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

by Stephen C. Meyer

For example, any bilaterian that manifests the characteristic exoskeleton of, say, an arthropod cannot also qualify as a plausible ancestor of a chordate, because chordates have internal skeletons or notochords.

The logic of these distinct body designs precludes sharing both anatomical characteristics. For this reason, any hypothetical bilaterian common ancestor could only have existed as a kind of lowest anatomical common denominator, or what evolutionary biologists call a “ground plan,” having only those few features that are common to all of the animal forms that allegedly evolved from it. But this creates a dilemma. If a fossilized form is simple enough to qualify as the common ancestor of later highly differentiated bilaterian phyla, then it will necessarily lack most of the important distinguishing anatomical features of those specific phyla. That means that all the interesting anatomical novelties that differentiate one phylum from another must arise along the separate lineages branching out from the alleged common ancestor well after its origin in the fossil record. Heads, jointed limbs, compound eyes, guts, anuses, antennae, notochords, stereoms, lophophores (a tentacled feeding organ), and numerous other distinguishing characteristics of many different animals must come later on many distinct lines of descent. Yet the gradual evolutionary origin of these characteristics is not documented in the Precambrian fossil record. These characteristics do not appear until they arise suddenly in the Cambrian explosion. For this reason, indistinct fossils such as Vernanimalcula—even if we take them as representing a common ancestor of many bilaterians—document little of the Darwinia...

If an alleged ancestral form manifests the distinguishing features of one of the specific Cambrian phyla—if, for example, Vernanimalcula or some other isolated form presented a convincing set of distinctively arthropod or chordate or echinoderm characteristics, then the very presence of those features would necessarily preclude the possibility of that specific animal form representing the common ancestor of all other Cambrian forms. The more an animal form manifests the characteristics of one phylum or group within the phylum, the less plausible it becomes as the ancestor of all the other animal phyla. And that is the dilemma in a nutshell. Highly differentiated and complex Precambrian forms by themselves could not have been ancestors common to all the Cambrian phyla; whereas undifferentiated forms simple enough to have been ancestral to all the Cambrian phyla leave no evidence, by themselves, of the gradual emergence of the complex anatomical novelties that define the Cambrian animals.

As Graham Budd and Sören Jensen state, “The known [Precambrian/Cambrian] fossil record has not been misunderstood, and there are no convincing bilaterian candidates known from the fossil record until just before the beginning of the Cambrian (c. 543 Ma), even though there are plentiful sediments older than this that should reveal them.”55 Thus they conclude, “The expected Darwinian pattern of a deep fossil history of the bilaterians, potentially showing their gradual development, stretching hundreds of millions of years into the Precambrian, has singularly failed to materialize.”56

the expected ancestral forms of the Cambrian animals—the very ones that Darwin hoped to find a hundred and fifty years ago—are still missing from the Precambrian fossil record.

Evolutionary biologists will acknowledge problems to each other in scientific settings that they will deny or minimize in public, lest they aid and abet the dread “creationists” and others they see as advancing the cause of unreason.

In a famous chapter in On the Origin of Species titled “The Mutual Affinities of Organic Beings,” Darwin made his case not on the basis of the fossil evidence, but on the basis of similar anatomical structures in many distinct organisms. He noted, for example, that the forelimbs of frogs, horses, bats, humans, and many other vertebrates exhibited a common five-digit (“pentadactyl”) structure or organization (see Fig. 5.1). To explain such “homologies,” as he called them, Darwin posited a vertebrate ancestor that possessed pentadactyl limbs in rudimentary form. As a menagerie of modern vertebrates evolved from this common ancestor, each retained in its own way the basic pentadactyl mode of organization. For Darwin, his theory of descent with modification from a common ancestor explained these similarities better than the received view of many older nineteenth-century biologists such as Louis Agassiz or Richard Owen, both of whom thought homologies reflected the common design plan of a creative intelligence.

In reconstructing the evolutionary history of life, most evolutionary biologists today emphasize the importance of homology. They assume that similarities in anatomy and in the sequences of information-bearing biomacromolecules such as DNA, RNA, and protein point strongly to a common ancestor.

