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It's not that science actively avoids explanation involving God--it's that science is only looking at theories that are potentially confirmable through observation. The judge seems to get confused in the distinction between these two points--he equates 'natural' with 'testable' and 'supernatural' with 'untestable.'
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There's no confusion. Supernatural things ARE untestable. Since supernatural means "not existing in nature or subject to explanation according to natural laws" it cannot be tested. Since it cannot be tested, it is untestable. While I agree that it was bad form (semantics) to phrase it how he did, they're interchangable. In order to create confirmable theories, we must explicitly reject supernatural explanations.