Naturalism faces a significant philosophical hurdle in attempting to establish the idea that everything—including human beings—is nothing more than physical matter. Man, therefore would be the equivalent of a biological computer. In order for Naturalism to be firmly established, everything about mankind must be explained by physical terms such as explaining the components of a car, or say how the components of Microsoft Windows operate. In defense of the naturalistic position, philosopher Daniel Dennett writes, “Our brains are made of neurons, and nothing else.” Steven Pinker writes, “…every aspect of our mental lives depends entirely on physiological events in the tissues of the brain.” In summation, Dennett and Pinker are clearly stating that emotions, thoughts, and even moral perceptions are rooted in this biological machine.
The difficulty of their proposition is that in a dogmatic sense of the Naturalistic view, the proposition is self-refuting. C.S. Lewis argues, “If my mental processes are determined wholly by the motions of atoms in my brain, I have no reason to suppose that my beliefs are true…and hence I have no reason for supposing my brain to be composed of atoms. It discredits our processes of reasoning or at least reduces their credit to such a humble level that it cannot longer support Naturalism itself.” In addition, humans do not live in such a way that thoughts are considered to be a result of physical processes, but that “most” thoughts have the idea of being valid. The dilemma for the Naturalist is plausibly obvious. Otherwise, we are left with a philosophy which puts the value of human reason in doubt—and if human reason is in doubt, there can be no way to establish it by using reason.  Thus the Naturalist’s argument commits philosophical and intellectual suicide.
Something does however take place inside the brain other than sending messages causing the arms and legs to move, and for the organs to operate efficiently. This must entail that events take place in the brain. Thoughts are a different type of event, which can be proven to be either true or false. Other types of events are not concerned with being true or false, nor are they about any particular thing.  A thought with reference to knowledge pertaining to the operating system of a car is wholly distinct and separate from the car itself. This must entail that there is something beyond atoms in the brain when thoughts or reasoning come about. A perfect example would be to consider a scientific theory. Wendell Berry comments, “At the root of the word, ‘theory’, is the word ‘theatre’; it has to do with watching, with observation. A scientific theory is an aid to observation.” The theory in and of itself cannot be explained by any type of physical process because it is a nonphysical theory about a physical object. In conjunction, Norman Geisler gives the following illustration: “A physics professor was once asked; ‘If everything is matter, then what is a scientific theory?’ His response was, ‘It is magic!’ When asked his basis for believing that, he replied, ‘Faith!’” When humans have thoughts or use the ability to reason, there must be something beyond physical matter, which cannot be measured or explained by physical processes.
However, Naturalists will attempt to challenge this notion. The best argument in support of their theory is how humans correlate with matter using the five senses. They further argue based on the effects of alcohol, exhaustion, and a harsh hit to the head. Alcohol can inhibit one’s ability to think. Navy Seals, undergoing Bud’s Training (also known as Hell Week), have been known to hallucinate due to the fact they stay awake for five consecutive days. Receiving a hard blow to the head will sometimes produce a state of unconsciousness. Mental diseases can produce one to lose the capacity to think clearly, and inhibit their physical abilities.
This argument however, can be dealt with in a reasonable and concise manner. CS Lewis argues that their must be a relation due to the fact that humans contain both physical and non-physical attributes. He states, “A man’s Rational thinking is just so much of his share in eternal Reason as the state of his brain allows to be come operative; it represents, so to speak, the bargain struck or the frontier fixed between Reason and Nature at that particular point. A nation’s moral outlook is just so much of its share in eternal Moral Wisdom as its history, economics, etc. lets through. What we call rational thought in a man always involves a state of the brain, in the long run a relation of atoms…and Reason is something more than cerebral biochemistry.”
What may be an even stronger argument against this philosophical view of Naturalism is the notion of morality. Naturalists, such as Richard Dawkins and Steven Pinker perceive morality as something derived from natural selection, in which the primary purpose of natural selection is to endure and reproduce; not to produce morality. This begs the question as to where they obtain the basis for their claim. Dawkins claims that morality is an enduring part of the plan of both survival and reproduction of the genes. This plan is seemingly programmed within the genes. However, if all forms of life come from a common ancestor—as natural selection suggests—how is it that humans differ from other types of species regarding thought and morality? Dr. Frans de Waal, who has meticulously studied chimpanzees writes, “It is hard to believe that animals weigh their own interests against the rights of others, that they develop a vision of the greater good of society, or that they feel lifelong guilt about something that they should not have done.”
