Table of Contents

Refuting Evolution 2, revised and expanded edition, 2011



Unit 1

Chapter 1

Argument: Creationism is religion, not science

Chapter 2

Argument: Evolution is compatible with Christian religion

Chapter 3

Argument: Evolution is true science, not ‘just a theory’

Unit 2

Chapter 4

Argument: Natural selection leads to speciation

Chapter 5

Argument: Some mutations are beneficial

Chapter 6

Argument: Common design points to common ancestry

Chapter 7

Argument: ‘Bad design’ is evidence of leftovers from evolution

Chapter 8

Argument: The fossil record supports evolution

Unit 3

Chapter 9

Argument: Probability of evolution

Chapter 10

Argument: ‘Irreducible complexity’

Chapter 11

Argument: Evolution of sex

Chapter 12

Argument: Evolution of mankind

Appendix 1

Common arguments for evolution that have been rejected

Appendix 2

Common arguments for creation that should not be used

Refuting Evolution 2

A sequel to Refuting Evolution that refutes the latest arguments to support evolution (as presented by PBS and Scientific American).

by with Michael Matthews

Argument: Creationism is religion, not science

Evolutionists say, ‘Creationism is a belief system that has nothing to do with science.’

First published in Refuting Evolution 2, Chapter 1

The two-hour premier episode of the PBS/Nova series ‘Evolution’ [see our online rebuttal of September 2002] sets the tone for this propaganda effort—ridiculing biblical religion as the enemy of true science, which had long shackled scientific study. Much of the first episode is a dramatization of the life of Charles Darwin (1809–1882). It opens with Darwin's famous voyage on HMS Beagle. Darwin introduces himself and Captain Robert FitzRoy (1805–1865) in broken Spanish to villagers in South America. The villagers then lead Darwin and FitzRoy to the skull of an extinct ground sloth, and this conversation ensues:

Darwin [D]: I wonder why these creatures no longer exist.

FitzRoy [F]: Perhaps the ark was too small to allow them entry and they perished in the Flood.

[D]: [laughs]

[F]: What is there to laugh at?

[D]: Nothing, nothing.

[F]: Do you mock me or the Bible?

[D]: Neither.

[F]: What sort of clergyman will you be, Mr. Darwin?

[D]: Dreadful, dreadful.

Then the drama moves to a scene on the Beagle, where Captain FitzRoy is reading from Genesis 1, and Darwin is below deck rolling his eyes.

There we have it—the alleged struggle between science and ‘fundamentalist’ religion. Of course, the representative of ‘fundamentalism,’ Captain FitzRoy, is made to spout a silly straw-man argument. Nowhere is there any hint that there could be any scientific objections to evolution.

But FitzRoy's argument is unbiblical—the Bible clearly states that two of every kind of land vertebrate animal was on the ark, and the ark had plenty of room for all the required animals.1

But then—not that we should be surprised—the PBS dramatization goes well beyond artistic license and actually falsifies history. Darwin's anti-Christianity hadn't fully developed by the time of the Beagle voyage, and he even attended church services, while FitzRoy, during that voyage, likely didn't believe in a global Flood. After all, FitzRoy himself had given Darwin a welcoming gift of the long-age­advocating book Principles of Geology by Charles Lyell (1797–1875), which was a great inspiration for Darwin's evolutionary ideas, as will be shown later in this book.

Philosophical assumption behind ‘modern science’—naturalism

The media is not subtle about its ridicule of ‘creation science.’ John Rennie, editor-in-chief of Scientific American, gets right to the point in ‘15 Answers to Creationist Nonsense’ [see our point by point response from June 2002]. He asserts,

‘Creation science’ is a contradiction in terms. A central tenet of modern science is methodological naturalism—it seeks to explain the universe purely in terms of observed or testable natural mechanisms. [SA 84]

Now we get to the key issue. It's not about scientific facts at all, but self-serving materialistic ‘rules of the game’ by which the evolutionary establishment interprets the facts. So it should be instructive for people to understand what's really driving Rennie and his ilk—a materialist or naturalist agenda that excludes God. This is not a tenet deducible by the experimental method, but a philosophical assumption from outside science.

