THE DISCOVERIES AND IDEAS discussed in this book are the fruit of many scientists’ efforts. Because the presentation is intended for a broad audience, I elected not to name every individual associated with every work pertinent to the story, nor to use footnotes in the text. In this section, I provide a summary of the books and papers upon which I relied, and I offer some suggestions for further reading on particular topics of interest. In most cases, the titles of journal articles are omitted; the reference given provides enough information for interested readers to locate them.
The inspiration for and accounts of Darwin’s, Bates’s, and Wallace’s travels can be found in both autobiographical and many biographical sources. I relied on Darwin’s Voyage of the Beagle (originally published 1839; many versions and editions since) and H. W. Bates, Naturalist on the River Amazons (London: John Murray, 1863). For key biographical background see the Introduction by A. Shoumatoff in the Penguin Nature Library 1988 edition of Bates’s classic, pp. vii–xviii. A. Desmond and J. Moore’s Darwin: The Life of a Tormented Evolutionist (London: Michael Joseph, 1991) is a rich source of insights into and facts of Darwin’s life. The friendship between Bates and Wallace and the role it played in taking them to the Amazon is well documented and appears in nearly every capsule biography.
Many authors have commented on the aesthetic dimensions of science. Foremost among these is Robert Root-Bernstein; I strongly recommend his exceptional book Discovering: Inventing and Solving Problems at the Frontiers of Scientific Knowledge (Cambridge, Mass.: Harvard University Press, 1989) and his article “The Sciences and Arts Share a Common Creative Aesthetic,” in The Elusive Synthesis: Aesthetics and Science, ed. A. Tauber, pp. 49–82 (Netherlands: Kluwer Academic Publishers, 1996). Scott Gilbert, a developmental biologist and science historian, has brought the aesthetic side of embryology to light in his article with Marion Taber, “Looking at Embryos: The Visual and Conceptual Aesthetics of Emerging Form,” also in Tauber’s The Elusive Synthesis, pp. 125–51. Among the works Gilbert and Taber single out, embryologist Paul Weiss’s “Beauty and the Beast: Life and the Rule of Order,” Scientific Monthly 81 (1955): 286–99, is an exceptional contribution.
The central role of embryology in Darwin’s formulation of evolutionary ideas is evident throughout The Origin of Species. It also arises frequently in his correspondence—see F. Darwin, ed., The Life and Letters of Charles Darwin. Thomas H. Huxley, too, discusses embryos and development as important evolutionary evidence in Evidence as to Man’s Place in Nature (1863).
The major components of the Modern Synthesis were treated in books on population genetics and evolution by Ronald A. Fisher, The Genetical Theory of Natural Selection (Oxford: Clarendon Press, 1930); J. B. S. Haldane, The Causes of Evolution (London: Longman, Green, 1932); and Theodosius Dobzhansky, Genetics and the Origin of Species (New York: Columbia University Press, 1937); on systematics by Ernst Mayr, Systematics and the Origin of Species (New York: Columbia University Press, 1942); and on paleontology by George Gaylord Simpson, Tempo and Mode in Evolution (New York: Columbia University Press, 1944). Julian Huxley’s Evolution: The Modern Synthesis (London: Allen and Unwin, 1942) integrated elements of genetics, systematics, paleontology, and botany.
Many authors have analyzed the impact and shortcomings of the Modern Synthesis, Stephen Jay Gould and Niles Eldredge, in particular. Their solo and joint works include N. Eldredge and S. J. Gould, “Punctuated Equilibria: An Alternative to Phyletic Gradualism” in Models in Paleobiology, ed. T. J. M. Schopf, pp. 82–115 (San Francisco: Freeman, Cooper, 1972); S. J. Gould and N. Eldredge, “Punctuated Equilibrium Comes of Age,” Nature 366 (1993): 223–27; N. Eldredge, Unfinished Synthesis: Biological Hierarchies and Modern Evolutionary Thought (Oxford: Oxford University Press, 1986); and S. J. Gould, The Structure of Evolutionary Theory (Cambridge, Mass.: Harvard University Press, 2002). Gould’s first analysis of the relationship between embryology and evolutionary processes was the landmark Ontogeny and Phylogeny (Cambridge, Mass.: Belknap Press, 1977).
A century before Gould’s opus, Rudyard Kipling published Just So Stories (New York: Doubleday, 1902). One can now find many editions of these tales online.
The emergence of evolutionary developmental biology has been chronicled in a series of books for the professional and student biologist. The first was Rudy A. Raff and Thomas C. Kaufman’s Embryos, Genes, and Evolution: The Developmental-Genetic Basis of Evolutionary Change (New York: Macmillan, 1983), which anticipated many of the fruitful questions and directions that were pursued in the decades following. More recent books include R. A. Raff, The Shape of Life (Chicago: University of Chicago Press, 1996); J. Gerhart and M. Kirschner, Cells, Embryos, and Evolution (Medford, Mass.: Blackwell Science, 1997); E. H. Davidson, Genomic Regulatory Systems: Development and Evolution (San Diego: Academic Press, 2001); A. Wilkins, The Evolution of Developmental Pathways (Sunderland, Mass.: Sinauer Associates, 2001); and a text I cowrote with my former students Jen Grenier and Scott Weatherbee, From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design, 2nd ed. (Medford, Mass.: Blackwell Science, 2005).
