PROLOGUE

References for “fish with arms, snakes with legs, and apes that can walk on two legs” include N. Shubin et al., “The Pectoral Fin of Tiktaalik roseae and the Origin of the Tetrapod Limb,” Nature 440 (2006): 764–71; D. Martill et al., “A Four-Legged Snake from the Early Cretaceous of Gondwana,” Science 349 (2015): 416–19; and T. D. White et al., “Neither Chimpanzee nor Human, Ardipithecus Reveals the Surprising Ancestry of Both,” Proceedings of the National Academy of Sciences 112 (2015): 4877–84.

1. FIVE WORDS

The seminar was taught by the late Farish A. Jenkins, Jr., who became a mentor of mine and a collaborator on the expeditions that led to the discovery of Tiktaalik roseae. The diagram that inspired me made its way into a fabulous little book on great transformations in vertebrate evolution: Leonard Radinsky, The Evolution of Vertebrate Design (Chicago: University of Chicago Press, 1987), figure 9.1, p. 78. Farish was close friends with Radinsky, who had shared drafts of the book’s illustrations, done by Sharon Emerson, with him for the course. Coincidentally, Radinsky was my predecessor as chair of the anatomy department at the University of Chicago. Little could I have known in graduate school that his diagram would inspire me to follow in his footsteps decades later.

Lillian Hellman’s quote appears in her autobiography, An Unfinished Woman: A Memoir (New York: Penguin, 1972). The biological translation for the concepts she expressed are exaptation and preadaptation. The subtle distinctions between them are discussed in Stephen J. Gould and Elisabeth Vrba, “Exaptation—A Missing Term in the Science of Form,” Paleobiology 8 (1982): 4–15. See also W. J. Bock, “Preadaptation and Multiple Evolutionary Pathways,” Evolution 13 (1959): 194–211. Both important papers contain numerous examples.

My history of St. George Jackson Mivart is taken from J. W. Gruber, A Conscience in Conflict: The Life of St. George Jackson Mivart (New York: Temple University Publications, Columbia University Press, 1960). Mivart’s On the Genesis of Species, published in 1871, is now available online at https://archive.org/details/a593007300mivauoft.

The sixth edition of Darwin’s On the Origin of Species is also available online, at https://www.gutenberg.org/files/2009/2009-h/2009-h.htm.

Gould’s take on “the 2% of a wing problem” is in Stephen Jay Gould, “Not Necessarily a Wing,” Natural History (October 1985).

My account of Saint-Hilaire’s life and work is derived from H. Le Guyader, Geoffroy Saint-Hilaire: A Visionary Naturalist (Chicago: University of Chicago Press, 2004), and from P. Humphries, “Blind Ambition: Geoffroy St-Hilaire’s Theory of Everything,” Endeavor 31 (2007): 134–39.

The original description of the Australian lungfish is in A. Gunther, “Description of Ceratodus, a Genus of Ganoid Fishes, Recently Discovered in Rivers of Queensland, Australia,” Philosophical Transactions of the Royal Society of London 161 (1870–71): 377–79. The history of the discovery is in A. Kemp, “The Biology of the Australian Lungfish, Neoceratodus forsteri (Krefft, 1870),” Journal of Morphology Supplement 1 (1986): 181–98.

On the developmental and evolutionary relationships between swim bladders and lungs, see Bashford Dean, Fishes, Living and Fossil (New York: Macmillan, 1895). His catalog of the armor collection at the Metropolitan Museum of Art is available digitally at http://libmma.contentdm.oclc.org/cdm/ref/collection/p15324coll10/id/17498. For a synopsis of his work and life, see https://hyperallergic.com/102513/the-eccentric-fish-enthusiast-who-brought-armor-to-the-met/.

Analyses of air breathing include K. F. Liem, “Form and Function of Lungs: The Evolution of Air Breathing Mechanisms,” American Zoologist 28 (1988): 739–59; and Jeffrey B. Graham, Air-Breathing Fishes (San Diego: Academic Press, 1997). Both show how lungs are the primitive condition for bony fish and corroborate the comparison between swim bladders and lungs.

Recent genetic comparisons between lungs and swim bladders have found deep similarities. See A. N. Cass et al., “Expression of a Lung Developmental Cassette in the Adult and Developing Zebrafish Swimbladder,” Evolution and Development 15 (2013): 119–32. Dean and his contemporaries would be proud.

The story of lungs is only one exemplar of the importance of a change in function at the origin of land-living fish.

Gunnar Säve-Söderbergh, at the age of twenty-two, was in charge of a small team of geologists exploring the rocks in the region for fossils. The hunt was a relatively simple and low-tech affair. Each day the team would disperse across the rocks and look for bones weathering out on the surface. When they found some, they would trace the fragments to attempt to identify the rock layer they came from. These were precisely the techniques that my team would use almost eighty years later in the Canadian Arctic to find the fishapod Tiktaalik roseae.

Säve-Söderbergh’s hunt was for the earliest creatures to walk on land. At the time, nobody had ever found a hint of limbed animals in Devonian-age rocks, which are about 365 million years old. His goal was to go to more ancient rocks to find a fishlike amphibian, a species that blurred the distinction between fish and amphibian.

Säve-Söderbergh was legendary for his energy; he’d work late nights and hike enormous distances to find fossils. He was also supremely confident. Pessimists don’t find fossils; you have to believe that there are fossils in the rocks to devote the long hours and many failed efforts required to find them. Each day his team were to place their findings in one of two boxes: P for fish (Pisces) and A for amphibians. It was a bold move. Nobody had ever found an amphibian in rocks of this age. As you can imagine, over the course of the 1929 field season, the fish box burgeoned with fossils and the amphibian box remained empty.

Near the end of the season, Säve-Söderbergh found a number of odd-looking fragments of bone in the rubble of Celsius Berg, a deep red butte adjacent to the ice of the East Greenland Sea. He collected nearly a dozen plates of bone, each of which was embedded in rock obscuring most of its structure. With their bumps and ridges, these plates looked like some of the fossil fish known at the time. Judging from what was preserved, they belonged in the fish box. They were clearly from a skull but were too flat to be associated with any fish known at the time. Säve-Söderbergh thought they might be amphibian. Ever the optimist, he threw them into the A box.

Returning to Sweden, Säve-Söderbergh began the laborious process of removing grains from the rock that surrounded each bone. Removing the layers revealed a true marvel. He had found what looked like a fish in body shape, but its head had the long snout and flat shape of an amphibian. Säve-Söderbergh had found his early amphibian.

The fossil became a celebrity. Säve-Söderbergh would have become one, too, but he died tragically from tuberculosis before his thirtieth birthday.

