It is only more recently in history that this 'pragmatic naturalism' has expanded to become an (unjustified) absolute. For Christian reasons, science began by talking about natural causes only, for science was just that - a method for investigating natural causes. In recent years, however, this has been turned on its head so as to claim that science therefore proves that natural causes are the only causes. This is a rather bizarre twist of logic, and only a little examination will show it to be unreasonable. Whether or not naturalism is true, it cannot be proved true by the very activity that pragmatically chooses not to discuss the alternative. The scientific method (as practised by the scientific community) will never 'discover' supernatural causes, since it does not look for them and by definition cannot accept them. This may or may not be a useful way to investigate the universe, but on its current constitution that is how science investigates the universe. A theory that incorporates supernatural intervention is, on current widely-accepted understanding not a scientific theory.
- p40, Unnatural Enemies by Kirsten Birkett (italics original)
That modern science came from Christians intending to discover the natural laws that God had woven into the world is indisputable. In order to discover the natural laws, they had to take on a pragmatic naturalism, that is, to leave out the discussion of all supernatural or spiritual explanations outside the labs in order to to focus on the natural causes, not implying that natural causes are the only causes in this universe.
Take heart scientists who are Christians, excel at what you do, for you are not and never will be discovering something that will explain away God's truth or His own existence. Only, remember to be steadfast and resist temptations to bend truths somehow to prove or support what you believe about God.