This is a response to a post by Frank Turek called WHY ATHEISM MAKES REASON IMPOSSIBLE. I will quote some of what he says for context.
If we are just molecules in motion as atheists assert, then every thought we have is the result of the non-rational laws of physics.
First of all, the molecule is not the smallest unit of reality. Physics also concerns itself with atoms and subatomic particles, not to mention weird stuff like wave/particle duality, quantum entanglement, and the role of the observer in determining the results of observations. So, the idea that atheists say we are just molecules in motion is a misrepresentation of both atheism and what many atheists actually believe. Scientists will readily admit that they do not know all the laws of physics and that the nature of consciousness remains a mystery. And maybe we’ll never crack the secret of consciousness, because, as Alan Watts has put it, this is like the eye trying to see itself. While science does have a better understanding of what isn’t conscious, this does not mean that atheists buy into the idea that everything is just unconscious pin balls bounced around by deterministic laws.
Although I am an atheist, I do not believe that thinking is a purely mechanical process that can be fully described at a level that does not reference thoughts. I can have thoughts about thoughts, which doesn’t make sense if thinking is just an unconscious mechanical process. Furthermore, I am aware of myself being conscious of various ideas and sensory inputs. My direct experience tells me there is more to reality than unconscious mechanics. I know consciousness exists, and I know it can make use of ideas and reasoning, because I have direct experience of that. So, no matter what an incomplete understanding of physics may tell me about the world, I know I’m not simply unconscious molecules bouncing around to something like Newton’s laws of motion.
logic, reason and our scientific ability to understand the orderly world are well explained by a theistic God whose very nature is rational—“in the beginning was the Word” (or rationality) as the opening line of John’s gospel declares.
So, I know I can think. I also know I can direct my thinking along logical lines. I have done lots of logical problem solving, such as math problems, symbolic logic proofs, and computer programming. I know how to frame a problem and use logical methods to come up with a solution. Furthermore, I know that some logical ideas are indisputably true. I understand that a meaningful proposition is either true or false, that no meaningful proposition can be both true and false, and that any particular thing will be identical to itself. This knowledge comes from my understanding of what a meaningful proposition is, what the terms true and false signify, and what identity is. I understand these to not only be indisputably true but necessarily true. When something is necessarily true, it is true no matter what. It is not thanks to anyone making it true that it is true. So, I know for a fact that God cannot be the author of logic. If God exists, God is just as subject to logic as the rest of reality.
Furthermore, the idea that God is in any way responsible for logic throws the utility of logic under the bus. If logic depends upon God, then God is not subject to logic, and it cannot be used to prove the existence of God. Arguments like the Ontological argument, the Cosmological argument, and the Teleological argument all become worthless if we must assume that God is above logic. The underlying presumption behind each of these arguments is that God is subject to logic. That is what allows any of them, if any of them indeed work, to prove that God exists. There can simply be no logical proof of any being who is responsible for creating logic.
Without an ability to think freely, science is lost too. As C. S. Lewis put it, “Unless human reasoning is valid no science can be true,” which would include the science of prominent atheists, Sam Harris, Lawrence Krauss, Richard Dawkins, and everyone else.
Let’s now turn to how the scientific method works. This is not a method of logically deducing facts about the world from mere observation, as if all it depends on is our ability to think straightforwardly. The scientific method is a trial-and-error process. It works through using experiments to rule out incorrect ideas about the world. In general, someone observes the world and forms an hypothesis about how something works. He then thinks of a test that should have one result if the world does work that way and another if it doesn’t. Then he does the test. This is the experiment. Getting the predicted result does not imply that his hypothesis is correct, but getting a different result will rule out that hypothesis. When a hypothesis is ruled out, it can be reformulated and tested again. Through repeated failures of hypotheses, various ideas can be ruled out, and scientists can gain a better understanding of how things work. Remember, this is not some house of cards that can fall apart if someone can somehow debunk freewill. This is a trial-and-error process of repeated reality testing, and it will hold up even if done by people who are not the best or most deliberate of thinkers.
Finally, I’ll mention that I have addressed this same issue before in previous posts. You will find further elaboration on some of the ideas in this post in these posts: