If SF is grounded in hard scientific fact, and science is killing God, then what place does that leave for divine intervention in the pages of SF literature? When I tweeted this question, @MirabilisDave gave Arthur C Clarke's famous dictum a twist, quipping that "Any sufficiently advanced technocrat will be indistinguishable from God."

Roger Zelazny could almost have written Lord of Light in response to this idea. In this classic of 1960s SF a group of human explorers colonise an Earth-like planet. But instead of creating a paradise, the original colonists keep control of their futuristic technology and set themselves up as gods over their fellow man. To mark themselves out they take on the aspects of the Hindu pantheon – Vishnu, Krisha, Kali and many others – and use their power to enslave generations of their own descendants in an enforced agrarian caste system.

But their conceit backfires when rebel colonist Sam sets himself up as the Buddha and, over the course of many lifetimes, makes spiritual and philosophical war against his god-like former colleagues. Zelazny's genius in Lord of Light is to show both how religious ideas can reinforce oppression, and how they offer a route to liberation and spiritual freedom. Religion is a battle ground, and walking away from it only concedes the war to your opponents.

If all technocrats were as charming and witty as the Minds of Iain M Banks's Culture novels, technocracy would be a far less chilling prospect. As @modulux points out, the artificially intelligent supercomputers, with the power to build worlds and govern billions of human lives, are at least "weakly god-like". So lovely are the Minds that they really rather win one over to the idea of a benign power taking over the world. Maybe Apple's Siri will one day take on the job!

That nightmare scenario might read more like Harlan Ellison's I Have No Mouth And I Must Scream. In Ellison's masterpiece of future horror AM, a supercomputer responsible for destroying humankind, tortures the last survivors for eternity, resurrecting them after each death, mutilating their bodies and perverting their minds. AM is the vengeful God we all hope and pray does not exist, and inspired both Terminator's Skynet and the human-hating machines of The Matrix.

Ted Kosmatka's Prophet of Bones is a sci-fi thriller that builds an alternate world from one simple idea: what if creationism had debunked Darwinism and the modern world believed it had existed for only 5,800 years? As a child Paul Carson researches evolution in mice, an experience which opens his mind to the scientific discovery that will help him bring scientific truth back to the world. But he is up against a conspiracy of silence that has kept that truth from the world for centuries.

Kosmatka's chilling high concept is grounded in the fact that our society lived in ignorance of evolution for centuries, when the evidence of it was right there for us to find at any time. New ideas always disrupt old ones, and the powers who benefit from the old ideas, be they the church or other institutions, never welcome the change. It raises the question of what ideas we are ignoring or repressing right now that could transform our understanding of life and the universe as profoundly as Darwin's theory of evolution.

Science fiction has always been a place where weird, disruptive and sometimes downright dangerous ideas have been allowed to express themselves. If there's one thing SF writers like to do, it's argue. Tell them God is good and they'll prove why he doesn't exist. Show them there is no God, and they'll invent one just to to prove you wrong. Science fiction isn't so much about science as it is about the quest for new ideas that will smash apart the old ones. That's why the best SF is always outside the mainstream. If it was winning literary awards, that would only prove it wasn't really doing its job.