Darwin's Doubt

by Stephen C. Meyer

  In summary, Behe and Snoke applied the principles derived from population genetics to evaluate the creative power of the standard neo-Darwinian model of gene evolution. They showed that the standard model encounters clear probabilistic limits if the structures it needs to build require more than two coordinated mutations in multicellular eukaryotic organisms.

  The Edge of Evolution and Its Critics

  Behe and Snoke are well-known critics of the creative power of the neo-Darwinian mechanism, so their conclusion might seem suspect to some observers. Nevertheless, evolutionary biologists attempting to defend the creative power of the neo-Darwinian mechanism have inadvertently confirmed Behe and Snoke’s conclusions.

  Two recent scientific publications tell this story. First, in 2007, Michael Behe published a book, The Edge of Evolution, amplifying the results of his 2004 paper with David Snoke. Using public-health data about a genetic trait—resistance to the antimalarial drug chloroquine in the one-celled organism that causes malaria—Behe provided another line of evidence and argument to support the conclusion that multiple coordinated mutations are often necessary to produce even minor genetic adaptations.

  Based on public-health data, Behe determined that resistance to chloroquine only arises once in every 1020 malaria-causing cells. Behe inferred, by working the problem backwards, that the trait probably required multiple—though not necessarily coordinated—mutations to develop. He called this trait a “chloroquine complexity cluster,” or a “CCC.”29 Behe wanted to explore what he called the “edge of evolution,” the limits to the creative power of mutation and selection at the genetic level. Having established that this trait could arise by random mutation in a reasonably short period of time, he wondered how much time would be required to produce traits of greater complexity in populations of various sizes.

  He asked his readers to consider a hypothetical genetic trait twice as complex as a CCC cluster—a feature requiring the origin of two coordinated traits, each as complex as a CCC. In other words, Behe wondered how long it would take to develop a hypothetical trait that required two genetic changes as complex as a chloroquine complexity cluster, if both changes had to occur together in the same organism—in a coordinated fashion—in order to produce the trait. He then showed, using the principles of population genetics, that multi-mutation traits of that complexity—the molecular equivalent of two coordinated CCCs—would require many more organisms or vastly more time than was reasonable given the history of life. Remember the Powerball lottery: waiting times increase exponentially with each additional coordinated change or winning element needed. Behe showed, for example, that if 1020 organisms were required to obtain one CCC, then the square of that amount—1040 organisms—would be required to evolve a trait that required two coordinated CCCs before providing any advantage.30 But, as we saw in Chapter 10, only 1040 total organisms have ever existed on earth, implying that the entire history of the earth would barely provide enough opportunities to generate a trait of this complexity.31

  Similarly, Behe reasoned that for organisms in smaller population sizes, developing a trait of twice the complexity of a CCC would require immensely long waiting times. He also determined that exceedingly long waiting times are typically required to generate even less complex genetic adaptations in smaller populations.

  Behe showed that the problem of coordinated mutations was particularly acute for longer-lived organisms with small population sizes—organisms such as mammals or, more specifically, human beings and their presumed prehuman ancestors. Behe estimated, based upon relevant mutation rates, known human population sizes, and generation times, the time required for two coordinated mutations to occur in the hominid line. He calculated that producing even such a modest evolutionary change would require many hundreds of millions of years. Yet, humans and chimps are thought to have diverged from a common ancestor only 6 million years ago. Behe’s calculation implied that the neo-Darwinian mechanism does not have the capacity to generate even two coordinated mutations in the time available for human evolution—and thus does not explain how humans arose.

  Here the story gets really interesting. Soon after the publication of The Edge of Evolution, two Cornell University mathematical biologists, Rick Durrett and Deena Schmidt, both defenders of neo-Darwinism, attempted to refute Behe’s conclusion by making their own calculations. Their paper, “Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution,” also applied a model based upon population genetics to calculate the amount of time necessary to generate two coordinated mutations in the hominid line. Although they calculated a shorter waiting time then Behe did, their result nevertheless underscored the implausibility of relying on the neo-Darwinian mechanism to generate coordinated mutations during the relevant evolutionary timescale. Their calculation suggested that it would take not several hundred million years, but “only” 216 million years to generate and fix two coordinated mutations in the hominid line—more than thirty times the amount of time available to produce humans and chimps and all their distinctive complex adaptations and differences from their inferred common ancestor.

  In seeking to refute Behe, Durrett and Schmidt inadvertently confirmed his main contention. As they acknowledged, their calculation implies that generating two or more coordinated mutations is “very unlikely to occur on a reasonable timescale.”32 In sum, calculations performed by both critics and defenders of neo-Darwinian evolution now reinforce the same conclusion: if coordinated mutations are necessary to generate new genes and proteins, then the neo-Darwinian math itself, as expressed in the principles of population genetics, establishes the implausibility of the neo-Darwinian mechanism.

