Alain de Botton has reinvigorated the conversation on religion. His new book moves away from the tedious debates of recent years to a more reflective consideration of the role of religion in sustaining values many people share.

Religion as a human phenomenon is too vast, pervasive and complicated to be discussed in simple binary terms of belief and unbelief. The evangelical atheists of the past few years may not be notable for sceptical doubt, but religious practitioners are often quite uncertain in their beliefs. De Botton is writing for the sceptics, whether they belong in any religion or not. It's a welcome shift of focus.

Atheists who aren't bigoted enemies of religion will agree that it has made many positive contributions. They are less likely to accept that they should have a religion of their own – complete with a temple in the City – as de Botton goes on to propose. Establishing atheist places of worship isn't exactly a new idea. As de Botton himself notes, an ambitious programme of atheist church-building was part of the Religion of Humanity, invented by the 19th-century French thinker Auguste Comte.

An obsessive and at times unbalanced personality, Comte – a fervent believer in phrenology, like many atheists at the time – developed an elaborate daily ritual that included tapping the forehead at the points where science had supposedly located the impulses of progress, altruism and order. He also created a "virgin mother of humanity", based on a married woman whom he had fallen in love with. When she died, he appointed her grave a place of pilgrimage.

Such eccentricities were not destined to last, but a number of atheist temples were established – not only in Paris, Comte's base, but in Rio de Janeiro, New York, Liverpool and London, where a church of humanity opened on Lamb's Conduit Street in 1870. In line with Comte's creed, these were temples where disciples could worship the new supreme being – humanity. As far as I know, none of the buildings is used for religious purposes today, though the Brazilian church seems to have been active until some time late in the 20th century.

When he proposes building a temple for unbelievers, de Botton is reinventing a wheel that never really turned. The fad for atheist temples lasted for perhaps 60 years, while places of worship dedicated to something bigger than humanity have been around for many millennia. There is a nice irony here. For all his loony notions, Comte was more intelligent than most of the atheists who came after him. He saw clearly that religion is an enduring human need that cannot be denied. Yet despite the formative influence it had on writers and philosophers such as George Eliot and John Stuart Mill, Comte's religion of humanity disappeared leaving hardly a trace – just a handful of sites, whose history as places of worship practically nobody remembers.

Even if Comte's church was ephemeral, he was right in predicting that religion would not die out. The world is awash with formless religiosity, much of it flowing through non-traditional channels. During most of the last century, politics was the principal vehicle for religion. Communism and the cult of the free market are examples of large, flimsy ideas being turned into articles of faith.

Today, faith is more often channelled through science. Not only the pseudo-science of crop circle enthusiasts and UFO cultists, but genuine advances in science and technology are being used to promote hopes and dreams that are quintessentially religious. People who believe that the human mind can be uploaded into virtual space and so be immune to death are recycling the fantasies of 19th-century spiritualists, who also argued that their beliefs were based on science.

Comte wanted his new religion to be based on science, so the temples of humanity pointed only as far as science could reach. That is why his new church failed. The very idea of a science-based religion is an absurdity. The value of religion is that it points beyond anything that can be known by the methods of science, showing us that a mystery would remain even if everything could be finally explained. The heart of religion isn't belief, but something more like what Keats described as negative capability: "being in uncertainties, mysteries, doubts, without any irritable reaching after fact and reason".

Rather than trying to invent another religion surrogate, open-minded atheists should appreciate the genuine religions that exist already. London is full of sites – churches, synagogues, mosques and other places of worship – that are evocative of something beyond the human world. Better spend the money that is being raised for the new temple on religious buildings that are in disrepair than waste it on a monument to a defunct version of unbelief.