Darwin's Doubt

by Stephen C. Meyer

  Chapter 5: The Genes Tell the Story?

  1. Dawkins, The Greatest Show on Earth, 111.

  2. According to Zvelebil and Baum, “The key assumption made when constructing a phylogenetic tree from a set of sequences is that they are all derived from a single ancestral sequence, i.e., they are homologous” (Understanding Bioinformatics, 239). Lecointre and Le Guyader note: “Cladistics can run into difficulties in its application because not all character states are necessarily homologous. Certain resemblances are convergent—that is, the result of independent evolution. We cannot always detect these convergences immediately, and their presence may contradict other similarities, ‘true homologies’ yet to be recognized. Thus, we are obliged to assume at first that, for each character, similar states are homologous, despite knowing that there may be convergence among them” (The Tree of Life, 16).

  3. Coyne, Why Evolution Is True, 10.

  4. Budd and Jensen, “A Critical Reappraisal of the Fossil Record of the Bilaterian Phyla,” 253–95; Budd and Jensen, “The Limitations of the Fossil Record and the Dating of the Origin of the Bilateria,” 166–89 (“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 … whatever the resolution of the misfit between the fossil record and molecular evidence for the origin of animals, it does not come about through a misunderstanding of the known fossil record … The known 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”); Jensen et al., “Trace fossil preservation and the early evolution of animals,” 19–29 (“A literal reading of the body fossil record suggests that the diversification of bilaterian animals did not significantly precede the Neoproterozoic–Cambrian boundary (ca. 545 Ma) … Despite reports to the contrary, there is no widely accepted trace fossil record from sediments older than about 560–555 Ma… . The above conclusions place serious constraints on the time of appearance of bilaterian animals. For example, assuming that key bilaterian features could only have been acquired in moderately large benthic animals, the absence of an ancient trace fossil record suggests that the Cambrian ‘explosions’ are a reality in terms of the relatively rapid appearance and diversification of macroscopic bilaterians”); Conway Morris, “Darwin’s Dilemma: The Realities of the Cambrian ‘Explosion’,” 1069–83 (“The ‘ancient school’ argues that animals evolved long before the Cambrian and that the ‘explosion’ is simply an artefact, engendered by the breaching of taphonomic thresholds, such as the onset of biomineralization and/or a sudden increase in body size. The alternative ‘realist school’, to which I largely subscribe, proposes that while the fossil record is far from perfect and is inevitably skewed in significant ways, none is sufficient to destroy a strong historical signal”); Peterson et al., “MicroRNAs and Metazoan Macroevolution: Insights into Canalization, Complexity, and the Cambrian Explosion,” 736–47; Fortey, “The Cambrian Explosion Exploded?” 438–39; Wray et al., “Molecular Evidence for Deep Precambrian Divergences Among Metazoan Phyla,” 568–73 (“Darwin recognized that the sudden appearance of animal fossils in the Cambrian posed a problem for his theory of natural selection. He suggested that fossils might eventually be found documenting a protracted unfolding of Precambrian metazoan evolution. Many paleontologists today interpret the absence of Precambrian animal fossils that can be assigned to extant clades not as a preservational artifact, but as evidence of a Cambrian or late Vendian origin and divergence of metazoan phyla. This would make the Cambrian the greatest evolutionary cornucopia in the history of the earth. Definitive representatives of all readily fossilizable animal phyla (with the exception of bryozoans) have been found in Cambrian rocks, as have representatives of several soft-bodied phyla. Recent geochronological studies have reinforced the impression of a ‘big bang of animal evolution’ by narrowing the temporal window of apparent divergences to just a few million years”) (internal citations omitted); Erwin et al., “The Cambrian Conundrum: Early Divergence and Later Ecological Success in the Early History of Animals,” 1091–97 (“When Charles Darwin published The Origin of Species (1), the sudden appearance of animal fossils in the rock record was one of the more troubling facts he was compelled to address. He wrote: ‘There is another and allied difficulty, which is much graver. I allude to the manner in which numbers of species of the same group, suddenly appear in the lowest known fossiliferous rocks’ (306). Darwin argued that the incompleteness of the fossil record gives the illusion of an explosive event, but with the eventual discovery of older and better-preserved rocks, the ancestors of these Cambrian taxa would be found. Studies of Ediacaran and Cambrian fossils continue to expand the morphologic variety of clades, but the appearance of the remains and traces of bilaterian animals in the Cambrian remains abrupt.”).

