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Is it just me or has the dialogue between science and religion become a bit stale? I thought as much recently while taking part in a conference on the debate. We were all so well defended in our respective corners – atheists, believers, agnostics. It seemed highly unlikely that what anyone said would seriously unsettle anyone else.

The smart and articulate apologists for theism were easily able to accommodate the challenges materialist science throws at faith. The smart and articulate atheists seemed content to accept the limits of the scientific worldview and not really be challenged by the insights of theology.

Something similar troubled me when I was asked to write The Big Questions: God for the series from Quercus (and indulge me if I add, out this week). Many of the contemporary big questions in theology arise from the impact of modern science, so could I find anything new to say? Well, I did find some new names to read, and while not often cited, I think they might yet find that their time will come.

One was the great German polymath Johann Wolfgang von Goethe. His place in the history of science is secure, having discovered that human beings possess an intermaxillary bone. Animals had long been known to possess this anatomical feature of the jaw. But in Goethe's day, there was a lively science-and-religion-type dispute as to whether human beings did too. The leading anatomist Petrus Camper denied it and further argued that this demonstrated that human beings were different from animals. Eventually, though, Goethe's research won the day.

It proved to be no trivial discovery but inspired the concept of homology, the study of anatomical features across different species. This proved crucial for Darwin's theory of evolution by natural selection. We have four limbs because our fish ancestors had four fins, and so on. What is interesting to reflect on now, though, is the means by which Goethe did his science.

His trouble with Camper alerted him to fashions in science – fashions that scientists find difficult to shake off because their reputations are likely to have been secured by those fashions. He was also convinced that good science embraces a subjective as well as objective dimension. This is because what scientists see in the natural world depends upon what they are prepared to contemplate seeing. He was prepared to contemplate the human intermaxillary bone. It demonstrated to him that imagination matters as much as investigation.

By imagination, Goethe meant something more than practical ingenuity or empirical creativity. He meant the capacity to discern the living world in all its aspects. Materialism, for example, does not. It treats the living world as a dead mechanism.

Annie Dillard explores the implications in her essay Teaching a Stone to Talk. She describes a man called Larry who is trying to listen to stones speaking. It seems mad but, Dillard asks, is not that hope what secretly drives the scientific impulse? Meteorologists record the wind's speed, but were they drawn to science because once they also heard the wind's cry? Geologists assess the age of stones, but do they sometimes also hear them "shout forth praise"? "What is the difference between a cathedral and a physics lab?" asks Dillard. "Are they not both saying: Hello?"

Popular science routinely trades on this sense of nature's aliveness. If you saw Brian Cox's TV series Wonders of the Universe you may recall how images of the cosmos were accompanied by the rising swell and celebratory trumpets of orchestral music. In fact, the producers received a number of complaints from viewers about the music being too loud. They could not hear Cox explain the hard science as he wistfully gazed heavenwards. And yet, you could be forgiven for concluding that the music was more important. It spoke more loudly and clearly to the meaning of being made of stardust. The music interpreted the physics for us. It made the stones speak. That is the sound we wanted to hear.

Another writer who has explored the power of the imagination in our engagement with the world is Owen Barfield. A philologist, he was fascinated by how words change their meaning over time. Take a word like "literal". Today it means straightforward or on the face of it. But when Saint Augustine, for example, wrote The Literal Meaning of Genesis, the last thing he read was that the world was created in six days. Literal then meant the true meaning, which could only be discerned by struggling with the text, as you might a poem.

The flattening out of the word "literal" is just one instance of a trend that Barfield detected across modern English. He proposed that it is tied up with materialism's mechanistic worldview. It flattens our imagination, thereby also deadening our experience of connection and meaning. Unlike our ancestors, we struggle to hear the stones speak.

Barfield argued that we need to recover our full imaginative capacities if we are deeply to know that the world is alive. Matter, he believed, would then be seen for what it once was, as an expression of spirit. ("Matter" is linked to "mater", or mother, remembered in the expression, mother earth.) This might not be so difficult to achieve because, actually, we experience it every day. When you perceive the matter called a human being speaking, you spontaneously know those perceptions as one person communicating with you, another person. You do not have a theory of other minds, as some philosophers have proposed, driven by a flattening scientistic ideology. We know such matter as spirited people – as souls, you might say.

The paradox that Goethe highlights is that materialism understands itself to be the champion of empiricism, when really it detaches us from the world as we experience it, in the name of objectivity. "All theory, dear friend, is grey," he wrote. "But the golden tree of actual life springs ever green."

Perhaps then, this is the problem with the contemporary dialogue between science and religion. Theology has felt obliged to secure a place for itself broadly within the materialist worldview, sensing its main task is apologetic. But perhaps the time is coming for thinkers to be braver, to push for a truer contemplation of nature, one that knows its aliveness, its spirit. Goethe and Barfield, to name just two, offer rich, imaginative resources.