The richness of life, the complexity of our DNA, and the universe at large attest to the majesty of our God who created it all. I am in full agreement with the concept of intelligent design insofar as God designed the universe and everything in it for His glory. The problem with this term, particularly when it is capitalized, is that it is used exclusively by pseudoscientific organizations, primarily the Discovery Institute, who leave no room for those who accept that God used biological evolution to accomplish the creation of the diversity of life. It’s clear that Intelligent Design (ID) can be supported as a science only if the definition of science itself is changed to include the supernatural. And this has been the Discovery Institute’s goal all along, as described in their “wedge” strategy document. They want to redefine science from the current definition to include metaphysics and spiritualism. In the famous Kitzmiller vs. Dover School District trial in 2005, long-time Intelligent Design proponent Michael Behe was sent by the Discovery Institute as an expert witness for their side in a bid to include an Intelligent Design textbook in the district’s science curriculum. Under oath, Dr. Behe admitted that by using the Discovery Institute’s definition of science, astrology would also be classified as a science. Judge Jones is a Christian, appointed by George W. Bush, and he sided with the parents who wanted an honest science education for their children, and against the school district’s use of the textbook.
Science uses the practice of methodological naturalism, and the very first scientists were known as naturalists. Science does not require or promote acceptance of philosophical naturalism or scientism — a very important distinction. Methodological naturalism means that a scientific theory does not invoke the supernatural in order to explain observations. It doesn’t mean that the supernatural does not exist.
Philosophical naturalism is a completely different concept that has nothing to do with science. It is a philosophy or worldview which states that the supernatural never interacts with nature, or does not exist at all. Someone who holds this view is an atheist, agnostic, or deist. As with any group of people, there are scientists who hold this view and scientists who don’t. However, Christians who accept methodological naturalism as the scientific method should not be confused with people who accept philosophical naturalism. A large percentage of real scientists hold the Christian faith just like anyone else, miracles and all.
Scientism is a recent pejorative term applied to the practice of methodological naturalism when the results it yields are improperly used to support statements that are outside of the realm of science. Understand that it is the rashly made statements that are incorrect, not the methodology of science itself. The most notable example is using the theory of evolution to prove that God does not exist or that the Bible is untrue. This one is a favorite of “evangelical atheist” Richard Dawkins. There are two problems with this: evolution implies neither claim about God or the Bible, and it isn’t the purpose of science to prove anything. If more people — Christians and atheists alike — understood this, our Christian witness to atheists would be much more effective.
Real science is a way of finding the best natural explanation for a phenomenon, past or present. And that is fine. It works very well as a methodology. Science doesn’t presume or declare or assume that there isn’t an intelligence — God — directing the changes that take place within the universe. It simply says that such activity cannot be described by the scientific method. Science requires its theories to be testable (either through direct observation or through forensics) and falsifiable. It doesn’t mean the supernatural doesn’t exist; it just means that the scientific method can have nothing to say about it. Maybe God used supernatural as well as natural methods. Certainly, the creation of the universe and all of the physical laws was a supernatural event, and so was God’s breath of life — Adam’s soul. Of course there is intelligent activity behind these actions, and such activity could only be the supernatural work of God. But what about the biological processes that drive life? Are those supernatural? Does the development of an embryo from a single cell to a baby defy the laws of statistics and thermodynamics? No. How are these biological processes qualitatively different from those of evolution?
Intelligent Design arguments, followed to their conclusion, always depend on a statistical model for some event to not happen “by chance”. The problem is, their reasoning is flawed because they don’t allow for any positive-feedback modifiers in the model. And more to the point, they suggest that we stop looking for them and simply throw up our hands and say “God did it.” The fact that a certain statistical model contradicts something that we see in nature is more likely to indicate a problem with the model than it is to be validated as a rigorous mathematical proof of a divine miracle, or of millions of miracles. As I show in another article, scientists have constructed combinatorial models showing that certain events could not happen in a measurable amount of time, and yet they did happen — events that could eventually be reproduced in the laboratory. It simply shows that making statistical models is a much more difficult part of science to get correct than the actual work of conducting biological and chemical experiments.