The story of Säve-Söderbergh’s work was told by a colleague and friend of his, Erik Jarvik. Jarvik, a member of the early expeditions, included a brief history of the Greenlandic expeditions in his hefty monograph on Ichthyostega, one of the first discovered Devonian tetrapods: E. Jarvik, “The Devonian Tetrapod Ichthyostega,” Fossils and Strata 40 (1996): 1–212. Carl Zimmer, At the Water’s Edge: Fish with Fingers, Whales with Legs (New York: Atria, 1999), discusses Säve-Söderbergh, Jarvik, and the larger history of the field in a highly readable account.

Five decades after Säve-Söderbergh, my colleague Jenny Clack, from Cambridge University, returned to Celsius Berg and his other sites to look with new eyes. Her team of paleontologists were well-versed in Säve-Söderbergh’s discoveries and notes. Their goal was to find missing parts of the skeleton, the ones that he did not collect. Lost in all the hoopla around the fossils was the fact that their limbs were poorly known. Hitting the rocks, Clack set out to correct that. With the right team, good weather, and the knowledge that the rocks held promise, she came back with a trove of fossils. And these fossils had well-preserved limb skeletons connected to them.

The limbs had the classic one bone–two bones–little bones–digits pattern seen in everything with limbs, whether a mammal, bird, amphibian, or reptile (see this page). The surprise lay in the hand and foot. These animals had more than five fingers and toes; they had as many as eight. The extra digits made the limbs broad and flat. Everything about them, from their proportions to the muscle scars on individual bones, implies that they were used as paddles or oars in water. The entire limb was more like a flipper than a hand.

What does this have to do with Darwin’s five words? The earliest animals possessing limbs with fingers and toes used them not to walk on land but to paddle about in water or maneuver through the shallows of swamps and streams. As with lungs, the earliest uses of these great inventions of land-living creatures was not to live on land but to make use of an aquatic environment in new ways. The organ arose early in one setting, with the big revolution—the shift to a new environment—coming about from repurposing it for a new function.

Clack’s magisterial Gaining Ground: The Origin and Evolution of Tetrapods (Bloomington: Indiana University Press, 2012) is the result of a lifetime of work on the origin of tetrapods by a person who brought that field into the modern age. Her book includes both the science and the history of the field along with an important personal account of her work in the Devonian sites in Greenland.

In animals both living and long extinct, lungs, arms, elbows, and wrists all first appear in aquatic animals. The major revolution from life in water to life on land didn’t involve new inventions. It involved changes in inventions that had come about millions of years before.

If history were a single path of change, where one step led inexorably to the next, each with a gradual improvement for a single function, major changes would be impossible. Every major transition would require waiting for not just one invention but a whole patent agency full of them to arise in concert. If, on the other hand, the inventions are already there, doing something else, a simple repurposing can open up new pathways of change. This capability for change is the power of Darwin’s five words.

Knowing that ancient creatures lived in water with lungs, arm bones, wrists, and even digits, our question about the invasion of land by fish changes. Instead of “How could creatures ever evolve to walk on land?,” the question becomes, “Why didn’t the transition happen sooner in the history of the planet?”

Rocks again hold clues. For billions of years, all of the rocks on Planet Earth lacked one thing. Rocks from 4 billion to about 400 million years ago hold evidence of vast oceans and smaller seaways, and on land, fast rivers capable of moving boulders and rocks. But, importantly, there was no evidence for plants on land.

Imagine a world without plants on land. Plants decay when they die and create soil. Plants have roots that hold soil together. This was a barren, rocky world lacking soil. It also lacked any food that animals could eat.

Land plants first appear in the fossil record about 400 million years ago, and insect-like creatures soon thereafter. The invasion of land by plants created a whole new world, one where bugs and insects could thrive. Some of the fossil plant leaves show damage, implying that they were eaten by these early bugs. With plants on land came detritus as they died and rotted. The resulting soils made possible shallow streams and ponds to serve as habitats for fish and amphibians.

The reason fish with lungs didn’t move to land earlier than 375 million years ago was that it was inhospitable until then. Plants, and the insects that followed them, changed everything; ecosystems now were habitable for any fish with the ability to spend short periods on land. Only when new environments appeared could our distant fish ancestors take those first steps, using organs that had already appeared while they were in water. Timing is everything.

Recent geological studies have shown how plants have changed the world, most notably how the invasion of land by plants changed the nature of the streams that existed in the Devonian. Plants with roots allow the formation of soils to form stable banks for shallow streams. For further discussion and analysis, see M. R. Gibling and N. S. Davies, “Palaeozoic Landscapes Shaped by Plant Evolution,” Nature Geoscience 5 (2012): 99–105.

For general reviews of dinosaur evolution and bird relationships, and popular accounts by dinosaur scientists, see Lowell Dingus and Timothy Rowe, The Mistaken Extinction (New York: W. H. Freeman, 1998); Steve Brusatte, The Rise and Fall of the Dinosaurs: A New History of a Lost World (New York: HarperCollins, 2018); and Mark Norell and Mick Ellison, Unearthing the Dragon (New York: Pi Press, 2005).

For a lovely popular account of Huxley’s work on Archaeopteryx and the origin of birds, see Riley Black, “Thomas Henry Huxley and the Dinobirds,” Smithsonian (December 2010).

On Baron Nopcsa, his colorful life, and his pathbreaking science, see E. H. Colbert, The Great Dinosaur Hunters and Their Discoveries (New York: Dover, 1984); Vanessa Veselka, “History Forgot This Rogue Aristocrat Who Discovered Dinosaurs and Died Penniless,” Smithsonian (July 2016); and David Weishampel and Wolf-Ernst Reif, “The Work of Franz Baron Nopcsa (1877–1933): Dinosaurs, Evolution, and Theoretical Tectonics,” Jahrbuch der Geologischen Anstalt 127 (1984): 187–203.

John Ostrom’s work was published in a number of papers in the 1960s and ’70s, including his formal description of Deinonychus: J. Ostrom, “Osteology of Deinonychus antirrhopus, an Unusual Theropod from the Lower Cretaceous of Montana,” Bulletin of the Peabody Museum of Natural History 30 (1969): 1–165. Papers that followed included J. Ostrom, “Archaeopteryx and the Origin of Birds,” Biological Journal of the Linnaean Society 8 (1976): 91–182; and J. Ostrom, “The Ancestry of Birds,” Nature 242 (1973): 136–39. For an account of Ostrom’s contributions, see Richard Conniff, “The Man Who Saved the Dinosaurs,” Yale Alumni Magazine (July 2014).

Recent surveys of the origin of features have spanned the fields of paleontology and developmental biology. See R. Prum and A. Brush, “Which Came First, the Feather or the Bird?,” Scientific American 288 (2014): 84–93; and R. O. Prum, “Evolution of the Morphological Innovations of Feathers,” Journal of Experimental Zoology 304B (2005): 570–79.

