Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design

by Stephen C. Meyer

Francis Crick and James Watson. Since my time as a Ph.D. student at Cambridge during the late 1980s, I have been fascinated by the way their discovery transformed our understanding of the nature of life. Indeed, since the 1950s, when Watson and Crick first illuminated the chemical structure and information-bearing properties of DNA, biologists have come to understand that living things, as much as high-tech devices, depend upon digital information—information that, in the case of life, is stored in a four-character chemical code embedded within the twisting figure of a double helix.

discoveries in molecular biology during the 1950s and 1960s established that DNA contains information in digital form, with its four chemical subunits (called nucleotide bases) functioning like letters in a written language or symbols in a computer code. And molecular biology also revealed that cells employ a complex information-processing system to access and express the information stored in DNA as they use that information to build the proteins and protein machines that they need to stay alive. Scientists attempting to explain the origin of life must explain how both information-rich molecules and the cell’s information-processing system arose.

The type of information present in living cells—that is, “specified” information in which the sequence of characters matters to the function of the sequence as a whole—has generated an acute mystery. No undirected physical or chemical process has demonstrated the capacity to produce specified information starting “from purely physical or chemical” precursors.

Although we don’t know of a material cause that generates functioning digital code from physical or chemical precursors, we do know—based upon our uniform and repeated experience—of one type of cause that has demonstrated the power to produce this type of information. That cause is intelligence or mind. As information theorist Henry Quastler observed, “The creation of information is habitually associated with conscious activity.”1 Whenever we find functional information—whether embedded in a radio signal, carved in a stone monument, etched on a magnetic disc, or produced by an origin-of-life scientist attempting to engineer a self-replicating molecule—and we trace that information back to its ultimate source, invariably we come to a mind, not merely a material process. For this reason, the discovery of digital information in even the simplest living cells indicates the prior activity of a

designing intelligence at work in the origin of the first life.

Natural selection assumes the existence of living organisms with a capacity to reproduce. Yet self-replication in all extant cells depends upon information-rich proteins and nucleic acids (DNA and RNA), and the origin of such information-rich molecules is precisely what origin-of-life research needs to explain. That’s why Theodosius Dobzhansky, one of the founders of the modern neo-Darwinian synthesis, can state flatly, “Pre-biological natural selection is a contradiction in terms.”5 Or, as Nobel Prize–winning molecular biologist and origin-of-life researcher Christian de Duve explains, theories of prebiotic natural selection fail because they “need information which implies they have to presuppose what is to be explained in the first place.”6 Clearly, it is not sufficient to invoke a process that commences only once life has begun, or once biological information has arisen, to explain the origin of life or the origin of the information necessary to produce it.

Leading figures in several subdisciplines of biology—cell biology, developmental biology, molecular biology, paleontology, and even evolutionary biology—now openly criticize key tenets of the modern version of Darwinian theory in the peer-reviewed technical literature. Since 1980, when Harvard paleontologist Stephen Jay Gould declared that neo-Darwinism “is effectively dead, despite its persistence as textbook orthodoxy,”7 the weight of critical opinion in biology has grown steadily with each passing year.

A steady stream of technical articles and books have cast new doubt on the creative power of the mutation and selection mechanism.8 So well established are these doubts that prominent evolutionary theorists must now periodically assure the public, as biologist Douglas Futuyma has done, that “just because we don’t know how evolution occurred, does not justify doubt about whether it occurred.”9 Some leading evolutionary biologists, particularly those associated with a group of scientists known as the “Altenberg 16,” are openly calling for a new theory of evolution because they doubt the creative power of the mutation and natural selection mechanism.

The fundamental problem confronting neo-Darwinism, as with chemical evolutionary theory, is the problem of the origin of new biological information. Though neo-Darwinists often dismiss the problem of the origin of life as an isolated anomaly, leading theoreticians acknowledge that neo-Darwinism has also failed to explain the source of novel variation without which natural selection can do nothing—a problem equivalent to the problem of the origin of biological information. Indeed, the problem of the origin of information lies at the root of a host of other acknowledged problems in contemporary Darwinian theory—from the origin of new body plans to the origin of complex structures and systems such as wings, feathers, eyes, echolocation, blood clotting, molecular machines, the amniotic egg, skin, nervous systems, and multicellularity, to name just a few.

As an increasing number of evolutionary biologists have noted, natural selection explains “only the survival of the fittest, not the arrival of the fittest.”

In On the Origin of Species, Darwin openly acknowledged important weaknesses in his theory and professed his own doubts about key aspects of it.

This book addresses Darwin’s most significant doubt and what has become of it. It examines an event during a remote period of geological history in which numerous animal forms appear to have arisen suddenly and without evolutionary precursors in the fossil record, a mysterious event commonly referred to as the “Cambrian explosion.” As he acknowledged in the Origin, Darwin viewed this event as a troubling anomaly—one that he hoped future fossil discoveries would eventually eliminate.

Part Two, “How to Build an Animal,” explains why the discovery of the importance of information to living systems has made the mystery of the Cambrian explosion more acute. Biologists now know that the Cambrian explosion not only represents an explosion of new animal form and structure but also an explosion of information—that it was, indeed, one of the most significant “information revolutions” in the history of life. Part Two examines the problem of explaining how the unguided mechanism of natural selection and random mutations could have produced the biological information necessary to build the Cambrian animal forms.

The twin pillars of his theory were the ideas of universal common ancestry and natural selection. The first of these pillars, universal common ancestry, represented Darwin’s theory of the history of life. It asserted that all forms of life have ultimately descended from a single common ancestor somewhere in the distant past. In a famous passage at the end of the Origin, Darwin argued that “all the organic beings which have ever lived on this earth have descended from some one primordial form.”1 Darwin thought that this primordial form gradually developed into new forms of life, which in turn gradually developed into other forms of life, eventually producing, after many millions of generations, all the complex life we see in the present.

THE ANOMALY: DARWIN’S DOUBT Despite the scope of his synthesis, there was one set of facts that troubled Darwin—something he conceded his theory couldn’t adequately explain, at least at present. Darwin was puzzled by a pattern in the fossil record that seemed to document the geologically sudden appearance of animal life in a remote period of geologic history, a period that at first was commonly called the Silurian, but later came to be known as the Cambrian.

During this geological period, many new and anatomically sophisticated creatures appeared suddenly in the sedimentary layers of the geologic column without any evidence of simpler ancestral forms in the earlier layers below, in an event that paleontologists today call the Cambrian explosion. Darwin frankly described his concerns about this conundrum in the Origin: “The difficulty of understanding the absence of vast piles of fossiliferous strata, which on my theory were no doubt somewhere accumulated before the Silurian [i.e., Cambrian] epoch, is very great,” he wrote. “I allude to the manner in which numbers of species of the same group suddenly appear in the lowest known fossiliferous rocks.”5 The sudden appearance of animals so early in the fossil record did not easily accord with Darwin’s new theory of gradual evolutionary change, and there was one scientist who would not let him forget it.

Of course, Darwin was well aware of these problems. As he noted in the Origin, “The abrupt manner in which whole groups of species suddenly appear in certain formations has been urged by several paleontologists—for instance, by Agassiz, Pictet, and Sedgwick—as a fatal objection to the belief in the transmutation of species. If numerous species, belonging to the same genera or families, have really started into life all at once, the fact would be fatal to the theory of descent with slow modification through natural selection.”

Agassiz, for his part, would have none of it. “Both with Darwin and his followers, a great part of the argument is purely negative,” he wrote. They “thus throw off the responsibility of proof. . . . However broken the geological record may be, there is a complete sequence in many parts of it, from which the character of the succession may be ascertained.” On what basis did he make this claim? “Since the most exquisitely delicate structures, as well as embryonic phases of growth of the most perishable nature, have been preserved from very early deposits, we have no right to infer the disappearance of types because their absence disproves some favorite [i.e., Darwinian] theory.”