2 They also assume that the degree of difference in such cases is on average proportional to the time elapsed since the divergence from a common ancestor. The greater the difference in the common feature or molecular sequence, the farther back the ancestor from which the feature or sequence arose.

Defenders of neo-Darwinism assert that these techniques have produced a coherent evolutionary picture of the early history of animal life. They assert that clues from the realm of genetics point unequivocally to Precambrian ancestral forms and to an evolutionary history that fossils have failed to document.

Many paleontologists and evolutionary biologists now concede that the long-sought-after Precambrian fossils, those necessary to document a Darwinian account of the origin of animal life, are missing.4 Scientists are especially candid about this when addressing each other in the technical peer-reviewed literature. Often, however, defenders of evolutionary orthodoxy raise another possibility—that the common ancestor of the Cambrian animals has been documented after all, not by fossil evidence, but by molecular or genetic evidence of what they call a “deep divergence” of animal life. In making such claims, these biologists clearly privilege molecular evidence over evidence from the fossil record. Proponents of deep divergence don’t deny that the fossil evidence has come up short. Instead, they adopt one of the versions of the artifact hypothesis to account for that missing evidence. They then argue that there was no “explosion” of animal forms in the Cambrian, but rather a “long fuse” of animal evolution and diversification lasting many millions of years leading up to what only looks like an “explosion” of animal life in the Cambrian, but this evolutionary history was hidden from the fossil record. Indeed, they argue that molecular evidence establishes a long period of undetected or cryptic evolution in Precambrian times, beginning from a common ancestor some 600 million to 1.2 billion years ago, depending upon which study of the molecular genetic data they cite. If correct, ...

Advocates of deep divergence use a method of analysis known as the “molecular clock.” Molecular clock studies also assume that the extent to which sequences differ in similar genes in two or more animals reflects the amount of time that has passed since those animals began to evolve from a common ancestor.

In theory, once the mutation rate has been determined, it can be used to calculate the divergence time of other present-day species, after their homologous genes have been compared for differences.

The Wray study concluded that the common ancestor of the animal forms lived 1.2 billion years ago, implying that the Cambrian animals took some 700 million years to evolve from this “deep-divergence” point before first appearing in the fossil record. Wray and his colleagues attempted to explain the absence of fossil ancestral forms during this period of time by postulating that Precambrian ancestors existed in exclusively soft-bodied forms, rendering their preservation unlikely.

They estimated that “the last common ancestor of all living animals arose nearly 800 million years ago.”13

They conclude: “Our results cast doubt on the prevailing notion that the animal phyla diverged explosively during the Cambrian or late Vendian, and instead suggest that there was an extended period of divergence during the mid-Proterozoic, commencing about a billion years ago.”

As Andrew Knoll, a Harvard paleontologist, states, “The idea that animals should have originated much earlier than we see them in the fossil record is almost inescapable.”

Nevertheless, there is now good reason to doubt this allegedly overwhelming genetic evidence. In the idiom of our forensic metaphor, other material witnesses (fossils) have already come forward to testify, the testimony of the genes (and other key indicators of biological history) is grossly inconsistent, and that genetic testimony has come to us through a translator, who is shaping the way the jury perceives the evidence. Let’s look at each of these problems in turn.

As we saw in Chapter 3, there is no currently plausible version of the artifact hypothesis. The preservation of numerous soft-bodied Cambrian animals as well as Precambrian embryos and microorganisms undermines the idea of an extensive period of undetected soft-bodied evolution. In addition, the claim that exclusively soft-bodied ancestors preceded the hard-bodied Cambrian forms remains anatomically implausible. A brachiopod cannot survive without its shell. An arthropod cannot exist without its exoskeleton. Any plausible ancestor to such organisms would have likely left some hard body parts, yet none have been found in the Precambrian. Yet the deep-divergence hypothesis, whatever its other merits, requires a viable artifact hypothesis to explain the absence of fossilized Precambrian ancestors.

Sometimes even different studies of the same or similar groups of molecules have generated dramatically different divergence times.