2. EMBRYONIC IDEAS

Duméril’s story is best related by his initial surprise, then his ultimate solving of the puzzle. After doing so, he set up a breeding colony of axolotls and generously gave them away to any researcher who wanted them. Descendants of that population are likely in labs today. You would not know it from the title, but a good recent account of Duméril is G. Malacinski, “The Mexican Axolotl, Ambystoma mexicanum: Its Biology and Developmental Genetics, and Its Autonomous Cell-Lethal Genes,” American Zoologist 18 (1978): 195–206. Some of Duméril’s early work appeared in M. Auguste Duméril, “On the Development of the Axolotl,” Annals and Magazine of Natural History 17 (1866): 156–57; and “Experiments on the Axolotl,” Annals and Magazine of Natural History 20 (1867): 446–49.

The field of embryology is blessed with some textbooks that are so good they have driven research in the field. These include Michael Barresi and Scott Gilbert, Developmental Biology (New York: Sinauer Associates, 2016); and Lewis Wolpert and Cheryll Tickle, Principles of Development (New York: Oxford University Press, 2010).

My treatment of von Baer (including his quote on misidentifying embryos in vials) and Pander is based in part on historical work by Robert Richards, available online at home.uchicago.edu/~rjr6/articles/von%20Baer.doc.

Stephen Jay Gould’s Ontogeny and Phylogeny (Cambridge, MA: Belknap Press, 1985) has a wonderful history of embryology in the first half, where he covers the work of von Baer, Haeckel, and Duméril. A short review paper is a superb follow-up: B. K. Hall, “Balfour, Garstang and deBeer: The First Century of Evolutionary Embryology,” American Zoologist 40 (2000): 718–28.

Over the years, while many learned Haeckel’s ideas in school, scientists in the field had a love/hate reaction to him: some were acolytes of his work, while others, like Garstang, thought him a fraud. Recent histories have held a variety of views, as seen in Robert Richards, The Tragic Sense of Life: Ernst Haeckel and the Struggle over Evolutionary Thought (Chicago: University of Chicago Press, 2008). Some recent embryologists believe that some of Haeckel’s original diagrams were, to put it charitably, drawn to emphasize his main points: M. K. Richardson et al., “Haeckel, Embryos and Evolution,” Science 280 (1998): 983–85.

Apsley Cherry-Garrard, The Worst Journey in the World (London: Penguin Classics, 2006), is a classic of expedition literature. I read it before my first Antarctic expedition. It made McMurdo Sound, Hut Point, and Mount Erebus feel like familiar landscapes when I saw them for the first time.

Walter Garstang, Larval Forms and Other Zoological Verses (Oxford: Blackwell, 1951), was republished by the University of Chicago Press in 1985.

Heterochrony has a vast literature stemming from the days of Garstang, if not before. Whole taxonomies of the rates and timing of development have been proposed. For a snapshot of some of the major approaches (with good references), see P. Alberch et al., “Size and Shape in Ontogeny and Phylogeny,” Paleobiology 5 (1979): 296–317; Gavin DeBeer, Embryos and Ancestors (London: Clarendon Press, 1962); and Stephen Jay Gould, Ontogeny and Phylogeny (Cambridge, MA: Belknap Press, 1985). Gould’s book had a large impact in the 1980s, leading to renewed interest in the approach.

Amphibian biology and metamorphosis are discussed in W. Duellman and L. Trueb, Biology of Amphibians (New York: McGraw-Hill, 1986); and D. Brown and L. Cai, “Amphibian Metamorphosis,” Developmental Biology 306 (2007): 20–33. Duellman and Trueb’s book is a thorough account of anatomy, evolution, and development.

Recently, analyses of genomes have identified tunicates, including sea squirts, as the closest living relatives of vertebrate animals. See F. Delsuc et al., “Tunicates and Not Cephalochordates Are the Closest Living Relatives of Vertebrates,” Nature 439 (2006): 965–68. Our understanding of vertebrate origins relies also on another living creature, amphioxus, whose genome is discussed in L. Z. Holland et al., “The Amphioxus Genome Illuminates Vertebrate Origins and Cephalochordate Biology,” Genome Research 18 (2008): 1100–11.

For a general review of Garstang’s hypothesis and the problem of vertebrate origins, see Henry Gee, Across the Bridge: Understanding the Origin of Vertebrates (Chicago: University of Chicago Press, 2018).

The iconic photo by Naef has generated significant discussion over the years. There is little doubt that he used mounted taxidermy specimens. See, most recently, Richard Dawkins, The Greatest Show on Earth (New York: Free Press, 2010). While the postures were likely posed, the similarity of the proportions of the cranial vault, face, and position of the foramen magnum between juvenile chimps and humans has been shown quantitatively in the references below.

The most prominent proponents of human paedomorphosis were Ashley Montagu, Growing Young (New York: Greenwood Press, 1989); and Stephen Jay Gould, Ontogeny and Phylogeny (Cambridge, MA: Belknap Press, 1985). An opposing view is B. T. Shea, “Heterochrony in Human Evolution: The Case for Neoteny Reconsidered,” Yearbook of Physical Anthropology 32 (1989): 69–101. While certain traits seem to be paedomorphic, others, such as bipedality, do not.

D’Arcy Wentworth Thompson, On Growth and Form (New York: Dover, 1992), originally published in 1917, launched a revolution in quantitative biology. Since his time, the field of morphometrics, the quantitative analysis of shape changes, has been an active area of inquiry.

The importance of the neural crest in development and evolution is reviewed in C. Gans and R. G. Northcutt, “Neural Crest and the Origin of Vertebrates: A New Head,” Science 220 (1983): 268–73; and Brian Hall, The Neural Crest in Development and Evolution (Amsterdam: Springer, 1999).

Julia Platt’s work and life is discussed in S. J. Zottoli and E. Seyfarth, “Julia B. Platt (1857–1935): Pioneer Comparative Embryologist and Neuroscientist,” Brain, Behavior and Evolution 43 (1994): 92–106.

3. MAESTRO IN THE GENOME

The apocryphal quote is taken from J. D. Watson, The Double Helix (New York: Touchstone, 2001). Watson and Crick’s full quote appeared in a two-page paper announcing the finding to science: “We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest.” J. D. Watson and F. Crick, “A Structure for Deoxyribose Nucleic Acid,” Nature 171 (1953): 737–38.

The story of uncovering the workings of DNA and the ways it makes proteins is discussed in Matthew Cobb, Life’s Greatest Secret: The Race to Crack the Genetic Code (New York: Basic Books, 2015). See also the classic work by Horace Freeland Judson, The Eighth Day of Creation: Makers of the Revolution in Biology (New York: Simon and Schuster, 1979).

Zuckerkandl and Pauling launched their new approach in a series of papers in the mid-1960s. Major ones include E. Zuckerkandl and L. Pauling, “Molecules as Documents of Evolutionary History,” Journal of Theoretical Biology 8 (1965): 357–66; and E. Zuckerkandl and L. Pauling, “Evolutionary Divergence and Convergence in Proteins,” 97–166, in V. Bryson and H. J. Vogel, eds., Evolving Genes and Proteins (New York: Academic Press, 1965).