Darwin himself accepted the validity of Agassiz’s objection.51 As he acknowledged elsewhere in the Origin, “To the question why we do not find rich fossiliferous deposits belonging to these assumed earliest periods prior to the Cambrian system, I can give no satisfactory answer. . . . The case at present must remain inexplicable; and may be truly urged as a valid argument against the views here entertained.”

Walcott, already the director of the Smithsonian Institution, was about to enter the most significant phase of his professional life. More than this, he was about to make perhaps the most dramatic discovery in the history of paleontology, a rich trove of middle Cambrian–era fossils, including many previously unknown animal forms, preserved in exquisite detail, suggesting an event of greater suddenness than had been known even in Darwin’s time and detailing a greater diversity of biological form and architecture than had hitherto been imagined.

Walcott’s discoveries, they too have noted several features of the Cambrian explosion that are unexpected from a Darwinian point of view11 in particular: (1) the sudden appearance of Cambrian animal forms; (2) an absence of transitional intermediate fossils connecting the Cambrian animals to simpler Precambrian forms; (3) a startling array of completely novel animal forms with novel body plans; and (4) a pattern in which radical differences in form in the fossil record arise before more minor, small-scale diversification and variations. This pattern turns on its head the Darwinian expectation of small incremental change only gradually resulting in larger and larger differences in form.

But the problem posed by the Burgess Shale is not the increase in complexity, but the sudden quantum leap in complexity. The jump from the simpler Precambrian organisms (further explored in the next chapters) to the radically different Cambrian forms appears to occur far too suddenly to be readily explained by the gradual activity of natural selection and random variations. Neither the Burgess Shale nor any other series of sedimentary strata known in Walcott’s day recorded a pattern of novel body plans arising gradually from a sequence of intermediates. Instead, completely unique organisms such as the bizarre arthropod Opabinia (see Fig. 2.9)—with its fifteen articulated body segments, twenty-eight gills, thirty flipper-like swimming lobes, long trunk-like proboscis, intricate nervous system, and five separate eyes12—appear fully formed in the Cambrian strata along with representatives of other fundamentally different body plans and designs of equal complexity. Darwin, as we know, regarded the sudden appearance of the Cambrian animals as a significant challenge to his theory.13 Where natural selection had to bridge yawning chasms from relatively simple life-forms to exquisitely complex creatures, it would require great expanses of time.

Darwin had hoped that later fossil discoveries would eventually eliminate what he regarded as the one outstanding anomaly associated with his theory. Walcott’s discovery was not that discovery. Not only did the Burgess Shale fail to reveal the expected ancestral precursors of the known Cambrian animal forms, but it revealed a motley crew of previously unknown animal forms and body plans that now demanded their own lengthy chain of evolutionary precursors, only complicating the task of explaining the Cambrian explosion in Darwinian terms.

In the spring of 2000, Discovery Institute, where I do my research, sponsored a lecture at the University of Washington geology department by renowned Chinese paleontologist J. Y. Chen (see Fig. 3.1). As the result of his role in excavating a new discovery of Cambrian-era fossils in southern China, Professor Chen’s standing in the scientific world was on the rise. The discovery, near the town of Chengjiang in the Yunnan Province, revealed a trove of early Cambrian animal forms. After Time magazine mentioned the Chengjiang discovery in a 1995 cover story about the Cambrian explosion,1 interest in the fossils surged. When he came to Seattle, Professor Chen had already published numerous scientific papers about this profusion of novel life-forms and had established himself as one of the foremost experts on the fossils in this unique geological setting.

