The Gene

by Siddhartha Mukherjee

  “Five years ago,” Kornberg wrote in 1960, “the synthesis of DNA was also regarded as a ‘vital’ process”—a mystical reaction that could not be reproduced in a test tube by the addition or subtraction of mere chemicals. “Tampering with the very genetic apparatus [of life] itself,” this theory ran, “would surely produce nothing but disorder.” But Kornberg’s synthesis of DNA had created order out of disorder—a gene out of its chemical subunits. The unassailability of genes was no longer a barrier.

  There is a recursion here that is worth noting: like all proteins, DNA polymerase, the enzyme that enables DNA to replicate, is itself the product of a gene.IV Built into every genome, then, are the codes for proteins that will allow that genome to reproduce. This additional layer of complexity—that DNA encodes a protein that allows DNA to replicate—is important because it provides a critical node for regulation. DNA replication can be turned on and turned off by other signals and regulators, such as the age or the nutritional status of a cell, thus allowing cells to make DNA copies only when they are ready to divide. This scheme has a collateral rub: when the regulators themselves go rogue, nothing can stop a cell from replicating continuously. That, as we will soon learn, is the ultimate disease of malfunctioning genes—cancer.

  Genes make proteins that regulate genes. Genes make proteins that replicate genes. The third R of the physiology of genes is a word that lies outside common human vocabulary, but is essential to the survival of our species: recombination—the ability to generate new combinations of genes.

  To understand recombination, we might, yet again, begin with Mendel and Darwin. A century of exploration of genetics illuminated how organisms transmit “likeness” to each other. Units of hereditary information, encoded in DNA and packaged on chromosomes, are transmitted through sperm and egg into an embryo, and from the embryo to every living cell in an organism’s body. These units encode messages to build proteins—and the messages and proteins, in turn, enable the form and function of a living organism.

  But while this description of the mechanism of heredity solved Mendel’s question—how does like beget like?—it failed to solve Darwin’s converse riddle: How does like beget unlike? For evolution to occur, an organism must be able to generate genetic variation—i.e., it must produce descendants that are genetically different from either parent. If genes typically transmit likeness, then how can they transmit “unlikeness”?

  One mechanism of generating variation in nature is mutation—i.e., alterations in the sequence of DNA (an A switched to a T) that may change the structure of a protein and thereby alter its function. Mutations occur when DNA is damaged by chemicals or X-rays, or when the DNA replication enzyme makes a spontaneous error in copying genes. But a second mechanism of generating genetic diversity exists: genetic information can be swapped between chromosomes. DNA from the maternal chromosome can exchange positions with DNA from the paternal chromosome—potentially generating a gene hybrid of maternal and paternal genes. Recombination is also a form of “mutation”—except whole chunks of genetic material are swapped between chromosomes.

  The movement of genetic information from one chromosome to another occurs only under extremely special circumstances. The first occurs when sperm and eggs are generated for reproduction. Just before the spermiogenesis and oogenesis, the cell turns briefly into a playpen for genes. The paired maternal and paternal chromosomes hug each other and readily swap genetic information. The swapping of genetic information between paired chromosomes is crucial to the mixing and matching of hereditary information between parents. Morgan called this phenomenon crossing over (his students had used crossing over to map genes in flies). The more contemporary term is recombination—the ability to generate combinations of combinations of genes.

  The second circumstance is more portentous. When DNA is damaged by a mutagen, such as X-rays, genetic information is obviously threatened. When such damage occurs, the gene can be recopied from the “twin” copy on the paired chromosome: part of the maternal copy may be redrafted from the paternal copy, again resulting in the creation of hybrid genes.

  Once again, the pairing of bases is used to build the gene back. The yin fixes the yang, the image restores the original: with DNA, as with Dorian Gray, the prototype is constantly reinvigorated by its portrait. Proteins chaperone and coordinate the entire process—guiding the damaged strand to the intact gene, copying and correcting the lost information, and stitching the breaks together—ultimately resulting in the transfer of information from the undamaged strand to the damaged strand.

  Regulation. Replication. Recombination. Remarkably, the three R’s of gene physiology are acutely dependent on the molecular structure of DNA—on the Watson-Crick base pairing of the double helix.

  Gene regulation works through the transcription of DNA into RNA—which depends on base pairing. When a strand of DNA is used to build the RNA message, it is the pairing of bases between DNA and RNA that allows a gene to generate its RNA copy. During replication, DNA is, once again, copied using its image as a guide. Each strand is used to generate a complementary version of itself, resulting in one double helix that splits into two double helices. And during the recombination of DNA, the strategy of interposing base against base is deployed yet again to restore damaged DNA. The damaged copy of a gene is reconstructed using the complementary strand, or the second copy of the gene, as its guide.V

  The double helix has solved all three of the major challenges of genetic physiology using ingenious variations on the same theme. Mirror-image chemicals are used to generate mirror-image chemicals, reflections used to reconstruct the original. Pairs used to maintain the fidelity and fixity of information. “Monet is but an eye,” Cézanne once said of his friend, “but, God, what an eye.” DNA, by that same logic, is but a chemical—but, God, what a chemical.