Zuckerkandl and Pauling sought to do more than uncover the relationships between species. They proposed to use the differences in proteins and genes as a kind of clock to tell how long species had been evolving independently of one another. If rates of change in the sequence of a protein are relatively constant over long timescales, then differences in proteins carry a way to interpret time.

The molecular clock hypothesis assumes that over long periods of time, the changes in the sequence of amino acids in a protein will be constant. One way of applying this concept relies on understanding amino acid sequences. Let’s take a completely hypothetical example, comparing a species of frog, a monkey, and a human. We would begin by sequencing the proteins. Then we would count the number of amino acids that differ between each of the species. Let’s say we’re looking at a protein in the skin, and the frog protein differs from both the human and the monkey one by eighty amino acids. Humans and monkeys differ by only thirty. To deploy the molecular clock, we would need to have a fossil date to fix the rate of amino acid change; then we could apply that rate to places where we don’t have fossils.

Let’s assume we have a fossil that suggests that frogs, monkeys, and people shared a common ancestor 400 million years ago. To calibrate the clock, we would divide 80 by 400 to give a rate of protein change of 0.2 percent over one million years. With this number, we could then calculate how long ago humans and monkeys shared a common ancestor by multiplying 0.2 times 30, to give six million years. This example is hypothetical, but it shows how we would first sequence the proteins, count the amino acid differences among them, use a fossil to estimate the rate of protein change, then apply that rate to understand ages of events for which we do not have fossils.

The account of Zuckerkandl and Pauling’s attempt to write an outrageous paper as well as the general historical context of their work is discussed in G. Morgan, “Émile Zuckerkandl, Linus Pauling, and the Molecular Evolutionary Clock,” Journal of the History of Biology 31 (1998): 155–78. Their resulting paper is E. Zuckerkandl and L. Pauling, “Molecular Disease, Evolution and Genic Heterogeneity,” 189–225, in Michael Kasha and Bernard Pullman, eds., Horizons in Biochemistry: Albert Szent-Györgyi Dedicatory Volume (New York: Academic Press, 1962).

For an oral history with Émile Zuckerkandl, see “The Molecular Clock,” https://authors.library.caltech.edu/5456/1/hrst.mit.edu/hrs/evolution/public/clock/zuckerkandl.html.

Allan Wilson and Mary-Claire King pursued this approach in their work. They were originally following up on an important and controversial molecular clock paper that suggested humans and chimpanzees had a relatively recent common ancestry. That paper is A. Wilson and V. Sarich, “A Molecular Time Scale for Human Evolution,” Proceedings of the National Academy of Sciences 63 (1969): 1088–93. Their goal was to add more proteins to this analysis to calibrate that clock more precisely. King’s epic paper is M. C. King and A. C. Wilson, “Evolution at Two Levels in Humans and Chimpanzees,” Science 188 (1975): 107–16. The two levels they were referring to were evolution at the level of protein coding and evolution at the level of gene regulation, i.e., the switches. Their data suggested that many of the differences between humans and chimpanzees are due to differences in when and where genes are active; hence, gene regulation.

More recent confirmation of their work is described in Kate Wong, “Tiny Genetic Differences Between Humans and Other Primates Pervade the Genome,” Scientific American, September 1, 2014; and K. Prüfer et al., “The Bonobo Genome Compared with Chimpanzee and Human Genomes,” Nature 486 (2012): 527–31.

Several web resources cover the history and impact of the Human Genome Project: “The Human Genome Project (1990–2003),” The Embryo Project Encyclopedia, https://embryo.asu.edu/pages/human-genome-project-1990-2003; “What Is the Human Genome Project?,” National Human Genome Research Institute, https://www.genome.gov/12011238/an-overview-of-the-human-genome-project/; and https://www.nature.com/scitable/topicpage/sequencing-human-genome-the-contributions-of-francis-686.

Major scientific papers on the project include International Human Genome Sequencing Consortium, “Finishing the Euchromatic Sequence of the Human Genome,” Nature 431 (2004): 931–45; and International Human Genome Sequencing Consortium, “Initial Sequencing and Analysis of the Human Genome,” Nature 409 (2001): 860–921.

Some relevant books on the Human Genome Project include Daniel J. Kevles and Leroy Hood, eds., The Code of Codes (Cambridge, MA: Harvard University Press, 2000); and James Shreeve, The Genome War: How Craig Venter Tried to Capture the Code of Life and Save the World (New York: Random House, 2004). A firsthand account is John Craig Venter, A Life Decoded: My Genome: My Life (New York: Viking Press, 2007).

The structure of the genome and the number of genes have a large literature, including a number of prominent multi-investigator projects. An introductory sampling, with good bibliographies, includes A. Prachumwat and W.-H. Li, “Gene Number Expansion and Contraction in Vertebrate Genomes with Respect to Invertebrate Genomes,” Genome Research 18 (2008): 221–32; and R. R. Copley, “The Animal in the Genome: Comparative Genomics and Evolution,” Philosophical Transactions of the Royal Society, B 363 (2008): 1453–61. The journal Nature has a good introductory website: https://www.nature.com/scitable/topicpage/eukaryotic-genome-complexity-437.

Powerful genome browsers allow scientists to compare genes and genomes of different species. Some of the most frequently used include ENSEMBL https://useast.ensembl.org/; VISTA, http://pipeline.lbl.gov/cgi-bin/gateway2; and the BLAST search tool, https://blast.ncbi.nlm.nih.gov/Blast.cgi. Check them out. They place a world of discovery at your fingertips.

François Jacob and Jacques Monod’s classic is one of the greatest papers in biology: “Genetic Regulatory Mechanisms in the Synthesis of Proteins,” Journal of Molecular Biology 3 (1961): 318–56. It is challenging for the novice to read. For a thorough yet readable breakdown, see this classic in scientific communication: Horace Freeland Judson, The Eighth Day of Creation: Makers of the Revolution in Biology (New York: Simon and Schuster, 1979).

For the incredible backdrop of Jacob and Monod’s work, see the gripping and authoritative account by Sean B. Carroll, Brave Genius: A Scientist, a Philosopher, and Their Daring Adventures from the French Resistance to the Nobel Prize (New York: Norton, 2013). I thought I knew everything about them, but this book opened an entire world for me.

Sean B. Carroll also wrote the classic on how gene regulation can impact evolution: Endless Forms Most Beautiful: The New Science of Evo Devo (New York: Norton, 2006).

The role of Sonic hedgehog in limb anomalies is discussed in E. Anderson et al., “Human Limb Abnormalities Caused by Disruption of Hedgehog Signaling,” Trends in Genetics 28 (2012): 364–73. Anomalies come about by changing the activity of Sonic or by disrupting the pathway of genes with which Sonic interacts.