A great introduction to the fossil fauna of Florida, including how to find them, is Mark Renz, Fossiling in Florida: A Guide for Diggers and Divers (Gainesville: University Press of Florida, 1999). Mark runs fossil-hunting excursions (contact Fossilx@earthlink.net) and I thank him for teaching me and my family how to search for fossils in Florida rivers and for helping us to identify what we found.
Ideas on modularity and serial repetition of structures were developed in W. Bateson, Materials for the Study of Variation (London: Macmillan, 1894). Williston’s Law is explained in S. W. Williston, Water Reptiles of the Past and Present (Chicago: University of Chicago Press, 1914). More recent treatments on the importance of modularity, homology, and serial homology are G. P. Wagner, American Zoologist 36 (1996): 36–43, and G. P. Wagner, Evolution 43 (1989): 1157–71.
The discovery of cyclopamine and the association of the lily Veratrum californicum with the induction of cyclopia are described in R. F. Keeler and W. Binns, Teratology 1 (1968): 5–10.
The classic experiments describing organizers in newt or frog embryos and the chick limb will be found in any modern text of developmental biology. Two such texts are Scott F. Gilbert, Developmental Biology, 7th ed. (Sunderland, Mass.: Sinauer Associates, 2003), and L. Wolpert et al., Principles of Development, 2nd ed. (Oxford: Oxford University Press, 2002). The experiments by Spemann and his student Hilde Mangold are described in H. Spemann, Embryonic Development and Induction (New Haven: Yale University Press, 1938), and those of John W. Saunders and his associate M. T. Gesseling in R. Fleischmajer and R. E. Bilingham, eds., Epithelial Mesenchymal Interactions (Baltimore: Williams and Wilkins, 1968), pp. 78–97. The experiments describing butterfly wing eyespot organizers were first described in H. F. Nijhout, Developmental Biology 80 (1980): 267–74.
The term “hopeful monsters” was coined by Richard Goldschmidt in his book The Material Basis of Evolution (New Haven: Yale University Press, 1940). See S. J. Gould’s introduction in a modern reprinting of the book (1982), pp. viii-xlii, for a discussion of the concept, as well as S. J. Gould’s “Helpful Monsters” in Hen’s Teeth and Horse’s Toes (New York: W. W. Norton, 1983), pp. 187–98.
For medical descriptions of polydactyly and statistics on its occurrence, I relied upon a review by W. F. Bakker et al. in the Electronic Journal of Hand Surgery, November 11, 1997, accessed online, and L. G. Biesecker, American Journal of Medical Genetics 112 (2002): 279–83. For anecdotal accounts of individuals with polydactyly, see BaseballLibrary.com for information on Antonio Alfonseca, Wikipedia.org for historical figures, and melungeanhealth.org for a description of polydactyly in a Turkish population. For a fascinating treatment of all sorts of human developmental abnormalities, see A. M. Leroi, Mutants: On Genetic Variety and the Human Body (New York: Viking Press, 2003).
The literature on homeotic mutants is enormous. Short descriptions will be found in the developmental textbooks I have cited above and in Gould’s “Helpful Monsters.” A lengthier exploration in the full context of the development of a fly is given in Peter Lawrence, The Making of a Fly (Cambridge, Mass.: Blackwell Science, 1992).
The origins of molecular biology, from the structure of DNA to the cracking of the genetic code, and Jacob and Monod’s discoveries of the logic underlying the control of lactose metabolism in E. coli are detailed in Horace Freeland Judson’s brilliant The Eighth Day of Creation: The Makers of the Revolution in Biology (New York: Simon and Schuster, 1979; reprint, with an updated preface, New York: Cold Spring Harbor Laboratory Press, 1996). This is one of the best written, most thoroughly researched books in the entire genre of science writing.
Explanations of how genetic information is encoded and decoded will be found in most college-level biology textbooks, and an online search for the keywords “DNA, RNA, and proteins” will lead to numerous short illustrated synopses. The control of beta-galactosidase production is detailed in most textbooks on genetics and molecular biology, and in a compendium of papers in J. H. Miller and W. S. Reznikoff, eds., The Operon (Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press, 1978).
The books by Jacques Monod and François Jacob to which I refer are J. Monod, Chance and Necessity (New York: Alfred A. Knopf, 1971); F. Jacob, The Logic of Life (New York: Pantheon, 1974); and F. Jacob, The Statue Within: An Autobiography (New York: Basic Books, 1988). François Jacob has also more recently written a book on advances in genetics and developmental biology, including the home-obox story, entitled Of Flies, Mice, and Men: On the Revolution in Modern Biology by One of the Scientists Who Helped Make It (Cambridge, Mass.: Harvard University Press, 1998).
