Exploring the conflict between science and religion
On December 11, 2006, the United States House Committee on Government Reform released a 29-page document titled “Intolerance and Politicization of Science at the Smithsonian: Senior Smithsonian Officials Enable Demotion and Harassment of scientists skeptical of Darwinism”. Evolution.” The skeptical scientist was Richard Sternberg, who authorized the publication of an article (“The Origin of Biological Information and Higher Taxonomic Categories”) defending Stephen Meyer’s Intelligent Design (ID) theory in The Proceedings of the Biological Society of Washington. The article is primarily a review of existing attempts to understand the evolution of protein organization in cells, cells in tissues, tissues in organs, and organs in organisms. At the end of the article, Dr. Meyer suggests that the DI was a better theory than Darwinism.
This was the first time a peer-reviewed journal published an article supporting the identification. The behavior of Smithsonian scientists and administrators toward Dr. Sternberg was deplorable and justifies the subtitle of the Congressional report. Dr. Sternberg and the three peer reviewers probably thought that Meyer’s mention of ID was an unimportant philosophical addendum that did not negatively affect the scientific value of the article.
In the article, Dr. Meyer offers no evidence that an intelligent designer exists. His only argument is that existing “materialist” explanations were deficient. He did not mention that existing theories could improve as more data is collected and the paradigm of natural selection acting on random mutations is improved. Indeed, James Shapiro, an evolutionary biologist at the University of Chicago, has already argued that “natural genetic engineering” will replace the random mutation paradigm in the 21st century.
Dr. Meyer probably knew better than Dr. Sternberg and the three anonymous reviewers that there would be consternation if the article were published. To my knowledge, he did not warn Dr. Sternberg about this because such a disclosure would not have been in his interest.
What this scandal proves is that there is emotional conflict over ID, not rational disagreement. Conflict between people causes anxiety, and anxiety prevents people from thinking rationally and intelligently and from behaving with integrity. Intelligence is usually a measure of how quickly or slowly it takes someone to understand a theory. People have difficulty understanding a theory that threatens their cherished beliefs. When the conflict involves religion, people have blind spots and exercise poor judgment.
The conflict over ID is certainly a conflict over religion. Most ID advocates believe in life after death, and many Darwinists, especially biologists, think this belief is irrational. One of the causes of the conflict over ID is that both sides do not understand the cosmological argument for the existence of God, which is the first of Thomas Aquinas’s five proofs. Aristotle pioneered the concept of the prime mover or unmoved mover, but Etienne Gilson improved on it in the early 1920s. My metaphysics professor in college was the author of The One and the Many: A Contemporary Thomistic Metaphysics.  Father Clarke told his metaphysics class in 1963 that St. Thomas did a better job of proving that God exists when he wasn’t trying to.
The contemporary cosmological argument is based on the observation that humans have free will and are finite beings. A finite being is a composition of two metaphysical principles: essence and existence. The essence of a finite being limits its existence, and an infinite being is a pure act of existence. An infinite being exists because a finite being needs a cause. In Western religions, the infinite being is called God.
This argument assumes or expects the universe to be intelligible, something that ID advocates and Darwinists don’t even consider. It also raises the question of what motivated God to create finite beings. The only thing that could motivate God to do something is self-love. Finite beings exist because God loved himself as giver. But God could also love himself without giving. This means that we do not understand why finite beings exist. God exists because a universe with only finite beings would be less intelligible than a universe with an infinite being. To me, this means that the Big Bang, the origin of life and evolution is evidence that God does not exist because it is evidence that the universe is not intelligible. I also consider it evidence that God inspired the human authors of the Bible because the Bible says that God created the universe out of nothing.
In a criminal trial, jurors reach different conclusions because they differ in their intelligence and judgment. It is usually clear whether a bit of evidence helps or hurts a defendant, but this is not necessarily the case. A particular display in the mind of one juror may help the defendant, but hurt the defendant in the mind of another. In the minds of ID advocates and Darwinists, the Big Bang is evidence for the existence of God. This means that both sides do not understand the cosmological argument. Neither does Wikipedia and the Stanford Encyclopedia of Philosophy, for that matter. This also means that ID advocates think that Darwinists have bad judgment and vice versa.