The work on the long-range switch, more formally known as a long-range enhancer, is in a series of beautiful papers: L. A. Lettice et al., “The Conserved Sonic hedgehog Limb Enhancer Consists of Discrete Functional Elements That Regulate Precise Spatial Expression,” Cell Reports 20 (2017): 1396–408; L. A. Lettice et al., “A Long-Range Shh Enhancer Regulates Expression in the Developing Limb and Fin and Is Associated with Preaxial Polydactyly,” Human Molecular Genetics 12 (2003): 1725–35; and R. Hill and L. A. Lettice, “Alterations to the Remote Control of Shh Gene Expression Cause Congenital Abnormalities,” Philosophical Transactions of the Royal Society, B 368 (2013), http://doi.org/10.1098/rstb.2012.0357.

Many of these long-range switches are now known. On their general biology and impacts on development and evolution, see A. Visel et al., “Genomic Views of Distant-Acting Enhancers,” Nature 461 (2009): 199–205; H. Chen et al., “Dynamic Interplay Between Enhancer-Promoter Topology and Gene Activity,” Nature Genetics 50 (2018): 1296–303; and A. Tsai and J. Crocker, “Visualizing Long-Range Enhancer-Promoter Interaction,” Nature Genetics 50 (2018): 1205–6.

The reduction in snake limbs and the correlation to changes in the Sonic long-range enhancer is discussed in E. Z. Kvon et al., “Progressive Loss of Function in a Limb Enhancer During Snake Evolution,” Cell 167 (2016): 633–42.

The role of changes in genetic regulatory elements (switches) has a large literature. See M. Rebeiz and M. Tsiantis, “Enhancer Evolution and the Origins of Morphological Novelty,” Current Opinion in Genetics and Development 45 (2017): 115–23; and Sean B. Carroll, Endless Forms Most Beautiful: The New Science of Evo Devo (New York: Norton, 2006). For the stickleback example, see Y. F. Chan et al., “Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer,” Science 327 (2010): 302–5.

4. BEAUTIFUL MONSTERS

Thomas Soemmerring was a polymath who described one of the first flying reptiles, pterosaurs, designed telescopes, developed vaccines, and analyzed mutants. His classic work on developmental anomalies is S. T. von Soemmerring, Abbildungen und Beschreibungen einiger Misgeburten die sich ehemals auf dem anatomischen Theater zu Cassel befanden (Mainz: kurfürstl. privilegirte Universitätsbuchhandlung, 1791).

An influential paper on how monsters—developmental anomalies—can be deeply informative is P. Alberch, “The Logic of Monsters: Evidence for Internal Constraint in Development and Evolution,” Geobios 22 (1989): 21–57.

For classical interpretations of developmental anomalies and teratology, see Dudley Wilson, Signs and Portents: Monstrous Births from the Middle Ages to the Enlightenment (New York: Routledge, 1993).

On the enduring contribution of Geoffroy and Isidore Saint-Hilaire to understanding developmental anomalies, see A. Morin, “Teratology from Geoffroy Saint Hilaire to the Present,” Bulletin de l’Association des anatomistes (Nancy) 80 (1996): 17–31 (in French).

For an informative website on the history and impact of studies of teratology on biology and medicine, see “A New Era: The Birth of a Modern Definition of Teratology in the Early 19th Century,” New York Academy of Medicine, https://nyam.org/library/collections-and-resources/digital-collections-exhibits/digital-telling-wonders/new-era-birth-modern-definition-teratology-early-19th-century/.

William Bateson’s classic work on variation is Materials for the Study of Variation Treated with Especial Regard to Discontinuity in the Origin of Species (London: Macmillan, 1894).

One of T. H. Morgan’s former students, an eminence in his own right, wrote his National Academy of Sciences Biographical Memoir: A. H. Sturtevant, Thomas Hunt Morgan, 1866–1945: A Biographical Memoir (Washington, DC: National Academy of Sciences, 1959), available online at http://www.nasonline.org/publications/biographical-memoirs/memoir-pdfs/morgan-thomas-hunt.pdf.

Calvin Bridges was the subject of a 2014 biopic, The Fly Room, reviewed in Ewen Callaway, “Genetics: Genius on the Fly,” Nature 516 (December 11, 2014), online at https://www.nature.com/articles/516169a.

Cold Spring Harbor Laboratory maintains a biographical website devoted to Calvin Bridges: Calvin Blackman Bridges, Unconventional Geneticist (1889–1938), at http://library.cshl.edu/exhibits/bridges.

For a history of Lewis and Bridges’s work, see I. Duncan and G. Montgomery, “E. B. Lewis and the Bithorax Complex,” pts. 1 and 2, Genetics 160 (2002): 1265–72, and 161 (2002): 1–10. Lewis was initially more interested in gene duplications than in development; hence his interest in this region of the chromosome.

The banding patterns on chromosomes as a road map to Bithorax and other mutants is described in C. B. Bridges, “Salivary Chromosome Maps: With a Key to the Banding of the Chromosomes of Drosophila melanogaster,” Journal of Heredity 26 (1935): 60–64; and C. B. Bridges and T. H. Morgan, The Third-Chromosome Group of Mutant Characters of Drosophila melanogaster (Washington, DC: Carnegie Institution, 1923).

Edward Lewis’s classic paper is E. B. Lewis, “A Gene Complex Controlling Segmentation in Drosophila,” Nature 276 (1978): 565–70.

The homeobox discovery was made in parallel by W. McGinnis et al., “A Conserved DNA Sequence in Homoeotic Genes of the Drosophila Antennapedia and Bithorax Complexes,” Nature 308 (1984): 428–33; and by M. Scott and A. Weiner, “Structural Relationships Among Genes That Control Development: Sequence Homology Between the Antennapedia, Ultrabithorax, and Fushi Tarazu Loci of Drosophila,” Proceedings of the National Academy of Sciences 81 (1984): 4115–19.

The homeobox discovery and its implications for evolution is given a full account, with references, in Sean B. Carroll, Endless Forms Most Beautiful: The New Science of Evo Devo (New York: Norton, 2006). Ed Lewis retrospectively reviewed the problem in E. B. Lewis, “Homeosis: The First 100 Years,” Trends in Genetics 10 (1994): 341–43.

Patel’s work with Parhyale is described in A. Martin et al., “CRISPR/Cas9 Mutagenesis Reveals Versatile Roles of Hox Genes in Crustacean Limb Specification and Evolution,” Current Biology 26 (2016): 14–26; and J. Serano et al., “Comprehensive Analysis of Hox Gene Expression in the Amphipod Crustacean Parhyale hawaiensis,” Developmental Biology 409 (2016): 297–309.