In the not-so-distant past, people believed that tornadoes and lightning were divine acts. No explanation could be found for how tornadoes formed. After all, the wind always blows in a certain direction, never in a circle. The basic, demonstrable laws of physics agreed with that. What natural force could possibly cause wind to move in tight circles with such tremendous force? Even the thought of it is ludicrous. Certainly, nothing approaching a tornado had ever been produced by man. No observable experiment could be devised to explain a tornado. “Micro-tornadoes” could be formed, certainly. People could accept that small natural variations in the wind could produce dust devils. But “macro-tornadoes?” Impossible. “The odds of such a thing occurring by chance are so remote that it could never happen within the timescale of the age of the universe, and here is the equation to prove it.” This argument may sound silly, but this is exactly the type of science that “Intelligent Design” reasoning produces. Of course, tornadoes have much less information content than do biological systems, but that is irrelevant to the discussion. The discussion is about the methodology for seeking answers. Without already knowing and trusting the science behind meteorology, Christians who favor an Intelligent Design methodology would be prone to say, “It’s obviously a divine act of God, and Bible verses can be found to support God’s supernatural activity in the weather. Therefore it must be true.” If we had stopped with the Intelligent Design answer hundreds of years ago, we’d still happily believe that weather phenomena were divine acts of God. As Christians, we can understand that the weather or anything else in nature is directed day-by-day, second-by-second by God’s providence. But are they miracles? Certainly not all of them. God may intervene with a miracle from time to time, as recorded in the Bible. But to ascribe a natural process to a miracle simply on the basis of us not understanding every detail of how it occurs is not glorifying God.
The Intelligent Design crowd will say that science, their science, disproves abiogenesis (the origin of life) and evolution (the diversification of life). Let’s be clear — real science does not have any currently workable theory for the origin of the first life and DNA. That being the case, accepting the Intelligent Design argument and to stop looking for natural explanations is not really science. They want to stop science dead in its tracks because they think their answer glorifies God. What if God did use natural mechanisms for the origin of life that we just haven’t discovered yet? We’d never find out if we accept their crude statistical model. By definition, the Intelligent Design argument precludes science because they think they have the answer.
Similar arguments are made for evolution, the diversification of the very first life form (or forms) into the myriad of species that we see today. Not only do they completely dismiss the tremendous volume of evidence which supports evolution and the common ancestry of living things on Earth. But to make this statement, they must include the supernatural in their definition of science. What if we go ahead and ascribe the origin of the first DNA to a miracle. Some number of billions of years after the Big Bang, let’s say God created the DNA ex-nihilo, as He did with the universe itself. The next question is, how did the diversification of the first DNA into modern species happen? Some Intelligent Design proponents say that God preloaded the DNA for all subsequent life forms into that first cell. If so, how was the DNA whose code was not expressed in any given life form preserved in the face of selective pressure? Did genetic variation and natural selection take its course unaltered? If not, what other miracles are needed to support the addition of genetic diversity over the subsequent four billion years of life on Earth? Where does that leave us for further research?
The Discovery Institute’s Phillip Johnson concedes that evolution may occur at stages up to the phylum level (for example, all vertebrates, including fishes, reptiles, and mammals, including man, are part of the same sub-phylum vertebrata.) However, Johnson “does not attempt to argue the question now, because certain crucial work in progress that bears on common ancestry has yet to be published.” . Mr. Johnson is a lawyer, not a scientist. As I don’t wish to misrepresent his position, I will state clearly that he denies the common descent of all life. But he cannot point to any specific weakness in evolutionary theory for explaining the common descent of genera (groups of species) and several higher taxa. Why stop there? If he’s open to evolution at the class, order, family, genus and species levels, is there some point in making an argument that we aren’t related to jellyfish? Since the time of Johnson’s statement, the difficulty of explaining evolution at the phylum level has collapsed due to the sequencing of Hox genes, comparative genomics and other recent advances in developmental biology. His “crucial work” has arrived. The intelligent design proponents’ pseudoscientific and false mathematical arguments fail, time and time again. Intelligent design is not credible as a science. Paul Nelson, senior fellow of the Discovery Institute, wrote in 2004:
“Easily the biggest challenge facing the ID community is to develop a fully-fledged theory of biological design. We don’t have such a theory right now, and that’s a problem. Without a theory, it’s very hard to know where to direct your research focus. Right now, we’ve got a bag of powerful intuitions, and a handful of notions such as ‘irreducible complexity’ and ‘specified complexity’ — but, as yet, no general theory of biological design.” 