Key papers on the genetics of the Antennapedia and Bithorax Complexes were E. Lewis, Nature 276 (1978): 565–70, and B. Wakimoto and T. Kaufman, Developmental Biology 81 (1981): 51–64. The homeobox was discovered in parallel by individuals working in two laboratories, one headed by Thom Kaufman at Indiana University, the other headed by Walter Gehring at the University of Basel. Accounts of the discovery can be found in Peter Lawrence, The Making of the Fly (Medford, Mass.: Blackwell Science, 1992), in W. Gehring, Master Control Genes in Development and Evolution: The Homeobox Story (New Haven: Yale University Press, 1999), and in W. McGinnis, Genetics 137 (1994): 607–11. The primary references are M. P. Scott and A. J. Weiner, Proceedings of the National Academy of Science, USA 81 (1984): 4115–19, and W. McGinnis et al., Nature 308 (1984): 428–33. The report of the similarity between the homeodomain and well-known bacterial and yeast regulatory proteins is A. S. Laughon and M. P. Scott, Nature 310 (1984): 25–31. The discovery of homeobox genes in other animals was reported in W. McGinnis et al., Cell 37 (1984): 403–8. Jonathan Slack’s article comparing the homeobox to the Rosetta stone appeared in Nature 310 (1984): 364–65. A commentary by Stephen Jay Gould on the significance of the homeobox appeared in Natural History 94 (1985): 12–23.
The discovery of the features of Hox gene organization in clusters and their expression along the body axes in vertebrates was reported by D. Duboule and P. Dollé, EMBO Journal 8 (1989): 1497–1505, and A. Graham, N. Papalapov, and R. Krumlauf, Cell 57 (1989): 367–78.
The homology of the Drosophila eyeless gene to the Small eye and Aniridia genes of mice and humans, respectively, was reported by R. Quiring et al., Science 265 (1994): 785–89, and the ability of the eyeless and Small eye gene products to induce eye tissue at additional sites in the fly was reported by G. Halder, P. Callaerts, and W. Gehring, Science 267 (1994): 1788–92. A commentary on this work was written by S. J. Gould, Natural History 103 (1994): 12–20. Richard Dawkins has written a terrific explanation of the evolution of eyes, “The Forty-Fold Path to Enlightenment,” in his Climbing Mount Improbable (New York: W. W. Norton, 1996), pp. 138–97.
The use of the Distal-less gene and its homologs in the formation of many kinds of appendages was reported by G. Panganiban et al., Proceedings of the National Academy of Science, USA 94 (1997): 5162–66. A discussion of the significance of the role of tinman and NK2 homeobox genes in the building of fly and vertebrate hearts is offered by R. Bodmer and T. V. Venkatregh, Developmental Genetics 22 (1998):181–86.
Enrst Mayr’s view of evolutionary distance can be found in his Animal Species and Evolution (Cambridge, Mass.: Harvard University Press, 1963), p. 609. Stephen Jay Gould’s comments in The Structure of Evolutionary Theory (Cambridge, Mass.: Harvard University Press, 2002) are found on p. 1065.
The first report of Nüsslein-Volhard and Wieschaus’s pioneering search for the genes that sculpt the pattern of the fruit fly embryo appeared in Nature 287 (1980): 795–801. It was many years later when the Drosophila hedgehog gene was isolated and, shortly therafter, its vertebrate homologs. The report of the ability of the Sonic hedgehog protein to mimic the activity of the ZPA in the chick limb was R. Riddle et al., Cell 75 (1993): 1401–16. The association of mutations in Sonic hedgehog with polydactyly in humans was reported by L. Lettice et al., Proceedings of the National Academy of Science, USA 99 (2002): 7548–53.
The induction of cyclopia by mutations in the Sonic hedgehog gene was reported by C. Chiang et al., Nature 383 (1996): 407–13. This observation, coupled with the discovery that some cancers are associated with mutations in other genes in the pathway, led to the testing of cyclopamine as a potential chemotherapy; see J. Taipale et al., Nature (2000): 1005–9, and commentary by A. E. Bale, Nature 406 (2000): 944–45.
The title wordplay was suggested by an anecdote in Scott Gilbert and Marion Taber’s “Looking at Embryos: The Visual and Conceptual Aesthetics of Emerging Forms” in The Elusive Synthesis: Science and Aesthetics, ed. A. Tauberg, pp. 125–51 (Netherlands: Kluwar Academic Publishers, 1996). They mentioned that in 1992 the Encyclopedia of the Mouse Genome carried the banner “The Complete Mouse” with “some assembly required” in parentheses. Gilbert and Taber are also the source of the Paul Weiss anecdote about getting the chicken back.
The analogy of embryology to mapmaking is explained in Stephen S. Hall, Mapping the Next Millennium: The Discovery of New Geographies (New York: Random House, 1992), pp. 193–214. Hall makes a compelling case throughout the book of the central role of mapmaking in the sciences; he is right on point with regard to genetics, embryology, and genomics.
The processes of embryonic development are also explained and illustrated in two books written for general audiences by great developmental biologists. Lewis Wolpert’s Triumph of the Embryo (New York: Oxford University Press, 1991) is a concise and very clear outline of the key steps in making embryos and structures. Enrico Coen’s Art of the Genes: How Organisms Copy Themselves (Oxford: Oxford University Press, 1998) has a unique perspective that intertwines embryology and art in illuminating how patterns are encoded and revealed.
Fate mapping is described in all developmental biology textbooks, including those I cited earlier for chapter 2. An excellent recent review of goals, strategies, and new methodologies in fate mapping is J. D. W. Clarke and C. Tickle, Nature Cell Biology 1 (1999): E103–9. Figures 4.1 and 4.2 are simplified from several sources including the above references and the fate maps of Volker Hartenstein published as a supplementary atlas in M. Bate and A. Martinez-Arias, eds., The Development of Drosophila melanogaster (Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press, 1993).