On the role of the homeobox genes in the development of vertebrae, see D. Wellik and M. Capecchi, “Hox10 and Hox11 Genes Are Required to Globally Pattern the Mammalian Skeleton,” Science 301 (2003): 363–67; and D. Wellik, “Hox Patterning of the Vertebrate Axial Skeleton,” Developmental Dynamics 236 (2007): 2454–63.

The “hand genes” are known more precisely as Hoxa-13 and Hoxd-13. The paper describing their deletion in mice is C. Fromental-Ramain et al., “Hoxa-13 and Hoxd-13 Play a Crucial Role in the Patterning of the Limb Autopod,” Development 122 (1996): 2997–3011.

Tetsuya Nakamura and Andrew Gehrke’s studies of homeobox genes in fin development are contained in T. Nakamura et al., “Digits and Fin Rays Share Common Developmental Histories,” Nature 537 (2016): 225–28. Their work was also reported in Carl Zimmer, “From Fins into Hands: Scientists Discover a Deep Evolutionary Link,” New York Times, August 17, 2016.

5. COPYCATS

Vicq d’Azyr is an underappreciated figure in the history of anatomy. He made many of the same observations that Richard Owen did about the similarity of form (such as homology) but never generalized them, so he is not as widely credited with their origin. See R. Mandressi, “The Past, Education and Science. Félix Vicq d’Azyr and the History of Medicine in the 18th Century,” Medicina nei secoli 20 (2008): 183–212 (in French); and R. S. Tubbs et al., “Félix Vicq d’Azyr (1746–1794): Early Founder of Neuroanatomy and Royal French Physician,” Child’s Nervous System 27 (2011): 1031–34.

A more modern take on this notion of duplicate organs in the body, known as serial homology, is in Günter Wagner, Homology, Genes, and Evolutionary Innovation (Princeton, NJ: Princeton University Press, 2018).

The small eyes mutant was first described in Sabra Colby Tice, A New Sex-linked Character in Drosophila (New York: Zoological Laboratory, Columbia University, 1913).

Bridges’s use of his chromosomal maps to reveal gene duplications is found in “Calvin Bridges, “Salivary Chromosome Maps: With a Key to the Banding of the Chromosomes of Drosophila melanogaster,” Journal of Heredity 26 (1935): 60–64.

The life of Susumu Ohno is covered in U. Wolf, “Susumu Ohno,” Cytogenetics and Cell Genetics 80 (1998): 8–11; and in Ernest Beutler, “Susumu Ohno, 1928–2000” Biographical Memoirs 81 (2012), from the National Academy of Sciences, online at https://www.nap.edu/read/10470/chapter/14.

Ohno’s work is in a number of papers and a book that synthesizes his work on duplications: Susumu Ohno, “So Much ‘Junk’ DNA in Our Genome,” 336–70, in H. H. Smith, ed., Evolution of Genetic Systems (New York: Gordon and Breach, 1972); Susumu Ohno, “Gene Duplication and the Uniqueness of Vertebrate Genomes Circa 1970–1999,” Seminars in Cell and Developmental Biology 10 (1999): 517–22; and Susumu Ohno, Evolution by Gene Duplication (Amsterdam: Springer, 1970).

Yves Van de Peer, Eshchar Mizrachi, and Kathleen Marchal, “The Evolutionary Significance of Polyploidy,” Nature Reviews Genetics 18 (2017): 411–24; and S. A. Rensing, “Gene Duplication as a Driver of Plant Morphogenetic Evolution,” Current Opinion in Plant Biology 17 (2014): 43–48.

T. Ohta, “Evolution of Gene Families,” Gene 259 (2000): 45–52; J. Thornton and R. DeSalle, “Gene Family Evolution and Homology: Genomics Meets Phylogenetics,” Annual Reviews of Genomics and Human Genetics 1 (2000): 41–73; and J. Spring, “Genome Duplication Strikes Back,” Nature Genetics 31 (2002): 128–29.

There are many examples of gene families and their evolution. One from the opsin genes used in seeing is a nice example. See R. M. Harris and H. A. Hoffman, “Seeing Is Believing: Dynamic Evolution of Gene Families,” Proceedings of the National Academy of Sciences 112 (2015): 1252–53.

Homeobox genes are another case of a gene family that arose by gene duplication. For different perspectives on the mechanisms and the impact of this duplication, see P. W. H. Holland, “Did Homeobox Gene Duplications Contribute to the Cambrian Explosion?,” Zoological Letters 1 (2015): 1–8; G. P. Wagner et al., “Hox Cluster Duplications and the Opportunity for Evolutionary Novelties,” Proceedings of the National Academy of Sciences 100 (2003): 14603–6; and N. Soshnikova et al., “Duplications of Hox Gene Clusters and the Emergence of Vertebrates,” Developmental Biology 378 (2013): 194–99.

Notch signaling and the duplication of genes in brain evolution was the subject of two papers published independently: I. T. Fiddes et al., “Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis,” Cell 173 (2018): 1356–69; and I. K. Suzuki et al., “Human-Specific NOTCH2NL Genes Expand Cortical Neurogenesis Through Delta/Notch Regulation,” Cell 173 (2018): 1370–84.

Roy Britten’s life is recounted by his longtime collaborator in Eric Davidson, “Roy J. Britten, 1919–2012: Our Early Years at Caltech,” Proceedings of the National Academy of Sciences 109 (2012): 6358–59. Davidson and Britten together published a speculative paper on the meaning of these sequences that was well ahead of its time and spawned research by a generation of scientists: R. J. Britten and E. H. Davidson, “Repetitive and Non-Repetitive DNA Sequences and a Speculation on the Origins of Evolutionary Novelty,” Quarterly Review of Biology 46 (1971): 111–38.

Britten’s paper describing the repeats and the techniques he used to find them is R. J. Britten and D. E. Kohne, “Repeated Sequences in DNA,” Science 161 (1968): 529–40. A simpler translation of the work and its context is R. Andrew Cameron, “On DNA Hybridization and Modern Genomics,” at https://onlinelibrary.wiley.com/doi/pdf/10.1002/mrd.22034.

Manyuan Long’s lab group described its work on the origin of new genes in W. Zhang et al., “New Genes Drive the Evolution of Gene Interaction Networks in the Human and Mouse Genomes,” Genome Biology 16 (2015): 202–26. The origin of new genes is an active area of inquiry. While many new genes arise by gene duplication, some do not, and the mechanisms for this are still under active inquiry. For an exemplar with references, see L. Zhao et al., “Origin and Spread of De Novo Genes in Drosophila melanogaster Populations,” Science 343 (2014): 769–72.

McClintock’s jumping gene discovery is first described in Barbara McClintock, “The Origin and Behavior of Mutable Loci in Maize,” Proceedings of the National Academy of Sciences 36 (1950): 344–55. For a retrospective celebration and explanation of the paper, see S. Ravindran, “Barbara McClintock and the Discovery of Jumping Genes,” Proceedings of the National Academy of Sciences 109 (2012): 20198–99.

