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Evolving Evolution

Despite much recent controversy about the theory of evolution, major changes in our understanding of evolution over the past twenty years have gone virtually unnoticed.1 At the heart of Darwin’s theory of evolution is an explanation of how plants and animals evolved from earlier forms of life that have long since disappeared; but his theory says nothing about the factors that determine the shape, color, and size of a particular fish, whale, or butterfly. Darwin and his contemporaries realized that understanding the evolution of animal forms and understanding how a fertilized egg develops into a whale, cow, or human being must be deeply connected; but they didn’t know how to make the connection.

Surprising discoveries in the 1980s have begun to tell us how an embryo develops into a mature animal, and these discoveries have radically altered our views of evolution and of the relation of human beings to all other animals. The new field of study in which these breakthroughs have been made is called Evo Devo, short for evolution and development, “development” referring to both how an embryo grows and how the newborn infant matures into an adult.

Sean Carroll, author of one of the books under review and a coauthor of another, has made important contributions to the understanding of evolution and development. From DNA to Diversity, written with two other scientists, is the second edition of a book that has become a classic for students of evolution. The title of Carroll’s other book, Endless Forms Most Beautiful, comes from the famous final sentence of The Origin of Species: “There is a simple grandeur in this view of life… that from so simple an origin, through the process of gradual selection of infinitesimal changes, endless forms most beautiful and most wonderful have been evolved.”

In 1830, nearly thirty years before Darwin published his book, two French naturalists—Georges Cuvier and Étienne Geoffroy St. Hilaire—debated the significance of the anatomical similarities between distantly related animals, such as the flippers of whales and the wings of bats. Cuvier held that form was dictated by function: the bat’s wing, needed for flying, had a separate origin from the whale’s flipper, needed for swimming.

Geoffroy St. Hilaire opposed this view, arguing that the underlying skeletal similarities pointed to the existence of a common archetype for both flippers and wings. While neither man claimed that animal forms could change over generations, St. Hilaire’s archetypal form foreshadowed some recent discoveries about development and evolution. No doubt this debate was in the mind of Charles Darwin as he formulated his theories in an attempt to account for the origins of animal forms.

The contemporary Darwinian theory of evolution is based on three ideas: natural selection, heredity, and variation. Small random changes—variations—occur in organisms through mutations of genes, and when these changes give an organism a greater chance of survival, they persist from one generation to the next through natural selection. That is, organisms with traits that make them better adapted to the environment they inhabit will have better reproductive success than other members of the same species that do not possess the advantageous traits. In each successive generation, then, an ever-larger proportion of the species in question will possess the mutation that produces the advantageous traits. “Natural selection,” Darwin wrote, “acts solely by accumulating successive, favorable variations.” Evolution in the Darwinian view was gradual: “it can act only by short and slow steps.” And since, in this view, all changes are random, there are no predetermined directions in which organisms evolve. All living organisms, Darwin claimed, are descended from one or a few common ancestors.

Neither Darwin nor any of his contemporaries knew about the workings of heredity—how we inherit the eye color of our father or the hair color of our mother. The work of the Czech monk Gregor Mendel, first published in 1865, had gone unnoticed in Darwin’s day and was only rediscovered around 1900. Mendel had shown that specific traits, such as the color of a pea, or the smoothness or roughness of its skin, could be inherited independently of one another. The new science of “genetics,” the idea that units called “genes” within each cell transmit specific traits, such as hair color, from one generation to the next, began in the first decade of the twentieth century. Studies of inherited traits in fruit flies in the following decades established convincing evidence for genes, but they remained invisible. Scientists still didn’t know how the gene made it possible for information to pass from one generation to the next, and how mutations in genes could, over many generations, lead to a new species that had a form different from its distant progenitor.

By the 1940s, though the structure of the gene was still unknown, scientists had introduced the idea of the gene into Darwinian theory. They now explained evolution as the consequence of small random changes in genes. This recasting of Darwinian theory was called the Modern Synthesis, following the 1942 publication of Julian Huxley’s book Evolution: The Modern Synthesis. The neo-Darwinian theory incorporated the Mendelian idea of genetics, explaining the mechanism of inheritance that was unknown to Darwin. The theory, however, did not account for how particular organisms develop from embryos in the womb to adult forms; that process, known as embryology, was not discussed.

The neo-Darwinian view was reinforced in 1953, when the double helix was discovered, showing how genes composed of the nucleic acid DNA transmitted hereditary characteristics. A molecule of DNA is made up of two long strands of chemical building blocks called nucleotides, each containing one of four bases: adenine, thymine, guanine, or cytosine, which are abbreviated A, T, G, and C. The order of the bases in each strand of DNA determines the information in the DNA molecule, information we can think of as providing an overall plan for producing enzymes and other proteins.

A gene was now understood to be a specific sequence of DNA bases. Genes vary considerably in size, most of them containing between 10,000 and 20,000 nucleotides, though they can be much longer or shorter. Each of our cells carries all our genes, although most genes remain inactive at any given moment. When a particular gene is activated it is first copied into RNA, a nucleic acid that carries instructions from DNA for assembling proteins. The RNA’s instructions are then decoded in a process called “translation,” and proteins, including the enzymes essential for cells to function, are produced. Proteins in turn form some 50 percent of all living cells.

How are particular genes activated? There are, according to recent research, as many as a hundred trillion cells in the human body, and each cell contains thousands of different types of molecules that vary considerably in size; many molecules move about freely inside the cell. All the cells in a given individual have the same DNA—it is contained in the largest molecules in each cell—and hence an identical set of genes. Which specific genes are activated in a particular cell depends, in part, on the cell’s location in the embryo or the adult body. Moreover, the activation of one combination of genes will give rise to a liver cell, while the activation of another will produce a brain cell.

The structure of the double helix made it apparent how changes, or mutations, in the base sequence of a gene could lead to variations in the characteristics of an organism; such mutations could, if advantageous, accumulate over time. The process appeared to confirm Darwin’s view that evolution is gradual. As he wrote in The Origin of Species, nature “can act only by short and slow steps. Hence, the saying Natura non facit saltum,” nature doesn’t make sudden jumps. The standard view, then, was that variation and selection could account for how the simple organisms of early life evolved into the complex forms of the contemporary biological world. After Mendel’s discoveries had been absorbed at the beginning of the twentieth century, it was assumed that as changes accumulated between one species and another, there would be less and less similarity in the kind and number of their genes. More advanced species would have many more genes than lower forms of life; and worms, for example, would have few, if any, genes similar to those of fish, mice, or human beings.

Yet it seemed astonishing that random mutations, even over enormous periods of time, could give rise to the remarkable complexity of an organ such as the human eye. “To suppose,” Darwin wrote in The Origin of Species,

that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree….

Nonetheless, he continued:

Reason tells me, that if numerous gradations from a simple and imperfect eye to one complex and perfect can be shown to exist, each grade being useful to its possessor, as is certainly the case; if further, the eye ever varies and the variations be inherited, as is likewise certainly the case; and if such variations should be useful to any animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, should not be considered as subversive of the theory.

The neo-Darwinian belief in small mutational changes in DNA molecules over hundreds of millions of years made the preservation of individual genes over long periods of time highly unlikely. It was thought that the diversity of living forms was the consequence of each animal having evolved its own unique set of genes over millions of years as well. Surely human beings, for example, would not have the same genes as worms.

Those assumptions were dramatically overturned when the rough draft of the human genome—the entire set of human genes—was announced in 2001. As it turned out, human beings have far fewer genes than expected—about 25,000 rather than the 60,000 or more that had been predicted. This was about the same number as mice have, and even the tiny worms called nematodes have about 14,000 genes. The number of genes in a given species, therefore, is not a measure of its complexity. Why had biologists so overestimated the number of genes in the human genome? Why is it unnecessary for complex animals such as mammals to have ten times as many genes as worms?

The answers to these questions were already hinted at more than four decades ago. At the time it was known that the bacteria E. coli, which normally live off the sugar glucose, are also capable of producing enzymes that digest other sugars, such as lactose. But biologists noticed that the bacteria only produce the enzyme when lactose is present in their immediate environment. Scientists could not explain how the E. coli somehow “knew” when the lactose-digesting enzyme would be needed.

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    For their critical readings and comments on this article, we would like to thank David Botstein, Nathaniel Heintz, Luisa Hirschbein, David Ish- Horowicz, and Richard Lewontin, none of whom should be held accountable for this text, for which we take full responsibility.

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