  In biology, there is an old distinction between two camps of scientists—anatomists, and physiologists. Anatomists describe the nature of materials, structures, and body parts: they describe how things are. Physiologists concentrate, instead, on the mechanisms by which these structures and parts interact to enable the functions of living organisms; they concern themselves with how things work.

  This distinction also marks a seminal transition in the story of the gene. Mendel, perhaps, was the original “anatomist” of the gene: in capturing the movement of information across generations of peas, he had described the essential structure of the gene as an indivisible corpuscle of information. Morgan and Sturtevant extended that anatomical strand in the 1920s, demonstrating that genes were material units, spread linearly along chromosomes. In the 1940s and 1950s, Avery, Watson, and Crick identified DNA as the gene molecule, and described its structure as a double helix—thereby bringing the anatomical conception of the gene to its natural culmination.

  Between the late 1950s and the 1970s, however, it was the physiology of genes that dominated scientific inquiry. That genes could be regulated—i.e., turned “on” and “off” by particular cues—deepened the understanding of how genes function in time and space to specify the unique features of distinct cells. That genes could also be reproduced, recombined between chromosomes, and repaired by specific proteins, explained how cells and organisms manage to conserve, copy, and reshuffle genetic information across generations.

  For human biologists, each of these discoveries came with enormous payoffs. As genetics moved from a material to a mechanistic conception of genes—from what genes are to what they do—human biologists began to perceive long-sought connections between genes, human physiology, and pathology. A disease might arise not just from an alteration in the genetic code for a protein (e.g., hemoglobin in the case of sickle-cell disease), but as a consequence of gene regulation—the inability to turn the right gene “on” or “off” in the appropriate cell at the right time. Gene replication must explain how a multicellular organism emerges from a single cell—and errors in replication might elucidate how a spontaneous metabolic illness, or a devastating me
ntal disease, might arise in a previously unaffected family. The similarities between genomes must explain the likeness between parents and their children, and mutations and recombination might explain their differences. Families must share not just social and cultural networks—but networks of active genes.

  Just as nineteenth-century human anatomy and physiology laid the foundation for twentieth-century medicine, the anatomy and physiology of genes would lay the foundation for a powerful new biological science. In the decades to come, this revolutionary science would extend its domain from simple organisms to complex ones. Its conceptual vocabulary—gene regulation, recombination, mutation, DNA repair—would vault out of basic science journals into medical textbooks, and then permeate wider debates in society and culture (the word race, as we shall see, cannot be understood meaningfully without first understanding recombination and mutation). The new science would seek to explain how genes build, maintain, repair, and reproduce humans—and how variations in the anatomy and physiology of genes might contribute to the observed variations in human identity, fate, health, and disease.

  * * *

  I. Monod and Jacob knew each other distantly; both were close associates of the microbial geneticist André Lwoff. Jacob worked at the other end of the attic, experimenting with a virus that infected E. coli. Although their experimental strategies were superficially dissimilar, both were studying gene regulation. Monod and Jacob had compared notes and found, to their astonishment, that both were working on two aspects of the same general problem, and they had combined some parts of their work in the 1950s.

  II. In 1957, Pardee, Monod, and Jacob discovered that the lactose operon was controlled by a single master switch—a protein eventually called the repressor. The repressor functioned like a molecular lock. When lactose was added to the growth medium, the repressor protein sensed the lactose, altered its molecular structure, and “unlocked” the lactose-digesting and lactose-transporting genes (i.e., allowed the genes to be activated), thereby enabling a cell to metabolize lactose. When another sugar, such as glucose, was present, the lock remained intact, and no lactose-digesting genes were allowed to be activated. In 1966, Walter Gilbert and Benno Muller-Hill isolated the repressor protein from bacterial cells—thereby proving Monod’s operon hypothesis beyond doubt. Another repressor, from a virus, was isolated by Mark Ptashne and Nancy Hopkins in 1966.

  III. Unlike cosmological turtles, this view is not absurd. In principle, the single-celled embryo does possess all the genetic information to specify a full organism. The question of how sequential genetic circuits can “actualize” the development of an organism is addressed in a subsequent chapter.

  IV. DNA replication requires many more proteins than just DNA polymerase to unfold the twisted double helix and to ensure that the genetic information is copied accurately. And there are multiple DNA polymerases, with slightly different functions, found in cells.

  V. The fact that the genome also encodes genes to repair damage to the genome was discovered by several geneticists, including Evelyn Witkin and Steve Elledge. Witkin and Elledge, working independently, identified an entire cascade of proteins that sensed DNA damage, and activated a cellular response to repair or temporize the damage (if the damage was catastrophic, it would halt cell division). Mutations in these genes can lead to the accumulation of DNA damage—and thus, more mutations—ultimately leading to cancer. The fourth R of gene physiology, essential to both the survival and mutability of organisms, might be “repair.”

