Table of Contents
Chapter I: Introduction
Chapter 2: The Scientific Method and the Mind-Body Problem
Chapter 3: The Method of Inquiry Called Metaphysics
Chapter 4: Popular Concepts of the Human Soul
Chapter 5: The Metaphysics, Theology, and Science of the Big Bang
Chapter 6: Origin of Life
Chapter 7: Scope of Darwinian Evolution
Chapter 8: The Complexity of Life
Chapter 9: Conclusion

Chapter I: Introduction
For twenty years, the Texas School Board required teachers to discuss the “strengths and weaknesses” of all scientific theories. The citizens who supported this proviso had in mind the Darwinian theory of evolution. This directive was changed somewhat in March of 2009 after the Texas School Board conducted a hearing. The New York Times took an interest in the dispute and said in an editorial:

At the end of a tense, confusing three-day meeting, Darwin’s critics claimed that this and other compromise language amounted to a huge victory that would still allow their critiques into textbooks and classrooms. One can only hope that teachers in Texas will use common sense and teach evolution as scientists understand it.

The criminal prosecution of John Scopes for teaching evolution in Tennessee in 1926 is well-known event in American history. Inherit the Wind is a 1960 movie about the trial with Spencer Tracy playing Clarence Darrow, Frederic March playing William Jennings Bryan, and Gene Kelley playing H. L. Mencken.

Later in the century, the shoe was on the other foot. In 1987, the United States Supreme Court ruled that a Louisiana law requiring the teaching of creation science violated the Establishment Clause of the First Amendment. In 2005, a United States District Court in Dover, Pennsylvania, ruled that intelligent design is not science and should not be taught to public school children.

WGBH-TV produced a documentary about the Pennsylvanian trial that included interviews with a daughter and her father who were residents of Dover. Speaking about the disagreement she had with her father, the daughter said:

He believed that God really should be in science class. He did not believe in science, and he was all worried about me and...because I believed in evolution. And he said, you know, ‘Well, do you really believe that we came from monkeys?’ At that point, I was pretty burned out from the trial, and I didn't really have the patience that I probably should have had with him, and I just said yeah, I mean, you know? ‘Yeah, I do believe in evolution, Dad,’ you know? And so we'd fight every morning.If you believe in heaven and hell, and you believe you have to be saved, nothing else could possibly matter. Not the First Amendment, not science, not rational debate. All that matters is that you're going to be rejoined with the people you love most on this Earth.

The father said:

Teaching the traditional evolutionary Darwinian concept that man evolved from lower forms of life, that's almost a slap in my face. That takes the dignity away from humanity, as far as I'm concerned. What gives dignity to man is that every one of us are made in the image of God. He is the creator, and he created the world with intention and with design. It upsets me deeply that now, in our educational system, we are indoctrinating our young people to think differently about humanity.

Through no fault of their own, the father and daughter are mistaken about evolution. There is no conflict between faith in God and evolutionary biology. In the court of conscience and reason, the study of evolution adds to the reasons there are to believe in the Bible and the Koran. I will attempt to show this by explaining evolutionary biology with a more thorough and objective application of the scientific method than is usually given. That there is a need for a layman, such as myself, to explain a branch of science that is expounded upon in so many textbooks and scholarly publications is not any more strange than the New York Times editorializing about a subfield of biology.

My first point is that evolution applies only to the bodies of human beings, not their spiritual souls. This is not explicitly stated in biology textbooks, but it is implied by omission. Biology textbooks don’t mention the properties of human beings that makes humans equal to each other and superior to animals: free will and conscious knowledge. We know humans possess these faculties because we have the ability to make ourselves the subject of our own knowledge. Free will and conscious knowledge are not scientific concepts or observables. One reason this limitation of evolution is not often mentioned is that biologists don’t understand the body-soul analysis and generally confuse it with the mind-body problem.