Thinking that someone who disagrees with you is having poor judgment can be a source of anxiety because it may be you who is having poor judgment. This is a hypothetical conversation about the cosmological argument:
ID Advocate: The Big Bang proves that God exists.
Darwinist: I am not convinced.
ID Defender: You have bad judgment.
Darwinist: No, you have bad judgment.
The ID advocate started the egotistical abuse, but the Darwinist should have admitted that he agreed that the Big Bang is evidence for God’s existence. ID advocates feel the need to persuade themselves that God exists. Darwinists are equally eager to justify their own thoughts to all educated, intelligent, rational people who believe in life after death. This neurotic conflict arises in the question of what caused microscopic organisms to become whales in a time span of about a billion years. This is the conversation above with evolution instead of the Big Bang being the bone of contention:
ID Defender: ID is a better theory than Darwinism.
Darwinist: Darwinism is a better theory than ID.
Since both statements are correct, this is not a rational exchange of views. ID is a better theory than Darwinism because Darwinism only explains the adaptation of species to the environment, not common descent. On the other hand, Darwinism is a better theory than ID because the evidence supports it. If ID proponents understood the contemporary cosmological argument for God’s existence, they might abandon ID. If this happens, Darwinists could be more forthcoming than they currently are about the limitations of Darwinism.
This conflict over DI is analogous to a conflict over a branch of physics dealing with temperature and other observables of real objects:
Creationist: Evolution violates the second law of thermodynamics.
Darwinist: Evolution does not violate the second law of thermodynamics.
According to the second law of thermodynamics, a gas will fill the entire container it is in because nature tends towards a disorderly arrangement of molecules. An ordered arrangement would result if the molecules remained packed in a small section of the container. This law does not apply to gases in outer space. Stars form when there are so many hydrogen atoms that the gravitational force between the atoms is not negligible and causes the atoms to get closer to each other. This law also does not apply to living organisms. A living organism is a complex piece of machinery, like a jet plane in flight. For this reason, it is incorrect to say that evolution violates the second law of thermodynamics.
This is not the reason Darwinists give. “Entropy and evolution”, the reference in footnote 4, for example, argues that evolution does not violate the second law of thermodynamics because the sun somehow pumps order into the biosphere. This reasoning is literally unintelligible. However, the article “Entropy and evolution” goes further. In fact, he performs a calculation in thermodynamics that shows that the second law of thermodynamics is not violated. This calculation was probably made in good faith as it is widely believed that the sun generates the order found in living organisms. However, since the error in the calculation has been pointed out, it is fair to call the AJP article a hoax promoted by Darwinists to squash ID and creationism.
 Shapiro, James A. 2011. Evolution: A View from the 21st Century, FT Press Science, Upper Saddle River, NJ.
 Clarke, W. Norris. 2001. The One and the Many: A Contemporary Thomistic Metaphysics, University of Notre Dame Press.
 “The history of life presents three great sources of wonder. One is adaptation, the marvelous fit between the organism and the environment. The other two are diversity and complexity, the enormous variety of living forms today, and the enormous complexity of its internal structure. Natural selection explains adaptation. But what explains diversity and complexity? (Kindle Rental Edition 78, McShae, Daniel and Brandon, Michael. 2010. The First Law of Biology: The trend of diversity and complexity to increase in evolutionary systems, University of Chicago Press)
 “Does the second law of thermodynamics forbid biological evolution? The erroneous answer ‘yes’ is sometimes presented in the creationist literature…” (Styer, Daniel. 2008. “Entropy and evolution”. Am. J. Phys. , vol 76, no 11)
 “Based on what we’ve said so far, some may be primed and ready to jump from the notion of accident accumulation to the second law of thermodynamics… We advise readers against this, for their own safety. We are Concerned that on the other side of that jump there may not be a firm footing, indeed, there may be an abyss, we first thought that the foundation of the ZFEL [zero-force evolutionary law] it lies in the theory of probability, not in the second law or any other law of physics. And second, our notions of diversity and complexity differ from entropy, in that entropy, unlike fundamental diversity and complexity, is not a level-related concept.” (location 220, op. cit.)
 McIntosh, Andrew C. 2009. “Top-Down or Bottom-Up Information and Entropy Development in Living Systems?” in t. J. of Design & Nature and Ecodynamics vol. 4, no. 4 351-385.