Skeptic Michael Shermer writes,
If [advocates of design] eschew all attempts to provide a naturalistic explanation for life, they abandon science altogether. There is no such thing as the supernatural or the paranormal. There is only the natural, the normal, and mysteries we have yet to explain.
Harvard zoologist Richard Lewontin boldly writes,
We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counterintuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is an absolute, for we cannot allow a Divine Foot in the door.
Are we engaging in mysticism when we claim that God could have a “Divine Foot in the door”?
RESPONSE: A number of observations can be made to this objection:
First, if we are going to deny possible supernatural causes, then we are admitting that we are no longer looking for the best explanation. If supernatural causes are ruled out before even looking at the evidence, then we are not looking for the most reasonable explanation. Instead, we are looking for the most reasonable naturalistic explanation. However, if this assumed criterion is false, then it could easily lead to false conclusions. Put another way, by stating, “Science only measures natural causes,” we are eliminating theism by definition –not by the evidence. This is special pleading at its worst.
To illustrate, consider if someone found some magnets on their refrigerator that spelled this: “Honey, I won’t be home for dinner tonight.” Now, imagine if someone said, “There must be some naturalistic explanation for this. The magnets must have assembled themselves together through gravity, chance, or some other natural, cause-and-effect sequence of events.” Of course, it’s easy to see the problem here. While this theory might be the best naturalistic theory, it is obviously not the most plausible theory. In the same way, if we just assume that nothing in our world can be intelligently caused, then we might neglect the most plausible explanation based on our previously ingrained assumptions, rather than the evidence itself. This previously biased assumption could distort our perception of reality. By contrast, there is nothing “spooky” about identifying intelligent causes (e.g. compare Mount Rushmore with the Grand Canyon). Instead, we do this all the time –every day –every hour. If we didn’t do this, we would hardly be able to get through a single day without encountering severe problems.
When investigating our world, our primary question should not be, “Is this the best naturalistic explanation?” Instead, the central question should be, “Is this the true explanation?” Put another way, how do we know that we aren’t excluding the true explanation –simply because of a naturalistic bias? If science has limits in its understanding, which theism can explain, then why wouldn’t we be open to this as a possible explanation?
Unfortunately, even theistic scientists have made this naturalistic assumption, presupposing that God’s work in nature would be so clever that it is undetectable to the scientific method. But, given the fact that the God of the Bible is an active and personal being, why would we ever assume that he would “blend in” with the natural process of cause and effect –especially considering the Scriptural warrant against this (Rom. 1:18-20; Ps. 19:1-4)?
Second, theistic explanations do not disagree with the scientific facts, but instead, they disagree with the interpretation of these facts. Scientific arguments for God’s existence do not distort the scientific data; instead, they suggest a Cause for the scientific data. Put another way, theists should be able to use the agreed upon scientific data to form a philosophical argument for the existence of God. In this way, theists are not engaging in “creation science,” by manipulating the data to fit their view. Instead, they are appealing to agreed upon scientific facts to affirm philosophical arguments for the existence of God. In this way, these arguments are not engaging in physics; they are engaging in metaphysics.
Third, atheists offer philosophical explanations for scientific facts, as well. For instance, in his book The God Delusion, Richard Dawkins offers the anthropic principle, as an explanation for the origin of life. But notice, this is not a scientific explanation for the origin of life; it is a philosophical one. Therefore, both naturalists and theists are trying to explain these “gaps” with philosophical explanations. For this reason, we might charge that men like Dawkins are creating “naturalism of the gaps” arguments. He is not making a scientific statement about science; instead, he is making a philosophical assumption to explain the scientific data.
Fourth, there is a difference between a reasonable supernatural explanation and an unreasonable supernatural explanation. Some naturalists argue, “If you allow supernatural explanations for scientific phenomena, then you will be opening up the door for explanations like fairies, unicorns, or anything else! We should keep this door shut to avoid nonsense like this!” However, there is a difference between a possible explanation and a probable one. By inferring a supernatural explanation, we are not opening the door for any explanation; instead, we are opening the door for a plausible or reasonable one.
In the same way, if we allow a naturalistic explanation for lung cancer, we will not accept any naturalistic explanation for lung cancer. Instead, we will only accept a narrow range of reasonable causes (e.g. cigarette smoking, second hand smoke, pollution, etc.). Here, we need to distinguish between the essential and the extra attributes of the cause in question. For instance, if you found someone had broken into your car, you would not know all of the qualities of the thief (e.g. race, gender, etc.). However, you would know the essential attributes (e.g. able to pick a lock, break into a car, turn a key, etc.). In the same way, we shouldn’t necessarily put a face on the cause in question. Instead, we should simply point out the essentialattributes of this cause.
 Shermer, Michael. Why Darwin Matters: The Case against Intelligent Design. New York: Times, 2006. 53.
 Emphasis mine. Richard Lewontin, “Billions and Billions of Demons,” New York Review of Books, January 9, 1997, p.31. Cited in Groothuis, Douglas R. Christian Apologetics: A Comprehensive Case for Biblical Faith. Downers Grove, IL: IVP Academic, 2011. 279.
 Dawkins writes, “The anthropic principle states that, since we are alive, eukaryotic and conscious, our planet has to be one of the intensely rare planets that has bridged all three gaps.” Dawkins, Richard. The God Delusion. Boston: Houghton Mifflin, 2006. 168-169.