He stands like a hotsy-totsy god with legs so far apart that the rising sun is momentarily framed by Gore-Tex-swathed thighs. "Once the remnants of the last stars have decayed away to nothing," he says portentously to an imaginary camera in one of those regional accents they like at the BBC, "the story of our universe will finally come to an end." He closes the book, looks moodily out of shot, then struts down the Kings Road like Liam Gallagher – ego the size of the Virgo Supercluster, swinging his arms like a chimp. What a great shot that would make, he thinks, before the credits.

But enough about me. I'm late for lunch with Professor Brian Cox OBE. When I arrive, he's sitting outside the Bluebird cafe, poised to order chicken pie. How very northern, I say to the Oldham-born cosmologist. "Mmm yes, it might be too stodgy. Spaghetti and rocket salad please," he tells the waiter. Even particle physicists have to watch their mass.

We're meeting to discuss the success of Wonders of the Universe, his four-part BBC2 series that ends on Sunday. It's accrued impressive viewing figures (6m watched the initial episode and it was the first BBC factual show to top the iTunes chart). It is also reportedly responsible for a hike in telescope sales. But, as night follows day, or as a planetary nebula becomes a white dwarf, it has its detractors. I show him two letters from the Radio Times. One suggests that Cox's presenting style is an unwitting homage to Paul Whitehouse's perma-smiling enthusiast for the wonders of nature on The Fast Show. "Isn't Einstein brilliant! Aren't black holes brilliant! Isn't Pauli's exclusion principle brilliant! Isn't the heat death of the universe, though somewhat depressing, fundamentally ... BRILLIANT!" You get the idea.

"I think that, as a TV presenter, if you can't be impersonated, you're probably not doing it right," retorts Cox cheerfully. He likes the fact that impressionist Jon Culshaw nails his voice. Being teased is tolerable – up to a point. Let's hope his skin's thick enough to enjoy the YouTube satire of him doing the rounds.

The other letter is more troubling. It lists the series' visual shortcomings. Incessant slow-mo footage; baffling CGI of putative cosmic objects whirling like a bad LSD trip; presenter legs akimbo on a mountain peak like a rutting stag to a soundtrack of bombastic power chords. Endless foreign-location sequences of questionable relevance that us increasingly impecunious dupes (licence-fee payers) are bankrolling. Carl Sagan (late US astrophysicist, cosmologist and one of Cox's idols) wouldn't have stooped to conquer viewers with such visual cliches.

"I accept some criticisms of the series," says Cox, 43. "I think the days of standing alone on a mountaintop while a helicopter circles round me are over. We're not going to do that again. But it's a challenge to suggest the epic, awe-inspiring nature of the universe. When Carl Sagan, whose work I loved from when I was a boy, made Cosmos [a 1980 TV series and book], he got a lot of stick. So do I. But it's hard: how do you keep the body of the documentary and remove all the visual cliches? To be honest, I'm a little bored of the grandiose thing and I want to move on."

He balks, though, at the suggestion he's cost licence-fee payers lots of money by travelling the world. "My foreign travel was hardly as costly as the CGI or the camera crew. Anyway, it's about the value we bring in the programme. You need epic locations to give the right resonance to what you're talking about." True, but some critics have pointed out the cosmic irony that extraterrestrial wonders are illustrated by shots of Earth's natural wonders.

Cox twirls his spaghetti crossly. It's as though he's trying to reduce his pasta from supernova to ultra-dense neutron star. (This, you will be pleased to learn, will be this article's first and last cosmological simile.) As Cox twirls, his smile fades. The last time I saw that smile disappear so thoroughly was last Sunday during the episode on gravity. There he brilliantly explained the differing gravitational forces on different planets while sitting in a centrifuge, and there is nothing like a centrifugal gravitational simulator to wipe the smile off someone's face.

What's he cross about? "What annoys me is that I can't get out my intellectual cricket bat with my critics, as I can when you're doing physics. There's a brutality in science because you're measuring yourself against reality. As a presenter, I have to be circumspect, but as an academic I just want to beat them into the ground." Who? "The people who accuse me of dumbing down. I may have been standing on a mountaintop, but what I was saying was about electro-weak symmetry breaking. Some people can't see the content for the style. I just want to get the script and say, 'Here's what I said about gravitational mass and inertial mass, or about Einstein's general theory of relativity or about entropy. Now you tell me what you fucking know about entropy.' I suspect they couldn't because they weren't paying attention. They're so bewitched by complaining that the style of Wonders isn't like the great TV documentaries from when they were young."

