Microcosm

by Carl Zimmer

  The question of why we slide this way toward death preoccupied George Williams. He was so fascinated by it that he charted his own decline. Beginning at age fifty-two, he would go once a year to a track near his home on Long Island and time how long it took him to run 1,700 meters. Some years he ran a little faster than he had the previous year, but over the course of twelve years he gradually slowed down. Why, Williams wanted to know, was he declining so steadily? If he had to die, why couldn’t he stay young and fit until his body suddenly gave out? And if he did have to get old, why did his decline follow the particular downward curve that it did? Why hadn’t he run so slowly in his twenties instead of in his fifties?

  After all, Williams could look to the natural world for an endless supply of alternatives. A clam may live for four centuries. At the other extreme are salmon, which return in peak condition to the streams where they were born. They find a mate, have baby salmon, then promptly grow old at catastrophic speed and die. In a few weeks the salmon age more than humans do in a few decades.

  As a graduate student in the 1950s, Williams had listened to his teachers explain that death existed for the good of the species. The old had to make way for the young, or else a species would become extinct. Williams thought that was nonsense. Instead, he considered how natural selection acting on individuals might create old age. Williams argued that it could be a side effect caused by genes that offered advantages in youth. As long as the advantages of these genes outweighed the disadvantages, they would become widespread. Cancer, declining stamina, deteriorating vision, and the other burdens of old age might all be the result of natural selection.

  Williams argued that organisms face these sorts of evolutionary tradeoffs throughout their lifetime. How much energy should they invest in maturing before they start to have babies, for example, or how much energy should they invest in raising offspring before they search for another mate? Natural selection ought to find the balance between those demands. Williams speculated that animals could also keep track of how those factors change over their lifetime and adjust their behavior accordingly, like an investor deciding which stocks to keep or sell.

  Over the past forty years, Williams’s theory has evolved into an experimental science of aging. Now scientists can predict which species will get old and why. In a 2005 study, to pick just one example from hundreds, scientists studied the sockeye salmon that return to Pick Creek, Alaska, each year. The salmon come back in July and August. Once the female salmon have mated, they select a spot to lay their eggs and dig a nest in the gravel bottom of the creek. After they lay their eggs, they cover them and guard them from other females that might want to take over the nest to lay their own eggs.

  The salmon of Pick Creek face just the sort of trade-off Williams proposed. Once they leave the ocean to travel to their breeding grounds, they stop eating for good. They have only a fixed amount of energy to divvy up among the things they do before they die. The females have to put some of their energy into their developing reproductive system in order to make eggs. They can also put some of their energy into maintaining their bodies so that they will live long enough to fight off other salmon. It’s a zero-sum game.

  The scientists predicted that salmon arriving at Pick Creek earlier in the season would live longer than the salmon that came later. A salmon that lays its eggs in July has weeks of battling ahead. If it puts all its energy into eggs and dies early, other salmon will take over its nest, and its genes won’t have a chance of getting into the next generation. If a late-arriving salmon invests its energy in long life, it’s wasting its effort, since it will still be alive when the rest of the salmon have died off. Late arrivers should invest in making extra eggs.

  When the researchers compared early and late arrivers, they found their predictions met. The early arrivers survived on average for twenty-six days at Pick Creek, whereas the late arrivers survived only twelve days. The early arrivers put roughly an equal amount of energy into maintaining their bodies and protecting their eggs. The late arrivers put twice as much energy into protecting their eggs as into maintaining their bodies.

  Williams’s predictions work not just for salmon but for fruit flies, vinegar worms, guppies, swans, humans, and many other species as well. But until recently experts on aging considered E. coli off limits. A trade-off between long life and reproduction seemed simply not to exist. E. coli did not have parents and children. An individual E. coli just duplicated its DNA and pulled itself apart into two new individuals. The parent became the children. Starvation might slow E. coli down, and chemical warfare and other assaults might kill the bacteria outright. But left to themselves with enough food, E. coli would reproduce forever, each new microbe as healthy as its forerunners.

  That was what scientists thought until Eric Stewart, a microbiologist now at Northeastern University, decided to take a very close look at E. coli. He and his colleagues built a sort of voyeuristic E. coli paradise. They injected a single microbe onto an agar-coated slide, covering the little shelter with glass and sealing the sides shut with silicon grease. The microbe carried a light-producing gene, making it easy to film through the top of the slide. The scientists mounted the slide on a microscope, and the entire apparatus was put in a box that was kept as warm as a healthy human gut.