  5. As Alan Cooper and Richard Fortey explain, “Molecular evidence indicates that prolonged periods of evolutionary innovation and cladogenesis lit the fuse long before the ‘explosions’ apparent in the fossil record. (“Evolutionary Explosions and the Phylogenetic Fuse,” 151.) Also, according to Welch, Fontanillas, and Bromham: “However, a wide range of molecular dating studies have suggested that the major lineages of animals arose long before the Cambrian, at over 630 mya [million years ago]. This raises the possibility that there was a long cryptic period of animal evolution preceding the explosion of fossils in the Cambrian” (“Molecular Dates for the ‘Cambrian Explosion,’ ” 672–73).

  6. “The molecular clock … is the assumption that lineages have evolved at equal rates” (Felsenstein, Inferring Phylogenies, 118).

  7. Smith and Peterson, “Dating the Time and Origin of Major Clades,” 72.

  8. Wray, Levinton, and Shapiro, “Molecular Evidence for Deep Precambrian Divergences Among Metazoan Phyla”; for another similar study of molecular sequence data that comes to the same conclusion, see Wang, Kumar, and Hedges, “Divergence Time Estimates for the Early History of Animal Phyla and the Origin of Plants, Animals and Fungi,” 163; see also Vermeij, “Animal Origins”; and Fortey, Briggs, and Wills, “The Cambrian Evolutionary ‘Explosion’ Recalibrated.”

  9. These proteins were ATP-ase, cytochrome c, cytochrome oxidase I and II, alpha and beta hemoglobin, and NADH I.

  10. The ribosomal RNA they used was 18S rRNA.

  11. These proteins were aldolase, methionine adenosyltransferase, ATP synthase beta chain, catalase, elongation factor 1 alpha, triosephosphate isomerase, and phosphofructokinase.

  12. The three RNA molecules they used were 5.8S rRNA, 18S rRNA, and 28S rRNA.

  13. Erwin et al., “The Cambrian Conundrum,” 1092.

  14. For example, Bronham and colleagues find that mitochondrial DNA and 18S rRNA data yielded divergence dates that varied by more than 1 billion years (“Testing the Cambrian Explosion Hypothesis by Using a Molecular Dating Technique”); Xun suggests that from a total of 22 nuclear genes the divergence time between Drosophila and vertebrates was about 830 mya (million years ago; “Early Metazoan Divergence Was About 830 Million Years Ago”); Doolittle and colleagues date the protostome-deuterostome split at 670 million years ago (“Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock”); Nikoh and colleagues date the split between eumetazoa and parazoa—animals with tissues, such as cnidarians, from those without, like sponges—at 940 mya, and the split between vertebrates and amphioxus at 700 mya (“An Estimate of Divergence Time of Parazoa and Eumetazoa and That of Cephalochordata and Vertebrata by Aldolase and Triose Phosphate Isomerase Clocks”); and Wang, Kumar, and Hedges suggest the basal animal phyla (Porifera, Cnidaria, Ctenophora) diverged between about 1200–1500 mya, and that nematodes were found to have diverged from the lineage leading to arthropods and chordates at 1177–79 mya (“Divergence Ti
me Estimates for the Early History of Animal Phyla and the Origin of Plants, Animals and Fungi”).

