Since people can learn about Darwin and still believe that God created them, I am sure they can go on believing in God whatever science finds out about human nature. So I am not as optimistic as Colin Blakemore.

As the giant combine harvester of science continues to round up the mousy believers in God, they will always find a way out – so, to stretch Colin's delightful metaphor, they will sprout wings, dig tunnels, or get crunched to bits by whirring blades and still come out squeaking "God did all this for a purpose, to test our faith, and we are stronger for it."

Leaving metaphors aside, determined believers may claim that God designed our brains to look as though natural selection designed them for religious belief; that God, not natural selection, made us social creatures; and that God endowed us with altruism and kindness.

Among the last defences, as Blakemore realises, are those central human capacities of consciousness and free will. Surely God gave them to humans (and to humans alone?) so that they could freely choose between good and evil, didn't he?

Well no. As Blakemore implies, the latest scientific theories suggest that both are more akin to visual illustions than powerful forces.

How can this be? It certainly feels as though I am conscious; as though I am some kind of inner self who looks out through my eyes at the world around me, and inhabits my body like a driver inside a magnificent machine that does my bidding by the power of thought. But this feeling is completely misleading. When neuroscientists look inside brains they do not find what Dan Dennett calls the Cartesian Theatre – that magical place where decisions are made and consciousness happens. There is no such place. The brain is simply not organised that way. Instead there are multiple parallel processes going on, no central headquarters, and no place where a self could lurk even if there were one.

For example, if a flying field mouse suddenly heads your way, you will probably either duck or catch it deftly. These actions have to be fast, so they are coordinated by one part of the visual system, the dorsal stream, that completes its job well before the much slower ventral stream whose job it is to work out what that flying object is. Brains are like this. They do lots of things at once.

So why do we feel as though we are having a single stream of conscious experiences? Perhaps it was useful for our past survival to have a false model of ourselves, to attribute our body's actions to an inner self, and to see the world in terms of spiritual forces and non-physical agents, when there are no such things. Perhaps it is possible to give up these illusions by practising watching the mind.

Where I disagree with Blakemore is that these misconceptions are "no more significant than a visual illusion". I think that belief in the illusion of free will is highly significant and becomes more so the more science learns.

For example, our legal system is largely based on belief in free will, which leads us into all kinds of tangles. For example, we accept that people who are too young or mentally disturbed are not responsible for their actions and should not be punished, while everyone else is. But then along comes evidence that, for example, Mr G carries the "murderer gene", or Ms T's kleptomania was caused by pre-natal trauma, or that Mr F couldn't resist the advertisements for sweet foods that made him violent. What do we do? We try to protect the idea of free will, while the possible space for its operation shrinks. The combine harvester comes round again and the terrified field mice squeal "But you can't take away our consciousness and our free will! The world will fall apart, our legal system will be destroyed, all hell will break loose."

Like many naturalists, I say it won't, and it is high time we faced up to the changes we need to make. We can do this personally by practising not thinking in terms of free will. We can do it communally by realising that our legal system can punish wrongdoers not because they could have done otherwise and freely chose to be bad, but because some punishments are effective. Indeed, I believe this approach would be better. Instead of asking how much punishment someone deserves, we should ask what actions we can take to make this person behave better in the future, and others not follow this bad example. More constructive use of prison and other kinds of sentences might even result.

So we should not despair. I am sorry the field mice are so frightened of losing what they hold so dear. I understand why they are, and why many will never give up their beliefs, but we are far better off taking scientific discoveries as our guide and finding out the truth about human nature and its origins.