Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design
Reviewed by Michael Buratovich, Biochemistry, Spring Arbor University
Stephen C. Meyer, director of the Discovery Institute’s Center for Science and Culture, is one of the most prolific and articulate proponents of the theory of Intelligent Design (ID), which holds that certain features of the universe and living things are best explained by an intelligent cause rather than undirected processes. His latest book, Darwin’s Doubt, builds upon his long argument for ID begun in his previous work, Signature in the Cell. Whereas Signature in the Cell examined the origin of life, Darwin’s Doubt examines the origin of complex animal life.
In the first few chapters, Meyer describes the problem the origin of animal life poses for evolutionary biology. Meyer summarizes the conundrum in this manner:
(1) the sudden appearance of Cambrian animal forms; (2) 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 minor, small-scale diversification and variations. (34)
However, according to Meyer, the dilemma for the theory of evolution goes deeper than that. Evolutionary biologists turn to genes when fossils fail to provide proper resolution of the tree of life. However, in Meyer’s view, genes turn out to be little to no help. Genetic studies have failed to produce a believable timeline for the divergence of major animal groups, since “different studies of different molecules generate widely divergent dates” (106). Furthermore, Meyer cites phylogenetic studies of the whole genomes of several different extant animals that failed even to generate a tree of life.
But wait; it gets worse. Making new body plans or new organisms requires new genes that encode novel proteins with innovative functions. But according to Meyer, when scientists have tried to determine the proportion of possible amino acid sequences that are functional, they repeatedly find that a vanishingly small proportion of possible amino acid sequences actually produce a protein that functions; numbers on the order of one sequence from 1 x 1063 possible sequences are commonplace. Therefore, Meyer thinks that generating the new proteins and genes necessary to make new animal forms seems wildly unlikely.
Then there is the veritable alphabet soup of possible ways to address these issues such as punctuated equilibrium, evo-devo, and so on. None of these, however, according to Meyer, seem to have the explanatory power to account for the origin of animals, their body plans, and the genetic information required to get those body plans off the ground.
What is the answer? Meyer draws on an argument known as “the inference to the best explanation,” in which “when trying to explain the origin of an event or structure from the past,” scientists “compare various hypotheses to see which would, if true, best explain it” (348). In the case of animal origins, animals look designed because they are designed, and the origin of genetic information requires a designer or mind of some sort. In Meyer’s own words: “It follows that the great infusion of such [genetic] information in the Cambrian explosion points decisively to an intelligent cause” (361). Meyer does not say anything about the designer, its identity or attributes. Instead he simply argues that the invocation of a designer to account for the origin of animal life is scientifically rigorous and should be a part of the origins debate.
Meyer’s argument has not been accepted by evolutionary biologists. Several highly negative reviews of Meyer’s book have appeared on the web and in print by phylogeneticist Nicholas Matzke,1 paleontologists Donald Prothero,2 and Charles R. Marshall,3 and science blogger John Farrell.4 To address these criticisms, the latest release of Meyer’s book has a section at the end of the book where he attempts to answer his critics.
I certainly agree with Meyer that living creatures look designed because they actually are, and we would probably agree that the designer is the God revealed in the pages of Scripture, who created all there is. Despite my agreement with his conclusions, I do not accept the means by which he arrived at them, and I am even more troubled by the solution he has proposed. There is only room to highlight a few examples.
The Cambrian Explosion refers to the relatively abrupt appearance of diverse and abundant fossils in the course of a specific window of time during the Cambrian period (542-488 million years ago). Meyer insists that the Cambrian explosion requires the creation of a host of new genes. This is in contrast to contemporary thinking that argues that the Cambrian explosion resulted not from the creation of new genes but the redeployment of already-existing genes. Surveys of the developmental genetics of a wide variety of animals show that the development of vertebrates, starfish, sea urchins, insects, and jellyfishes utilizes largely the same genes but varies as to how those genes are used. Meyer breaks with this conclusion because the perturbation of modern gene regulatory networks during development almost always results in lethality. However, Meyer makes the unwarranted extrapolation that the gene regulatory networks in ancient animals were as inflexible as those in modern animals, which is inconceivable given the over half a billion years that have elapsed since the Precambrian and Cambrian periods.
