The atheist will explain the whole show of reality (universe/life) as a mechanic would explain the workings of pistons in a car; in terms of mechanisms, laws and principals (leaving aside for now that the engine of the car was designed by a personal intelligent agency). Science to a degree explains how things work in the universe as far as laws, principals and mechanisms are concerned and such an explanation is a wonderful explanation at one level, but the problem I have is when atheists try to interpret EVERYTHING at this one single level of explanation to the exclusion of explanation at a different level. For example when we talk about God the atheist will say that God is not a scientific explanation; but for us God is an explanation at a different level.
God is not in competition with the explanation of mechanisms, laws and principals; God is the explanation of personal agency in regards to the origin of these very mechanisms, laws and principals. How does it work? (The scientific principals) and why does it exist, and what’s behind it? (Personal agency) are not in opposition but complimentary explanations at different levels. So to be forced to exclude one in preference of the other is to be offered nothing more than a reductionist dogma of false alternatives.
For the atheist to merely assert that there was/is no personal agency behind these mechanisms, laws and principals that govern the universe is to be committing the fallacy of argument from omniscience in so far as the atheist CANNOT KNOW that the whole show was not ultimately unguided and undirected. Atheism and science should not be conflated – they are not synonymous. Atheism is a philosophy whereas science attempts to remove philosophy as much as possible from its evaluation of the natural world and its phenomenon (though such a goal is often thwarted when science is removed from its proper context and used as a philosophical tool against theism). The assumption that there isn’t anything outside the system is the mother of all assumptions. There is no way to get outside the present system so there is no way to prove that assumption. You can believe it, but it has to be by faith. It is the presupposition that matter produced consciousness and that the universe and life did not come into existence through God but were the direct result of impersonal mindless haphazard processes that came from nothing and for no particular reason. The philosophical position that grounds atheism is NOT scientific – you cannot prove that the natural world is all that there is. In this regard atheism is not an objective unbiased viewpoint but geared from the very outset to reject any interpretation of reality that does not hold its own viewpoint central and foundational.
*(The underlying idea in this article was not an original thought but was borrowed from physicist John Pokinghorne.)