Arrival of the Fittest: Solving Evolution's Greatest Puzzle (22 page)

An especially remarkable protein in this circuit is called
engrailed
. Guided by the circuit’s choreography, it becomes expressed in seven highly regular stripes across the embryo. Seven regions that produce engrailed alternate with seven other regions that don’t, and the stripes of engrailed expression demarcate the nascent fourteen segments of the fly. Engrailed and other regulators then control many further genes that specify each segment’s identity, specifying whether a segment will carry legs, or support wings, or be part of the abdomen.
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All this and more happens in a matter of hours, but it’s not only their speedy development that made fruit fly embryos a boon to developmental biology: Until segmentation is well under way, the embryo’s cells are not separated by walls. This means that molecules can drift freely through the growing embryo. In most other species, cells are walled off right after fertilization, which makes communication between them more challenging.

Not impossible, though. The male reproductive apparatus in humans—the penis and scrotum—is an instructive example. When a male fetus is about eight weeks old, clusters of so-called Leydig cells release chemical signals called androgens near the area where sex organs will eventually form. These signals are hormones like testosterone that are crucial for sculpting sexual organs. Released from the Leydig cells, they instruct nearby cells to specialize in forming the penis, the scrotum, and, much later, sperm cells. Once an androgen hormone molecule has been released by a Leydig cell, it drifts through the space between cells, and because its chemical structure allows it to penetrate the cellular membrane, it eventually enters another cell. Inside, an androgen receptor, a special protein that can recognize the hormone’s shape, is already waiting for it. And when the two connect, the receptor protein changes its shape—yet another turning lock. Its new shape allows the protein to bind specific words on DNA and activate nearby genes. The androgen receptor turns on many genes, some of which make regulators that eventually arouse hundreds of genes to create unique cellular identities within the male sexual organs.
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From flies to humans, hundreds of similar signals crisscross every tiny sliver of tissue during every moment of an embryo’s development. This unimaginably complex communication process instructs cells about their location and fate, like the bicoid-expressing cells that “know” they are near the front. These signals also command cells to divide, move, swell, shrink, flatten, and, eventually, to acquire an identity and shape a body. And they are involved whenever cells acquire new identities that lead to innovative shapes and body plans.

If we could predict the regulatory dance that shapes embryos from flies to humans, we could predict how organs, tissues, and cells form, and why different organisms have very different body plans. That would be quite a feat. Unfortunately, a circuit’s expression pattern can be extremely complicated, even for a simple circuit like that of figure 16. If A activates B and C represses B, whereas B activates C, and D represses C, it’s not immediately obvious which gene expression pattern would result. And worse, many circuits contain many more genes than this one, dozens of regulators that form a dense filigree of interwoven regulation, complex beyond our mind’s grasp. But there is hope, in the form of computers that can describe a circuit’s choreography through mathematical equations, process these equations in their silicon brains, and predict a circuit’s gene expression patterns.

One remarkable computational scientist who devotes his life to this task is John Reinitz. I first met John when I was a graduate student at Yale in the 1990s. He was a few years my senior, and what they call a character, chain-smoking filterless cigarettes at a time when smokers were already ostracized, and dressing in ways that made casual Friday look like a formal banquet. He drove a fossilized Volkswagen Beetle, whose rear seats had disappeared beneath a landfill of discarded fast-food packaging. John’s nonconformism surely was an asset in his research, because he swam with bold strokes against the mainstream.

At the time, many scientists studied fly embryos, but they used computers for little more than writing their research papers. Instead they studied regulation by changing the DNA text of a gene, or manipulating a regulator in the laboratory, and measuring how such changes altered segmentation. Their experiments were productive: Among other things, they established which among thousands of genes formed the fruit fly’s embryo. But their efforts to understand a circuit’s entire expression patterns, one gene at a time, were doomed to fail, because a whole circuit is so much more than the sum of its parts. Today this is widely accepted, but in the early 1990s John’s efforts to emulate fly development in a computer made him an outsider. His work was ignored by many and belittled by some.

This work was analogous to building one of those flight simulators that are indispensable for training military and commercial pilots—by reproducing not only all the complex machinery of a cockpit, but also disturbances like turbulence and instrument failures. Similarly, John’s fly simulator collected mountains of data about the regulators of early fly embryos and how they regulate each other, encapsulated this information in equations, and simulated them in a computer. And like a good flight simulator, this one worked—not a small achievement. It can mimic the early development of fruit flies, and does so at enormously accelerated speed. It can be run over and over again, to tease out patterns that might be missed in isolated examples. And more than reenacting the choreography of a normal embryo, it can also simulate the plane crashes of regulator malfunction, and explain how mutant genes lead to deformed embryos.
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As I write these lines, John has devoted decades of his life to building this simulator, often in the face of ignorant and condescending peers. His dedication often crosses my mind when I am about to swat a fly. (Then I swat.)

Beyond sharing a backbone and a spinal cord, the more than sixty thousand species of vertebrates
,
which include fish, mammals, amphibians, reptiles, and birds, have incredibly diverse bodies. This diversity is built on similar structures, however, because all vertebrates can trace their lineage back to a common ancestor that appeared more than five hundred million years ago. For example, the paired fins—one pair in front, one in the back—that help fish push and steer themselves through water gave rise to the arms and legs of animals that crawl, walk, jump, and run on land. And the forearms of some of these animals—dinosaurs—changed into the wings of birds.