My second point is that the theory of evolution only explains the adaptation of species to their habitats. It does not explain the increase in complexity that occurred in the descent of hominids from the tiny bacteria-like cells that appeared on Earth three billion years ago. I am saying there is no disagreement between scientists who advocate intelligent design and scientist who are against intelligent design and creationism. This debate about evolution is a proxy for something else. The disputants are guilty of deceiving themselves just as they are guilty of deceiving the father and daughter in Dover. My hope is that my analysis and explanation of evolutionary biology will help the reader understand what is going on.

Chapter 2: The Scientific Method and the Mind-Body Problem
This chapter will explain the scientific method and illustrate the difference between an observation and a theory by comparing a bad theory of adaptation (Lamarkism) with a good theory of adaptation (Darwinism).

I will explain that the free will and conscious knowledge of human beings are not observables and can’t be defined. This means they can’t be included in a scientific model or theory, except to exclude the concepts. I will explain Descartes’ irrational solution of the mind-body problem and explain why humans are embodied spirits.

Chapter 3: The Method of Inquiry Called Metaphysics
I will explain the three act-potency concepts of metaphysics (substance-accidence, form-matter, essence-existence) and contrast science with metaphysics. Essentially, metaphysics poses questions that can be answered and science poses questions that are hard to answer. Metaphysics is a method of inquiry different from science, but connected to it by the metaphysical concept we refer to as reason.
The proof of God’s existence starts with the proposition that human beings have free will. Free will means each of us possesses a center of action that makes us unified with respect to ourselves but different from other beings. Hence, we are finite beings. God is a being that is totally other—not finite or infinite. An infinite being exists because finite beings need a cause. If all beings in the universe needed a cause, the universe would not be intelligible.

Chapter 4: Popular Concepts of the Human Soul
Using Chapters 2 and 3, I will analyze a number of quotes from biologists concerning human spirituality:

Catholics could believe whatever science determined about the evolution of the human body, so long as they accepted that, at some time of his choosing, God had infused the soul into such a creature. I also knew that I had no problem with this statement, for whatever my private beliefs about souls, science cannot touch such a subject and therefore cannot be threatened by any theological position on such a legitimately and intrinsically religious issue.( Stephen Jay Gould, Natural History, March 1997, 13th paragraph)

Two major puzzles of human evolution remain. One puzzle is the genetic basis of the ape-to-human transformation…The other puzzle is the brain-to-mind transformation. We know that the 30 billion neurons in our brains communicate between themselves and with other nerve cells by chemical and electrical signals. How do these signals become transformed into perceptions, feelings, ideas, critical arguments, aesthetic emotions, and ethical and religious values? And how, out of this diversity of experiences, does a unitary reality emerge, the mind or self? The soul created by God, you might say, accounts for both transformations: ape to human and brain to mind. This religious answer may be satisfactory for believers, but it is not scientifically satisfactory. I still want to know how the anatomical and behavioral traits that differentiate us from apes emerge out of our genetic differences; I also want to know the biological correlates that account for mental experiences. (Francisco J. Ayala, Darwin's Give to Science and Religion, p.10)

And certain properties of the human brain distinguish our species from all other animals. The human brain is, after all, the only known collection of matter that tries to understand itself. To most biologists, the brain and the mind are one and the same; understand how the brain is organized and how it works, and we’ll understand such mindful functions as abstract thought and feelings. Some philosophers are less comfortable with this mechanist view of the mind, finding Descartes’ concept of a mind-body duality more attractive. (Neil Campbell, Biology, 4th edition, p. 776)

I’ll show that these biologists think the human soul is some kind of attempt to explain the mind-body problem. The body-soul analysis is a metaphysical explanation of why humans are different from one another and yet members of the same category of being. The mind of the mind-body problem makes people good or bad, whereas the body of the soul-body analysis makes people good or bad.

Chapter 5: The Metaphysics, Theology, and Science of the Big Bang
The key quote in this chapter will be:

As far as we are concerned, events before the Big Bang can have no consequences and so should not form part of a scientific model of the universe. We should therefore cut them out of the model and say that the big bang was the beginning of time. This means that questions such as who set up the conditions for the big bang are not questions that science addresses.

