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Evolving Evolution

In fact, vertebrates—reptiles, birds, chickens, mice, pythons, and humans—do have more genes than insects, though far fewer than had been expected before the human genome was revealed. The increase in the number of genes in these animals is partly responsible for their complexity and diversity. But as Carroll notes, “frogs and snakes, dinosaurs and ostriches, giraffes and whales, have evolved around a similar set of four Hox gene clusters. So again, the mere number of Hox genes does not tell us how these forms evolved.” The diversity of these animals comes from changes in the ways genes are turned on and off.

For example, though the giraffe has a long neck, it has seven cervical vertebrae, the same number as humans, whales, and all other mammals. Hox genes control this number, but they may also control cell proliferation and consequently the size of the vertebrae. The giraffe’s larger vertebrae may have developed because of mutations in the Hox genes controlling the size of vertebrae. Giraffes with large vertebrae and longer necks could feed off tall trees and were consequently selected over other giraffes. Changes in gene regulation, not new genes, gave rise to the long-necked giraffe.

Evolution, then, depends on new patterns of gene regulation rather than the creation of new genes. Indeed, it is not meaningful to talk about the function of a single gene in isolation. Genes only function in the context of the organism. There is no single gene for an eye, a limb, or language, much less such tendencies as homosexuality. Genes function in relation to other genes and intercellular signals, much as words vary in meaning and function depending on the way they are used in sentences and the contexts in which they are spoken. It is the combinations of gene activity, which may be different in different species, that create the form of the organism. “We can begin to think of individual groups—insects, spiders, and centipedes, or birds, mammals, and reptiles, as well as their long extinct fossil relatives—not so much in terms of their uniqueness, but as variations on a common theme,” Carroll writes. And surprising, too, is the evidence that all animals, from worms to humans, probably descend from one or a few primitive bacteria. Darwin would have been pleased to discover molecular evidence for his “common descent.”

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A powerful new theory adds considerable weight to this view, putting Carroll’s work in a larger perspective. In The Plausibility of Life, Marc W. Kirschner and John C. Gerhart take a broader view than Carroll’s on the questions of development and evolutionary biology. They agree that Hox genes make an important contribution to the mechanisms of evolution, but they argue that there are a number of other fundamental properties of organisms that give direction to evolution. The weakness of Darwinian theory—and one that has been seized upon by secular critics of evolutionary theory—is its failure to explain how the gene determines the observable traits of the organism. From an evolutionary point of view, how can complex organs such as eyes, arms, or wings evolve over long periods of time? What about the intermediary forms?

The Darwinian view was that early evolutionary forms of arms, legs, or wings might have initially served other purposes (insect legs, for example, might have evolved from gills their ancestors used for respiration). Such transformations of purpose are certainly important in evolution, Kirschner and Gerhart argue, but there must be other mechanisms at work as well. Concerning the human eye, for example: How is it possible for the different parts of an eye to evolve simultaneously—the lens, the iris, the retina, along with the blood vessels necessary for supplying the eye with oxygen and nutrition as well as the nerves that must receive signals from the retina and send signals to the muscles of the eye? Could these precise nerve and vascular networks be created by gradual random changes in genes over long periods of time, as Darwin claimed? Similarly, how can random mutations and natural selection create not only the necessary muscles and bone that make up the arm, for example, but organize the blood supply and nerves so that, after hundreds of thousands of years, an animal evolves with functioning arms, legs, and eyes? The Darwinian view that developing organs can serve different purposes at different times seems incomplete at best.

Darwin thought that at any given time variations in the forms of organisms were purely random. This is true of the neo-Darwinian view as well. However, recent research has shown that even though mutations are random, the effects of a mutation will be restricted, and may alter only one part or trait of an organism. A good example of the restricted effects of mutation is provided, as Kirschner and Gerhart point out, by the body plans created by Hox genes. Because they are contained within the different compartments of the embryo established by the body plan, individual parts of an animal can evolve independently of each other. For example, the lizard has limbs, the python has vestigial limbs, and the advanced snake has no limbs at all. These variations in limb structure have evolved without major changes in other parts of the body plan.

This independence means that mutations can occur within a single region of an embryo that may or may not be beneficial; in any case, fewer of the mutations will be lethal for the developing organism. In other words, while evolution is constrained by the body plan created by the Hox genes, this constraint gives nature a much greater freedom to experiment with variant forms through random mutations. If there were no body plans with separate parts, most variations would be lethal to the entire organism and evolution would be much, much slower. Suppose we wanted to design new windows for airplanes that would improve the visibility for passengers, resist cabin pressure, and better insulate passengers from the cold. We would test the new window designs without changing their positions on the body of the plane. If we had to redesign the entire plane every time we changed the window design, we would be much slower in developing new and more efficient planes. Similarly, Hox genes can, through mutations, shift the pattern of organization within a part of the embryo, allowing evolution to experiment with new forms, such as wings and longer necks, without affecting other parts of the embryo.

Kirschner and Gerhart thus place the activity of Hox genes inside the embryo in a broader perspective. They agree that Hox genes are important in organizing the embryo into discrete parts, a process they call the invisible anatomy (it is only visible with the aid of recent technology). But they argue that the function of Hox genes is only one of a number of “core processes” that act as constraints on evolution. The storage of genetic information in DNA and the mechanisms for translating that information in the synthesis of proteins are examples of core processes. Other kinds of core processes that are used by cells include biochemical mechanisms, such as the digestion of nutrients by enzymes. These mechanisms were established at an early stage in evolution and are still used in human cells, worms, and bacteria. Because of these core processes, natural selection is presented with a variety of forms that are more likely to succeed than if there were no constraints on variation at all. Should a new advantageous process arise by mutation, it can be incorporated into the functional repertory of the organism, and it is then inherited over generations.

Another kind of core process that can, by constraining development, create forms that are more likely to succeed is what Kirschner and Gerhart call “exploratory behavior,” such as the method used by ants when foraging for food. Ants leave their nest and take random paths. As they move about they secrete a chemical substance called a pheromone that leaves a scent along the path they are following. If an ant fails to find food it will eventually return to the nest, using the pheromones it has deposited to guide it back to the nest. However, an ant that finds food will deposit more pheromones as it returns to the nest. This will reinforce the scent of the trail that led to food and other ants will now follow the reinforced trail.

Nonetheless, not all the ants will follow the successful trail. Some ants will set out on random paths in search of other sources of food and if successful they, too, will establish paths for subsequent ants. Eventually, the ants will have established a detailed map of paths to food sources. An observer might think that the ants are using a map supplied by an intelligent designer of food distribution. However, what appears to be a carefully laid out mapping of pathways to food supplies is really just a consequence of a series of random searches.

Other exploratory processes are important for the development of the vascular and nervous systems in a growing embryo. While the details of the individual processes vary considerably, the guiding principles are similar to those of ant foraging: just as the ants randomly explore the terrain around their nest, capillary vessels sprout off from the larger blood vessels and randomly explore the surrounding tissues for the signals coming from cells deprived of oxygen; they then can bring blood containing oxygen to the cells. And just as contact with food makes the ant reinforce the path that led to the food, the sprouting capillary vessels establish permanent contacts whenever they encounter tissue with oxygen-deprived cells. Similarly, fine nerve endings extend themselves randomly, establishing stable connections between nerves and muscles whenever they receive electrical and chemical signals coming from muscles.

Hence, unlike the eye or hand, whose forms follow from the body plan that is programmed by Hox genes in the developing embryo, the apparently well-designed and integrated nervous and vascular systems that serve such organs do not require predetermined paths and wirings. Darwin’s view that small simultaneous changes would give rise to organs as complex as the eye is in principle true, but in need of modification. It is the very constraints created by the Hox genes and the other core processes (e.g., the exploratory behavior of capillaries and nerve endings) that permit complex designs to emerge over a relatively short period of time from a biological point of view (hundreds of thousands of years, or perhaps even less). As Carroll and Kirschner and Gerhart observe, some alteration of genes is still necessary if the changes are to be passed on from one generation to another. But the genetic alterations are considerably simpler and fewer in number than had been formerly imagined.

While Carroll argues—a claim that is at the heart of Evo Devo—that embryological development gives us the deepest clues to the mechanisms of evolution, Kirschner and Gerhart move beyond embryology to show that metabolic and physiological processes are also critical to evolutionary change. Their approach, which they call the theory of “facilitated variation,” attempts to show how the regulation of genes inside the embryo, as described by Carroll, is part of a larger set of processes that allow organisms to experiment with evolution in a tightly controlled way. According to this theory, the mutations, or variations, needed to drive evolutionary change can occur with little disruption either to the basic organization of an organism or to the core processes that make its cells function.

We now have a far deeper understanding of evolution than even a decade ago.4 And although our knowledge is still incomplete, our new understanding, as the books under review admirably show, has opened the way toward a comprehensive account of evolution and has supplied solid answers to the critics of evolutionary theory.

  1. 4

    While classical genetics relies on changes in the order of the bases in the DNA strands, other heritable changes have been discovered—changes in the chemical makeup of the bases that control gene activities, for example—and are increasingly recognized as important in development and evolution. For example, the base cytosine might undergo a chemical modification involving the addition of a single carbon atom.

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