One of the ground rules of science, espoused by agencies such as the National Academy of Sciences, is that scientists cannot appeal to any supernatural causes in their scientific work. This is often presented as one of the key distinguishing factors between science and pseudoscience – a rule known as “methodological naturalism.” While this principle may (or may not) be valid, it means that scientists are not allowed to follow the evidence wherever it leads. That is, if the evidence pointed to a supernatural cause (such as God), scientists would not be allowed to acknowledge that. This is an important fact to keep in mind when atheists point to science as proof of their worldview. What these atheists fail to realize is that if science is not allowed to consider God, it is illegitimate to use it to prove that which has been assumed from the outset. To do so is to engage in circular reasoning.
Some atheists recognize this problem and are lobbying for change. For example, the atheist-physicist, Dr. Sean Carroll, wants to see the scientific community reject methodological naturalism. In his opinion, science should be a search for truth that is free of constraints.
Science should be interested in determining the truth, whatever the truth may be—natural, supernatural, or otherwise. This stance known as methodological naturalism, while deployed with the best of intentions by supporters of science, amounts to assuming part of the answer ahead of time. If finding truth is our goal, that is just about the biggest mistake we can make.
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Reference
Sean M. Carroll, The Big Picture: On the Origins of Life, Meaning, and the Universe Itself, Reprint ed. (New York: Dutton, 2017), 133.