The descriptions of tool kit gene expression are drawn from work in my laboratory, many primary literature reports, information provided by colleagues who contributed images, as well as textbook sources. Again, the developmental biology textbooks cited will contain most of this information in much greater detail. Peter Lawrence, The Making of the Fly (Cambridge, Mass.: Blackwell Science, 1992), contains much detail about genes expressed in the fly embryo, and Sean B. Carroll, Jen Grenier, and Scott Weatherbee, From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design, 2nd ed. (Medford, Mass.: Blackwell Science, 2005), also describes the steps involved in building flies and vertebrates. Some reviews that cover particular topics in depth include: for early vertebrate embryos, E. M. De Robertis et al., Nature Reviews Genetics 1 (2000): 171–81; the making of segments in vertebrates, O. Pourquie, Science 301 (2003): 328–30; the building of the vertebrate limb, F. Moriani and G. R. Martin, Nature 423 (2003): 319–25; the making of the hindbrain, C. B. Moens and V. E. Prince, Developmental Dynamics 224 (2002): 1–17.
The description of lateral inhibition is generalized from numerous examples, such as the positioning of bristles and feather buds. This concept is discussed in detail and numerous examples reviewed in H. Meinhardt and A. Gierer, BioEssays 22 (2002): 753–60. There are some excellent tutorials and animations on these authors’ Web site concerning the generation of periodic and spacing patterns: www.eb.tuebingen.mpg.de/dept4/meinhardt/home.html.
François Jacob’s quotation of Jean Perrin appears in his essay “Evolution and Tinkering,” Science 196 (1977): 1161–66. Jean Perrin was a Nobel laureate in Physics (1926) who was cited for his work on colloids and Brownian motion. He wrote a very popular book, Les Atomes (1913), from which the quotation is taken.
I first encountered “dark matter” in Brian Greene’s The Elegant Universe (New York: W. W. Norton, 1999), a very engaging book about the structure of the universe from the very smallest to the largest scale, and in Martin Rees’s excellent Just Six Numbers: The Deep Forces That Shape the Universe (New York: Basic Books, 2001). For additional articles, see Dennis Overbye, “From Light to Darkness: Astronomy’s New Universe,” The New York Times, April 10, 2001, and Vera Rubin, Scientific American Presents 9, no. 1 (1998), 106–10.
There are several texts that focus on the properties of genetic switches in detail. Mark Ptashne’s classic A Genetic Switch, 2nd ed. (Cambridge, Mass.: Blackwell Science, 1992), is a short, very well illustrated, step-by-step tutorial on genetic switches, primarily in bacteriophage, but with some examples from more complex organisms. Eric H. Davidson, Genomic Regulatory Systems: Development and Evolution (San Diego: Academic Press, 2001) is an advanced text that explains the logic and operations of the more complicated switches of animal genes.
Estimates of the amount of “junk” DNA in our genome and the fraction that is regulatory are based upon studies of the human genome sequence, and comparisons with other species, particularly the mouse, as described by the Mouse Genome Sequencing Consortium, Nature 420 (2002): 520–62.
Key references for the operation of genetic switches in positioning stripes and clusters of cells are: D. Stanojevic, S. Small, and M. Levine, Science 254 (1991): 1385–87; S. Small, A. Blair, and M. Levine, EMBO Journal 11 (1992): 4047–57; G. Vachon et al., Cell 71 (1992): 437–50; J. Jiang and M. Levine, Cell 72 (1993): 741–52; S. Gray, P. Szymanski, and M. Levine, Genes and Development 8 (1994): 1829–38; S. Gray and M. Levine, Genes and Development 10 (1996): 700–710; P. Szymanski and M. Levine, EMBO Journal 14 (1995): 2229–38; and J. Cowden and M. Levine, Developmental Biology 262 (2003): 335–49. The signature sequences bound by particular tool kit proteins are derived from these references and S. Jun et al., Proceedings of the National Academy of Sciences, USA 95 (1998): 13720–725; S. Knirr and M. Frasch, Developmental Biology 238 (2001): 13–26; and S. C. Ekker et al., EMBO Journal 13 (1994): 3551–60.
Examples of Turing-like models of pattern formation are discussed in S. Kauffman’s The Origins of Order (Oxford: Oxford University Press, 1993) and P. Ball, The Self-Made Tapestry: Pattern Formation in Nature (Oxford: Oxford University Press, 1999). It is interesting to compare the analyses of fly development in the two books. Kauffman’s treatment is longer and more complex and did not incorporate the discovery of switches for making individual stripes (made a couple of years before publication). Ball’s treatment is greatly simplified and clarified by the description of how switches transform fuzzy patterns into sharper patterns. Still, the central importance of genetic switches to pattern formation has not yet fully penetrated the computational modeling world; for example, see S. Wolfram, A New Kind of Science (Champaign, Ill.: Wolfram Media, 2002). The continuing mistake is being seduced into believing that simple rules that can generate patterns on a computer screen are the rules that generate patterns in biology.
