In fact science has no way to have absolute certainty of anything because all its conclusions are falsifiable. For example, when science says phlogiston does not exist, it is not for it to be 100% sure that it does not exist, but because it is more prudent to consider that it does not exist until proven otherwise. The inexistence is the rule and the existence is the exception, and that the existence of phlogiston is not necessary to explain absolutely nothing of the natural world. The same can be said about God, it is a hypothesis to "explain" things of the natural world, but nowadays it is no longer needed. All supernaturalism is unnecessary for science.