When John K Clark entered the department of murals and stained glass at Glasgow School of Art, he had no intention of studying the 1,000-year-old craft of stained glass painting.

As a teenager he was dedicated to mosaics. Were it not for the encouragement of his mentor and teacher Alfredo Avella, he might never have taken up the profession that has made his name and brought colour and coruscation to some of the country's most famous panes of glass.

“I started out working in tile mosaic and even started cutting stone,” he says, recalling his days as a student in the late 1970s. “Alfredo told me I should try stained glass. It didn’t really appeal to me, but when I cut the glass for the first time I thought, ‘Oh, hold on, that’s really nice’.

It also helped that there was money to be made in stained glass. “I did a small stained glass piece to start off,” says Clark. “My second piece was actually a commission. When I made the third window it sold immediately, and this was before the end of my second year. My degree piece, Bird in Flight, is in Kelvingrove Art Gallery and Museum.”

His latest windows were commissioned by Colin Beattie, the owner of Oran Mor, the entertainment venue in the west end of Glasgow that was formerly Kelvinside Parish Church, as a tribute to the Dunbar conservationist John Muir. They were shipped from Clark’s studio near Frankfurt in Germany, where he makes all his glasswork with the assistance of a team of specialist stained glass artists. It’s quite a hike, but a necessary one — there is no similar facility in Scotland.

Beattie has filled Oran Mor with art in addition to Clark’s windows. Alasdair Gray has painted a mural on the ceiling and there are works on display by Sheila Tandy, a sculptor.

Clark knew little about Muir until he was given the job, but was soon up to speed with the life and writings of the eccentric naturalist, who devoted his life to the preservation of the wild lands of California and in 1892 founded the Sierra Club, still one of America’s leading conservation organisations. The stained glass windows have been placed in the Oran Mor restaurant, which has been renamed the John Muir room in his honour.

“I am often astonished by the depth of my ignorance at the beginning of a project,” says Clark. “First I agree to do it and then I go and find out what it’s all about.”

Beattie, a keen conservationist himself, is a fan of Muir. He has donated money to the trust set up in his name and taken a pilgrimage to his birthplace in Dunbar. However, he stayed out of the creative process.

“Colin just told me to do what I wanted with the project, which was brilliant,” says Clark. The room features a quotation by Muir written in glass. It reads, in part: “How infinitely superior to our physical senses are those of the mind . . . The Sierra canyons are full of avalanche debris — we hear them boom again, and we read the past sounds from present conditions. Again we hear the earthquake rock-falls. Imagination is usually regarded as a synonym for the unreal. Yet is true imagination healthful and real, no more likely to mislead than the coarse senses. Indeed, the power of imagination makes us infinite.”

An admirer of the philosophies of the American transcendentalists Emerson and Thoreau, Muir’s writings strongly influenced the formation of the modern environmental movement. The four windows, reminiscent of the tall mountain peaks of the Sierra Nevada, are inspired by the quotation.

“The John Muir windows are the first time I’ve used an abstract approach,” says Clark. “Although they are nominally based on landscapes, they are completely abstract landscapes. They have a sense of the landscape he described — the high mountains, the layers of the plains and the glaciated mountain lakes. These were the qualities I wanted to evoke. His was fantastically lyrical, poetical language. It was a case of using an appropriate quotation that made sense of the abstract landscapes.”

The John Muir windows are only half the story. On the stone path at the bottom of the steps outside Oran Mor, Clark has created a mosaic called Wee Folk Dancing, a motif of a group of Scottish dancers seen from above. The piece is a labour of love for Clark and he plans to let more dancing figures loose around the city. The idea originated with a small roundel for the Piping Centre in Glasgow, made in 1997, showing a stick figure version of a dashing white sergeant dance. More than a decade later, the wee folk are finally dancing a more expansive jig. A third mural, for St Andrews in the Square, is currently awaiting planning permission, but Clark won’t stop there. He has met with Steven Purcell, the leader of Glasgow city council, with a view to working on other sites around the city.

“I have always loved the idea of making a large dance in the middle of George Square, but I think the city has other plans for that location,” he says. “I would love to see the idea spreading through the city creating trails of one or two dancers, making small groups of several dancers at important buildings and some complete dances like the eightsome reel or strip the willow. The works should have the feeling of a ceilidh and not just a series of illustrations.”

Clark, originally from Dumbarton, prefers to think of himself as an anonymous artist and, to many, his work will be more familiar than his name. Take the majestic Millennium Window in Glasgow cathedral or Flock of Fishes in Cafe Gandolfi, instantly recognisable to anybody who has spent a pleasant afternoon swathed in the blue-green light it casts in one of the city’s most famous restaurants.

In 1991 he created the Lockerbie Memorial Window in Lockerbie’s Lesser Town Hall to commemorate the victims of the 1988 Pan Am air disaster. He has also designed a window for the chapel at Pangbourne College in Berkshire that commemorates those who died during the Falklands war. In Glasgow, his most famous commission so far has been a series of windows for the Queen’s Park synagogue. It was a project dear to Clark’s heart and he was “devastated” when the synagogue closed down and the windows were moved to Giffnock synagogue in 2005.

“I had a key for that building,” he says ruefully. “I could go in any time I wanted. I’ve never had a relationship like that with a building where I’ve created art. It felt like the building was mine. It was such a wrench.”

Though Glasgow is where he takes his inspiration, Clark spends most of his time in Germany at the Derix Glass Studio near Wiesbaden, one of the leading stained glass workshops in the world. Germany is where it’s at in stained glass, but even there Clark has noticed the craft is experiencing something of a slump.

“It’s a funny time for stained glass,” says Clark, who says he only works in the medium when a commission he likes comes along. “Over the last few years it’s been done as cheaply as possible. I’m not really sure why, but I have a sense that people aren’t willing to invest in it. When you create a piece of stained glass for a building it’s with a view to it being there for hundreds of years. I have a sneaky feeling that people aren’t looking that far ahead any more. It’s not part of the zeitgeist at the moment.”

Clark uses traditional methods where possible. He is wary of more contemporary, time-saving techniques such as enamelling or using Photoshop images that are screen-printed straight onto glass. New technology is all very well, but it lacks the purity and beauty of mouth-blown glass.

“In the past, whenever enamelling has taken the upper hand in stained glass, the art form goes into serious decline,” he says.

Clark’s expertise is indispensable. If the craft is to survive for another millennium it will need artists like him to preserve its traditions.