For information on the genetic switches of the BMP5 gene I relied on personal communications with Dr. David Kingsley of Stanford University and on R. J. Di Leone et al., Proceedings of the National Academy of Sciences, USA 97 (2000): 1612–17. The logic of how Hox proteins and other tool kit proteins differentiate modules in animal bodies is summarized in S. D. Weatherbee and S. B. Carroll, Cell 97 (1999): 283–86.
There are several excellent books for the general reader that deal entirely or in part with the Cambrian Explosion. S. J. Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W. W. Norton, 1989) was the first to bring the phenomenon of the Cambrian to a wide audience. Simon Conway Morris, The Crucible of Creation: The Burgess Shale and the Rise of Animals (New York: Oxford University Press, 1998) tells the story from the viewpoint of one of the leading paleontologists working on the fossils, and is more up-to-date with respect to interpretation and the inclusion of insights from other Cambrian sites. Andrew H. Knoll, Life on a Young Planet: The First Three Billion Years of Evolution on Earth (Princeton: Princeton University Press, 2003) covers the entire known history of life up to and including the Cambrian—it is a terrific synthesis of geology, geochemistry, and paleontology. Derek E. G. Briggs, Douglas H. Erwin, and Frederick J. Collier, The Fossils of the Burgess Shale (Washington, D.C.: Smithsonian Institution Press, 1994) is a handsome catalog describing Burgess fossils.
The first description of Urbilateria was E. M. De Robertis and Y. Sasai, Nature 380 (1996): 37–40. Additional articles pertaining to Urbilateria are: De Robertis, Nature 387 (1997): 25–36; C. B. Kimmel, Trends in Genetics 12 (1996): 329–31; N. Shubin, C. Tabin, and S. Carroll, Nature 388 (1997): 639–48; D. Arendt and J. Wittbrodt, Philosophical Transactions of the Royal Society of London B 350 (2001): 1545–63; D. Arendt, U. Technau, and J. Wittbrodt, Nature 409 (2001): 81–85; A. H. Knoll and S. B. Carroll, Science 284 (1999): 2129–37; D. H. Erwin and E. H. Davidson, Development 129 (2002): 3021–32; and A. Peel and M. Akam, Current Biology 18 (2003): R708–10.
The quote from Darwin on mankind’s genealogy comes from his letter to Charles Lyell of January 10, 1860, published in The Life and Letters of Charles Darwin, ed. E Darwin, vol. 2 (London: John Murray, 1887).
For background on the evolution of lobopodians, I relied upon G. E. Budd, Lethaia 29 (1996): 1–14, and personal communications with Dr. Graham Budd of the University of Uppsala, Sweden.
Lewis’s “new genes” hypothesis appears in E. B. Lewis, Nature 276 (1978): 565–70. The description of the Hox genes of Onychophorans is J. K. Grenier et al., Current Biology 7(1997): 547–53. The literature on the shifting of Hox zones in arthropods is substantial and growing; key references are M. Averof and M. Akam, Nature 376 (1995): 420–23; S. B. Carroll, Nature 376 (1995): 479–85. M. Averof and N. H. Patel, Nature 388 (1997): 682–87; C. L. Hughes and T. C. Kaufman, Development 129 (2002): 1225–38; and N. C. Hughes, BioEssays 28 (2003): 386–95.
The detailed description of Haikouichthys is in D. G. Shu et al., Nature 421 (2003): 526–29. The analysis of cephalochordate Hox genes is in J. Garcia-Fernandez and P. W. Holland, Nature 370 (1994): 563–66; of lamprey and hagfish Hox genes in H. Ecriva et al., Molecular and Biological Evolution 19 (2002): 1440–50, and C. Fried, S. J. Prohaska, and P. F. Stadler, Journal of Experimental Zoology Part B Molecular and Developmental Evolution 299 (2003): 18–25; and of sharks in C.-B. Kim et al., Proceedings of the National Academy of Sciences, USA 97 (2000): 1055–60. The innovations of vertebrates are discussed in S. M. Shimeld and P. W. Holland, Proceedings of the National Academy of Sciences, USA 97 (2000): 4449–52, and G. P. Wagner, C. Amemiya, and F. Ruddle, Proceedings of the National Academy of Sciences, USA 100 (2003): 14603–606. The expression of Hox genes in different vertebrates is detailed in A. C. Burke et al., Development 121(1995): 333–46, and M. J. Cohn and C. Tickle, Nature 399 (1999): 474–79. The evolution of a vertebrate Hox gene switch is reported in H.-G. Belting, C. Shashikant, and F. H. Ruddle, Proceedings of the National Academy of Sciences, USA 95 (1998): 2355–60.
For a discussion of the role of ecology in the Cambrian, see Knoll’s Life on a Young Planet.
The histories of the knife and fork and paper clips are described in A. B. Duthie, Journal of Memetics—Evolutionary Models of Information Transmission 8 (2003), available at http://jom-emit.cfpm.org/2004/vol8/duthie_ab.html, and H. Petroski, The Evolution of Useful Things (New York: Vintage Books, 1992). Darwin’s discussion of the importance of multifunctionality and redundancy is in chapter 6, “Difficulties of the Theory,” in The Origin of Species.
