Darwin's Doubt

by Stephen C. Meyer

  There are two aspects of this endeavor. First, by analyzing the genes of existing animals representing phyla that first arose in the Cambrian, scientists have attempted to establish when the common ancestor of the Cambrian animal forms lived. This effort has generated what is known as the “deep-divergence hypothesis,” which holds that the common ancestor of all animal life arose long before the Cambrian explosion. Second, by analyzing anatomical and molecular similarities, biologists have attempted to reconstruct the Precambrian–Cambrian tree of life, mapping the course of evolution during a cryptic period before the Cambrian.

  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.

  This chapter will examine what genes tell us about the alleged universal common ancestor of all animals; the next chapter will consider whether the analysis of genes (and other features of organisms) yield a coherent treelike picture of the Precambrian prehistory of animal life. Genetic analyses have indeed revealed a trove of clues. The question is: Do those genetic clues establish the Precambrian ancestor and history that fossils have failed to document, or, as sometimes occurs in criminal investigations, has there been a rush to judgment?

  Deep Divergence

  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, the Cambrian phyla may have had many hundreds of millions of years to evolve from a common ancestor.5

  The Molecular Clock

  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. A small difference means a short time; a big difference, a long time. To determine exactly how short or long, these studies estimate the mutation rate by analyzing genes in two species or taxa that are thought to have evolved from an ancestor whose presence in the fossil record can be discerned and dated accurately. For example, many molecular-clock studies of birds and mammals are calibrated based on the age of an early reptile thought to be the most recent common ancestor of both.

  FIGURE 5.2

  The idea behind the molecular clock. The two animals and their homologous gene sequences at the right of the figure show the molecular distance between two present-day animals, that is, how many mutational differences have accumulated over time since they diverged on the tree of life. The animal at the left of the figure (a mammal-like reptile) represents the common ancestor from which these animals presumably evolved. Knowing how long ago the common ancestor (the mammal-like reptile) lived, and how many mutational differences have accumulated in its descendants during that time, allows scientists to calculate a mutation rate. 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.

  Genetic comparisons enable evolutionary biologists to estimate the number of mutational changes since divergence, and dating of the strata containing presumed fossil ancestors tells how long ago the divergence occurred. Assuming that different lineages evolve at the same rate,6 together the two pieces of information enable evolutionary biologists to calculate a baseline mutation rate. They can then use that rate to determine how long ago some other pair of animals diverged from each other on the evolutionary tree (see Fig. 5.2).7

  Advocates of the deep-divergence hypothesis have applied this method to analyzing similar genes, RNA molecules, or proteins in pairs of animals belonging to phyla that first arose in the Cambrian period. In this way they estimate how long it took for the different animal phyla to diverge from a common Precambrian ancestor.

  Deep and Deeper: Evidence for Deep Divergence

  In the 1990s, evolutionary biologists Gregory A. Wray, Jeffrey S. Levinton, and Leo H. Shapiro performed a major study of Cambrian-relevant molecular sequence data. In 1996, they published their results in a paper entitled “Molecular Evidence for Deep Precambrian Divergences Among Metazoan Phyla.”8 Wray’s team compared the degree of difference between the amino-acid sequences of seven proteins9 derived from several different modern animals representing five Cambrian phyla (annelids, arthropods, mollusks, chordates, and echinoderms). They also compared the nucleotide base sequences of a ribosomal RNA molecule10 from the same animal representatives of the same five phyla.

  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.

  More recently, Douglas Erwin and several colleagues performed a study comparing the degree of sequence difference between other genes—seven nuclear housekeeping genes11 and three ribosomal RNA genes12 across 113 different species of living Metazoa. (The term “Metazoa” refers to animals with differentiated tissue. The term “metazoan” refers to one such animal or can be used as an adjective, as in “the metazoan phyla.”) They estimated that “the last common ancestor of all living animals arose nearly 800 million years ago.”13

  Many similar studies affirm a very ancient or “stratigraphically deep” divergence of the animal forms, in opposition to those who claim that the Cambrian animals appeared suddenly within just a few million years.14 Each of these studies affirms the gradual emergence of animal life that most researchers expected to find on the basis of a Darwinian picture of the history of animal life. Indeed, a major aim of the Wray study was to challenge the view “that the animal phyla diverged in an ‘explosion’ near the beginning of the Cambrian period.”15 Wray and his colleagues argue instead that “all mean divergence time estimates between these four phyla and chordates, based on all seven genes, substantially predate the beginning of the Cambrian period.”16 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.”17

  From an orthodox Darwinian point of view, the conclusions of these studies seem almost unavoidable since (1) the neo-Darwinian mechanism requires vast amounts of time to produc
e anatomical novelty and (2) such phylogenetic analyses assume that all the animal forms descended from a common ancestor. Many evolutionary biologists claim that clues long hidden in DNA now confirm these Darwinian axioms and, consequently, the existence of an extremely ancient, Precambrian ancestor of the Cambrian animals. 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.”18

  Reasonable Doubt

  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.

  Fossil Testimony

  Recall that the deep-divergence hypothesis has two components. One of them—a version of the artifact hypothesis—provides an explanation for why the Precambrian ancestral fossils are missing. And here the deep-divergence hypothesis first runs into trouble. 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.

  The Testimony of Genes: Conflicting Stories

  There is a second, more telling reason to doubt the deep-divergence hypothesis: the results of different molecular studies have generated widely divergent results. Yet presumably there was only one common ancestor of all the Metazoa and only one ultimate divergence point.