If histones change too slowly to provide an accurate calibration of the molecular clock, then which molecules do change at the correct rate—and how do we know that they do? The answer to these questions for most evolutionary biologists usually runs something like this. We already know that the animal phyla evolved from a common ancestor and we also know roughly when they did; therefore, we must reject studies based on histone sequences because the conclusions of these studies would contradict that date. But do we really know these things, and if so how? Assumptions about the window of time in which the first metazoan, the ancestor of all animals, must have lived are clearly not derived from the testimony of molecular genetics alone, since the results of sequence comparisons vary so greatly and include dates, depending upon the molecule studied, that fall outside that window.

The subjective quality of these conclusions, where scientists “cherry-pick” evidence that conforms to favored notions and discard the rest, casts further doubt on the extent to which molecular comparisons yield any clear historical signal.

These comparisons assume the accuracy of molecular clocks—that mutation rates of organisms have remained relatively constant throughout geological time. These studies also assume, rather than demonstrate, the theory of universal common descent. Both assumptions are problematic.

So great is this variation that one paper in the journal Molecular Biology and Evolution cautions, “The rate of molecular evolution can vary considerably among different organisms, challenging the concept of the ‘molecular clock.’ ”

“the idea that there is a universal molecular clock ticking away has long since been discredited.”38

these studies assume the existence of such ancestors, and then merely attempt, given that assumption, to determine how long ago such ancestors might have lived.

to invoke molecular studies that assume the existence of a common ancestor as evidence for such an entity only begs the question. Certainly it provides no reason for using molecular evidence to trump fossil evidence. Perhaps the Precambrian rocks do not record ancestors for the Cambrian animals because none existed. To foreclose that possibility, and to resolve the mystery of the missing Precambrian ancestral fossils, evolutionary biologists cannot use studies that assume the existence of the very entity their studies are thought to establish.

the design logic and arrangement of parts necessary to provide the foundation for one mode of animal life preclude it from providing the foundation for other modes of animal life—just as a system of parts providing one mode of transportation (with a bicycle, for example) will typically preclude functioning as another (as with a submarine, for example).43

For this reason, biologists thinking about the characteristics of the earliest ancestor of all the metazoan phyla—the actual animal at the deep-divergence point—have typically postulated an extremely simple form of life—what one evolutionary biologist described to me as a “shmoo,” after the blob-like cartoon character made famous by Al Capp in the 1940s and 1950s.

Could there have been an animal form simple enough to serve as a viable ancestor common to all the animal phyla? Perhaps. But positing such a form only deepens the required depth of the divergence point and intensifies the already significant problem of Precambrian–Cambrian fossil discontinuity.

The results of different studies diverge too dramatically to be conclusive, or even meaningful; the methods of inferring divergence points are fraught with subjectivity; and the whole enterprise depends upon a question-begging logic.

he concludes, “A deep history extending to an origination in excess of 1,000 Myr [million years] is very unlikely.”

In 2009, in honor of the bicentennial anniversary of Darwin’s birth, a piece of artwork was created to adorn the ceiling of an exhibit room at the Natural History Museum in London. A paper in the journal Archives of Natural History noted that the inspiration for the artwork, titled “TREE,” came from a diagram that Darwin had sketched in one of his notebooks—a diagram that later came to be known as the “tree of life” (see Fig. 2.11a). One BBC radio program called the TREE exhibit the “Darwinian Sistine Chapel.”1 Another article in Archives of Natural History, a journal published by the University of Edinburgh, remarked that, “TREE celebrates Darwinian evolutionism” and “secular science and reason.”2

Though the fossil record does not directly attest to many of the expected intermediate forms represented on Darwin’s tree, leading authorities assert that other lines of evidence, particularly from genetics, firmly establish Darwin’s tree as the correct picture of the history of life.

The tree of life as a whole, however, is another matter. Many evolutionary biologists think the case for universal common descent is something close to unassailable because, they argue, analysis of both anatomical and genetic similarities converges on the same basic pattern of descent from a universal common ancestor. As Richard Dawkins asserts, “when we look comparatively at . . . genetic sequences in all these different creatures—we find the same kind of hierarchical tree of resemblance. We find the same family tree—albeit much more thoroughly and convincingly laid out—as we did with . . . the whole pattern of anatomical resemblances throughout all the living kingdoms.”5 Likewise, Jerry Coyne argues that gene sequences independently confirm the same set of evolutionary relationships—the same basic tree—established from the analysis of anatomy.6 Oxford University chemist Peter Atkins is even more emphatic: “There is not a single instance of the molecular traces of change being inconsistent with our observations of whole organisms.”7 As a result of this confidence, evolutionary biologists often dismiss the missing Precambrian fossil precursors and intermediates as a minor anomaly—one awaiting explanation by an otherwise completely adequate theory of the history of life.

