity.

• This article was amended on 18 September 2013. The original referred to Dawkins as former professor for public understanding of life rather than science.