  15. Wray, Levinton, and Shapiro, “Molecular Evidence for Deep Precambrian Divergences Among Metazoan Phyla,” 568.

  16. Wray, Levinton, and Shapiro, “Molecular Evidence for Deep Precambrian Divergences Among Metazoan Phyla,” 569.

  17. Wray, Levinton, and Shapiro, “Molecular Evidence for Deep Precambrian Divergences Among Metazoan Phyla,” 568.

  18. Quoted in Hotz, “Finding Turns Back Clock for Earth’s First Animals,” A1, A14.

  19. See, e.g., Xun, “Early Metazoan Divergence Was About 830 Million Years Ago”; Aris-Brosou and Yang, “Bayesian Models of Episodic Evolution Support a Late Precambrian Explosive Diversification of the Metazoa.” See also an early study by Bruce Runnegar in 1982, which measured the percent sequence difference between globin molecules in various animal phyla and, from this, postulated that “the initial radiation of the animal phyla occurred at least 900–1000 million years ago” (Runnegar, “A Molecular-Clock Date for the Origin of the Animal Phyla,” 199). For other examples, see Bronham et al., “Testing the Cambrian explosion hypothesis by using a molecular dating technique,” 12386–12389 (finding that mitochondrial DNA and 18S rRNA data yielded divergence dates that varied by more than 1 billion years); Xun, “Early Metazoan Divergence Was About 830 Million Years Ago,” 369–71 (suggesting “From a total of 22 nuclear genes, we estimate that the divergence time between Drosophila and vertebrates was about 830 million years ago (mya)”); Doolittle, “Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock,” 470–77 (dating the protostome-deuterostome split at 670 million years ago); Nikoh et al., “An Estimate of Divergence Time of Parazoa and Eumetazoa and That of Cephalochordata and Vertebrata by Aldolase and Triose Phosphate Isomerase Clocks,” 97–106 (dating the split between eumetazoa and parazoa—animals with tissues from those without, like sponges—at 940 mya, and the split between vertebrates and amphioxus at 700 mya); Wang et al., “Divergence Time Estimates for the Early History of Animal Phyla and the Origin of Plants, Animals and Fungi,” 163–71 (suggesting “the basal animal phyla (Porifera, Cnidaria, Ctenophora) diverged between about 1200–1500 Ma” and “Nematodes were found to have diverged from the lineage leading to arthropods and chordates at 1177–79 Ma”).

  20. Valentine, Jablonski, and Erwin, “Fossils, Molecules and Embryos,” 851.

  21. Nikoh et al., “An Estimate of Divergence Time of Parazoa and Eumetazoa and That of Cephalochordata and Vertebrata by Aldolase and Triose Phosphate Isomerase Clocks.”

  22. Wang, Kumar, and Hedges, “Divergence Time Estimates for the Early History of Animal Phyla and the Origin of Plants, Animals and Fungi,” 163.

  23. Bronham et al., “Testing the Cambrian Explosion Hypothesis by Using a Molecular Dating Technique.”

  24. Xun, “Early Metazoan Divergence Was About 830 Million Years Ago.”

  25. Aris-Brosou and Yang, “Bayesian Models of Episodic Evolution Support a Late Precambrian Explosive Diversification of the Metazoa.” Other literature surveys report that molecular clock-based estimates of the split between protostomes and deuterostomes have ranged from 588 million to 1.5 billion years ago. See Erwin, Valentine, and Jablonski, “The Origin of Animal Body Plans”; and Benton and Ayala, “Dating the Tree of Life.”

  26. Graur and Martin, “Reading the Entrails of Chickens: Molecular Timescales of Evolution and the Illusion of Precision.”

  27. Graur and Martin, “Reading the Entrails of Chickens,” 85. Smith and Peterson also note: “The second area where molecules and morphology are in serious disagreement concerns the origins of the metazoan phyla. Although the difference between the molecular and morphological estimates for bird and mammal origins may be as much as 50 million years, the discord between the two for the animal phyla may be as much as 500 million years, almost the entire length of the Phanerozoic” (“Dating the Time and Origin of Major Clades,” 79).

  28. Ayala, Rzhetsky, and Ayala, “Origin of the Metazoan Phyla.”

  29. Ayala and his team eliminated the 18S rRNA, an RNA-coding gene because of problems with obtaining a reliable alignment. They also added an additional twelve protein-coding genes.

  30. Ayala, Rzhetsky, and Ayala, “Origin of the Metazoan Phyla,” 611.

  31. Valentine, Jablonski, and Erwin, “Fossils, Molecules and Embryos,” 856.

  32. Behe, “Histone Deletion Mutants Challenge the Molecular Clock Hypothesis.”

  33. Some evolutionary biologists have attempted to explain their extreme conservation (similarity) by “strong selection” for their essential functional role: the close packing, or wrapping, of DNA in eukaryotic chromosomes. This hypothesis is hard to square, however, with experimental data showing that yeast tolerates dramatic deletions in their H4 histones. Behe, “Histone Deletion Mutants Challenge the Molecular Clock Hypothesis.”

  34. As Baverstock and Moritz explain in more detail: “The single most important component … of a phylogenetic analysis is the decision as to which method(s) or sequence(s) are appropriate to the phylogenetic question at hand. The method chosen must yield sufficient variation as to be phylogenetically informative, but not so much variation that convergence and parallelisms overwhelm informative changes” (“Project Design,” 25).

  35. Valentine, Jablonski, and Erwin, “Fossils, Molecules and Embryos,” 856.

  36. Ho et al., “Accuracy of Rate Estimation Using Relaxed-Clock Models with a Critical Focus on the Early Metazoan Radiation,” 1355.