Rennie illustrates his view of ‘modern science’ with an example from physics:

Physics describes the atomic nucleus with specific concepts governing matter and energy, and it tests those descriptions experimentally. Physicists introduce new particles, such as quarks, to flesh out their theories only when data show that the previous descriptions cannot adequately explain observed phenomena. The new particles do not have arbitrary properties, moreover their definitions are tightly constrained, because the new particles must fit within the existing framework of physics. [SA 84–85]

What has this to do with evolution? Creationists agree that the particles would not behave arbitrarily, because they were created by a God of order. But an atheist has no philosophical justification from his underlying religious premise, i.e., ‘God does not exist,’ for a belief in an orderly universe.

Deceptive attacks on creation ‘science’

Evolutionists tend to lump all opponents of materialistic ‘science’ under the same category, whether they call it ‘creation science’ or ‘intelligent design,’ ignoring the profound differences among the various camps. As a result, they make some outlandish claims that simply do not apply to Bible-believing Christians. For instance, Scientific American attacks ‘creation science’ because it promotes some shadowy intelligence that is beyond scientific inquiry and that offers few answers to scientific questions:

Intelligent-design theorists invoke shadowy entities that conveniently have whatever unconstrained abilities are needed to solve the mystery at hand. Rather than expanding scientific inquiry, such answers shut it down. (How does one disprove the existence of omnipotent intelligences?)

Intelligent design offers few answers. For instance, when and how did a designing intelligence intervene in life's history? By creating the first DNA? The first cell? The first human? Was every species designed, or just a few early ones? Proponents of intelligent-design theory frequently decline to be pinned down on these points. They do not even make real attempts to reconcile their disparate ideas about intelligent design. [SA 85]

In reality, the founders and leaders of modern ‘creation science’ base their views on the Bible, believing it is God's inspired account of history given to mankind. It is wrong to confuse this group with other, more recent advocates of ‘intelligent design’ who wish to avoid all appeals to biblical authority. Christians don't advocate just any ‘designer’ who may or may not be capricious. Rather, they identify the Designer with the faithful triune God of the Bible.

We base our science on the biblical framework of history, which provides much information about when and how the Designer performed special acts of design. That is, during creation week about 6,000 years ago, He created distinct kinds of creatures. Shortly after that, Adam sinned and brought death and mutations into the world. About 1,500 years later, God judged the world by a global Flood that produced most of the world's fossils. But two of every kind of land vertebrate (seven of the few ‘clean’ ones and birds) were rescued on an ocean-liner­sized ark. After they landed on the mountains of Ararat, the ark animals migrated and diversified, adapting to different environments—including some speciation. Mankind disobeyed God's command to fill the earth, and migrated only when God confused the languages at Babel about 100 years later. This explains why human fossils are higher in the post-Flood fossil record than other mammals.

Evolutionists often attack advocates of intelligent design for perfectly admissible types of logical arguments (which evolutionists also use). For instance, Scientific American condemns advocates of intelligent design because ‘they pursue argument by exclusion—that is, they belittle evolutionary explanations as far-fetched or incomplete and then imply that only design-based alternatives remain.’ [SA 85]

This is not wrong. It is simple logic, called the law of the excluded middle.2 Evolutionists from Darwin to today have used the same tactic, i.e., ‘God wouldn't have done it that way, therefore evolution must explain it.’

It's notable that Darwin often used pseudo-theological arguments against design rather than direct arguments for evolution. But this form of argument presupposes the ‘two-model approach,’ i.e., that creation and evolution are the only alternatives, so evidence against creation is evidence for evolution. Ironically, many evolutionists scream loudly if creationists use this same form of logic to conclude that evidence against evolution is support for creation!

