The first cause
     Naturalism and theism are two opposing philosophies. We cannot prove either one empirically, but we can ask at the philosophical level, which one provides a logical basis for science? Which one justifies the idea of an orderly cosmos?
     Let’s start by identifying a first cause: what Aristotle called the “unmoved mover” and Thomas Aquinas called the “uncaused cause,” something that put the whole shebang into motion. Did the cosmos get itself into motion, or did God do it?
     Bertrand Russell said, “If there can be anything without a cause, it may just as well be the world as God.”  In other words, if the universe had no cause, we wouldn’t need to add anything to the equation. Ockham’s razor would have us go with the simpler explanation.
     Of course, we do need another explanation. The first cause must explain the authority of truth. The first cause is the source of knowledge, the reason for reason, and the basis for science.
     I would also point out that an impersonal object does not act on its own initiative. For example, if you saw a stone fall down a hill, and I asked you why the stone fell, any answer you might give would point to something other than the stone as the cause.
     Because naturalism rejects a final authority, it is relativistic. It treats the laws of nature as ultimately uncaused; things simply happen. Naturalism hides behind a mask of generic terms such as science and reason and inquiry and freethinking, but while it holds these concepts in high esteem, it gives no explanation for any of them being here in the first place.
     What about the human mind? Did an unthinking cosmos give us minds that can discern truth? To gain science, we must trust that the human mind is reliable. With God, we have reason to believe so.
     Where did reason come from? It’s not a human invention. We discovered it, but it exists whether we acknowledge it or not. Did an unthinking cosmos give us a standard for judging our thoughts? Perhaps God would be a better explanation. 
     Some people say that God cannot explain it either, because God might be illogical. Let me explain something. If the laws of logic are authoritative, they reflect an authority. They do not stand above the highest authority and judge whether he is complying with them or not. That wouldn’t be logical.
     Also, note that the laws of logic are not material. They are as intangible as the thoughts and minds that they govern. We wouldn’t have laws in a materialistic world.
     What about the laws of nature? Gravity didn’t depend on Newton’s efforts to figure it out. According to naturalism, the laws of science describe properties inherent in nature; there’s no further explanation. Yet, it seems that there must be an explanation for these laws governing the universe. 
     What about the value of life? Many say that science is neutral in this respect, because science studies the impersonal cosmos. The order of nature does not answer the ultimate questions of value and meaning.
     I would agree that science does not prove the value of life but not that science is neutral to it. The value of life is another concept that is presupposed in order for science to make sense. As with anything else we do, we assume that scientific pursuits are worthy of human effort. The value of life must already be true, and science must be relevant to that truth. Life is worth living before science is worth knowing.    
     Naturalists like to point out that theists have personal motives for believing in God. They say that theists want to feel that they have a special place in the universe. This is true. Theists have personal reasons for their beliefs. That still leaves unanswered the question of why people want to feel valuable. 
     Naturalists also have personal reasons for their beliefs. Many desire a purposeless world so that they can fill the vacuum with their own value and purpose. Without a final authority, they are free to make their own rules. Aldous Huxley said, “I had motives for not wanting the world to have a meaning . . . the philosophy of meaninglessness was essentially an instrument of liberation . . .”  Stephen Jay Gould said, “Once you find out that there is no superior wisdom, no superior cause, it is liberating, if not exhilarating.”  Naturalism and theism both have personal implications.
     Theism does seem to have one weakness regarding science. Doesn’t the concept of miracles interfere with science? Certainly, if God wanted to throw a miracle into our experiments for the fun of confusing us, he could do so (as long as this matches his character). The primary cause has the prerogative to intervene in any manner. Hence, naturalists believe in chance.
     Naturalists insist that they do not believe that everything happens by chance, but let’s think about it. If a cosmos with no preordained purpose happened for no reason, isn’t this chance? Then everything proceeds from this. From the naturalist perspective, any time an event follows the laws of nature, it is essentially a “miracle.”
See details: Bias
* From Russell’s Why I Am Not a Christian. At the time, Russell did not believe the world had a beginning.
In the debate with Greg Bahnsen, Gordon Stein described the laws of logic as human “conventions that are self-verifying.”
Aldous Huxley Ends and Means, pg 270, 1937.
Quoted by Ravi Zacharias in his lecture, Unplugging Truth in a Morally Suicidal Culture.