Steven Pinker is a scientist and public intellectual, provocative, informed and informative. He is resolutely atheist, but not of the 'religion poisons everything' variety; he thinks institutional religion – while based on an entirely false premise – can evolve and be a force for good.

Where he draws the line, however, is the believer's conviction that there is a God who intervenes in the world. Like Scotty from Star Trek, he thinks you cannot change the laws of physics. Even if there were a God, there are no miracles: the world is as it is, and that's that.

And in an interview with Hugh Hewitt for MSNBC, one of the arguments he puts forward to justify that is the Florida shooting, which he says casts doubt on 'the idea that there is a benevolent shepherd who looks out for human welfare. What was the benevolent shepherd doing in Florida while the teenager was massacring his classmates?'

Earlier he says of his book Enlightenment Now: 'It is not against religion. It is certainly against the belief that God interferes with the laws of the universe and that by praying to him we can make the world better. I think that is a dangerous belief because it's not true. If we want to make the world better, we have to figure out how to do it ourselves.'

There's a challenge here for Christians on two levels. One is his fundamental question about whether God intervenes at all – whether there are miracles. The other is whether the Florida massacre is a knock-down argument in his favour.

Most Christians would answer the first with, 'Of course he does.' The Bible is full of miracles. We pray constantly for people and situations that trouble us, and we wouldn't do it if we didn't think it 'worked'.

But Pinker's line is that the more we find out about the world, the less we need to call on the miraculous to account for what's going on. So is there room for an interventionist God in a scientifically sophisticated world?

One answer comes from Christian scientists like John Polkinghorne and David Wilkinson. The latter – an astrophysicist and principal of St John's College, Durham – wrote a little book called, When I Pray, What Does God Do? in which he addresses this problem.

He says the problem with the idea that the physical world runs on rails and is in principle completely predictable is that it's based on out of date science – a mechanistic, Newtonian view of the world in which cause and effect can be plotted exactly. But that's not how the world works. Quantum theory tells us that the small-scale structure of the world is, as Polkinghorne puts it, 'radically random': 'It is a world that is unpicturable, uncertain, and in which the cause of events cannot be fully specified,' says Wilkinson. There's room for God to act because the system isn't closed; he can push electrons around and alter the course of events in the world without breaking any of the laws of nature. Quantum theory doesn't answer all our questions, Wilkinson says cautiously, but it 'may be one dimension of how God works in the world'.

He also writes about 'chaos theory', another challenge to the idea that the world is predictable. It isn't – most systems are very sensitive to small changes, like the 'butterfly effect' named after meteorologist Edward Lorenz, who asked in 1979, 'Does the flap of a butterfly's wings in Brazil set off a tornado in Texas?'

This means that at the macro level as well as the micro, the idea that the world is fixed and predictable is just wrong, and that arguments against an interventionist God don't work. So, Wilkinson says, chaos might give 'space for God to work in unusual and specific ways within the scientific description of the world'. Again, he quotes John Polkinghorne, who says that chaos means that the world is open to the future: 'This means that we can pray and God responds by working in the openness of a chaotic system.'

It's not outdated and foolish to believe in an interventionist God. But what about Florida? Why, if God can intervene, did he not do so last Wednesday – or yesterday, when Syrian forces bombarded Eastern Ghouta and killed 100 civilians in what's been described as an outbreak of 'hysterical' violence? Or when Myanmar's army murders and drives out hundreds of thousands of Rohingyas, or...?

The truth is that Christians have lived with these questions for the last two millennia. And as Pinker himself showed in his 2014 book The Better Angels of Our Nature: Why Violence Has Declined, those questions were even more urgent in centuries gone by, when Florida-style atrocities and worse were even more frequent. We know why bad things happen: it's because God gives human beings freedom to do them – and freedom to do good things, too. The Florida shooting doesn't mean God doesn't exist, or that if he exists he can't intervene. It means – and this is a hard thing to hear, but it's the only thing a Christian can say – that he has chosen not to.

Pinker's other criticism in his MSNBC interview is that believing God intervenes to make the world a better place means believers won't bother doing it for themselves. 'If we want to cure disease, we have got to come up with antibiotics and vaccines and not prayer. If we want to stave off global warming, we can't assume God won't let terrible things happen,' he says.

Of course, it's a straw man argument. Christianity has encouraged scientific progress (it's the Christian belief that the world is ordered and rational that was to lead to science replacing magic) and Christians have been in the forefront of medical attempts to cure disease. But that doesn't quite let Christians off the hook: the best answer to such criticisms is to prove that those who criticise Christians for retreating into 'thoughts and prayers' rather actually doing something to change things are wrong.

Can the Florida massacre become a catalyst for changing US gun laws? Perhaps – and if, alongside costly personal ministry to survivors and their families, Christians can become lead voices in challenging a toxic firearms culture, that might be a better answer to Steven Pinker than reams of intellectual argument.

Mark Woods is the author of Does the Bible really say that? Challenging our assumptions in the light of Scripture (Lion, £8.99). Follow him on Twitter: @RevMarkWoods