Naturalistic explanations are in many cases, fully compatible with theism and, indeed, Christianity.
To those who see an unbridgeable gap between “naturalistic science” and “creation science”: What if… just what if God created natural mechanisms capable of producing the diversity of life that we see? What if He didn’t just go “POOF” and make mankind and other species fully formed?
The intelligent design methodology would never be able to arrive at the answer of how God did it, because it would never ask the question. Whereas the traditional scientific method can go a long way toward discovering these mechanisms. The “creation science” explanation for the diversity of life is, “God did it! Stop looking further!”
A better Christian scientific answer is, “God did it! We’ve seen that created the elements, stars, planets, and other incredible complexity in this universe using natural mechanisms. If He created species in the same way, let’s learn how, and let’s do it with integrity.”
To include metaphysics, spiritualism, and other supernatural philosophies in what we currently practice as science will cause us to disassemble a working methodology that has given us all of the (non-accidental) scientific discoveries made with the past 400 years. If we need to postulate that God had to have jumped in with millions of miracles of speciation just to make His already created order work, how could we possibly apply scientific reasoning? How can we include God as part of the scientific method? Is God testable? Is God falsifiable? Both of these ideas border on blasphemy. I believe in all of the miracles of the Bible, but I don’t think that we should redefine science to include God’s actions of jumping in and “fixing” his creation in order to diversify the species on this planet before Adam was around to even see them. There’s surprisingly little Biblical basis for God definitively creating species individually, and no scientific basis, whatsoever. I think He got it right using the mechanisms of biology and chemistry which He designed. Genesis states that God spoke and caused the earth and the waters to “bring forth” life.
Isaac Newton was a brilliant scientist. Newton is upheld by the Intelligent Design community as a great example of how Christians should engage science because he mentioned God in his book, the Principia Mathematica. But he is also an example of the very problems that become apparent when we use God as a pseudoscientific tool to close a gap caused by our own ignorance. It’s a good lesson for us today. For all his brilliance, Newton made a critical error in reasoning, and that was to apply an “Intelligent Design” answer to a problem he had with gravity. Newton’s laws of motion predicted the orbits of the planets around the Sun. Because he used approximations when calculating the forces of the planets upon each other, he came to the conclusion that the orbits are unstable and would decay after thousands of years. Newton suggested that God occasionally intervened with a miracle, by sending a comet or other object with just the right direction, size, and velocity, to gravitationally nudge the planets back into their correct orbits.
Years after Newton, Pierre Laplace found better methods to solve Newton’s equations, showing that the planetary orbits are indeed stable. When asked by Napoleon, “Monsieur Laplace, why wasn’t the Creator mentioned in your book on celestial mechanics?”, Laplace replied, “Sir, I have no need for that hypothesis.” Laplace was likely an atheist, but we now know that his findings about planetary motion were true. If he were a believer, he could have just as well said, “We don’t need to explicitly invoke God’s miraculous intervention when describing planetary motion.”
In the one area where Newton inserted God’s supernatural action as part of a scientific explanation, he was later shown to be wrong, and to add insult to injury, he was shown up by an atheist. Intelligent Design proponents leave out this detail when they talk about Newton.
I think this is a good lesson for us regarding what methodology to use in discerning the truth about how God created the diversity of life on Earth. I believe in the Intelligent Designer. His design of the universe brought about mankind, made in His image, that we would come to know Him. And He upholds the universe day by day. It is appropriate and productive to discuss Intelligent Design in a philosophy classroom. But Intelligent Design is not a science, and it should not be taught in any science classroom, Christian or otherwise. I believe this movement causes much unneeded confusion and tension between scientific and Christian communities.