  Testing the CoOption Option

  But does generating novel genes and proteins require coordinated mutations? Behe and Snoke inferred as much based upon an undisputed fact of molecular biology: many proteins rely on sets of amino acids acting in close coordination in order to perform their functions. In addition, in The Edge of Evolution, Behe argued on functional grounds that many complex biological systems would require coordinated adaptive mutations since in these systems, the absence of even one or a few gene products (proteins or traits) will cause them to lose function. Behe specifically showed that several molecular machines within cells (such as the cilium and intraflagellar transport system, and the bacterial flagellar motor33) require the coordinated interaction of multiple protein parts in order to maintain their function. Nevertheless, in making this argument, Behe did not address an alternative idea about the pathway by which new genes and proteins might have evolved, and thus did not establish conclusively that new genes and proteins themselves represent complex adaptations.

  Some neo-Darwinists have proposed a model of protein evolution known as “cooption.” In this model, a protein that performs one function is transformed, or “co-opted” to perform some other function. This model envisions new features requiring multiple “mutations” arising in a step-by-step way to produce some protein, call it “Protein B,” from some other protein that lacked those features, call it “Protein A.” In proposing a series of single separate mutations, advocates of cooption acknowledge that the initial individual amino-acid changes, the first few steps in evolution, from Protein A, the protein lacking the multisite feature, would not allow Protein A to perform the function of Protein B. Nevertheless, they propose that these initial changes might have allowed Protein A to perform some other advantageous function, thus making it selectable and preventing protein evolution from terminating due to diminution or loss of its initial function. Eventually, as mutations continued to generate new proteins with slightly different functions, they would have generated a protein close enough in sequence and structure that just one or a very few additional changes would suffice to convert it into Protein B.

  Aware of these imaginative scenarios, Douglas Axe and his colleague, molecular biologist Ann Gauger (see Fig. 12.5), now working together at the Biologic Institute in Seatt
le, decided to put them to an ingenious experimental test.34 In so doing, they sought to determine whether the evolution of new multisite features does indeed typically require multiple coordinated mutations, or instead whether such a feature could arise by cooption.

  FIGURE 12.5

  Ann Gauger. Courtesy Laszlo Bencze.

  Axe and Gauger scoured protein databases looking for proteins that are as similar as possible in sequence and structure, but that nevertheless perform different functions. They identified two proteins that meet those criteria. One of these proteins (Kbl2) is needed for breaking down an amino acid called threonine, and the other (BioF2) is needed for building a vitamin called biotin. (See Fig. 12.6.)

  Gauger and Axe realized that if they could transform Kbl2 into a protein performing the function of BioF2 with just one or very few coordinated amino-acid changes, then that might demonstrate (depending upon how few) that the two proteins were close enough in sequence that a conversion in function of the kind envisioned by cooption advocates is plausible in evolutionary time. What’s more, because they knew the difficulty scientists have had in showing any real change of protein function to be feasible, a positive result would suggest that they had at last discovered a functional gap that one or very few mutations could plausibly jump—as cooption envisioned.

  If, however, they found that many coordinated mutational changes were needed, then that could establish—depending upon how many were needed—that the Darwinian mechanism could not accomplish the functional jump from A to B in a reasonable time. That would imply that an even greater degree of structural similarity between proteins would be needed for the cooption hypothesis to be plausible. Having carefully examined the structural similarities between members of a large class of structurally similar enzymes, they knew that Kbl2 and BioF2 were about as close in sequence and structure as any two known proteins that performed different functions. Thus, if it turned out that converting one protein function into the other required many coordinated mutations—more than could be expected to occur in a reasonable time—then the outcome of their experiment would have devastating implications for standard accounts of protein evolution. If proteins that perform two different functions have to be even more similar than Kbl2 and BioF2 in order for mutational changes to convert the function of one to the other, then for all practical purposes cooption would not work. There simply aren’t many known jumps that small.

  FIGURE 12.6

  The proteins, Kbl2 (left) and BioF2 (right) are enzymes that use similar catalytic mechanisms to accelerate different chemical reactions in the bacterium E. coli. Courtesy Ann Gauger and Douglas Axe.

  Axe and Gauger first identified those amino-acid sites that were most likely, if mutated, to cause a change from Kbl2 function to BioF2 function. They then systematically mutated those sites individually and in groups involving various amino-acid combinations. Their results were unambiguous. They found that they could not induce, with either one or a small number of amino acids, the change in function they sought. In fact, they found that they could not get Kbl2 to perform the function of BioF2, even if they mutated larger numbers of amino acids in concert—that is, even if they made many more coordinated mutations than could plausibly occur by chance in all of evolutionary history.

  Although their attempts to convert Kbl2 to perform the function of BioF2 failed, their experiment did not. It allowed them to establish experimentally for the first time that the cooption hypothesis of protein evolution lacks credibility—simply too many coordinated mutations would be required to convert one protein function to another, even in the case of extremely similar proteins. That implied that generating new genes and proteins would require multiple coordinated mutations, and thus, the waiting times that Behe and Snoke had calculated do present a problem for neo-Darwinian theory.

