The Influence of Christian Theology
Methodological naturalism is a convention that has been around really only since the late 19th century. Science actually got started in a very explicitly theistic—indeed Christian—milieu. The period of time that historians call the Scientific Revolution is roughly 1300 to 1700. There’s debate about when it actually started and how much the Protestants versus Catholics were responsible, but clearly theological ideas—Christian theological ideas—had a huge in the formation and foundation of modern science.
One of those key ideas was the idea of intelligibility: that nature is intelligible. There’s an order and design that can be understood and discerned by the scientist because nature is the product of a rational mind, namely the mind of God, and that that same mind or creator who made nature with that rational order built into it made us and our reason, so that we could perceive and understand the reason that he built into nature. That was what gave people confidence to do the hard work of investigation to figure out the hidden order, the design that is beneath the appearances of natural phenomenon.
Since the order in nature is contingent on the act of the Creator, we have to go and look and see what kind of order he put into it.

The Order of Nature
The first thing to say is that science did not arise because of a set of naturalistic presuppositions. It actually arose because of a conviction that there was a lawful order in nature, that human beings could discern and understand it because they’d been made in the image of the creator of that order, and that also they needed to go investigate. While they might expect that there’s a rational order there (the Greeks believe the same), they also knew the rational order was contingent on the choice of the creator.
This was a product of recovering the doctrine of creation in the late Middle Ages. Since the order in nature is contingent on the act of the Creator, we have to go and look and see what kind of order he put into it. We can’t just simply sit in our armchairs and deduce it from logical first principles.

The Greeks and ptolemaic astronomy were a good example of this. They figured that since the most perfect form of motion is a circle, and since the planets are in a heavenly realm, they must be inscribing circular orbits. But, in fact, they were doing ellipses.
So the early modern scientists broke with the ancient Greeks and said since nature is created by God and he could have done otherwise, we need to go and find out not what he must have done, as Robert Boyle said, but what he did do—which means empirical investigation. You’ve got to look and see.

There were a number of ways in which Christianity gave rise to modern science, and the idea that a set of naturalistic assumptions is necessary to do science is just historically false.
Stephen Meyer (PhD, University of Cambridge) is the director of the Discovery Institute’s Center of Science and Culture.