Occidental College geologist Donald Prothero explains, “If the fossil record is poor in one particular group, we look to other sources of data.” He concludes that two such sources of data, anatomical and molecular data, now “converge on a common answer”—one “that is almost certainly ‘the truth’ (as much as we can use that term in science).”10 But is all of this true? Does analysis of the genetic and anatomical similarity of the Cambrian animals really establish that the history of animal life is best depicted as a continuously branching tree? Does the pattern of a branching tree accurately depict the history of Precambrian and Cambrian animal life, and in so doing establish the existence of Precambrian forms that the fossil record fails to document?

History happened once. And if Richard Dawkins is correct that “there is, after all, one true tree of life, the unique pattern of evolutionary branchings that actually happened,”11 then evolutionary history also happened once. Consequently, if we think of evolutionary trees describing the relationships of animal groups as hypotheses about an unobserved history (which is what they are), then having two or more conflicting hypotheses about only one history—the history that actually happened—means that we haven’t figured out what did happen. A widely used textbook on phylogenetic methods explains this: “The fact that there is only one true tree . . . provides the basis for testing alternative hypotheses. If two hypotheses are generated for the same group of species, then we can conclude that at least one of these hypotheses is false. Of course, it is possible that both are false and some other tree is true.”

When a body of evidence supports multiple conflicting historical hypotheses, the evidence cannot be sending a definitive historical signal about what happened in the past. That raises the possibility that it may not be sending a signal at all. Conversely, when the evidence leads investigators to converge around a single historical hypothesis, when one hypothesis best explains a whole group of clues, it is much more likely that the evidence is telling us what actually happened.

Consider, by way of illustration, a case in which we know a true history of ancestor–descendant relationships to see how evidence can converge around a single (unequivocal) history. Between 1839 and 1856, Charles Darwin and his wife, Emma, produced ten children, listed below in alphabetical order: Anne Charles Elizabeth Francis George Henrietta Horace Leonard Mary William This alphabetical listing, of course, is not their actual birth order. Instead, it is one of a large number of possible birth orders for Darwin’s children, only one of which is the correct sequence. Indeed, only one of these arrangements can represent the actual Darwin family history. Now, suppose I gave you and some friends a pile of historical evidence about Darwin’s children, and asked you to “solve for their birth order.” No one would consider the problem solved if you came back with more than one order. On the other hand, if you came back and presented a single coherent hypothesis of the birth order supported by evidence from birth records, family letters, and photographs from the Darwin family archives, that would provide persuasive evidence that you had obtained the correct solution. Since only one true history exists, once you find it the evidence will tend to fall naturally into place.

There are several reasons to doubt that evidence of genetic and anatomical similarity is sending a reliable signal of the early history of animal life.

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?”

Nevertheless, he concedes that a century and a half after The Origin of Species, “a complete and accurate tree of life remains an elusive goal.”

Their article brings the discussion of the Cambrian explosion full circle from an attempt to use genes to compensate for the absence of fossil evidence to the acknowledgment that genes do not convey any clear signal about the evolutionary relationships of the phyla first preserved by fossils in the Cambrian.

Thus, the inability to reconstruct the evolutionary history of the animal phyla from the molecular data not only fails to establish a Precambrian pattern of descent; it ironically also reaffirms the extreme rapidity of the origin of the Cambrian animal forms.

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.

germ cells receive external signals from surrounding tissues to become primordial germ cells (PGCs, illustrated by solid white squares in Fig. 6.3b).

Germ-cell formation has indisputable evolutionary importance. To evolve, a population or a species must leave offspring; to leave offspring, species of animals must generate primordial germ cells. No PGCs, no reproduction; no reproduction, no evolution.

there has been a long history of scientific controversy about just how much novelty natural selection can produce and about whether natural selection is a truly creative process.

In fact, between 1870 and 1920 classical Darwinism entered a period of eclipse, because many scientists thought that it could not explain the origin and transmission of new heritable variation.1