Unfortunately, this tension is as much a fault of our Christian community as it is the fault of the “evangelical” atheists. We chide militant atheist scientists such as Richard Dawkins for turning scientific arguments into philosophical arguments disproving God, and as a Christian community we then turn around and turn scientific arguments into philosophical arguments proving God. Both are an abuse of the minds that God has given us. God wants our faith, not scientific proofs of His existence and work. I have more to say about God’s desire for our faith in another article. This is not to say that apologetics overall is an unworthy discipline — far from it. But God’s providential workings in the universe should not be made into a scientific tool, a tool to be used in apologetics like so many others. Even though Newton suggested God’s miraculous intervention as a solution to his problem in celestial mechanics, he never proposed this as a tool to prove God’s existence. Dietrich Bonhoeffer wrote, “A god who let us prove his existence would be an idol.”
In the 13th century, St. Thomas Aquinas wrote that God has given us two books: the book of Scripture, and the book of Nature. God reveals truth in both, but for different purposes. Centuries later, Protestant theologian Jonathan Edwards wrote, “All truth is given by revelation, either general or special, and it must be received by reason. Reason is the God-given means for discovering the truth that God discloses, whether in his world or his Word.” Special revelation is what God has provided to us in the Bible. General revelation is everything else — what God has provided to us within His created order. Through a grounded theology and the witness of the Holy Spirit present in us as believers, we can understand special revelation. Through the painstaking methodology of science, we can understand God’s creation.
When God created the universe and everything in it, He saw that it was good. This is stated not once, but seven times in Genesis, and the seventh indicates that God’s creation was very good. Adam’s fall did not cause the laws of the universe to suddenly become corrupt in such a way that all of the consistent scientific evidence for the age of the universe or of the common ancestry of living things would be planted so as to deceive us. God is not capricious, nor is He capable of deception. The Bible clearly states that God reveals the truth, not a deception, in His creation:
“The heavens declare the glory of God;
the skies proclaim the work of His hands.
Day after day they pour forth speech;
night after night they display knowledge.”
Psalm 19:1-2 (NIV)
I believe that it is impossible for a truth that is revealed in the world (general revelation) to contradict a truth that is revealed in the Bible (special revelation), because truth is an absolute quality. But how do we find the truth? Science by itself will never give us any absolute truth, as it is a self-refining process that can only give us the best explanation available at any given time. The only absolute Truth is Christ Himself as revealed in the gospel message. However, the scientific method is still a worthwhile endeavor to seek out knowledge about God’s creation in a fashion that espouses honesty and integrity. In 1 Timothy 6:20, Paul warns Timothy to “turn away from godless chatter and the opposing ideas of what is falsely called knowledge (Greek gnosis, sometimes translated as science), which some have professed and in so doing have wandered away from the faith.” Almost every creation science organization ascribes this verse to evolution, the Big Bang, and recently, even global warming! Incredible. The modern physical and biological sciences did not exist in Paul’s time. Paul is warning Timothy about the influence of gnosticism on the church, and it still refers to ideas which are falsely called science. That should make us pause to consider where creation science is leading us.
For those Christians who are in (or who desire to enter) scientific fields, we should practice science — real science — and give God the glory for whatever we discover about the universe. There are Christian organizations which espouse honesty and integrity in science. A short list is below in “Online Resources.” And we should know well that whatever we discover is subject to change, for science will never have the ultimate answer or proof of anything. Whatever we find about creation through its methodology, there can be no injury to a true Christian faith. Regardless of how God accomplished His creative work, we can and should give glory to God for creation — and more importantly, for Who He Is, for the nature of our relationship to Him, and for what He does in our lives today. That is the real message of Genesis.
 Johnson, Phillip E., Lamoureux, Denis O. Darwinism Defeated: The Johnson-Lamoureux Debate on Biological Origins. 1999, Regent College Publishing. pp. 49, 118.
 Miller, Kenneth R. Only a Theory: Evolution and the Battle for America’s Soul. 2008, Penguin Books. p. 178