He's still cross that complaints about the noisiness of the musical soundtrack led producers to turn down the volume on later episodes. "That was a mistake. It was only a handful of complaints. When I worked as a science adviser with Danny Boyle on Sunshine [the 2007 sci-fi film set 50 years in the future in which a team of astronauts are sent to reignite the dying Sun] he said that music is an integral part of the emotional presentation of a film. It's the same for Wonders: this is supposed to be a documentary about the wonders of the universe and the music should be in the same emotional register. It's not a lecture."

Cox argues that the BBC could have made two different soundtracks available for the series as it was screened. One authentically loud, presumably for the kids whom Cox wants to lure into studying science and engineering; the other muted for more venerable demographics likely to send why-oh-why complaints to Points of View. "It would be similar to making subtitles available, an option you could choose with your remote. It wouldn't cost much. It would be like having wheelchair lifts to buses." After the interview, the BBC press officer chaperoning Cox tells me it would be prohibitively expensive to provide such audio options.

His insistence on his documentary having an emotional dimension underwritten by epic images and loud music highlights is what we might call Cox's Paradox. "I'm trying to get viewers to feel my first reaction to science, which was awe at the universe and astonishment at what we've learned." But at the same time, his vision of science is one devoid of emotion. "Sagan always said this – people don't need to know when the universe began; people need to know how science works, that it's not got an agenda, and that it is a process that is utterly dispassionate."

So you're trying to get younger viewers to have a passionate reaction to something that is methodologically dispassionate? "It's a paradox, but it's what I'm doing. I'm fighting for reason. With scientific education in a democracy, which is what this is about, you have to accept that reason is radical. We live in a culture where people can say 'I don't like nuclear power' or 'I don't think wind farms are pretty', whereas PhD scientists are valuable precisely because they instinctively strip away emotional responses and say, 'Here's the evidence. Here are reasons.' I want Britain to be more reason-based."

As a Royal Society University Research Fellow, Cox has a brief to educate Britons about science and to instil enthusiasm about science and engineering in young people. Why's the latter important? "Britain is squandering its lead in science and engineering. We once led the world, and we can again."

I catch a sidelong glance of Cox as he talks. High-cheekboned, plump-lipped, favoured with serene brown eyes, flecks of grey dignifying his Madchester hairdo – he is not an ugly man. Such improperly non-dispassionate assessments, though, about his looks and their corollary, his alleged egotism, drive the professor nuts. He's just concluded a Twitter war with Sarah Vine, Times columnist and wife of education secretary Michael Gove. In a hyperbolically rude outburst, Vine wrote that Cox's ego was a "giant intergalactic body of energy, an object so large and indomitable that it threatens to obscure even the light of the sun. . . Not even Narcissus himself would have had the brass neck to stipulate . . . long, lingering shots of the handsome professor silhouetted against a night sky."

Cox tweeted: "Sarah Vine should speak to her husband about the impact of science and history programming before scribbling her drivel in the Times". He added that it was Gove's job to encourage young people to into the fields. Then he tweeted Vine: "Your article offends me, and I dare say everyone who has an interest in encouraging more young people into science." Vine snapped back: "If someone can point me towards an ugly scientist who objects to my piece as much as @ProfBrianCox then I will take his objection seriously." Cox replied: "Surely age/sex/appearance has nothing to do with it. Perhaps scientific track record would be a better barometer?"

It's edifying – isn't it? – to see two footsoldiers of Rupert Murdoch's evil empire (Cox writes a column for the Sun) mash each other up as the Milky Way and Andromeda galaxies will do in 3bn years' time? (Another cosmological metaphor. Sorry). Don't you guys realise you love each other, I ask Cox. "Well, I'm glad she's admitted she was wrong. I know what it's like to be a journalist – you get called at 2pm and told to file something at 4 on something topical."

