The Limits of Science
Science is a way of knowing about the natural world. It is limited to explaining the natural world through natural causes. Science can say nothing about the supernatural. Whether God exists or not is a question about which science is neutral.
(US National Academy of Science).
Thus, the correct position for the skeptic who appeals to science is agnosticism. Atheism is a faith-based belief system decided ultimately on other grounds – psychological, emotional, existential. It is a presupposition brought to the table by those who hide behind scientific rationalism as an excuse for their atheism.