Scientific American goes on to claim:

Logically, this is misleading: even if one naturalistic explanation is flawed, it does not mean that all are. [SA 85]

This attack overlooks the obvious fact that the ‘intelligent design’ arguments are based on analogy, a common scientific procedure, about what we can observe being produced by intelligent and unintelligent causes. There is nothing wrong or ‘misleading’ about that approach. The article continues with another misleading objection:

Moreover, it does not make one intelligent-design theory more reasonable than another. Listeners are essentially left to fill in the blanks for themselves, and some will undoubtedly do so by substituting their religious beliefs for scientific ideas. [SA 85]

Here Scientific American is accusing their opponents of doing something that evolutionists do all the time. Editor John Rennie has no objection to substituting (and confusing) his own atheistic religious ideas for scientific ones, but he finds it offensive when other people's religious ideas are brought into the discussion!

Confusing ‘origins science’ with ‘operational science’; the real origins of science

Scientific American also repeats the common claim that evolution and ‘methodological naturalism’ are the basis for modern advances in science:

Time and again, science has shown that methodological naturalism can push back ignorance, finding increasingly detailed and informative answers to mysteries that once seemed impenetrable: the nature of light, the causes of disease, how the brain works. Evolution is doing the same with the riddle of how the living world took shape. [SA 85]

This fails to note the distinction between normal (operational) science, and origins or historical science.3 Normal (operational) science deals only with repeatable observable processes in the present, while origins science helps us to make educated guesses about origins in the past.

Operational science has indeed been very successful in understanding the world, and has led to many improvements in the quality of life, e.g., putting men on the moon and curing diseases. And it's vital to note that many historians, of a wide number of religious persuasions, from Christians to atheists, point out that the founders of operational science were motivated by their belief that the universe was made by a rational Creator. An orderly universe makes perfect sense only if it were made by an orderly Creator. But if atheism or polytheism were true, then there is no way to deduce from these belief systems that the universe is (or should be) orderly.

Genesis 1:28 gives us permission to investigate creation, unlike say animism or pantheism that teach that the creation itself is divine. And since God is sovereign, He was free to create as He pleased. So where the Bible is silent, the only way to find out how His creation works is to experiment, not rely on man-made philosophies as did the ancient Greeks.

These founding scientists, like modern creationists, regarded ‘natural laws’ as descriptions of the way God upholds His creation in a regular and repeatable way (Col. 1:15–17), while miracles are God's way of upholding His creation in a special way for special reasons. Because creation finished at the end of day 6 (Gen. 2:1–3), creationists following the Bible would expect that God has since mostly worked through ‘natural laws’ except where He has revealed in the Bible that He used a miracle. And since ‘natural laws’ are descriptive, they cannot prescribe what cannot happen, so they cannot rule out miracles. Scientific laws do not cause or forbid anything any more than the outline of a map causes the shape of the coastline.

Because creation finished at the end of day 6, biblical creationists would try to find natural laws for every aspect of operation science, and would not invoke a miracle to explain any repeating event in nature in the present, despite Scientific American's scare tactics. This can be shown in a letter I wrote to an inquirer who believed that atoms had to be held together by miraculous means:

‘Natural laws’ also help us make predictions about future events. In the case of the atom, the explanation of the electrons staying in their orbitals is the positive electric charge and large mass of the nucleus. This enables us to make predictions about how strongly a particular electron is held by a particular atom, for example, making the science of chemistry possible. While this is certainly an example of Colossians 1:17, simply saying ‘God upholds the electron’ doesn't help us make predictions.

And in my days as a university teaching assistant before joining CMI, I marked an examination answer wrong because it said ‘God made it so’ for a question about the frequency of infrared spectral lines, instead of discussing atomic masses and force constants.

So, Scientific American is wrong to imply that creationists are in any way hindered in real operational scientific research, either in theory or in practice.

In contrast, evolution is a speculation about the unobservable and unrepeatable past. Thus, it comes under origins science. Rather than observation, origins science uses the principles of causality (everything that has a beginning has a cause4) and analogy (e.g., we observe that intelligence is needed to generate complex coded information in the present, so we can reasonably assume the same for the past). And because there was no material intelligent designer for life, it is legitimate to invoke a non-material designer for life. Creationists invoke the miraculous only for origins science, and as shown, this does not mean they will invoke it for operational science.