Dawkins attempts to defend his claim, in his book The Selfish Gene, when he wrote, “we have the power to turn against our creators. We, alone on earth, can rebel against the tyranny of the selfish replicators…if we understand our own selfish genes are up to…we may then at least have the chance to upset their designs.” How is it possible that morality is not only found within the genes, but that we can turn from them? The Naturalist seems to be delving back into the metaphysical world, which ironically requires a bit of “faith” on his part. Assuming he is correct, why is Dawkins & Co. so concerned with vehemently proclaiming Naturalism if all they do is rebel against it? Perhaps that is a separate issue, but it appears that Dawkins has somewhat cornered himself in espousing the idea that morality can be traced to the genetics of the human body. If he claims morals to be somewhat useful, where is his foundation for knowing for certain? Even Dawkins’ counterpart, Pinker admits, “Human behavior makes the most sense when it is explained in terms of beliefs and desires, not in terms of volts and grams.” Thus in a sense Pinker seems to challenge their own views!
If there is no basis for showing morality comes from the genes, some may appeal to an individual and societal experience. If this is the case then morals must have been learned by the way of an extremely long, historical process by the way of “majority rule”. However, this is insufficient as well for providing a basis for moral conduct. Lewis states, “…until there were thinkers, there was no truth or falsehood.” If there was no truth to begin with, “majority rule” cannot create truth with the passing of time. Only a “truth-claim” can come as a result. Thus there is no foundation for Naturalism to firmly plant its feet.
As a result however, society doesn’t live as if there is no truth concerning morals. Immanuel Kant said that not only is it unacceptable but it is impossible for humans to live as if there is no truth concerning morality. Donald Brown discovered in his work, Human universals, over three hundred standardized patters of conduct, which included many moral beliefs commonly “shared by all cultures.” All people have within themselves moral precepts, which say, “ought to” do something and “not ought to” do something. When people invoke phrases such as these, we actually plead to a standard of human judgment shared by all with is outside of ourselves. Lewis states, “The moment you say that one set of moral ideas can be better than another, you are, in fact, measuring them both by a standard, saying that one of them conforms to that standard more nearly than the other. But the standard that measures two things is something different from either. You are in fact, comparing them both with some Real Morality, admitting that there is such a thing as real Right, independent of what people think, and is some people’s ideas get nearer to that real Right than others. Or put it this way. If your moral ideas can be truer, and those of the Nazis less true, there must be something—some Real Morality—for them to be true about.”
If there is a “Real Right” and a “Real Morality” then both must have come from a “Real Something.” This “Something” cannot be based on genetics, nor can it be based on some type of learned historical process in which the majority rules. This “Something” cannot be concretely established via scientific or natural methods, therefore the source must have a supernatural origin; and if there is a supernatural origin, the ancient Biblical writer stated correctly when he said that the law must have been written on the hearts of people. Thus Naturalism has failed and is insufficient in providing a philosophical foundation for human behavior.
Naturalism faces yet another significant hurdle based on a probability standpoint. Probability is used in all aspects of life. Meteorologists use it to predict the weather. Businessmen use probability in dealing with the stock market. It is also used in the realm of science. Former Yale professor of biophysics, Harold Morowitz, said, “Randomness itself displays certain properties which have been turned into powerful tools in the study of behavior and atoms.” Randomness is dealt with by probability and therefore can shed some light on the subject of Naturalism.
Dr. Emile Borel is credited with formulating what mathematicians refer to as the “law of probability.” This law of probability states that if any event occurs where the chances are beyond one in one followed by 50 zeroes, that event—can be stated with certainty—will never take place; regardless of how much time is allowed and the number of possible opportunities could exist in order for the event to take place. The question then is what is the probability that Naturalism could be true regarding the origin and maintaining of life as we know it? There are an abundant amount of factors to consider if this is a probabilistic and logically acceptable.