However, it is not only new genes that the Cambrian explosion required but, according to Meyer, the generation of novel protein folds: “explosions of new life forms must have involved bursts of new protein folds as well” (191). A protein fold is a particular arrangement of the local structures formed by a protein chain relative to each other in three-dimensional space. Different protein folds are often associated with particular functions. For example, a protein fold called a Rossman fold is associated with binding ATP or related molecules.5 It is entirely possible to generate new genes without producing new protein folds6, and Meyer never explains why new animal diversity requires the generation of new protein folds rather than the innovative use of already-existing protein folds; it is merely assumed. However, Meyer then provides tiny numbers from papers that subjected very well-characterized proteins to random amino acid substitutions in order to determine which substitutions these proteins could tolerate before they lost their ability to function properly. Such experiments allow scientists to assess quantitatively the structural flexibility of the protein and estimate the percentage of amino acid sequences that might assume the proper structure and allow the protein to execute its specific function. Experiments with proteins such as the phage lambda repressor yielded numbers like one in 1063 of the total number of possible 92-amino acid sequences would yield a protein that folded properly and executed its function. Other experiments with beta-lactamase yielded an estimate of between one in 1053-1077 and theoretical experiments with cytochrome c give an estimate within this range.7 First, these experiments provide estimates and these estimates are highly dependent on the methods and assumptions employed by the researcher. Secondly, these estimates predict the probability of finding a particular amino acid sequence that will allow a protein to execute a specific function and say nothing about whether or not alternative sequences can perform a different function. Therefore to state that these experiments demonstrate there is a 1 in 1077 chance of a new protein fold forming from an existing protein is an abuse of these estimates. In fact Meyer uses these small numbers to state that “protein-to-protein (or functional gene-to-functional gene) evolution is a no-go where the mutation and selection mechanism must produce a new protein fold” (196), and “the gradual transformation of one functional fold into another was a complete nonstarter” (197). However these assertions are demonstrably false. Philip Bryan at the University of Maryland Biotechnology Institute and his colleagues converted one protein that formed a specific protein fold and bound to Human Serine Albumin into a protein that assumed a completely different fold in three-dimensional space and bound to Immunoglobulin G with only one amino acid substitution.8 Also, Suat Özbek from the University of Heidelberg and his collaborators have shown that single amino acid changes in the cysteine-rich domains of the nematocyst outer wall antigen can cause the protein to interconvert into two vastly different protein structures.9 Furthermore, Meyer limits his discussion to amino acid substitutions, when, in fact, the universe of natural-occurring mutations is far more diverse and includes insertions, deletions, duplications, gene fusions, transpositions, and a wide variety of gene rearrangements. When these others types of mutations are considered, then a wide variety of new proteins and new protein folds can be created by means of phenomena such as structural drift, circular permutation, D-events (duplication, swapping and deletion), strand invasion/withdrawal, or several other mechanisms.10
- Nicholas Matzke, “Meyer’s Hopeless Monster, Part II,” accessed June 19, 2013. http://pandasthumb.org/archives/2013/06/meyers-hopeless-2.html.
- Donald Prothero, “Stephen Meyer’s Fumbling Bumbling Amateur Cambrian Follies,” accessed August 28, 2013. http://www.skepticblog.org/2013/08/28/stephen-meyers-fumbling-bumbling-amateur-cambrian-follies/.
- Charles R. Marshall. “When Prior Belief Trumps Scholarship,” Science 341, no. 6152 (2013): 1,344.
- John Farrell. “How Nature Works,” National Review 65, no. 16 (2013): 35.
- M. G. Rossman and P. Argos, “Protein Folding,” Annual Reviews of Biochemistry 50 (1981): 497-532.
- Manyuan Long, et al., “New Gene Evolution: Little Did We Know,” Annual Review of Genetics 47 (2013): 307-333.
- Douglas D. Axe, “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds,” Journal of Molecular Biology 341 (2004): 1,295–1,315; Herbert P. Yockey, “The Information Content of Cytochrome C,” Journal of Theoretical Biology 67 (1977): 345-376.
- Patrick A. Alexander, et al., “A Minimal Sequence Code for Switching Protein Structure and Function,” Proceedings of the National Academy of Sciences U.S.A. 106, no. 50 (2009): 21,149–21,154.
- Sebastian Meier, et al., “Continuous Molecular Evolution of Protein-Domain Structures by Single Amino Acid Changes,” Current Biology 17 (2007): 173–178.
- Nick Grishin, “Fold Changes in Evolution of Protein Structures,” Journal of Structural Biology 134 (2001): 167–185; William Taylor, “Evolutionary Transitions in Protein Fold Space,” Current Opinion in Structural Biology 17 (2007): 354-361; S. Sri Krishna and Nick V. Grishin, “Structural Drift: A Possible Path to Protein Fold Change,” Bioinformatics 21, no. 8 (2005): 1,308–1,310.