© Tiktaalik, Field Museum, by Eduard Solà [CC BY-SA 3.0], via Wikimedia Commons.
Editor's note: Phillip E. Johnson, Berkeley law professor and author of Darwin on Trial and other books, died on November 2. Evolution News is sharing remembrances from Fellows of Discovery Institute. Dr. Behe's most recent book is Darwin Devolves. The following essay appeared originally as the Foreword to the 20th Anniversary edition of Darwin on Trial.
Twenty years can be a virtual eternity in modern science, so rapidly do new discoveries accumulate. Twenty years ago the idea of determining the entire DNA sequence of even a tiny living organism such as a bacterium, let alone the genetic endowment of a large animal such as a mammal, seemed a dream. Yet shortly before I wrote this foreword, the 1000th kind of bacterial genome was sequenced. The DNA code of humans was completed a decade ago. That of other familiar creatures, such as dog, rice, mosquito, and more, are also now public knowledge.

It's not only the genome sequences of organisms that has been brought to light in the past two decades. DNA is the "instruction manual" that tells cells how to go about building pieces of molecular machinery that actually run the cell. But, like trying to picture the end result of an instruction manual written in a foreign language, it is usually not very straightforward for a scientist to determine what kind of machines are going to result simply by looking at the DNA instructions. However, by performing clever laboratory experiments, investigators can probe the machinery directly. In the past two decades whole new classes of molecular machines have been discovered. One of the most interesting is a class of RNA molecules that helps regulate DNA. RNA (as you of course remember from your high school biology class) is a chemical "cousin" of DNA, and an "intermediate" between the information coded in DNA and its translation into proteins, which are the usual components of molecular machines. But other roles have been discovered for RNA including, most surprisingly, the ability to decide when some DNA genes are turned on and off.

In other areas of biology besides the micro-world, too, discoveries have been pouring in. New fossil finds, new ways that the brain communicates, and more, have dazzled the scientific community and the world.

Science and Logic

Phillip E. Johnson

Phillip E. Johnson
Twenty years can be a virtual eternity in modern science — but in logic, not so much. Arguments that rest on faulty premises and strained reasoning are not helped at all by the passage of time. It is the brilliance of Phillip Johnson, Jefferson E. Peyser Professor of Law, Emeritus, at the University of California Berkeley and an expert in the way arguments are framed and the unspoken premises they rest on, to have written a book, Darwin on Trial, that, despite the intervening years and progress of science, is as fresh and relevant today as when it was first printed.

Johnson's classic masterpiece came about rather serendipitously. While on sabbatical in England over two decades ago, he chanced to pick up two books concerning evolution. The first was The Blind Watchmaker by Oxford biologist and world-renowned atheist Richard Dawkins. Dawkins's book is widely acknowledged even today to be the most vigorous defense of Darwinian evolution available for a general readership. The second book was the less well-known, but soon-to-be-influential, Evolution: A Theory in Crisis, by an English geneticist, Michael Denton, who at the time was working in Australia. Denton, an agnostic, was fed-up with the claims Darwinists made for their theory when he saw many problems with it. In the book he detailed his scientific criticisms of Darwinism with nary a single Bible verse to bolster them.

Reading side-by-side books by knowledgeable, secular scientists alternately criticizing and extolling the dominant scientific theory of our age, Johnson was enchanted. Clearly, he realized, something more than just the undisputed facts entered into the weighing of the evidence. And when a large theory such as evolution cuts across many disciplines, no one can claim to be expert in all of the evidence. Rather, the evidence is much better evaluated by a generalist trained to evaluate the logic of arguments and the assumptions lying behind them, as Johnson himself was exquisitely qualified to do.

Help Wanted: A Generalist

If you thought tendentious theories and outlandish alibis were confined to courtroom shenanigans, Johnson will quickly disabuse you. Partisan strategies find their way into even the most abstruse scientific arguments. Johnson argues that Darwin's theory of evolution relies heavily on the highly tendentious, usually unstated, assumption of materialism: the idea that the only things that really exist are matter and energy in the physical universe. If one begins with that assumption, then one has neatly gotten rid of the chief rival to evolution which has seemed much more plausible to the greatest minds throughout history: that a supernatural entity, God, possessed of great power and intellect, designed the cosmos and the life it contains. If, by postulate, no such Being exists, then something like evolution pretty much has to be true. The universe alone exists, so the universe alone must have produced life.

A neat little trick, and one which saves an awful lot of scientific work. If a scientist can beguile the world into thinking that his theory must be true by definition, and that others must be ruled out from the start, then evidence becomes decidedly secondary, and no rival theories need apply.

But what if one is unwilling to concede that postulate? What if one suspects that there may indeed be a Mind beyond the universe, capable of affecting it, as the overwhelming number of people throughout history have thought? In that case, Johnson argues persuasively, the typical evidence brought forward for Darwinian evolution looks far less compelling than its boosters make it out to be. If Darwinism simply has to be true, then two breeds of finches with slightly different beak shapes seems like stunning confirmation of the theory. If it doesn't have to be true, then you just have two birds with slightly different beaks, and the question of what formed finches in the first place stands. Soon the skeptic of Darwinism comes to the conclusion that a large part of the modern worldview is built not on solid scientific evidence, but on philosophical bias enforced with sociological prejudice.