So there was little doubt about the significance of the discoveries that Chen came to report that day. What was soon in doubt, however, was Chen’s scientific orthodoxy. In his presentation, he highlighted the apparent contradiction between the Chinese fossil evidence and Darwinian orthodoxy. As a result, one professor in the audience asked Chen, almost as if in warning, if he wasn’t nervous about expressing his doubts about Darwinism so freely—especially given China’s reputation for suppressing dissenting opinion. I remember Chen’s wry smile as he answered. “In China,” he said, “we can criticize Darwin, but not the government. In America, you can criticize the government, but not Darwin.”

Nevertheless, those in the audience that day soon learned that Professor Chen had good reasons for questioning Darwin’s picture of the history of life. As Chen explained, the Chinese fossils turn Darwin’s tree of life “upside down.” They also cast doubt on a surviving version of Charles Walcott’s artifact hypothesis, a crucial prop in the case for Darwinian gradualism.

Whittington, a trilobite expert, understood this as well as anyone. In 1971, he published the first comprehensive taxonomic review of the Burgess biota. In his review, he broke decisively with Walcott’s previous attempt to lump all Cambrian forms into a few preexisting taxonomic categories. In so doing, he reemphasized the morphological disparity present in the Burgess animal biota and, in the process, deprived evolutionary biologists of one part of Walcott’s two-part strategy for minimizing the Cambrian problem. By lumping all Burgess animals into existing phyla and classes, Walcott had seemingly diminished the problem of disparity by reducing the number of novel phyla for which connecting intermediates were required. By recognizing the disparity clearly on display in the Burgess, Whittington partially undercut Walcott’s solution to the Cambrian mystery and highlighted what would become its central unsolved problem: the origin of novel biological form.

Until the early 1990s, most paleontologists thought the Cambrian period began 570 million and ended 510 million years ago, with the Cambrian explosion of novel animal forms occurring within a 20- to 40-million-year window during the lower Cambrian period.

Two developments have led paleontologists and geochronologists to revise those estimates downward. First, in 1993, radiometric dating of zircon crystals from formations just above and below Cambrian strata in Siberia allowed for a precise redating of Cambrian strata. Radiometric analyses of these crystals fixed the start of the Cambrian period at 544 million years ago,58 and the beginning of the Cambrian explosion itself to about 530 million years ago (see Fig. 3.8). These studies also suggested that the explosion of the novel Cambrian animal forms occurred within a window of geologic time much shorter than previously believed, lasting no more than 10 million years, and the main “period of exponential increase of diversification” lasting only 5 to 6 million years.

Geologically speaking, 5 million years represents a mere 1/10 of 1 percent (0.11 percent, to be precise) of earth’s history. J. Y. Chen explains that “compared with the 3-plus-billion-year history of life on earth, the period [of the explosion] can be likened to one minute in 24 hours of one day.”60

Likewise, a 2012 paper in Biological Reviews acknowledges that “phylogenetic conflict is common, and frequently the norm rather than the exception.”14 Echoing these views, a January 2009 cover story and review article in New Scientist observed that today the tree-of-life project “lies in tatters, torn to pieces by an onslaught of negative evidence.” As the article explains, “Many biologists now argue that the tree concept is obsolete and needs to be discarded,” because the evidence suggests that “the evolution of animals and plants isn’t exactly tree-like.”

The New Scientist article cited a study by Michael Syvanen, a biologist at the University of California at Davis, who studied the relationships among several phyla that first arose in the Cambrian.15 Syvanen’s study compared two thousand genes in six animals spanning phyla as diverse as chordates, echinoderms, arthropods, and nematodes. His analysis yielded no consistent tree-like pattern. As the New Scientist reported, “In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories.” Syvanen himself summarized the results in the bluntest of terms: “We’ve just annihilated the tree of life. It’s not a tree anymore, it’s a different topology [pattern of history] entirely. What would Darwin have made of that?”

My point in summarizing these disputes is simply to note that the molecular and anatomical data commonly disagree, that one can find partisans on every side, that the debate is persistent and ongoing, and that, therefore, the statements of Dawkins, Coyne, and many others about all the evidence (molecular and anatomical) supporting a single, unambiguous animal tree are manifestly false. As can readily be seen by comparing Figures 6.1a and 6.1b,36 these hypotheses—Coelomata and Ecdysozoa—contradict each other. Although both might be false, both cannot be true.