Morowitz estimated the chance of life developing from a “simple living organism” is one part in 1x10^340,000,000 This number far surpasses the “upper limit” fifty that Borel established in his law of probability. It is so enormous that the mind can hardly fathom it. What’s even more amazing is that there also must be a vast number of factors concerning the universe for even the simplest living organism to exist!
One example would be to consider the number of electrons in the universe. Ross shows that this number must equal the number of protons to an accuracy of one part in 10^37 or better. If the accuracy was off the mark even by an extremely small factor, then electromagnetic forces involved would prevail over gravity. The results would be that galaxies, stars, or planets would not have been created; therefore no life would exist. In order to understand this more clearly, he gives the following example: “Cover the entire North American continent in dimes, all the way up to the moon, a height of about 239,000 miles. Next, pile dimes from here to the moon on a million other continents the same size as North America. Paint one dime red and mix it into the billions of piles of dimes. Blindfold a friend and ask him to pick out one dime. The odds he will pick the red dime are 10^37th power.”
The example above is one out of about 128 parameters Hugh Ross gives in order for life to exist on any give planet such as earth. Considering that there are billions upon billions of stars in the universe, the probability—based on a naturalistic viewpoint—that a planet such as earth would be able to sustain life would be 1 x 10^-144th power. This number turns out to be one in a trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion, trillion. Ross comments that one would have a better chance of being killed by a sudden reversal of the 2nd law of thermodynamics. Probabilistically, it stands to reason that Naturalism is beyond the scope of ever achieving mathematical certainty. The evidence is completely overwhelming. Even Richard Dawkins stated, “The more statistically improbable a thing is, the less we can believe it happened by blind chance. Superficially the obvious alternative to chance is an intelligent Designer."
 Dinesh D’Souza. What’s So Great About Christianity, (Washington D.C., Regnery Publishing, 2007), page 240.
 Dinesh D’Souza. What’s So Great About Christianity, (Washington D.C., Regnery Publishing, 2007), page 241.
 CS Lewis, Miracles, (New York, Harper Collins, edition 2001), page 22.
 CS Lewis, Miracles, (New York, Harper Collins, edition 2001), page 33.
 CS Lewis, Miracles, (New York, Harper Collins, edition 2001), page 25.
 Wendell Berry, Life is a Miracle, (Washington D.C., Counterpoint, 2002), page 18.
 Norman Geisler, Baker’s Encyclopedia of Christian Apologetics, (Grand Rapids, MI: Baker, 1999) pg 522.
CS Lewis, Miracles, (New York, Harper Collins, edition 2001), page 62-63.
 Dinesh D’Souza. What’s So Great About Christianity, (Washington D.C., Regnery Publishing, 2007), page 227.
 Dinesh D’Souza. What’s So Great About Christianity, (Washington D.C., Regnery Publishing, 2007), page 241. “Interesting that Dawkins uses the word, “design.”
 Dinesh D’Souza. What’s So Great About Christianity, (Washington D.C., Regnery Publishing, 2007), page 245. (Immanuel Kant statement taken from the same page).
 CS Lewis, Miracles, (New York, Harper Collins, edition 2001), page 28.
 Dinesh D’Souza. What’s So Great About Christianity, (Washington D.C., Regnery Publishing, 2007), page 230.
 CS Lewis, Mere Christianity, (New York, Simon and Schuster, 1996 edition), page 25.
 Bert Thompson, The Scientific Case for Creation, (Montgomery, Apologetics Press, 1986), page 68.
 Bert Thompson, The Scientific Case for Creation, (Montgomery, Apologetics Press, 1986), page 70.
 Hugh Ross, Creator and the Cosmos, (Colorado Springs, Navpress, 2001), page 150.
 Hugh Ross, Creator and the Cosmos, (Colorado Springs, Navpress, 2001), page 194.
 Bert Thompson, The Scientific Case for Creation, (Montgomery, Apologetics Press, 1986), page 75.