The difference between operational and origins science is important for seeing through common silly assertions such as:

… evolution is as thoroughly established as the picture of the solar system due to Copernicus, Galileo, Kepler, and Newton.5

However, we can observe the motion of the planets, but no one has ever observed an information-increasing change of one type of organism to another.

To explain further: the laws that govern the operation of a computer are not those that made the computer in the first place. Much anti-creationist propaganda is like saying that if we concede that a computer had an intelligent Designer, then we might not analyze a computer's workings in terms of natural laws of electron motion through semiconductors, and might think there are little intelligent beings pushing electrons around instead. Similarly, believing that the genetic code was originally designed does not preclude us from believing that it works entirely by the laws of chemistry involving DNA, RNA, proteins, etc. Conversely, the fact that the coding machinery works according to reproducible laws of chemistry does not prove that the laws of chemistry were sufficient to build such a system from a primordial soup. The PBS producer even admitted that the naturalistic origin of life was a major problem for evolution.

For some specifics, it's notable that creationists have made many of the great scientific advances that Scientific American and other evolutionary magazines like to mention! Isaac Newton discovered the spectrum of light (as well as co-inventing calculus and formulating the laws of motion and gravity); James Clerk Maxwell discovered the laws of electromagnetism which led to the prediction of electromagnetic radiation; Louis Pasteur formulated the germ theory of disease and disproved spontaneous generation; Joseph Lister pioneered antiseptic surgery; Raymond Damadian pioneered magnetic resonance imaging (MRI) that is a vital tool in brain research.

In spite of the evidence, Scientific American asserts,

Creationism, by any name, adds nothing of intellectual value to the effort. [SA 85]

This blind assertion shows John Rennie's willing ignorance concerning the contributions made by creationists to the major branches of modern science in general and to his own magazine in particular.

Example of the naturalistic assumptions driving evolution

Scientists have a reputation for impartiality and rigid honesty in their treatment of the facts, but it does not take much digging to find examples of how powerfully a materialistic mindset can cloud a scientist's judgment. One of the greatest influences on Darwin, for example, was a book he took on the Beagle voyage, Principles of Geology by Charles Lyell, which pushed the idea of slow and gradual geological processes occurring over millions of years, and denied Noah's Flood. Modern evolutionists acknowledge that Lyell was biased and unscientific, driven by anti-biblical philosophical assumptions, whereas the ‘catastrophists’ of his day (who believed in one or more Flood catastrophes) were rigid followers of the scientific method. Stephen Jay Gould (1941–2002), himself a leading evolutionist, wrote:

Charles Lyell was a lawyer by profession, and his book is one of the most brilliant briefs published by an advocate. … Lyell relied upon two bits of cunning to establish his uniformitarian views as the only true geology. First, he set up a straw man to demolish. … In fact, the catastrophists were much more empirically minded than Lyell. The geologic record does seem to require catastrophes: rocks are fractured and contorted; whole faunas are wiped out. To circumvent this literal appearance, Lyell imposed his imagination upon the evidence. The geologic record, he argued, is extremely imperfect and we must interpolate into it what we can reasonably infer but cannot see. The catastrophists were the hard-nosed empiricists of their day, not the blinded theological apologists.6

One infamous example of Lyell's bias was his decision to ignore eyewitness accounts of the rate of erosion of Niagara Falls, and publish a different figure to suit his purpose.7

But Lyell convinced Darwin, who eventually linked slow and gradual geological processes with slow and gradual biological processes. For example, he said that mountains were products of thousands of small rises. PBS Episode 1 portrays Darwin saying, ‘Time, unimaginable tracts of time, is the key,’ and arguing that just as small changes over ages can throw up mountains, why couldn't small changes accumulate over ages in animals to produce new structures?

Not only Darwin, but also many prevailing churchmen of his day had capitulated to Lyell's ideas. The prominent view was that God created organisms in their present locations. In his arguments against creation and for evolution, Darwin wondered why God would create not-quite-identical finches in almost identical islands.