A Prejudice with Teeth

Make no mistake, however — that sociological prejudice has teeth. From ridicule to shunning to dismissal from a job, a variety of unpleasant consequences can be brought to bear on folks in vulnerable situations who don't get with the Darwinian program. You are about to read a dangerous book.

That's what happened to me. When it first came out in 1991 I saw an advertisement for Darwin on Trial, ordered a copy, and devoured it in two days. Having earlier read Denton's Evolution: A Theory in Crisis (the same book that Johnson read on his sabbatical in London), I realized that Darwin's theory had a lot of problems. But Phil's book got me to see why it was popular with scientists nonetheless: it was the only game in town — the only slightly plausible explanation for life that did not invoke intelligent causes. Then one fine day in 1991 I was strolling through the department office and noticed the latest edition of Science magazine. I stopped to look at the table of contents and noticed there was a news item on an anti-evolution book from an unusual source — a U.C. Berkeley professor. I read the item and saw it wasn't so much a story as a warning to faculty to keep their students away from this book — it might confuse them....

The Irishman

I'm half Irish on my mother's side, so when I see such blatant tendentiousness I get ticked off. I fired off a letter to the editor of Science pointing out that this Johnson fellow seemed pretty bright, noticed grand claims being made for evolution with little data, and was likely to make up his own mind about Darwin's theory, thank you very much. A person like that, I wrote, should be argued with, not condescended to. Much to my surprise, Science printed the letter, and to my further surprise a few days later I got a letter in the mail from Phil, thanking me for writing the letter.

Little did I know it at the time, but I was now in the circle of Phil Johnson's useful contacts. Over the years, more academics gathered in Phil's circle and joined the high intellectual adventure of battling a decrepit idea that had managed to hang on through a combination of bad science and bad philosophy. Over the years we had our victories and defeats, but because of Phillip Johnson's leadership no informed person will ever again honestly say that Darwin's theory flows straight from the data.

In Darwin on Trial Phillip Johnson discusses a number of strands of scientific evidence that in the 1990s purportedly supported Darwin's theory, and he neatly shows they are at best inadequate, at worst contradictory. Let's revisit several of these topics and see if the intervening years have been kinder to Darwin. The three areas I'll briefly discuss are, in turn, mutations, fossils, and the origin of life.

Random Mutations

Ultimately the fodder for Darwinian evolution is random mutation. Deep in the genetic endowment of some creature a change occurs that makes it genetically different from its parents. Since the DNA of living creatures is highly functional, usually the change is for the worse. The poor creature thus finds itself at a disadvantage in the struggle for life and its line quickly dies out in the process of natural selection. But on rare occasions, the mutation is actually for the better. The lucky creature has an advantage over its brothers and sisters, and its offspring over theirs. Over time the offspring of the fortunate mutant come to dominate the population. Repeat this scenario over and over again, and the result is Darwinian evolution. Or so the story goes.

In Darwin on Trial Johnson discussed what was known about mutation up until the early 1990s, which was mostly speculative. But since that time, with the newly developed easy ability to sequence DNA, evolution experiments can actually be done in real time in the laboratory, and the exact mutations that give organisms an advantage can be tracked down. What have these experiments shown? Just about the time Darwin on Trial was being written a scientist named Richard Lenski at Michigan State University began the largest laboratory evolution experiment ever. Lenski, a microbiologist, decided to grow cultures of the common bacterium E. coli in his lab. Because it is so small, the bacterium can reproduce very quickly (in less than an hour) and grow to enormous numbers (billions in a single test tube). Once the growing bacteria had exhausted the food in one test tube, Lenski and his colleagues would transfer a small portion of them to a fresh test tube. When that test tube became saturated with bacteria, they would transfer another small portion to another fresh tube. They have been repeating this procedure for decades, which in bacterial terms is upward of 50,000 generations and a cumulative population size of hundreds of trillions! This is roughly the number of generations and population size that it supposedly took for some primate ancestor to evolve into modern humans.

Along the way Lenski saw that his bacteria were improving — they could grow faster than the starting bacteria could. However, the big surprise came when he and his coworkers tracked down the beneficial mutations. It turned out that mutations in the "improved" bacteria had broken a lot of genes and thrown others away. In other words, just as it may be beneficial to throw sophisticated-but-heavy computers and machinery off a sinking ship, it was beneficial for the bacteria to toss out sophisticated genes that normally were useful. That actually made the mutant bacteria grow faster than their relatives, but it hardly answers the question of where sophisticated genes come from in the first place. In the end, after 50,000 generations, not only did a new kind of organism not evolve, but rather the original organism was degraded. This is currently our best evidence of what random mutation is capable of: Most mutations are harmful, and the few that are beneficial break genes.

