Science assumes that things can be understood because they operate according to rules, resulting in predictable and testable outcomes. However, a philosophy of science that excludes God introduces an assumption that some things, at least, and fundamental things, in particular, happen by chance, and are, therefore, neither predictable nor testable.
This results in an atheism (or a theism which assumes that God is not relevant, i. e., deism) that depends for its rational basis on holding two mutually-exclusive presuppositions simultaneously. That is, to use the terminology of logic, it holds "A" and "not-A" together, in violation of the Law of Non-Contradiction. This basic law of logic says simply that a premise and its contrary cannot both be true at the same time.
In contrast, positing God as the origin, not chance, provides the basis of rationality on which science depends. It is the biblical God who testifies that it is "in Him [that] we live and move and have our being" (Acts 17:28). It is His a priori rationality that gives order and comprehensibility to all other things: "He is before all things, and in Him all things hold together" (Colossians 1:17).
In other words, the logic of science requires, not the exclusion of the concept of God, but rather the assumption of the biblical God. When scientists perform their research or their experiments, they are assuming the very rationality of God, while repudiating it in their conscious statements. In fact, that is the only way that science can function, by acting on principles that it denies, while advocating principles which undermine its very existence.
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