This chapter will argue that the Big Bang is a reason for believing in revelation because Genesis and John’s Gospel say God created the universe ex nihilo. The discovery of cosmic background radiation in the 1960s confirmed the Big Bang, which is a sign that God inspired the human authors of the Bible.

Many people seem to think there is a need to make a decision about whether or not God exists apart from whether or not God has revealed himself to mankind. Whether or not to believe in revelation is really the only decision that has to be made.

If there was no revelation, what difference does God’s existence make? The proof of God’s existence is hypothetical. It is based on the assumption that the universe is intelligible and that metaphysical propositions have content. This is why, in my opinion, it is wrong to call the proof of God an argument rather than a proof. Calling it an argument implies that a person should decide whether or not God exists and those who decide God doesn’t exist should not be criticized. Persons expose themselves to criticism when they don’t understand the concept of God and don’t tell the truth about God.

This chapter will outline the Big Bang model from 13.7 billion years ago up until the appearance of life on Earth 3 billion years ago.

Chapter 6: Origin of Life
The following will be the key quotes in this chapter:

Everything about evolution before the bacteria-like life forms is sheer conjecture, so we start this narrative with the bacteria-like ancestor and its complex collection of biochemical and molecular biological core processes. (Marc W. Kirschner and John C. Gerhart, The Plausibility of Life: Resolving Darwin’s Dilemma, Yale University Press, 2005, p. 50)

Evolution is not the study of life’s ultimate origin as a path toward discerning its deepest meaning. Evolution, in fact, is not the study of origins at all. Even the more restricted (and scientifically permissible) question of life’s origin on our earth lies outside its domain. (This interesting problem, I suspect, falls primarily within the purview of chemistry and the physics of self-organizing systems.) There is presently no generally accepted theory of how the first life-form arose, but several options have been proposed. The raw materials, of course, were not alive, but were capable of assembling into a complex structure with the capacity to reproduce itself. And once reproduction was initiated, evolution began.

There are eight transformations or changes in being that are worth discussing scientifically and metaphysically:
1. Vacuum or nothingness to the Big Bang
2. Protons and electrons to hydrogen atoms
3. Big Bang to the condensation of Earth
4. Nonliving chemicals to prokaryotes (small cells without nuclei)
5. Prokaryotes to eukaryotes
6. Single-celled eukaryotes to hominids
7. Plants to animals
8. Animals to human beings

I have a joke about No. 1. Michael Behe (ID advocate), Francisco Ayala (anti-ID advocate), and Jean-Paul Sartre (atheistic existentialist) were stranded on an island and were discussing the Big Bang. Behe said the Big Bang was created ex nihilo by an angel. Ayala said the Big Bang was a vacuum fluctuation. Sartre said there was no angel and no vacuum.

Concerning No. 2, my Ph.D. thesis was a calculation of the binding energy of hydrogen (actually positronium) using quantum electrodynamics. The calculation proves that the properties of a hydrogen atom can be derived from the properties of a proton and an electron. To give it an even more metaphysical cast, protons and electrons have the potential to become hydrogen atoms. Quantum electrodynamics is not mathematically rigorous. Physicists are proud of how well the calculations explained the observations, but a mathematician obsessed with rigor might say there was no explanation at all.

Concerning Nos. 3 and 4, the transformation from prokaryotes to eukaryotes took three times longer than the transformation from single celled eukaryotes to chimpanzees and other apes.

Transformation No. 8 is entirely metaphysical. You can, however, make the transformation entirely scientific with the metaphysical concepts of form (soul) and matter (body).