On the discovery and workings of jumping genes, see L. Pray and K. Zhaurova, “Barbara McClintock and the Discovery of Jumping Genes (Transposons),” Nature Education 1 (2008): 169.

The National Library of Medicine has an online repository of McClintock’s papers, including her quotes used here and the quote by Nixon at her National Medal of Science ceremony: https://profiles.nlm.nih.gov/ps/retrieve/Narrative/LL/p-nid/52.

6. OUR INNER BATTLEFIELD

Ernst Mayr’s classic book is Animal Species and Evolution (Cambridge, MA: Harvard University Press, 1963).

Richard Goldschmidt’s book is The Material Basis of Evolution (New Haven, CT: Yale University Press, 1940). The paper that so enraged Mayr is Goldschmidt, “Evolution as Viewed by One Geneticist,” American Scientist 40 (1952): 84–98.

For Goldschmidt’s life, see Curt Stern, Richard Benedict Goldschmidt, 1878–1958: A Biographical Memoir (Washington, DC: National Academy of Sciences, 1967), at http://www.nasonline.org/publications/biographical-memoirs/memoir-pdfs/goldschmidt-richard.pdf.

The era when Mayr did his major work is known as the time of the Evolutionary Synthesis; it culminated in the late 1940s, when findings from genetics were incorporated into the fields of taxonomy, paleontology, and comparative anatomy. During our continued teas, Mayr often spoke of a whole new synthesis being on the horizon in the 1990s, one that would extend the work of his generation into molecular biology and developmental genetics. Accordingly, he encouraged the graduate students in his retinue to stay current in that scientific literature.

Ronald Fisher’s enormously influential work was The Genetical Theory of Natural Selection (London: Clarendon Press, 1930).

Vincent Lynch’s papers are V. J. Lynch et al., “Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome During the Evolution of Mammalian Pregnancy,” Cell Reports 10 (2015): 551–61; and V. J. Lynch et al., “Transposon-Mediated Rewiring of Gene Regulatory Networks Contributed to the Evolution of Pregnancy in Mammals,” Nature Genetics 43 (2011): 1154–58.

Lynch reviewed the general problem in G. P. Wagner and V. J. Lynch, “The Gene Regulatory Logic of Transcription Factor Evolution,” Trends in Ecology and Evolution 23 (2008): 377–85; and G. P. Wagner and V. J. Lynch, “Evolutionary Novelties,” Current Biology 20 (2010): 48–52. The inspiration for this work was McClintock herself in B. McClintock, “The Origin and Behavior of Mutable Loci in Maize,” Proceedings of the National Academy of Sciences 36 (1950): 344–55; and the seminal paper by R. J. Britten and E. H. Davidson, “Repetitive and Non-Repetitive DNA Sequences and a Speculation on the Origins of Evolutionary Novelty,” Quarterly Review of Biology 46 (1971): 111–38.

The conversion of jumping genes into useful parts of the genome (their so-called domestication) is an active area of research. A sampling of papers and references includes D. Jangam et al., “Transposable Element Domestication as an Adaptation to Evolutionary Conflicts,” Trends in Genetics 33 (2017): 817–31; and E. B. Chuong et al., “Regulatory Activities of Transposable Elements: From Conflicts to Benefits,” Nature Reviews Genetics 18 (2017): 71–86.

A good review of the syncytin work is C. Lavialle et al., “Paleovirology of ‘Syncytins,’ Retroviral env Genes Exapted for a Role in Placentation,” Philosophical Transactions of the Royal Society of London, B 368 (2013): 20120507; and H. S. Malik, “Retroviruses Push the Envelope for Mammalian Placentation,” Proceedings of the National Academy of Sciences 109 (2012): 2184–85. The syncytin discoveries are in S. Mi et al., “Syncytin Is a Captive Retroviral Envelope Protein Involved in Human Placental Morphogenesis” Nature 403 (2000): 785–89; J. Denner, “Expression and Function of Endogenous Retroviruses in the Placenta,” APMIS 124 (2016): 31–43; A. Dupressoir et al., “Syncytin-A Knockout Mice Demonstrate the Critical Role in Placentation of a Fusogenic, Endogenous Retrovirus-Derived, Envelope Gene,” Proceedings of the National Academy of Sciences 106 (2009): 12127–32; and A. Dupressoir et al., “A Pair of Co-Opted Retroviral Envelope Syncytin Genes Is Required for Formation of the Two-Layered Murine Placental Syncytiotrophoblast,” Proceedings of the National Academy of Sciences 108 (2011): 1164–73.

For a general review of the role of retroviruses in the evolution of the placenta, see D. Haig, “Retroviruses and the Placenta,” Current Biology 22 (2012): 609–13.

Syncytins have also now been found in other species that have placenta-like structures, such as lizards. See G. Cornelis et al., “An Endogenous Retroviral Envelope Syncytin and Its Cognate Receptor Identified in the Viviparous Placental Mabuya Lizard,” Proceedings of the National Academy of Sciences 114 (2017): E10991–E11000.

The search for long-dead or domesticated viruses is a field unto itself, known as paleovirology. For more information, see M. R. Patel et al., “Paleovirology—Ghosts and Gifts of Viruses Past,” Current Opinion in Virology 1 (2011): 304–9; and J. A. Frank and C. Feschotte, “Co-option of Endogenous Viral Sequences for Host Cell Function,” Current Opinion in Virology 25 (2017): 81–89.

Jason Shepherd’s work with Arc is in E. D. Pastuzyn et al., “The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein That Mediates Intercellular RNA Transfer,” Cell 172 (2018): 275–88. Ed Yong reviewed the paper for a more general audience in “Brain Cells Share Information with Virus-Like Capsules,” Atlantic (January 2018).

7. LOADED DICE

The book that emerged from Gould’s lectures was Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: Norton, 1989).

For Ray Lankester’s work on degeneration and multiples in evolution, see E. R. Lankester, Degeneration: A Chapter in Darwinism (London: Macmillan, 1880); and E. R. Lankester, “On the Use of the Term ‘Homology’ in Modern Zoology, and the Distinction Between Homogenetic and Homoplastic Agreements,” Annals and Magazine of Natural History 6 (1870): 34–43.

For a discussion of convergent and parallel evolution, see Simon Conway Morris, Life’s Solution: Inevitable Humans in a Lonely Universe (Cambridge, UK: Cambridge University Press, 2003). Conway Morris takes the hard stand that all of evolution is inevitable. By contrast, Jonathan Losos, Improbable Destinies: Fate, Chance and the Future of Evolution (New York: Riverhead, 2017), is a finely balanced view of the relationship between chance and inevitability.

Good footage of salamander tongue flipping is at https://www.youtube.com/watch?v=mRrIITcUeBM.