The structure and importance of biramous limbs are discussed at length in S. J. Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W. W. Norton, 1989), and scenarios for their origin are discussed in G. E. Budd, Lethaia 29 (1996): 1–14, and N. Shubin, C. Tabin, and S. Carroll, Nature 388 (1997): 639–48. The expression of the Distal-less limb-building gene in arthropod and Onychophoran limbs is reported in G. Panganiban et al., Science 270 (1995): 1363–66, and Panganiban et al., Proceedings of the National Academy of Sciences, USA 94 (1997): 5162–66.
The evidence for the evolution of the insect wing from the gill branch of an aquatic ancestor is M. Averof and S. M. Cohen, Nature 385 (1997): 627–30. The scenario for the evolution of insect wing number is derived from S. B. Carroll, S. D. Weatherbee, and J. A. Langeland, Nature 375 (1995): 58–61, and based partly on fossil evidence in J. Kukalova-Peck, Journal of Morphology 156 (1978): 53–126.
The evidence for the evolution of spider spinnerets, book lungs, and tubular tracheae from an ancestral gill branch is W. G. M. Damen, T. Saridaki, and M. Averof, Current Biology 12 (2002): 1711–16. The different Hox zones in spiders are reported in W. G. M. Damen et al., Proceedings of the National Academy of Sciences, USA 95 (1998): 10665–670, and A. Abzhanov, A. Popadic, and T. C. Kaurman, Evolution and Development 1 (1999): 77–89. The evolution of the insect hindwing under the control of the Ultrabithorax protein is based upon S. D. Weatherbee et al., Current Biology 11 (1999): 109–15.
For a detailed treatment of the evolution of the vertebrate limb, both in adapting to land and back to water, see Carl Zimmer, At the Water’s Edge: Macroevolution and the Transformation of Life (New York: Free Press, 1998). Descriptions of Sauripteris, Acanthostega, Tulerpeton, and other fossils are in E. B. Daeschler and N. Shubin, Nature 391 (1998): 133, and M. I. Coates, J. E. Jeffrey, and M. Rut, Evolution and Development 4 (2002): 390–401. The evolution of the autopod with respect to Hox genes is described in P. Sardino, F. van der Hoeven, and D. Duboule, Nature 375 (1995): 678–81; N. Shubin, C. Tabin, and S. Carroll, Nature 388 (1997): 639–48; and M. Kmita et al., Nature 420 (2002): 145–50.
The evolution of the different forms of vertebrate wings is the focus of Pat Shipman’s Taking Wing: Archeopteryx and the Evolution of Bird Flight (New York: Simon and Schuster, 1998). The developmental basis of limblessness in snakes is reported by M. J. Cohn and C. Tickle, Nature 399 (1999): 474–79. The evolution of spine reduction in threespine stickleback fish is described in M. D. Shapiro et al., Nature 428 (2004): 717–23, and the exceptional high-resolution fossil record of sticklebacks is described in M. A. Bell, J. V. Baumgartner, and E. C. Olsen, Paleobiology 11 (1985): 258–71.
Although the quote at the beginning of the chapter is often cited, Monod never said it—which bears some explanation. In Le Hasard et la Nécessité (Paris: Editions du Seuil, 1970), Monod wrote, “Hasard capté, conserve, reproduit per la machinerie de l’invariance et ainsi converti en ordre, régie, nécessité” (p. 128). His English-language translator, Austryn Wainhouse, chose to translate “hasard capté” as “randomness caught on the wing,” but more literally it would be “chance [or, randomness] captured.” Stuart Kauffman, in At Home in the Universe (New York: Oxford University Press, 1995), first quotes Monod as saying “chance caught on the wing” (p. 71) and later extends the quote to “Evolution is chance caught on the wing” (p. 97). A wonderful phrase, well worth quoting, but neither Monod nor his translator ever wrote it.
The statistics on Bates’s collections are in H. W. Bates, Naturalist on the River Amazons (London: John Murray, 1863). The letter quoted from Bates to Darwin was received on March 28, 1861. Darwin’s enthusiastic comment on Bates’s paper on mimicry was written on November 20, 1862, and appears in The Life and Letters of Charles Darwin, ed. F. Darwin, vol. 2 (London: John Murray, 1887). Darwin’s appreciation of Bates’s book was published in the Natural History Review 3 (1863). All of the quoted passages about butterflies are from Naturalist on the River Amazons. For more on Nabokov, see K. Johnson and S. Coates, Nabokov’s Blues: The Scientific Odyssey of a Literacy Genius (Cambridge, Mass.: Zoland, 1999).
The most comprehensive analysis of butterfly wing patterns is H. Frederik Nijhout, The Development and Evolution of Butterfly Wing Patterns (Washington, D.C.: Smithsonian Institution Press, 1991), which explains much of the background I cover on the structure and diversity of wing patterns. The tool kit gene associated with the development of scales is reported in R. Galant et al., Current Biology 8 (1998): 807–13.
The discovery of Distal-less gene expression in spots in developing wings is S. B. Carroll et al., Science 265 (1994): 109–14; see also S. B. Carroll, Natural History, February 1997, pp. 28–37. The comparison of Distal-less expression in different species is illustrated in P. M. Brakefield et al., Nature 384 (1996): 236–42. The tool kit proteins that mark the outer rings of eyespots are reported in C. R. Brunetti et al., Current Biology 11 (2001): 1578–85.
