For example,suppose that the universe was in fact created by a supernatural god as told in some religions. Suppose for the moment that this scenario is the true one. Now, Rejecting the possibility that supernatural explanations are true will lead science to a wrong conclusion about the origin of the universe.
So, adapting a materialistic philosophy can make science deviating from truth. In this case we have two possibilities, the first is to say that the aim of science is not to discover the true nature of things but that it gives us just a possible materialistic model of how things work. The other is to allow the room of metaphysical explanations.
We can give similar scenarios in Biology say in the origin of life or origin of mind and Consciousness.
So, the question is:
How should the scientific method be treated? Is it a mean towards objective truth? or just a materialistic model-builder? Is it necessary that the scientific method exclude supernatural explanations?