A scientific breakdown of the anatomy behind this amazing feature is S. M. Deban et al., “Extremely High-Power Tongue Projection in Plethodontid Salamanders,” Journal of Experimental Biology 210 (2007): 655–67.

Wake’s original paper on tongue projection is a classic: R. E. Lombard and D. B. Wake, “Tongue Evolution in the Lungless Salamanders, Family Plethodontidae IV. Phylogeny of Plethodontid Salamanders and the Evolution of Feeding Dynamics,” Systematic Zoology 35 (1986): 532–51.

The remarkable multiple evolution of tongue projection is shown in D. B. Wake et al., “Transitions to Feeding on Land by Salamanders Feature Repetitive Convergent Evolution,” 395–405, in K. Dial, N. Shubin, and E. L. Brainerd, eds., Great Transformations in Vertebrate Evolution (Chicago: University of Chicago Press, 2015).

The frozen salamander analysis is in N. H. Shubin et al., “Morphological Variation in the Limbs of Taricha Granulosa (Caudata: Salamandridae): Evolutionary and Phylogenetic Implications,” Evolution 49 (1995): 874–84. The evolutionary interpretation and predictability of their patterns is discussed in N. Shubin and D. B. Wake, “Morphological Variation, Development, and Evolution of the Limb Skeleton of Salamanders,” 1782–808, in H. Heatwole, ed., Amphibian Biology (Sydney: Surrey Beatty, 2003); N. Shubin and P. Alberch, “A Morphogenetic Approach to the Origin and Basic Organization of the Tetrapod Limb,” Evolutionary Biology 20 (1986): 319–87; N. B. Fröbisch and N. Shubin, “Salamander Limb Development: Integrating Genes, Morphology, and Fossils,” Developmental Dynamics 240 (2011): 1087–99; N. Shubin and D. Wake, “Phylogeny, Variation and Morphological Integration,” American Zoologist 36 (1996): 51–60; and N. Shubin, “The Origin of Evolutionary Novelty: Examples from Limbs,” Journal of Morphology 252 (2002): 15–28.

Wake wrote some general papers on how multiples in evolution reveal general mechanisms of change: D. B. Wake et al., “Homoplasy: From Detecting Pattern to Determining Process and Mechanism of Evolution,” Science 331 (2011): 1032–35; and D. B. Wake, “Homoplasy: The Result of Natural Selection, or Evidence of Design Limitations?,” American Naturalist 138 (1991): 543–61.

Another scholarly review of multiples in evolution is B. K. Hall, “Descent with Modification: The Unity Underlying Homology and Homoplasy as Seen Through an Analysis of Development and Evolution,” Biological Reviews of the Cambridge Philosophical Society 78 (2003): 409–33.

The work on Caribbean lizards is reviewed in Jonathan Losos, Improbable Destinies: Fate, Chance and the Future of Evolution (New York: Riverhead, 2017).

Rich Lenski’s laboratory at Michigan State University has been carrying out a long-term experiment with bacteria that began in 1998. This venture, bold at the time, has allowed for direct observation of many major kinds of evolutionary change, giving us the tools to see these events in action. This review reveals the complex relationship of determinism and contingency in evolution: Z. Blount, R. Lenski, and J. Losos, “Contingency and Determinism in Evolution: Replaying Life’s Tape,” Science 362:6415 (2018): doi: 10.1126/scienceaam5979.

8. MERGERS AND ACQUISITIONS

Lynn Margulis’s original paper is L. [Margulis] Sagan, “On the Origin of Mitosing Cells,” Journal of Theoretical Biology 14 (1967): 225–74. Her wide-ranging book on her theory is Lynn Margulis, Symbiosis in Cell Evolution: Life and Its Environment on the Early Earth (San Francisco: Freeman, 1981). Her retrospective quote is taken from a 2011 interview in Discover magazine, available online at http://discovermagazine.com/2011/apr/16-interview-lynn-margulis-not-controversial-right.

For recent perspectives including references, see J. Archibald, One Plus One Equals One: Symbiosis and the Evolution of Complex Life (Oxford: Oxford University Press, 2014); L. Eme et al., “Archaea and the Origin of Eukaryotes,” Nature Reviews Microbiology 15 (2017): 711–23; J. M. Archibald, “Endosymbiosis and Eukaryotic Cell Evolution,” Current Biology 25 (2015): 911–21; and M. O’Malley, “Endosymbiosis and Its Implications for Evolutionary Theory,” Proceedings of the National Academy of Sciences 112 (2015): 10270–77.

Compelling and informative resources on the earliest phases of life’s history include Andrew Knoll, Life on a Young Planet: The First Three Billion Years of Evolution on Earth (Princeton, NJ: Princeton University Press, 2004); Nick Lane, The Vital Question: Energy, Evolution, and the Origins of Complex Life (New York: Norton, 2015); and J. William Schopf, Cradle of Life: The Discovery of Earth’s Earliest Fossils (Princeton, NJ: Princeton University Press, 1999).

Schopf’s collaborative work on the carbon isotopic analysis of the Apex Chert structures is in J. W. Schopf et al., “SIMS Analyses of the Oldest Known Assemblage of Microfossils Document Their Taxon-Correlated Carbon Isotope Compositions,” Proceedings of the National Academy of Sciences 115 (2018): 53–58.

The meaning and evolution of individuality is discussed in a little book that had a big impact: Leo Buss, The Evolution of Individuality (Princeton, NJ: Princeton University Press, 1988). Buss focuses on what an individual is and shows how natural selection operates as new individuals and levels of selection emerge.

An approach to the origin of new types of individuals, and their impact on evolution, is in John Maynard-Smith and Eörs Szathmáry, The Major Transitions in Evolution (Oxford: Oxford University Press, 1998).

Nicole King’s wonderful lecture “Choanoflagellates and the Origin of Animal Multicellularity” is online at https://www.ibiology.org/ecology/choanoflagellates/.

For work on choanoflagellates, see T. Brunet and N. King, “The Origin of Animal Multicellularity and Cell Differentiation,” Developmental Cell 43 (2017): 124–40; S. R. Fairclough et al., “Multicellular Development in a Choanoflagellate,” Current Biology 20 (2010): 875–76; R. A. Alegado and N. King, “Bacterial Influences on Animal Origins,” Cold Spring Harbor Perspectives in Biology 6 (2014): 6:a016162; and D. J. Richter and N. King, “The Genomic and Cellular Foundations of Animal Origins,” Annual Review of Genetics 47 (2013): 509–37.

A good primer on CRISPR-Cas genome editing, including its history, was co-written by one of its pioneers: Jennifer Doudna and Samuel Sternberg, A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution (New York: Houghton Mifflin Harcourt, 2017).

EPILOGUE

Mount Ritchie lies in Victoria Land in Antarctica. We were there as part of a U.S. Antarctic Program project funded by the National Science Foundation Grant 1543367.

FURTHER READING AND NOTES