Chapter 7: Scope of Darwinian Evolution
There are numerous statements in the scientific literature saying that the Darwinian mechanism of mutations and natural selection does not explain the complexity of living organisms and molecular biology. The following quote, for example, is from mainstream biologists whose work is considered an improvement over Darwinian evolution. Notice that the authors refer only to adaptation, not to the increase in complexity:

Facilitated variation is not like orthogenesis, a theory championed by the eccentric American paleontologist Henry Osborn (1857–1935), which imbues the organism with an internal preset course of evolution, a program of variations unfolding over time. Natural selection remains a major part of the explanation of how organisms have evolved characters so well adapted to the environment. (Marc Kirschner and John Gerhart, The Plausibility of Life: Resolving Darwin’s Dilemma, p. 247)

The following three quotes—I could add four more— indicate the limited scope of Darwinism. Authorities who advocate intelligent design and those who are against intelligent design agree that common descent is proven. However, there are no authorities on the subject of evolution that say natural selection explains the complexity of living organisms. Most authorities criticize creationism and intelligent design, however, this is not the same as saying the Darwinian mechanism explains the complexity of organ systems, individual proteins, molecular machinery with dozens of proteins, and the biological blueprints in zygotes (fertilized eggs) that controls their development.

The theory sketched suggests something like a solution to the problem of how evolution leads towards what may be called “higher” forms of life. Darwinism as usually presented fails to give such a explanation. It can at best explain something like an improvement in the degree of adaptation. (Marc W. Kirschner and John C. Gerhart, The Plausibility of Life: Resolving Darwin’s Dilemma, Yale University Press, 2005)

Considered thermodynamically, the problem of neo-Darwinism is the production of order by random events. (“Chance or Law,” in Beyond Reductionism: New Perspectives in the Life Sciences, The Macmillan Company, 1969, page 76)

P. falciparum, HIV, and E. coli are all very, very different from each other. They range from the simple to the complex, have very different life cycles, and represent three different fundamental domains of life: eukaryote, virus, and prokaryote. Yet they all tell the same tale of Darwinian evolution. Single simple changes to old cellular machinery that can help in dire circumstances are easy to come by. This is where Darwin rules, in the land of antibiotic resistance and single tiny steps…There is no evidence that Darwinian process can take the multiple, coherent steps needed to build new molecular machinery, the kind of machinery that fills the cell. Michael Behe, The Edge of Evolution: The Search for the Limits of Darwinism, p. 162)

Chapter 8: The Complexity of Life
The primary structure of proteins is an aspect of the complexity of life that can be quantized. The laws of probability can be used to calculate how long it would take to get a particular sequence of amino acids by random chance. The following quote is not from an advocate of intelligent design but from a textbook used by 65% of the biology majors in the United States:

Each of the four identical polypeptide chains that together make up transthyretin is composed of 127 amino acids…The primary structure is like the order of letters in a very long word. If left to chance, there would be 20127 different ways of making a polypeptide chain 127 amino acids long. (Neil Campbell, Biology, 7th edition, p. 82)

The following quote from mainstream biologists shows how large 20127 is. A sonnet can be thought of as a protein with 600 amino acids with 26 (instead of 20) possible amino acids at every location:

By comparison, if we question how long it would take a high-speed computer to write randomly a specific Shakespearean sonnet, we are asking that all the letters of the words of the sonnet will come up simultaneously in the correct order. It is an impossible task, even if all the computers in the world today had been working from the time of the big bang to the present. Even to compose the phrase, “To be or not to be,” letter by letter, would take a typical computer millions of years. (Marc W. Kirschner and John C. Gerhart, The Plausibility of Life: Resolving Darwin’s Dilemma, Yale University Press, 2005, p.32

Kirschner and Gerhart did the above calculation. To explain their ideas about evolution, they modified the calculation for “to be or not to be.” If the computer generated only dictionary words (facilitated variation) and stopped every time it got part of the phrase right (natural selection), a computer could generate an epigram in a short length of time. However, as I pointed out, they don’t claim to have explained the complexity of life. They only claim to have explained adaptation.

Chapter 9: Conclusion
I have proven the following: 1) There is no explanation for the Big Bang. 2) There is only speculation about the origin of life. 2) Darwinian evolution only explains adaptation. 4) The existence of human beings lies outside the methodology of science.

Concerning this last point, we can give credit to Descartes for expressing the indefinability of human beings very concisely: I think, therefore I am. In other words, all you can say about humans is that they are aware of their own existence. It is true that we can conclude from the existence of finite beings that an infinite being exists, but this has no explanatory power. It just raises the question of why the infinite being created finite beings.