Of course, my family reunion illustration breaks down as an analogy to the history of animal life, because if we could trace the history of all the people at the reunion back far enough we would find that they are all related by common ancestry. Though we can choose to assume that the same is true of the Cambrian animals, neither the fossil evidence nor the evidence of genetics and comparative anatomy actually establishes that.

Paleontologists Douglas Erwin and James Valentine exposed this problem in 1987 in a seminal paper titled “Interpreting Great Developmental Experiments: The Fossil Record.”20 They questioned the ability of both of the main evolutionary theories of the time—punctuated equilibrium and neo-Darwinism—to explain the pattern of fossil appearance in the Precambrian–Cambrian fossil record.21 Clearly, neo-Darwinism does not explain this pattern. But, as Valentine and Erwin argue, neither does punctuated equilibrium. As they conclude, the mechanism of species selection requires a large pool of species upon which to act. Thus, Valentine and Erwin conclude: “The probability that species selection is a general solution to the origin of higher taxa is not great.”

Many critics of punctuated equilibrium have noted this problem. As Richard Dawkins wrote in 1986: “What I mainly want a theory of evolution to do is explain complex, well-designed mechanisms like hearts, hands, eyes and echolocation. Nobody, not even the most ardent species selectionist, thinks that species selection can do this.”31 Or as paleontologist Jeffrey Levinton argued in 1988, “It is inconceivable how selection among species can produce the evolution of detailed morphological structures. . . . Species selection did not form an eye.”32

When I was a college professor, I used to ask my students a question: “If you want your computer to acquire a new function or capability, what do you have to give it?” Typically, I would hear a smattering of similar answers from the class: “code,” “instructions,” “software,” “information.” Of course, all these are correct. And thanks to discoveries in modern biology, we now know that something similar is true of life: to build a new form of life from a simpler preexisting form requires new information.

Shannon emphasized that the kind of information his theory described needs to be carefully distinguished from our common notions of information. As Warren Weaver, one of Shannon’s close collaborators, made clear in 1949, “The word ‘information’ in this theory is used in a special mathematical sense that must not be confused with its ordinary usage.”23 By ordinary usage, Weaver, of course, was referring to the idea of meaningful or functional communication.

Murray Eden (see Fig. 9.1), a professor of engineering and computer science at MIT, was accustomed to thinking about how to build things. But when he began to consider the importance of information to building living organisms, he realized something didn’t add up. His critics said that he knew just enough biology to be dangerous. In retrospect, they were probably right. In the early 1960s, just as molecular biologists had confirmed Francis Crick’s famed sequence hypothesis, Eden began to think about the challenge of building a living organism. Of course, Eden wasn’t contemplating building a living organism himself. Rather, he was thinking about what it would take for the neo-Darwinian mechanism of natural selection acting on random mutations to do the job. He wondered whether mutation and selection could generate the needed functional information.

In 1966, a distinguished group of mathematicians, engineers, and scientists convened a conference at the Wistar Institute in Philadelphia called “Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution.” Prominent among the attendees were Marcel-Paul Schützenberger, a mathematician and physician at the University of Paris; Stanislaw Ulam, the codesigner of the hydrogen bomb; and Eden himself. The conference also included a number of prominent biologists, including Ernst Mayr, an architect of modern neo-Darwinism, and Richard Lewontin, at the time a professor of genetics and evolutionary biology at the University of Chicago.