  The single E. coli feasted and divided. Its descendants spread out in a layer one cell deep. At regular intervals a camera mounted on the microscope took a picture of the glowing colony. Comparing one picture with the next, Stewart could track the fate of every branch of his E. coli dynasty. He could time how long it took each microbe to divide and then how long its two offspring needed and then its four grandchildren. Given that all the microbes were genetically identical and all were living in the same perfect conditions for growth, they all should have grown at the same rate. But they didn’t. Some individuals grew more slowly than their siblings, and over time their descendants lagged farther and farther behind.

  Some bacteria, Stewart discovered, were getting old. Each time a microbe reproduces, it builds itself a ring in order to cut itself in half. At the same time, it builds two new caps to cover the new ends of its daughter cells. When those two daughter cells split, each will build new caps as well. After several generations, some bacteria will have old poles and others will have new ones. In the diagram below, the numbers show how many generations have passed since a cap has been created:

  Stewart discovered that as the caps on microbes got older, the microbes grew more slowly. He estimates that the aging E. coli were slowing down so quickly that after a hundred generations they would stop dividing altogether.

  Once more the Williams-Hamilton decoder ring can help. Old age must have some evolutionary advantage over immortality for E. coli. Its edge may come from the inescapable damage that strikes the bacteria. Proteins become snarled; genes mutate. When a microbe divides, it may pass down its defective proteins and genes to one or both of its descendants. Over the generations, more and more damage can pile up like a cruel, compounding legacy. Of course, E. coli can fix this damage, and it does fix a lot of it. Yet that repair doesn’t come free. A microbe must use up a lot of energy and nutrients to repair itself. If it spent all its resources on repair, a more careless microbe would outcompete it.

  There is another way to cope with damage: push it all into one place. In E. coli’s case, the dumping grounds are its poles. E. coli does not put much effort into repairing them, and when it divides, each of its descendants gets an old, damaged pole along with a new one on the other end. Over the generations, some of the poles can get very old—and presumably accumulate a lot of damage to their proteins. Instead of trying to be a perfectionist, Stewart suggests, E. coli may just turn its poles into garbage cans. A microbe that lets some of its descendants get old while the rest stay young may have found the best strategy for evolutionary success.

  What once seemed like a major exception to Monod’s rule has now vanished. Once again E. coli has hit on the same strategy we humans have. Wh
en a fertilized human egg begins to grow into an embryo, it soon develops into two types of cells: cells that can become new people (eggs and sperm) and all the others. We invest a great deal of energy in protecting eggs and sperm from the ravages of time and much less on protecting the rest of our bodies. From this unconscious choice, we allow our progeny to live on while we die. For both humans and E. coli, the privilege of life must be paid with death.

  Seven

  DARWIN AT THE DRUGSTORE

  LIFE AGAINST LIFE

  THE BACTERIA IN THE DISH on my desk are a long way from home. Their ancestors left the body of a diphtheria patient in California eighty-five years ago and have never returned to another human gut. They were transported into another dimension—of flasks and freezers, centrifuges and X-rays. These laboratory creatures have enjoyed a strange comfort, gorging themselves on amino acids and sugar. And over hundreds of thousands of generations they have evolved. They have become fast breeders and have lost the ability to survive for long in the human gut. They avoid extinction only because they have become so dear to the biologists who carry them from flask to freezer to incubator.

  Over those eighty-five years their wild cousins have gone on with their own lives. They have continued to colonize guts, and they have evolved as well. The microbes that live inside us today are not the same as the ones that lived inside people in 1920. We are the source of much of that change.

  The most obvious way we have changed E. coli is by trying to fight infections with drugs. E. coli and other bacteria have responded to those drugs with a rapid burst of evolution. They can now resist drugs that once would have wiped them out. Scientists are now left scrambling to find new drugs to replace the failed ones, and there’s little reason to think E. coli and other microbes won’t evolve resistance to them as well.

  While some scientists have observed E. coli evolve in their laboratories, we have also launched a global, unplanned experiment in E. coli evolution. Like laboratory experiments, the rise of resistant E. coli is offering its own clues to the workings of evolution. Resistance can evolve through the familiar course of random mutations and natural selection. But in some ways, E. coli is not fitting into the conventional picture. In the evolution of resistant E. coli, some researchers claim to have found evidence that the microbe can alter the way it mutates to suit the conditions it faces. And while Darwin erected his theory on the idea that organisms inherit traits from their direct ancestors, E. coli has acquired much of its resistance to antibiotics from other species of bacteria, which can trade genes like business cards. These discoveries are significant not only because they may help in the battle against drug-resistant pathogens. They may also reveal forces that have been shaping life for the past 4 billion years.

  The era of antibiotics began suddenly, but it followed a long, slow prelude. Traditional healers long knew that mold could heal wounds. In 1877, Louis Pasteur found that he could halt the spread of anthrax-causing bacteria by introducing “common bacteria” in their midst. No one knew what the common bacteria did to stop the anthrax, but scientists gave it a name anyway: antibiosis, the ability of one creature to kill another.