  For example, comparing the Wray-led study and the Erwin-led study generates a difference of 400 million years. In the case of other studies, even greater differences emerge. Many other studies have thrown their own widely varying numbers into the ring, placing the common ancestor of animals anywhere between 100 million and 1.5 billion years before the Cambrian explosion (some molecular clock studies, oddly, even place the common ancestor of the animals after the Cambrian explosion).19 As Douglas Erwin, writing with fellow paleontologists James Valentine and David Jablonski, acknowledged in 1999: “Attempts to date those branching[s]” from a common Precambrian ancestor “by using molecular clocks have disagreed widely.”20 How can this be?

  In the first place, different studies of different molecules generate widely divergent dates. In addition to the studies I have already cited, a 1997 paper by Japanese biologist Naruo Nikoh and colleagues examined two genes (aldolase and triose phosphate isomerase), and dated the split between eumetazoa and parazoa—animals with tissues (like cnidarians) from those without (like sponges)—at 940 million years ago.21 Compare that to a 1999 paper by Daniel Wang, Sudhir Kumar, and S. Blair Hedges based on the study of 50 different genes, showing that “the basal animal phyla (Porifera, Cnidaria, Ctenophora) diverged between about 1200–1500 Ma.”22

  Sometimes contradictory divergence times are reported in the same article. For instance, a refreshingly forthright paper by evolutionary biologist Lindell Bromham of Australian National University and colleagues in Proceedings of the National Academy of Sciences USA analyzed two different molecules, mitochondrial DNA and 18S rRNA, to yield individual gene-based divergence dates that differed by as much as 1 billion years.23 Another study investigating the divergence between arthropods and vertebrates found that depending on which gene was used, the divergence date might be anywhere between 274 million and 1.6 billion years ago, the former date falling almost 250 million years after the Cambrian explosion.24 That paper in its conclusion chose to split the difference, confidently reporting an arithmetic average of about 830 million years ago. Likewise, bioinformaticians Stéphane Aris-Brosou, now at the University of Ottawa, and Ziheng Yang, at University College London, found that depending on which genes and which estimation methods were employed, the last common ancestor of protostomes or deuterostomes (two broadly different types of Cambrian animals) might have lived anywhere between 452 million and 2 billion years ago.25

  A survey of recent deep-divergence studies, by molecular evolutionists Dan Graur and William Martin, notes one study in which the authors claim to be 95 percent certain that their divergence date for certain animal groups falls within a 14.2-billion-year range—more than three times the age of the earth and clearly a meaningless result.26 Graur and Martin conclude that many molecular-clock estimates “look deceptively precise,” but, given the nature of this field, their “advice to the reader is: whenever you see a time estimate in the evolutionary literature, demand uncertainty!”27 The title of their paper, published in Trends in Genetics, made the point still more vividly: “Reading the Entrails of Chickens: Molecular Timescales of Evolution and the Illusion of Precision.”

  Sometimes even different studies of the same or similar groups of molecules have generated dramatically different divergence times. For example, Francisco Ayala and several colleagues have recalculated the divergence times of Metazoan phyla, using mostly the same protein-coding genes as Wray’s team.28 Correcting for “a host of statistical problems”29 in the Wray study, Ayala and colleagues found that their own estimates “are consistent with paleontological estimates”—not with the deep-divergence hypothesis. “Extrapolating to distant times from molecular evolutionary rates estimated within confined datasets,” they conclude, is “fraught with danger.”30 Or as Valentine, Jablonski, and Erwin conclude, “The accuracy of the molecular clock is still problematical, at least for phylum divergences, for the estimates vary by some 800 million years depending upon the techniques or molecules used.”31 Reported Precambrian divergence times would vary even more dramatically were it not that evolutionary biologists and molecular taxonomists ignore certain molecules in their studies to avoid grossly contradictory results. Consider, for example, histones—proteins found in all eukaryotes involved in packing DNA into chromosomes. Histones exhibit little variation from one species to the next.32 They are never used as molecular clocks. Why? Because the sequence differences between histones, assuming a mutation rate comparable to that of other proteins, would generate a divergence time at significant variance with those in studies of many other proteins.33 Specifically, the small differences between histones yield an extremely recent divergence, contrary to other studies. Evolutionary biologists typically exclude histones from consideration, because those times do not confirm preconceived ideas about what the Precambrian tree of life ought to look like.

  But that raises obvious questions. If we don’t have fossils documenting a common animal ancestor, and if genetic studies produce such different and contradictory divergence times, how do we know what the tree of life should look like and when the first animals began to diverge from a common ancestor? 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 tes
timony 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. Instead, as one widely used textbook euphemistically puts it, evolutionary biologists must choose “phylogenetically informative” data.34 By this, they mean sequences that exhibit neither too little nor too much variation—where too much and too little are determined by preconceived considerations of evolutionary plausibility, rather than by reference to independent criteria for determining the accuracy of molecular methods.

  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. Only one divergence point could represent the actual universal common ancestor of all animals. If, however, comparative sequence analyses generate divergence times that are consistent with nearly all possible evolutionary histories, with the divergence event ranging from a few million to a few billion years ago, then clearly most of these possible histories must be wrong. They tell us little about the actual time of the Precambrian divergence, if such an event really happened.

  Questionable Assumptions

  Other problems run even deeper, having to do with the assumptions that make comparative sequence analyses possible in the first place. 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.