  The experimental work also enabled Axe to calculate expected waiting times for various numbers of coordinated mutations given different variables and factors. Axe developed a refined population-genetics mathematical model to calculate various waiting times. His results roughly confirmed the previous calculations of Behe and Snoke. He found, for example, that if he took into account the probable fitness cost to an organism of carrying unnecessary gene duplicates (as was necessary to give the evolution of a new gene a reasonable chance), that the probable waiting time for even three coordinated mutations exceeded the duration of life on earth.

  He therefore effectively determined an upper bound of two for the number of coordinated mutations that could be expected to occur in a duplicate gene during the history of life on earth (taking into account the negative effects of carrying gene duplicates in the evolutionary process). He also calculated six coordinated mutations as an upper bound, neglecting the fitness cost of carrying gene duplicates. Nevertheless, in their experiments, he and Gauger could not induce a functional change in a single gene with more than six coordinated mutations. So, even that more generous—and, again, unrealistically generous upper bound—does little to render the cooption hypothesis credible. Indeed, Axe and Gauger’s experiments showed that the smallest realistically conceivable step exceeded what was plausible given the time available to the evolutionary process. In their words, “evolutionary innovations requiring that many changes … would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth.”

  What It All Means

  By showing the implausibility of the cooption model of protein evolution and the need for multiple coordinated mutations in order to generate multisite features in proteins, Axe and Gauger confirmed that genes and proteins themselves represent complex adaptations—entities that depend upon the coordinated interaction of multiple subunits that must arise as a group to confer any functional advantage.

  The need for coordinated mutations means that evolutionary biologists cannot just assume that mutations will readily generate new genes and traits, as neo-Darwinists have long presupposed. Indeed, by applying mathematical models based on the standard principles of population genetics to the questions of the origin of genes themselves, Behe and Snoke, Durrett and Schmidt (inadvertently), Axe and Gauger, and other biologists35 have recently shown that generating the number of multiple coordinated mutations needed to produce even one new gene or protein is unlikely to occur within a realistic waiting time. Thus, these biologists establish the implausibility of the neo-Darwinian mechanism as a means of generating new genetic information.

  There is one other aspect of this. The body of work published between 2004 and 2011 also provides additional confirmation of Axe’s research showing the rarity of genes and proteins in sequence space. In fact, that research helps to explain why such long waiting times are necessary. If functional sequences are rare in sequence space, it stands to reason that finding them by purely random and undirected means will take a long time. Moreover, waiting times increase exponentially with each additional necessary mutation. Thus, long waiting times for the production of new functional genes and proteins is exactly what we should expect if indeed functional genes and proteins are rare, and if coordinated mutations are necessary to produce them. Thus, the various experiments and calculations performed between 2004 and 2011 indirectly confirm Axe’s earlier conclusion about the rarity of functional genes and proteins and supply further evidence that the neo-Darwinian mechanism cannot generate the information necessary to build new genes, let alone a new form of animal life, in the time available to the evolutionary process.

  The Math and the Mechanism

  There is a concluding irony in all this. The researchers calculating waiting times for the appearance of complex adaptations have in each case done so using models based on the core principles of population genetics, the mathematical expression of neo-Darwinian theory. In a real sense, therefore, the neo-Darwinian math is itself showing that the neo-Darwinian mechanism cannot build complex adaptations—including the new information-rich genes and proteins that would have been necessary to build the Cambrian animals. To
adapt a metaphor that Tom Frazzetta might appreciate, the snake has eaten its own tail.

  13

  The Origin of Body Plans

  Rarely have the implications of a Nobel Prize–winning scientific discovery received so little notice. Of course, the discovery itself received great acclaim. But the deeper meaning was another matter.

  Starting in the autumn of 1979, at the European Molecular Biology Laboratory in Heidelberg, two venturesome young geneticists, Christiane Nüsslein-Volhard and Eric Wieschaus (see Fig. 13.1), generated thousands of mutations to investigate the genomes of tens of thousands of fruit flies (species: Drosophila melanogaster). They hoped to get them to divulge the secrets of embryological development. In technical jargon, Nüsslein-Volhard and Wieschaus performed “saturation mutagenesis” experiments. After feeding male flies the potent mutation-causing chemical (i.e., mutagen) ethyl methane sulphonate (EMS), Nüsslein-Volhard and Wieschaus bred the males with virgin females. They then examined the offspring larvae for visible defects.

  In generating many thousands of mutants, thereby “saturating” the Drosophila genome, Nüsslein-Volhard and Wieschaus induced variations in the small subset of genes that specifically regulate embryonic development. These regulatory genes normally control the expression of many other genes that build the fly embryo, progressively subdividing it into regions that will become the head, thorax, and abdomen of the adult fly. The EMS mutagen disrupts DNA replication, thereby mutating genes. These mutations affect the process of development, leaving visible defects in the fly larvae. By observing the damaged larvae, Wieschaus and Nüsslein-Volhard inferred how specific genes regulate the development of different parts of the fly body plan. In essence, Wieschaus and Nüsslein-Volhard reverse-engineered the fly’s genome to determine the function of the different genes, including the regulatory genes crucial to fly development.1