Does science disprove the existence of God, souls, spirits, and the supernatural? The problem with answering this claim in the affirmative is that science, as it is currently defined, cannot acknowledge any evidence for the supernatural. This is because scientists while doing their scientific work, are told that they must assume supernatural causation does not occur. This view is known as “methodological naturalism” and it prevents scientists from following the evidence wherever it might lead. If any scientist does try to use science to point to the supernatural, it is immediately dismissed as "pseudoscience." What this means is that science is not an unqualified search for truth but rather a search for the best explanation assuming that supernatural causes do not exist and that natural causes are the only causes. But science cannot “prove” what it assumes. For an atheist to use science to disprove the supernatural (i.e. without appreciating the limits of science) is to simply make a circular argument. The philosopher and atheist, Bradley Monton, points this out.
If science really is permanently committed to methodological naturalism, it follows that the aim of science is not generating true theories. Instead, the aim of science would be something like: generating the best theories that can be formulated subject to the restriction that the theories are naturalistic. More and more evidence could come in suggesting that a supernatural being exists, but scientific theories wouldn’t be allowed to acknowledge that possibility.
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Reference
Bradley John Monton, Seeking God in Science: An Atheist Defends Intelligent Design (Peterborough, Ont: Broadview Press, 2009), 58.