Limbs are key innovations of land-living vertebrates. They have three familiar parts, the upper arm and upper leg, the lower arm and lower leg, and the hands and feet. The major bones in our arms and legs correspond to arm and leg bones in horses, dogs, eagles, bats, pigs, crocodiles, and many other animals. Transform their sizes, as evolution did, and many specialized functions become possible, such as the slender limbs of horses custom-made for running, and the light bones of wings perfected for flying.

Limbs—old and new—owe their existence to a family of regulators that are used in building the bodies of thousands of organisms, from jellyfish to humans.
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Though these regulators are essential for normal body development, the name for the genes that encode them—homeobox, or Hox, genes—comes from their role in homeosis, a process that creates malformed organisms when these genes are mutated, such as flies with (useless) legs sprouting from their heads in place of antennae. For better or for worse, changing life’s recipes can have dramatic effects.
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The homeobox is a protein sequence of sixty amino acids that binds DNA and allows Hox regulators to control gene expression. In organisms as different as fruit flies and humans, these regulators are lords over hundreds of other genes that give texture to cells, tissues, and organs. Hox regulators also regulate one another’s expression. That is, they form a regulator circuit like that of figure 16, but much more complex, because animals can have forty or more of them. This circuit shapes important parts of many bodies—including ours. Among these parts are the thirty-three vertebrae in our spinal column and their unique identities—two vertebrae in our neck with flexible joints, twelve vertebrae in our thorax with attached ribs, and so on.

The Hox gene circuit expresses different combinations of genes in the neck, thorax, and abdomen as our backbone develops in the womb. Each of these combinations is a
gene expression code,
an on-off pattern of Hox genes that is specific to each body region. One on-off pattern specifies neck vertebrae, another specifies thoracic vertebrae, and so on.

Hox genes mold not just the human body but also the bodies of vertebrates like pythons and other snakes whose body plan—another ancient innovation—allows them to slither, burrow, and swim. Some snakes have more than three hundred vertebrae, most of them identical and rib-carrying like our twelve thoracic vertebrae. Hox genes are responsible for these differences between snakes and other animals: In most vertebrates, the Hox code for the thorax is expressed in only a small region of the embryo, but this region stretched like a rubber band when snakes evolved from lizards more than a hundred million years ago. The thoracic Hox code became expressed along most of the main body axis, and allowed snakes to build the hundreds of vertebrae that define their new body plan.
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Hox genes shape not only the main axis of an organism’s body—the axis defined by the backbone in vertebrates—but evolution also co-opted them to mold another ancient innovation, the fins of fish.
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And it did not stop there. Over millions of years, evolution transformed these fins into limbs, by altering, refining, and differentiating the fins’ Hox code. Eventually it created a three-part code in organisms that walk or fly, a specific combination of Hox genes for the upper arm, another for the lower arm, and a third for the hand. We know all this from the effects of mutations that garble this code and appear as horrific birth defects that are well studied in animals. When two genes called Hoxa11 and Hoxd11 are not expressed while limbs develop, the results can be no lower arms at all, or a hand sprouting from somewhere near the elbow. Likewise, missing fingers or palms in a newborn can result from a failure to express two hand-specific Hox genes—Hoxa13 and Hoxd13. If the expression of a third group of Hox genes fails, only the upper arm will form.
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Most of the time, though, Hox genes do their job very well. And they do it in an impressive number of locations, helping form structures from the pelvis to the vertebrate brain. They also help to build the bodies of organisms as different as shrimp, jellyfish, worms, and even fruit flies, where the Hox circuit is as important as the segmentation circuit. In fact, the two work sequentially. After the segmentation circuit establishes segment
numbers,
the Hox circuit specifies segment
identities
—which segments will carry legs, which ones wings, and so on. And these circuits are only two among many that flies and most animals use to build their bodies, and have used ever since the first animals emerged hundreds of millions of years ago.

Hox gene circuits were instrumental in the origin of new body
parts
—like limbs—as well as new body
plans,
like those of snakes. How exactly these innovations originated may be forever lost in the mists of life’s deep history, but one principle is crystal clear: They originated through changes in regulation.

The same principle is just as clear in other, more ancillary innovations.

Imagine a slender lizard that weaves its way through a dense meadow hunting for its next meal when suddenly a huge pair of eyes stares into its face. It freezes, knowing that it will be torn to pieces in a moment. But then two wings flap, and the eyes are gone like a mirage. No predator was near, just two enormous colored spots on the wings of a tasty butterfly.

The eyespots of butterflies are lifesaving bluffs, formed by an unusually versatile regulator protein called
distalless.
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A member of a circuit that molds the legs, wings, and antennae of flies, distalless has also been co-opted to paint eyespots on the butterfly’s wings. We know that distalless
is part of an eyespot-specific expression code, because developing butterfly larvae make distalless exactly where the eyespots will later form. Some butterflies have smaller eyespots, others larger eyespots, some have only one eyespot, others several. Regardless, developing butterflies unfailingly express distalless in the location of their eyespots. And distalless
is really a cause of eyespots rather than just correlated with their appearance: If one transplants distalless-producing cells of a developing wing to different wing locations, development will paint an eyespot there.
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