Albemarle Street, just off Piccadilly, was the first street in London to be designated "one-way". This historic moment in 19th-century traffic management was caused, hard though it is to believe in these days of Britain's Got Talent, by the huge popularity of scientific lectures at the Royal Institution, which still occupies No 21. The Christmas lectures in particular - delivering a secular creed at Christianity's primary festival - created such a crush of people and vehicles that one-way traffic proved the only safe response.

With the mumbo-jumbo of alternative medicine nestling into previously sane minds and the garbled nonsense of Intelligent Design inching its way ever closer to British schools, beleaguered rationalists could be forgiven for thinking those days are gone for good. Surprisingly, however, the vanguard of the Enlightenment's fightback includes a small group of young, bright and strangely lo-fi comedians - most of whom will be performing at this year's Edinburgh Fringe - based around an occasional roaming comedy night called the School for Gifted Children.

Last Christmas, the School was behind a series of wilfully secular nights at the Bloomsbury Theatre and the Hammersmith Apollo in London, called Nine Lessons and Nine Carols for Godless People, in which Richard Dawkins, Simon Singh and Dr Ben Goldacre shared the stage with Ricky Gervais, Dara O'Briain, Chris Addison, Mark Thomas, Stewart Lee and Jarvis Cocker, and preached the glories of evolution and the material world - but with the funny.

“The show wasn't an attack on religion," says the stand-up and writer Robin Ince. "Personally, I would like to see a world without religion but the way to do that is not by saying: 'Your book is stupid.' It's better to say, 'Here is something you may not know that shows how this wonderful world could come to be without a creator.'"

Ince is the mastermind behind the School for Gifted Children - for which the scientists first teamed up with comedians in early 2008 - and its literary predecessor, the Book Club. He organises his events in pub basements, arts centres, bookshops, the Museum of London, even the British Library. Ince's regulars read like a Who's Who of new comedy, from Josie Long (an en­thusiastic stand-up who likes to hand-draw her own posters) through Isy Suttie (a sharp-tongued comic-song performer with hints of the young Victoria Wood) to the dark and surreal Danielle Ward, as well as the character comedian Jo Neary, the high-energy sketch troupe Pappy's Fun Club and the erudite Gavin Osborn. Loosely affiliated fellow-travellers include Will Adamsdale, Natalie Haynes, Tim Key and Wil Hodgson as well as the older hands Mark Thomas, Dave Gorman and Stewart Lee.

“I was excited when these younger comedians came along, as I'd be on bills where I just didn't fit," Lee says. "When I started on the circuit, there were all sorts of weirdos, but after Baddiel and Skinner and the new lad thing it became very homogenised. But seeing people like Josie, Will and Danielle, it seemed more like it was 20 years ago, when there were more weirdos about."

Lee's new weirdos deliver material ranging from the explicitly political through to the quirky and offbeat. Josie Long, for instance, recently curated a week at the Battersea Arts Centre in London with new comedians such as Hatty Ashdown and Sara Pascoe as well as short films and cupcake-making, while her own show, All of the Planet's Wonders, combined history, astronomy and anthropology.

“When alternative comedy started, it was about, well, being alternative," Ward says. "Since then, it's become an industry where, if you have 20 minutes of observational comedy, you can just work the chain-store comedy clubs every weekend - it's like comedy as a trade. We're reacting against the likes of Jongleurs clubs where innovative, weird stuff is actively discouraged. We're all trying to put a little bit of theatre into what we do, trying to say and do things in ways they haven't been done before."

Unlike the work of the early alternative comics, there is very little explicit bashing of politicians and very few ideological gags. Instead, there's
a joyous celebration of emotion and ideas. All share an intellectual approach to the world and to comedy itself, unashamedly believing it to be as valid an art form as any other. In part, they've banded together because many established acts found this approach incomprehensible.

“When I started on the circuit," says Suttie, "the reaction I got from many of the comics was: 'This is not your world.' We didn't plan a movement, but it's really important to know there are other people who are more fragile in their comedy - not least so you have someone to ring and ask for help." Ward credits Daniel Kitson with being the inspiration for most of the under-thirties in this new wave. "He's the daddy of this sort of comedy," she says.

Kitson, now 32, who won the Perrier Comedy Award in 2002 with a show attacking corporate sponsorship of comedy, writes plays as well as stand-up, organises his own tours rather than join a management company, and shuns TV, describing Peter Kay's Phoenix Nights - in which Kitson appeared at the start of his career - as "lazy". Many share his reluctance to appear on the small screen; in fact, their material is often too complex and long-winded to make for Fast Show-style sketches or a job as a quick-fire panellist on Mock the Week. Which is why eager comedy fans should trek this summer to Edinburgh, where most of them have hour-long shows, or chase up the School for Gifted Children and its offspring at oddball venues.

The troupe has influence on the mainstream in subtle ways, however. Long wrote for the first two series of the Channel 4 teen drama Skins; Suttie has taken her chair for series three and four, and has a role in Peep Show. Ince, meanwhile, has film scripts and radio shows in development. All of them will be on the road in one form or another this autumn.

And the rationalist pebbles they began to throw two years ago are sending ripples out further and further. Both Ricky Gervais (whom Ince often supports when he plays live) and Eddie Izzard are touring explicitly atheist shows this autumn - Gervais with Science, which previews at Edinburgh, and Izzard with Stripped. Ince is keen to point out that this is not about attacking any particular faith. "There are plenty of religious comics," he says. "It's just that some of us are intrigued by the ideas of science - we come from the Bertrand Russell point of view: OK, who made God? But we're not picking on Christianity. For one thing, to say that Stephen Green of Christian Voice, who hounded Stewart Lee over Jerry Springer: the Opera, represents Christianity is like saying The Black and White Minstrel Show represents multiculturalism. In a way, it's unfortunate we picked Christmas first. We definitely need to do a rational Ramadan."

Wil Hodgson's "Punk Folk Tales" is at the Pleasance Dome (5-31 August). Danielle Ward's "Lies" is at the Pleasance Courtyard (5-30 August). Robin Ince's "Bleeding Heart Liberal"
is at Medina and Negociants (19-30 August). Stewart Lee's "If You Prefer a Milder Comedian, Please Ask for One" is at the Stand (5-30 August). Ricky Gervais's "Science" is at the Edinburgh Playhouse (25 August)