In this case, Darwin rightly thought that the island animals were descended from mainland ones. But this is what biblical creationists would believe too, with a global Flood and subsequent migration from Ararat via continents to islands. So Darwin's arguments work only against a compromised creationist view, not the biblical view. (Present-day ‘progressive creationists’ hold essentially the same view as Darwin's opponents, so they are trying to fight a battle that was lost 150 years ago but wouldn't have been if Christians had not compromised on the earth's age and the global Flood.)

Darwin's attempt to explain variations between finches underscores a fundamental point in the debate between evolution and creation: that facts do not speak for themselves, but are always interpreted within a framework. Creationists don't deny a single observation an evolutionist makes, but find that they virtually always make better sense when interpreted within the biblical framework, as opposed to a compromised one. Therefore, it shouldn't be surprising that many of the alleged ‘evidences’ for evolution actually turn out to support the biblical model.

Scopes trial and Sputnik

Evolutionists frequently point to two emotion-charged incidents in the 20th century that supposedly confirm the danger of mixing creation and science—the famous Scopes trial (1925) and the launch of Sputnik (1957). PBS 7 talks about the Scopes trial and says that William Jennings Bryan was victorious, and that it had the ‘chilling effect’ of expunging evolution from science curricula from many states. Surprisingly, for a series containing millions of dollars worth of misinformation, it didn't present the play and film Inherit the Wind as a serious account of the trial. A good thing, because of its gross distortions documented in the article Inherit the Wind—an Historical Analysis.’8

Then PBS 7 showed Sputnik, and claimed that American authorities were so alarmed that the Soviets beat them into space that they decided to make science education a priority. Somehow, evolution was smuggled in there. However, the science that put spacecraft on the moon is nothing like evolution. Rocket science involves repeatable experiments in the observable present; evolution is a just-so story to explain the unobservable past without God's direct intervention. It's especially ironic that the leader of the Apollo program, Wernher von Braun, was a creationist!

It's also blatantly revisionist history to claim that the Scopes trial paved the way for the Sputnik. During this alleged scientific nadir between Scopes and Sputnik, American schools produced more Nobel prizes than the rest of the world combined. America produced twice as many as all other countries—this was especially pronounced in the biological field (physiology and medicine), supposedly one that can't do without evolution. The Soviet Union beat the USA into space merely because the totalitarian government made it a top priority. While the USA had a good space program, there were other spending priorities, such as helping a war-torn world to rebuild. When the USA put its mind to it, it quickly surpassed the USSR, and was the first to land men on the moon in 1969. If it had needed scientists trained in evolution, the moon landing wouldn't have happened till the next generation had gone through the public school system.9

PBS and science journals are not the only ones trying to equate ‘science’ with evolution. One of the most vociferous anti-creationist organizations is the pretentiously named National Center for Science Education. This is a humanist-founded organization, and its chief spokesperson, Eugenie Scott, is the winner of humanist awards and was also a consultant for the PBS series. It's significant that the only ‘science education’ NCSE seems interested in is evolution—not chemistry, physics, astronomy, or even experimental biology (or rocket science for that matter).10

Creation in public schools?

The debate about religion and science has practical ramifications today, and it has spilled over into the public schools again. Evolutionists are terrified that criticisms of evolution (which they equate with teaching biblical creation—when it suits them!) may be allowed into the schools, and they are doing everything they can to stop it. (It's important to note that, although it would be nice to give teachers the freedom to present alternatives to evolution, Creation Ministries International and other major creationist organizations have not been lobbying for compulsory creation in schools, despite common accusations. For one thing, one school of thought is that sending kids to public schools is like Joshua sending the Israelite children to Canaanite schools. But mainly, would Christians want an atheistic teacher to be forced to teach creation, and deliberately distort it?)

PBS 7 extensively featured Jefferson High School in Lafayette, Indiana. A student petition requested that the science curriculum should include the creation model. One teacher admitted that the signatories included ‘outstanding students’ and even some teachers. Of course this shows that one can be a top student without swallowing the evolutionary story.