  From Genes to Genesis

  In the beginning, there was simplicity.

  —Richard Dawkins, The Selfish Gene

  Am not I

  A fly like thee?

  Or art not thou

  A man like me?

  —William Blake, “The Fly”

  While the molecular description of the gene clarified the mechanism of the transmission of heredity, it only deepened the puzzle that had preoccupied Thomas Morgan in the 1920s. For Morgan, the principal mystery of organismal biology was not the gene but genesis: How did “units of heredity” enable the formation of animals and maintain the functions of organs and organisms? (“Excuse my big yawn,” he once told a student, “but I just came from my own lecture [on genetics].”)

  A gene, Morgan had noted, was an extraordinary solution to an extraordinary problem. Sexual reproduction demands the collapse of an organism into a single cell, but then requires that single cell to expand back into an organism. The gene, Morgan realized, solves one problem—the transmission of heredity—but creates another: the development of organisms. A single cell must be capable of carrying the entire set of instructions to build an organism from scratch—hence genes. But how do genes make a whole organism grow back out of a single cell?

  It might seem intuitive for an embryologist to approach the problem of genesis forward—from the earliest events in the embryo to the development of a body plan of a full-fledged organism. But for necessary reasons, as we shall see, the understanding of organismal development emerged like a film run in reverse. The mechanism by which genes specify macroscopic anatomical features—limbs, organs, and structures—was the first to be deciphered. Then came the mechanism by which an organism determines where these structures are to be placed: front or back, left or right, above or below. The very earliest events in the specification of an embryo—the specification of the body axis, of front and back, and left versus right—were among the last to be understood.

  The reason for this reversed order might be obvious. Mutations in genes that specified macroscopic structures, such as limbs and wings, were the easiest to spot and the first to be characterized. Mutations in genes that specified the basic elements of the body plan were more difficult to identify, since the mutations sharply decreased the survival of organisms. And mutants in the very first steps of embryogenesis were nearly impossible to capture alive since the embryos, with scrambled heads and tails, died instantly.

  In the 1950s, Ed Lewis, a fruit fly geneticist at Caltech, began to reconstruct the formation of fruit fly embryos. Like an architectural historian obsessed with only one building, Lewis had been studying the construction of fruit flies for nearly two decades. Bean shaped and smaller than a speck of sand, the fruit fly embryo begins its life in a whir of activity. About ten hours after fertilization of the egg, the embryo divides into three broad segments, head, thorax, and abdomen, and each segment divides into further subcompartments. Each of these embryonic segments, Lewis knew, gives rise to a congruent segment found in the adult fly. One embryonic segment becomes the second section of the thorax and grows two wings. Three of the segments grow the fly’s six legs. Yet other segments sprout bristles or grow antennae. As with humans, the basic plan for the adult body is furled into an embryo. The maturation of a fly is the serial unfolding of these segments, like the stretching of a live accordion.

  But how does a fly embryo “know” to grow a leg out of the second thoracic segment or an antenna out of its head (and not vice versa)? Lewis studied mutants in which the organization of these segments was disrupted. The peculiar feature of the mutants, he discovered, was that the essential plan of macroscopic structures was often maintained—only the segment switched its position or identity in the body of the fly. In one mutant, for instance, an extra thoracic segment—fully intact and nearly functional—appeared in a fly, resulting in a four-winged insect (one set of wings from the normal thoracic segment, and a new set from the extra thoracic segment). It was as if the build-a-thorax gene had incorrectly been commanded in the wrong compartment—and had sanguinely launched its command. In another mutant, two legs sprouted out of the antenna in a fly’s head—as if the build-a-leg command had mistakenly been launched in the head.

  The building of organs and structures, Lewis concluded, is encoded by master-regulatory “effector” genes that work like autonomous units or subroutines. During the normal genesis of a fly (or any other organism), these effector genes kick into action at specified sites and at s
pecified times and determine the identities of segments and organs. These master-regulatory genes work by turning other genes on and off; they can be likened to circuits in a microprocessor. Mutations in the genes thus result in malformed, ectopic segments and organs. Like the Red Queen’s bewildered servants in Alice in Wonderland, the genes scurry about to enact the instructions—build a thorax, make a wing—but in the wrong places or at the wrong times. If a master regulator shouts, “ON with an antenna,” then the antenna-building subroutine is turned on and an antenna is built—even if that structure happens to be growing out of the thorax or abdomen of a fly.

  But who commands the commanders? Ed Lewis’s discovery of master-regulatory genes that controlled the development of segments, organs, and structures solved the problem of the final stage of embryogenesis, but it raised a seemingly infinite recursive conundrum. If the embryo is built, segment upon segment and organ by organ, by genes that command the identity of each segment and organ, then how does a segment know its own identity in the first place? How, for instance, does a wing-making master gene “know” to build a wing in the second thoracic segment, and not, say, the first or third segment? If genetic modules are so autonomous, then why—to turn Morgan’s riddle on its head—are legs not growing out of fly’s heads, or humans not born with thumbs emerging from our noses?