The Fossil Record

In Darwin on Trial Phillip Johnson criticizes the state of the fossil record circa 1990, and shows that it is not at all what Darwin expected it to turn out to be when he wrote The Origin of Species in 1859. The scarcity of transitional forms, frequency of punctuated equilibrium, the Cambrian explosion, the ever-shifting categorization of, and scandals over, supposedly human-ancestral fossils — all gave the skeptic strong reason to think that Darwinism was less of a scientific citadel than a scientific Potemkin village. Yet anyone who glances at a newspaper or watches TV knows that major new fossil finds have been announced about every month or so for the past few decades. Do they make Johnson's argument outdated?

No, they re-enforce it. Let's look at just two fossils that have been among the more prominently publicized recently. In the mid 2000s several fossils were discovered in northern Canada of a strange fish-like creature dubbed Tiktaalik. The fossils were dated to hundreds of millions of years ago, to a time when there were thought to be fish but no vertebrate land animals, or "tetrapods." On close examination the fossils were seen to have structures — in particular, bones that resembled wrists — that were thought to make them good candidates for transitional forms between fish and tetrapods. For several years Tiktaalik was hailed as the missing link between fish and land vertebrates. But its moment of fame was cut short in early 2010 with the discovery of fossil footprints in Poland of true tetrapods which were at least ten million years older than Tiktaalik. At a stroke, the Canadian fossil could no longer be a transitional form, since it appeared later in the fossil record than its supposed descendants. Thus, as Johnson argued in 1991, it continues to be true that fossils don't tell their own stories, and the tale of ancestors being modified into descendants still relies on Darwinian theory to fill in 99 percent of the details. Question the theory and the hard evidence is much less impressive.

In Chapter Six of Darwin on Trial Johnson describes a preview in 1984 for a group of anthropologists of a new exhibit of fossils related to human evolution. It was reported that everyone spoke in reverential hushed tones, and a sociologist remarked "Sounds like ancestor worship to me." Intense interest concerning possible human fossils continues unabated — and so does the exploitation of that interest. In the middle of 2009, the 200th anniversary of Darwin's birth and the 150th anniversary of the publication of The Origin of Species, a major new fossil find was announced of a lemur-like animal classified as Darwinius masillae and nicknamed "Ida." It was initially billed as the "earliest ancestor" of humanity. Oddly, the discovery was announced by New York Mayor Michael Bloomberg, accompanied not only by a scientific paper in Science magazine, but also a book, a web site, and a documentary released within a week of the unveiling. It seemed that the announcement was choreographed in the hopes of cashing in on the year of Darwin. Unfortunately, "Ida" was quickly reclassified by unprejudiced scientists as an organism that could not be on the line to humans. The Ida brouhaha, and a remarkably similar one several months later over a fossil nicknamed "Ardi," demonstrate Johnson's continuing point that the wish is too often the father of the ancestor in Darwinian theory.

The Origin of Life

Two decades ago Phillip Johnson also criticized reigning scientific theories of the origin of life as built upon little evidence and much interpretation. Today the advance of science has shown that there are even more severe roadblocks to chemical evolution than were recognized back then, so that the situation for materialistic origin of life theories has gotten substantially worse. Broadly speaking, for decades there have been two categories of origin-of-life theories: the "metabolism-first" view, where metabolic reactions in an enclosed space precede the occurrence of genetic material; and the "genetics-first" view, where a DNA-like polymer that is capable of carrying information precedes cells. The partisans of both camps have offered devastating criticisms of each other's views, so that none are left standing. A paper published by the Proceedings of the National Academy of Sciences USA in early 2010 by the prominent Hungarian scientist Eörs Szathmáry and co-workers offered a mathematical model that ruled out metabolism-first, and an article in 2007 in Scientific American by New York University chemist Robert Shapiro showed the massive roadblocks facing the genetics-first scenario. Bereft of plausible theories, the only reason at present to believe in a materialistic origin of life is if one holds it as a postulate that life must have had a materialistic origin.

The early years of life on earth, when bacteria and other single-celled organisms reigned, are getting stranger and stranger from a Darwinian point of view. Although Phil Johnson didn't touch on the subject in the early 1990s, the great advance in DNA sequencing of microbes in the past twenty years have given scientists much to think about. And one conclusion that seems increasingly firm, as leading geneticists have voiced, is that Darwin's idea of a "tree of life" — where a single primordial cell gave rise to all subsequent organisms — is dead. The DNA sequence data cannot be made to fit with the idea. What sort of model, if any, will emerge to take its place in scientific circles is hard to guess, but there is no reason to think that early life was dominated by Darwinian processes.

Twenty years ago Darwin's theory seemed a truism, simply because rival explanations had been ruled out of bounds from the start. Then Phillip Johnson's epic Darwin on Trial cut to the heart of the debate. It wasn't about evidence; it was about assumptions. And like the proverbial drunk looking for his car keys, no one searched beyond Darwin's lamppost. Two decades later, even as scientific advances accumulate, Johnson's insight remains key. We must cast off arbitrary assumptions. If we are ever to arrive at the solution the search for answers to the question of how life arose and developed has to be free to follow the evidence wherever it leads.