  37. Smith and Peterson, “Dating the Time and Origin of Major Clades,” 73.

  38. Smith and Peterson, “Dating the Time and Origin of Major Clades,” 73. Smith and Peterson elaborate: “All molecular clock approaches require one or more calibration points using dates derived either from the fossil record or from biogeographic constraints. There are two approaches—either calibration can rely on one or a small number of ‘well documented’ dates where paleontological evidence seems highly reliable, or calibration can be achieved using a large number of independent dates so that a range of estimates is arrived at. The former approach has been criticized by both Lee (1999) and Alroy (1999) for placing too much reliance on a single paleontological date without considering its error” (75). See Lee, “Molecular Clock Calibrations and Metazoan Divergence Dates”; and Alroy, “The Fossil Record of North American Mammals.” Dan Graur and William Martin concur. They note that gross uncertainties often afflict assumptions about (1) the age of fossils used to calibrate the molecular clock, (2) the rate of mutations in various genes, and (3) the conclusions of comparative sequence analyses based upon the use of molecular clocks (“Reading the Entrails of Chickens”).

  39. Conway Morris, “Evolution,” 5–6.

  40. Valentine Jablonski, and Erwin, “Fossils, Molecules and Embryos,” 856.

  41. Zvelebil and Baum, Understanding Bioinformatics, 239.

  42. Lecointre and Le Guyader, The Tree of Life, 16.

  43. For a related discussion see Wagner and Stadler, “Quasi-Independence, Homology and the Unity of Type.”

  44. Osigus, Eitel, Schierwater, “Chasing the Urmetazoon: Striking a Blow for Quality Data?” 551–57; Conway Morris, “The Cambrian ‘Explosion’ and Molecular Biology,” 505–506.

  45. Osigus, Eitel, Schierwater, “Chasing the Urmetazoon: Striking a Blow for Quality Data?” 551–57. As Osigus and colleagues note: “The sum of molecular trees based on large numbers of gene sequences does not resolve phylogenetic relationships at the base of the Metazoa. Conflicting scenarios have been published in short sequence and each single analysis can be criticized for one or the other reason. It is unclear to many whether the base of Metazoa can ever be resolved by means of sequence data even if whole genomes and extensive taxon sampling is used” (555).

  46. Conway Morris, “Early Metazoan Evolution,” 870.

  47. Graur and Martin, “Reading the Entrails of Chickens”; Smith and Peterson, “Dating the
Time and Origin of Major Clades”; Valentine, Jablonski, and Erwin, “Fossils, Molecules and Embryos.”

  Chapter 6: The Animal Tree of Life

  1. “The Darwinian Sistine Chapel,” April 14, 2009, www.bbc.co.uk/darwin/?tab=21 (accessed October 31, 2012).

  2. Hellström, “The Tree as Evolutionary Icon,” 1.

  3. Ruse, Darwinism Defended, 58.

  4. Dobzhansky, “Nothing in Biology Makes Sense Except in the Light of Evolution,” 125.

  5. Dawkins, The Greatest Show on Earth, 315.

  6. As Coyne has asserted, “both the visible traits of organisms and their DNA sequences usually give the same information about evolutionary relationships” (Why Evolution Is True, 10).

  7. Atkins, Galileo’s Finger, 16.

  8. Coyne, Why Evolution Is True, 7.

  9. An enormous literature exists analyzing how “similarity,” which can be directly observed and measured, comes to be interpreted as “homology,” a theoretical construct that cannot be directly observed. The two terms should not be equated. According to Van Valen, “For molecular biologists … a good touchstone is that homology is always an inference, never an observation. What we observe is similarity or identity, never homology” (“Similar, but Not Homologous,” 664).

  10. Prothero, Evolution, 140.

  11. Dawkins, A Devil’s Chaplain: Reflections on Hope, Lies, Science, and Love, 112.

  12. Wiley and Lieberman, Phylogenetics, 6.

  13. Degnan and Rosenberg, “Gene Tree Discordance, Phylogenetic Inference and the Multispecies Coalescent,” 332.

  14. Dávalos et al., “Understanding Phylogenetic Incongruence: Lessons from Phyllostomid Bats,” 993.

  15. Syvanen and Ducore, “Whole Genome Comparisons Reveals a Possible Chimeric Origin for a Major Metazoan Assemblage,” 261–75.

  16. Quoted in Lawton, “Why Darwin Was Wrong About the Tree of Life,” 39.

  17. Rokas, “Spotlight: Drawing the Tree of Life.”

  18. Rokas, Krüger, and Carroll. “Animal Evolution and the Molecular Signature of Radiations Compressed in Time,” 1933–34.