But several teachers claimed the petition was dangerous (i.e., for them to listen to students and parents). One teacher, Clare McKinney, claimed to be a Christian, but she claimed that science can't involve God, swallowing the belief that science and religion do not overlap. Yet this claim is only possible if the Bible and the real world have nothing to do with each other, or if God and reason are mutually exclusive.

Another teacher at the school said that science is peer-reviewed, testable, and repeatable. He failed to explain how a claim such as ‘a reptile turned into a bird 150 million years ago’ is testable or repeatable! Although evolutionists like to condemn creation as non-science, they have a hard time coming up with a definition of ‘science’ that includes evolution and excludes creation unless it's blatantly self-serving. Sometimes these definitions are self-contradictory, e.g., some evolutionists, including Gould, have claimed that creation is not scientific because it's not testable, then explained how it has allegedly been tested and shown to be wrong.

The school board, led by School Superintendent Ed Eiler, refused the Jefferson High School petition, claiming that creation is not part of science. Amazingly, the teacher Clare McKinney lamented how biology would be unteachable if evolution were censored, but that was not what the petitioners requested. Ironically, they wanted the curriculum to teach more about evolution than the establishment wants the students to learn! But the upshot was that any criticisms of evolution are censored instead.

There are numerous instances of teachers who face severe discrimination simply because they want to present their classes with the scientific evidence against evolution. One chemistry teacher was constructively dismissed simply for having [former] Answers in Genesis (US) speaker Geoff Stevens, who is qualified in physics as well as theology, address his class on chemical evolution, surely an appropriate topic for chemistry class. Mr Stevens presented a purely scientific case that non-living chemicals could not form a living cell by natural processes (see chapter 9), and he didn't mention God or religion at all. But Eiler issued a formal letter of reprimand to the teacher of the class, Dan Clark, falsely accusing him of introducing ‘religion’ to his classes. The real problem was that ardent evolutionists refused to tolerate any challenges to their materialist faith.

When tested by logic and reality, the evolutionists' contention that ‘creationism is a religion that has nothing to do with science’ is hypocritical. Both creationists and evolutionists accept the same facts of science, they just interpret them based on different frameworks. One interpretation is based on atheistic materialism, and the other is based on God's perfect, revealed Word.

References and notes

  1. J. Sarfati, How Did All the Animals Fit on Noah's Ark? Creation 19(2):16–19, March–May 1997; J. Woodmorappe <>, Noah's Ark: A Feasibility Study, El Cajon, CA, Institute for Creation Research, 1996.
  2. J. Sarfati, Loving God with All Your Mind: Logic and Creation, Journal of Creation 12(2):142–151, 1998.
  3. N.L. Geisler and J.K. Anderson, Origin Science: A Proposal for the Creation-Evolution Controversy, Grand Rapids, MI, Baker Books, 1987.
  4. J. Sarfati, If God Created the Universe, Then Who Created God? Journal of Creation 12(1)20–22, 1998.
  5. Levitt as quoted by L.S. Lerner in Good Science, Bad Science: Teaching Evolution in the States, Thomas B. Fordham Foundation, 2000.
  6. S.J. Gould, Natural History, p. 16, February 1975.
  7. L. Pierce, Niagara Falls and the Bible, Creation 22(4):8–13, September–November 2000.
  8. D. Menton, Inherit the Wind—an Historical Analysis, Creation 19(1):35–38, December 1996–February 1997; see also Q&A: Scopes Trial.
  9. The Discovery Institute's critique makes these good points in Getting the Facts Straight: A Viewer's Guide to PBS's Evolution, Seattle, WA, Discovery Institute Press, 2001.
  10. See How Religiously Neutral Are the Anti-Creationist Organizations? and A Who's Who of Evolutionists, Creation 20(1):32, December 1997–February 1998.

Note about citations: Quotations from the Scientific American article by John Rennie will be labeled ‘SA,’ followed by the page number. Quotations from, and other mentions of, the PBS-TV series Evolution will be labeled ‘PBS,’ followed by the episode number, e.g., ‘PBS 6’ refers to Episode 6. Return to article.

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