"I suspect we're not the only family in the country that likes to have a friendly row on Christmas Day," admits Jim Al-Khalili, sitting in his office in the physics department at the University of Surrey. "I guarantee we will have the usual Al-Khalili religion debate. My wife gets very frustrated about it. It's the same old argument every year."

But this year might be a little more fraught than most. Mr Khalili's mother is still a devout, church-going Christian but, next week, her 40-year-old son will become the next president of the British Humanist Association, the ever-expanding organisation for, in its own words, "people who seek to live good lives without religious or superstitious beliefs".

"She felt somewhat disappointed that I had taken on this role," he admits. "I said: 'You shouldn't be. You shouldn't be any more disappointed than I am that you go to church every Sunday.'"

Mr Khalili, who grew up in Iraq with his Christian mother and his "bordering on agnostic Muslim" father, is a theoretical physicist and also presents The Life Scientific on Radio 4.

A scientist-atheist then – which makes comparisons with Professor Richard Dawkins inevitable. But Mr Khalili is keen to portray himself as more cuddly than the man dubbed "Darwin's Rottweiler". Cuddly?

"Yes. Cuddly. I am a cuddly atheist. Someone who doesn't feel the need to tell you that what you believe in is stupid. Take my mother, I will tell her: 'I'm happy for you, because I know your religious faith fills a hole in your life.' I can see how important it is to her to have this faith. What right do I have to destroy it?

"I'd like to see her one day say: 'You know, I don't think God exists,' but I'm not going to be arguing and pushing that she is wrong.

"I am against creationism being taught in schools because there is empirical evidence that it is a silly notion, but I don't put religious faith in that bracket. I have no evidence to prove there is no God. The burden of proof is on them, yes, but I don't force it upon them to prove it. If they want to have a religious faith that is up to them. I won't dictate to them.

"I'm not going to have a debate with someone whose religious faith is very important to them and expect them to say: 'Ah, of course, you're right. There is no God.' It's not going to happen. If people turn away from religion it is because they see there is no need in their worldview for a supernatural being guiding how they live their lives."

But he is no shrinking violet. At a time when Christianity in Britain is on a downward trajectory, according to recent census results, he is adamant that the humanist voice must be heard. "I am passionately concerned about the rise in pseudo-science; in beliefs in alternative medicine; in creationism. The idea that somehow it is based on logic, on rational arguments, but it's not. It doesn't stand up to empirical evidence.

"In the same way in medicine, alternative medicines like homeopathy or new age therapies – raiki healing – a lot of people buy into it and it grates against my rationalist view of the world. There is no evidence for it. It is deceitful. It is insidious. I feel passionately about living in a society with a rationalist view of the world.

"I will be vocal on issues where religion impacts on people's lives in a way that I don't agree with – if, for instance, in faith schools some of the teaching of religion suggests the children might have homophobic views or views that are intolerant towards other belief systems."

Despite being an atheist, Mr Khalili got married in a church, a right that should clearly be extended to gay people. "Why shouldn't they have the right to be able to do what heterosexual couples do? Getting married in a church has a cultural resonance that has nothing to do with religion. I got married in a unitarian church. At the time I was an atheist, but it was nice."

He added: "I find it quite difficult to ridicule people of faith. I've debated on stage with the Archbishop of Canterbury, with the Chief Rabbi, but one thing I do feel very strongly about is this idea that they have the moral high ground. Many people of religious faith assume that if you're an atheist you're an empty shell. That you have no moral guidance whatsoever. Humanism says the opposite of that. If you have faith in humankind and all the qualities that we like to encourage – compassion, empathy and so on – these are things that make us human.

"I am totally against, for example, bishops in the House of Lords. Why should someone of a particular religious faith have some preferential treatment over anyone else? This notion that the Church of England is the official religion of the country is utterly outmoded now.

Once, so-called scientists were convinced they could turn lead into gold. History has a persistent habit of making scientists look like fools – so while they now fire atoms at each other at high speed in tunnels under the Swiss Alps, how can they criticise religion when their own beliefs sometimes turn out to be wrong?

"But the difference between my beliefs and having a religious faith is that I am prepared to change my views in light of new evidence," he says.

"But someone of a religious faith will just stick their fingers in the ears and say: 'I'm not listening, there's nothing you can say that will make me change my mind.'"

For anyone interested in listening, Mr Khalili's voice is one you can expect to be hearing quite often in the next few years.

This life: Jim al-Khalili

Last place went to dinner: Clarke's in Kensington, London.

Last album listened to: The Eagles Greatest Hits (in the car on a drive back from Yorkshire)

Last book read: Erwin Schrödinger's What is Life? (well, reread)

Last gig: Paloma Faith

Last film: The Hobbit