The role of reduced eyespots for hiding on dead leaf litter is examined in A. Lytinen et al., Proceedings of the Royal Society of London B 271 (2004): 279–83. The expression of Distal-less in butterflies reared at different temperatures is reported in P. M. Brakefield et al., op. cit. The Spotty mutant is described in P. M. Brakefield and V. French, Acta Biotheoretica 41 (1993): 447–68. The use of artificial selection to evolve lines of butterflies with different eyespot sizes is described in A. F. Monteiro, P. M. Brakefield, and V. French, Evolution 48 (1994): 1147–57. A general overview of recent studies of butterfly wing-pattern evolution is P. Beldade and P. M. Brakefield, Nature Reviews Genetics 3 (2002): 442–52.
Mimicry in the tiger swallowtail is described in J. M. Scriber, R. H. Hagen, and R. C. Lederhouse, Evolution 50 (1996): 222–36. There is a large literature on mimicry in Heliconius butterflies; see J. Mallet and M. Joron, Annual Rev. Ecol. Syst. 30 (1999): 201–33.
For more work by Hugh B. Cott, see The Royal Engineers Journal 52 (1938): 501–17, and Looking at Animals: A Zoologist in Africa (New York: Charles Scribner Sons, 1975).
For a broad discussion of melanism see M. Majerus, Melanism: Evolution in Action (Oxford: Oxford University Press, 1988). Recent scrutiny of the biology of industrial melanism in peppered moths is provided by B. N. Grant, Evolution 53 (1999): 980–84, and J. Mallet, Genetics Society News 50 (2003): 34–38; the latter responds to J. Hopper, Of Moths and Men: Intrigue, Tragedy, and the Peppered Moth (New York: Fourth Estate, 2002).
An excellent review of melanism in mammals is M. E. N. Majerus and N. I. Mundy, Trends in Genetics 19 (2003): 585–88. The primary references are: for the jaguar and jaguarundi, E. Eizirik et al., Current Biology 13 (2003): 448–53; for the bananaquit, E. Theron et al., Current Biology 11 (2001): 550–57; for the rock pocket mouse, M. Nachman et al., Proceedings of the National Academy of Science, USA 100 (2003): 5268–73; and for the Kermode bear, K. Ritland et al., Current Biology 11 (2001): 1468–72. Field studies of the rock pocket mice of the deserts of the American southwest are L. Dice and P. M. Blossom, Studies of Mammalian Ecology in Southwestern North American with Special Attention for the Colors of Desert Mammals (Washington, D.C.: Carnegie Institution of Washington, 1937), pub. no. 485, and L. R. Dice, Contributions from the Laboratory of Vertebrate Biology (University of Michigan) 34 (1947): 1–20.
Gould’s essays on zebras are in Hen’s Teeth and Horse’s Toes (New York: W. W. Norton, 1983), pp. 355–65 and 366–75. J. L. Bard’s analysis is in Journal of Zoology (London) 183 (1977): 527–39.
The general formulas for the time required for advantageous mutants to spread in a population, or the probability of disadvantageous mutations being lost from a population, are in most any population genetics text; see, for example, W.-H. Li, Molecular Evolution (Sunderland, Mass.: Sinauer Associates, 1997).
Darwin’s reactions to observing orangutans are described in A. Desmond and J. Moore, Darwin: The Life of a Tormented Evolutionist (New York: Warner, 1997). Queen Victoria’s diary entry on Jenny is quoted in R. A. Keynes, Annie’s Box (London: Fourth Estate, 2001). The quote from Erich Fromm appeared in his Man for Himself (New York: Rinehart, 1947).
A broad overview of the physical and genetic history of human evolution is found in J. Klein and N. Takahata, Where Do We Come From? The Molecular Evidence for Human Descent (Berlin: Springer-Verlag, 2002). Some of the topics addressed here are examined in S. B. Carroll, Nature 422 (2003): 849–57.
The story of the discovery of the first Neanderthal is told in R. McKie, Dawn of Man: The Story of Human Evolution (London: Dorling Kindersley, 2000), and its first meaningful interpretation was detailed in T. H. Huxley, Evidence as to Man’s Place in Nature (1863). The Athenaeum’s review of Huxley’s book appeared on February 28, 1863. The oldest H. sapiens specimen is described in T. D. White et al., Nature 423 (2003): 742–47.
The data represented in figures 10.3 and 10.5 are compiled from many sources. I have received guidance from paleontologists with differing views on the number and identity of distinct hominin species. I chose a more conservative rather than all-inclusive picture here. For differing views, see B. Wood, Nature 418 (2002): 133–35, and T. White, Science 299 (2003): 1994–96.
For more information on the footprints at Laetoli, see N. Agnew, Scientific American 279 (1998): 51–54. Data on fossil brain sizes are derived from R. B. Ruff, E. Trinkhaus, and T. Holliday, Nature 387 (1997): 173–76; G. Conroy et al., American Journal of Physical Anthropology 13 (2000): 111–18; P. Brunet et al., Nature 418 (2002): 145–51; and B. Wood, Science 284 (1999): 65–71. J. M. Allman, Evolving Brains (New York: Scientific American Library, 1999) was a source of much information on primate and human brain structure and evolution, behavior, and climatic change. The mosaic pattern of brain evolution is described by R. A. Barton and P. Harvey, Nature 408 (2000): 1055–58; W. de Winter and C. E. Oxnard, Nature 409 (2001): 710–14a; and D. A. Clark, P. P. Mitra, and S. S. H. Wang, Nature 411 (2001): 189–93.