Sir Peter Medawar, a Nobel laureate and the director of the North London Medical Research Council’s laboratories, chaired the meeting. In his opening remarks, he said, “The immediate cause of this conference is a pretty widespread sense of dissatisfaction about what has come to be thought of as the accepted evolutionary theory in the English-speaking world, the so-called neo-Darwinian theory.”2

Although fully aware of this range of mutational options at nature’s disposal, Eden argued at Wistar that such random changes to written texts or sections of digital code would inevitably degrade the function of information-bearing sequences, particularly when allowed to accumulate.3 For example, the simple phrase “One if by land and two if by sea” will be significantly degraded by just a handful of random changes such as those in bold: “Ine if bg lend and two ik bT Nea.” At the conference the French mathematician Marcel Schützenberger agreed with Eden’s concerns about the effect of random alterations. He noted that if someone makes even a few random changes in the arrangement of the digital characters in a computer program, “we find that we have no chance (i.e., less than 1/101000) even to see what the modified program would compute: it just jams.”

As evolutionary biologists Jack King and Thomas Jukes put it in 1969, “Natural selection is the editor, rather than the composer, of the genetic message.”

And that was the problem, as the Wistar skeptics saw it: random mutations must do the work of composing new genetic information, yet the sheer number of possible nucleotide base or amino-acid combinations (i.e., the size of the combinatorial “space”) associated with a single gene or protein of even modest length rendered the probability of random assembly prohibitively small. For every sequence of amino acids that generates a functional protein, there are a myriad of other combinations that don’t.

Consider another illustration. The two letters X and Y can be combined in four different two-letter combinations (XX, XY, YX and YY). They can be combined in eight different ways for three-letter combinations (XXX, XXY, XYY, XYX, YXX, YYX, YXY, YYY), sixteen ways for four-letter combinations, and so on. The number of possible combinations grows exponentially—22, 23, 24, and so on—as the number of letters in the sequence grows. Mathematician David Berlinski calls this the problem of “combinatorial inflation,” because the number of possible combinations “inflates” dramatically as the number of characters in a sequence grows

The combinations of bases in DNA are subject to combinatorial inflation of just this sort. The information-bearing sequences in DNA consist of specific arrangements of the four nucleotide bases. Consequently, there are four possible bases that could occur at each site along the DNA backbone and 4 × 4, or 42, or 16 possible two-base sequences (AA AT AG AC TA TG TC TT CG CT CC CA GA GG GC GT). Similarly, there are 4 × 4 × 4, or 43, or 64 possible three-base sequences. (I’ll refrain from listing them all.) That is, increasing the number of bases in a sequence from 1 to 2 to 3 increases the number of possibilities from 4 to 16 to 64. As the sequence length continues to grow, the number of combinatorial possibilities corresponding to sequences of increasing length inflates exponentially. For example, there are 4100, or 1060, possible ways of arranging one hundred bases in a row.

The amino-acid chains are also subject to such inflation. A chain of two amino acids could display 202, or 20 × 20, or 400 possible combinations, since each of the twenty protein-forming amino acids could combine with any one of that same group of twenty in the second position of a short peptide chain. With a three-amino-acid sequence, we’re looking at 203, or 8,000, possible sequences. With four amino acids, the number of combinations rises exponentially to 204, or 160,000, total combinations, and so on.

Now, the number of combinatorial possibilities corresponding to a chain with four amino acids only marginally outstrips the combinatorial possibilities associated with the five-dial lock in my first illustration (160,000 vs. 100,000). It turns out, however, that many necessary, functional proteins in cells require far, far more than just four amino acids linked in sequence, and necessary genes require far, far more than just a few bases. Most genes—sections of DNA that code for a specific protein—consist of at least one thousand nucleotide bases. That corresponds to 41000—an unimaginably large number—possible base sequences of that length.

Moreover, it takes three bases in a group called a codon to designate one of the twenty protein-forming amino acids in a growing chain during protein synthesis. If an average gene has about 1000 bases, then an average protein would have over 300 amino acids, each of which are called “residues” by protein chemists. And indeed proteins typically require hundreds of amino acids in order to perform their functions. This means that an average-length protein represents just one ...

Putting these numbers in perspective, there are only 1065 atoms in our Milky Way galaxy and 1080 elementary p...