He tells me he did just that recently, in a column for the Sun in which he eviscerated Saint Vince of Cable because the coalition business secretary seemed poised to cut science funding by 20% in the comprehensive spending review. "The Sun illustrated my article with a Spitfire flying from a double helix, with the headline that cutting back on science now would be like cutting back on the Spitfire programme in 1938. Bang on."

Excellent. But didn't Vine have a point? Where are TV's ugly presenters? Doubtless in some BBC Television Centre holding pen, poor hideous brutes. Would Patrick Moore have been given air time in a TV culture that privileges lookers over thinkers?

"I guess my answer is what you're looking for is someone people want to watch. It's the same for actors. It's not all about looks. If you look at the BBC's science output now it's all middle-aged academics – Marcus du Sautoy, Alice Roberts, Ian Stewart, Jim Al-Khalili, me. It's not like we're Take That."

Casting Professor Cox as a boyband member, though fun, is wrong. He played keyboards for Dare in the 80s and for D:Ream in the 90s, but his rock'n'roll years are long over.

What happened? Picture the scene: it's Manchester in the early 90s, probably raining. A physics undergraduate who only got a D in A-level maths and used to enjoy bus-spotting, is presented with an unimaginably glamorous offer – to tour sunny Australia with a band with a misplaced colon in its name. "It was a really exciting prospect. But I decided I needed to concentrate on my studies."

It was a Damascene moment: down one path lay sex, drugs and rock'n'roll; down the other, gluons, muons and the quest to find the hypothesised Higgs boson particle. He chose the latter. Why? "Physics excited me more. I felt so energised by the process of learning – the intensity of learning – you don't get that very often." He looks wistful: "Actually, I'm trying to get space to get that feeling back. I like going on learning curves and doing TV has given me that but nothing's been as thrilling as the intensity of learning physics."

In 1997, one of his last performances with D:Ream was at Labour's election night party at the Royal Festival Hall. Their song Things Can Only Get Better had been co-opted as the Blairite anthem. "It became a hit again as a result, but I don't think I got any money."

Were you a New Labour supporter? "No, I wasn't politicised. I've never been party political. I only became political in 2007 when Labour was cutting science funding. I got to work in the Particle Physics Action group to fight it. I had a horror of politics then – everybody knew it was wrong to cut science funding, but nobody admitted that they had made a mistake. That's how politics differs from science. In science, you're peer-reviewed into admitting your mistakes. In politics, you don't have to, in fact you have a vested interest in not doing so."

The year after playing for dad-dancing New Labourites, Cox got his PhD in high-energy particle physics at Manchester. He became a member of the High-Energy Physics group at the University of Manchester and worked on the Atlas experiment at Cern, aimed at investigating basic forces that have shaped our universe since the beginning of time and that will determine its fate. Put that way, it's not hard to see why Cox chose physics over rock'n'roll.

In 2004, he married US blogger and film-maker Gia Milinovich at Cern. They have a son called George, who will be two in May. His middle name is Eagle after the first spacecraft to land on the moon. Two years ago he became professor of particle physics at Manchester, aged only 41.

Between now and September he will collaborate on a book on quantum mechanics and start filming a five-part BBC TV series called The Wonders of Life. It follows his two successful series (the first of which last week earned Cox a Royal Television Society award) and will be a physicist's take on what life is. Didn't David Attenborough's Life on Earth series cover the same ground? "His was a naturalist's perspective; mine goes back to the time when there's an argon content in water and you had living organisms in uranium in rock. It will be about how life was brought about by chemical reaction." Will it be as grandiose as the previous series? "I hope not." We'll see, when the series is screened later next year.

Just before Cox's cab drops me off and he heads to his publisher where he must sign copies of his new book, Cox tells me one of his heroes is physicist Richard Feynman. "He was one of the greatest minds of the 20th century but people always expressed frustration that he didn't concentrate on one thing more. He could have achieved more." Isn't the same true of you? After all, you're doing TV, writing for the Sun, signing books, rather than knuckling down to the hard stuff: understanding the natural laws of the cosmos. "Well, he got a Nobel prize. I won't. I'm not Feynman. I'm not a genius like him!"

The cab pulls away. Inside it, there is someone whose ego is not intergalactically proportioned but, so far as I can judge, more modest.

• This article was amended on 25 March 2011. The original referred to Brian Cox as a fellow of the Royal Society. This has been corrected.