The first study of Neanderthal DNA was M. Krings et al., Cell 90 (1997): 19–30; see also D. Serre et al., Public Library of Science/Biology 2 (2004): 0313–0317.
The quote from Emerson Pugh is from his The Biological Origin of Human Values (New York: Basic Books, 1977).
Evidence for anatomical asymmetries in great ape brains is discussed in C. Cantalupo and W. D. Hopkins, Nature 414 (2001): 505, but is strongly countered by C. C. Sherwood et al., The Anatomical Record Part A 271 (2003): 276–85. Studies of patients with situs invertus are D. Kennedy et al., Neurology 53 (1999): 1260–65, and S. Tanaka et al., Neuropsychologia 37 (1999): 869–74.
The arithmetic of human DNA sequence evolution is derived from the full human genome sequence and comparable data available for chimpanzees—see, for instance, S. B. Carroll, Nature 422 (2003): 849–57. The comparison with the mouse is based upon the Mouse Genome Squence Consortium, Nature 420 (2002): 520–62, and an update presented by Dr. Eric Lander, Breckinridge, Colorado, January 2004.
The classic reference on human-chimpanzee differences is M.-C. King and A. C. Wilson, Science 188 (1975): 107–16. Additional early views were E. Zuckerkandl and L. Pauling in Evolving Genes and Proteins, ed. V. Bryson and J. H. Vogel, pp. 97–166 (New York: Academic Press, 1965), and R. J. Britten and E. H. Davidson, Quarterly Review of Biology 46 (1971): 111–38.
The association of a myosin gene mutation with reduction in human jaw musculature is reported by H. Stedman et al., Nature 428 (2004): 415–18.
The discovery of the FOXP2 gene associated with a speech and language disorder is in C. S. L. Lai et al., Nature 413 (2001): 519–23; imaging of patients with the disorder is described by F. Liégeois et al., Nature Neuroscience 6 (2003): 1230–36; the molecular evolution of the FOXP2 sequence is reported in W. Enard et al. Nature (2002) 418: 869–872; FOXP2 expression in the human brain is reported in C. S. Lai et al., Brain 126 (2003): 2455–62; FOXP2 expression in rats and mice brains is described in K. Takahashi et al., Journal of Neuroscience Research 73 (2003): 61–72, and R. J. Ferland et al., Journal of Comprehensive Neurology 460 (2003): 266–79.
For more on genes, experience, and human behavior, see M. Ridley, Nature via Nurture: Genes, Experience, and What Makes Us Human (New York: HarperCollins, 2003).
The earlier versions of passages in The Origin of Species are found in The Foundations of the Origin of Species: Two Essays Written in 1842 and 1844 by Charles Darwin, ed. Francis Darwin (Cambridge: Cambridge University Press, 1909).
For additional perspective on the tendency of evolution to repeat itself at various levels, see Simon Conway Morris’s Life’s Solution: Inevitable Humans in a Lonely Universe (Cambridge: Cambridge University Press, 2003).
Data on the public understanding of evolution are from G. Bishop, The Public Perspective 9 (1998): 39–44. Further information on the state of evolution education can be found on the Web site of the National Center for Science Education (www.natcenscied.org).
Detailed information on the various changes made between editions of The Origin of Species can be found in Morse Peckham, ed., The Origin of Species by Charles Darwin: A Variorum Text (Philadelphia: University of Pennsylvania Press, 1959). Pope John Paul II’s statement on evolution and various individual reactions to it are discussed in E. C. Scott, The Quarterly Review of Biology 72 (1997): 401–6. Charles Harper’s comments appear in Nature 411 (2001): 239–40. Scott Gilbert’s views on teaching evolution through developmental genetics and his critique of M. Behe’s Darwin’s Black Box: The Biochemical Challenge to Evolution (New York: Free Press, 1996) appear in Nature Reviews Genetics 4 (2003): 735–41.
Thoreau talks of the long haul in his 1849 A Week on the Concord and Merrimack Rivers. The views of John F. Haught are from Science and Religion: From Conflict to Conversation (New York: Paulist Press, 1995). Excerpts of his writings can be found at www.aaas.org/spp/dser/evolution/perspectives/haught.shtml.
The statistics on population growth and its history are taken from the Population Reference Bureau (www.prb.org).
The story of the thylacine is told in D. Owen, Thylacine: The Tragic Tale of the Tasmanian Tiger (Crows Nest, NSW: Allen and Unwin, 2003). Further information on species extinction is found in E. O. Wilson and F. M. Peter, eds., Biodiversity (Washington, D.C.: National Academy Press, 1988), and E. O. Wilson, The Diversity of Life (New York: Penguin, 1992).
Huxley’s address to the Royal Institution in February 1860 is quoted in A. Desmond and J. Moore, Darwin: The Life of a Tormented Evolutionist (New York: Warner, 1991), p. 489.