Sometimes, ungodly people get science mixed up with Naturalism or with Materialism.  If you run into such a person, you only need to ask them to prove to you, using science, that Naturalism is part of reality.  You need to ask them for the scientific experiments that can be done to prove this.  You need to get all the steps and detail of these experiments. 

Of course, there is no way to prove such irrational claims as Naturalism, Materialism, Atheism, or any such thing.  What you will find is that the Atheist changes the subject, becomes abusive or rude, or goes to some other diversion.  They can’t deal with the question which is basic to all of their beliefs.  If they face the question honestly, their entire paradigm shakes and falls, but they don’t want to acknowledge God.

Naturalism is an arbitrary assumption and is irrational. It is irrational to make arbitrary claims. Followers of Christ speak of their actual experience with Christ. They know Him. There is no place to be irrational in such a thing. And their eye-witness accounts of the goodness of Christ are verified by the millions of Christians who have the same experience.