  In 1928, Alexander Fleming, a Scottish bacteriologist, discovered a molecule that could kill bacteria. He noticed that one of his petri dishes had become contaminated with mold. There were no bacteria near it. He ran tests on the mold and discovered that it could halt the spread of bacteria. Yet it did not harm human cells. Fleming isolated the mold’s antibiotic and named it penicillin.

  At first, penicillin did not look like a promising drug. For one thing, Fleming could extract only tiny amounts of it from mold, and it proved too fragile to be stored for very long. It took ten years for penicillin to live up to its promise. Howard Florey and Ernst Chain at Oxford University figured out how to coax the mold to make enough penicillin to test on mice. They infected mice with streptococci and injected some with penicillin. The treated mice all survived, and the others all died. In 1941, Florey and Chain persuaded American pharmaceutical companies to adopt their penicillin production scheme and expand it to an industrial scale. By 1944, wounded Allied soldiers were being cured of infections that would have killed them a year before. In the next few years, a rush of other antibiotics came along, mostly derived from fungi and bacteria.

  Antibiotics, scientists discovered, kill bacteria in many ways. Some attack enzymes that help replicate DNA. Others, such as penicillin, interfere with the construction of the peptidoglycan mesh that wraps around E. coli and other bacteria. Gaps in the mesh form, and the high-pressure innards of the microbes burst out. Organisms naturally make only trace amounts of antibiotics, but drug companies began to produce them in enormous bulk, rearing fungi and bacteria in giant fermenters or synthesizing drugs from scratch. It would take billions of microbes to produce the antibiotics in a single pill. In such a concentrated form, antibiotics had a staggering effect on disease-causing bacteria. They didn’t just reduce infections. They got rid of them altogether, and with few noticeable side effects. The war against infectious diseases seemed to have suddenly become a rout.

  But even in those heady days of early victory, there were signs of trouble. At one point in their research, Florey and Chain discovered that their cultures of mold had been invaded by E. coli. The bacteria were able to survive in a soup of penicillin by producing an enzyme that could cut the antibiotic molecule into feeble fragments.

  As penicillin was being introduced to the world, microbiologists were discovering how mutations arose in E. coli. In 1943, Delbrück and Luria showed that mutations spontaneously made E. coli resistant to viruses. In 1948, the Yugoslavian-born geneticist Milislav Demerec showed that the same held true for antibiotics. He bred resistant strains of E. coli and Staphylococcus aureus. Both species became increasingly resistant as they picked up a series of mutations. In the same year that Demerec published his results, doctors reported that penicillin was beginning to fail in their Staphylococcus-infected patients.

  These disturbing discoveries did nothing to halt the rise of antibiotics. Today the world consumes more than ten thousand tons of antibiotics a year. Some of those drugs save lives, but a lot of them are wasted. Two-thirds of all the prescriptions that doctors hand out for antibiotics are useless. Antibiotics can’t kill viruses, for instance. Many farmers today practically drown their animals with antibiotics because the drugs somehow make the animals grow bigger. But the cost of the antibiotics is greater than the profit from the extra meat.

  Along with the rise in antibiotics has come a rise in antibiotic resistance. Drugs that were once fatal to bacteria are now useless. E. coli’s story is typical. Resistant strains of E. coli first emerged in the 1950s. At first only a small fraction of E. coli could withstand any particular antibiotic, but over several years resistant microbes became more common. Soon the majority of E. coli could withstand the drug. As one drug faltered, doctors would prescribe another—a stronger drug with harsher side effects or a more recently discovered molecule. And in a few years that drug would begin to fail as well. Before long, strains of E. coli emerged that could resist many antibiotics at once.

  E. coli uses many tricks to dodge antibiotics. As Florey and Chain discovered, it can secrete enzymes that cut penicillin into harmless fragments. In some cases, E. coli’s proteins have taken on new shapes that make it difficult for antibiotics to grab them. And in other cases, E. coli uses special pumps to hurl antibiotics out of its interior. For every magic bullet science has found for E. coli, E. coli has acquired an equally magic shield.

  SKIN OF FROG

  E. coli has evolved its resistance to antibiotics almost entirely out of view. It was not trapped in a laboratory flask, where a scientist could track every mutation from one generation to the next. Its flask was the world.

  The pieces of evidence scientists have assembled are enough for them to reconstruct some of its history. The genes that now provide E. coli with resistance to antibiotics did not suddenly appear in 1950. They descend from old
er genes that originally had other functions. Some of the pumps that flush antibiotics out of E. coli probably evolved from pumps bacteria use to release signaling molecules. Others originally flushed out the bile salts E. coli encounters in our guts.

  When E. coli first encountered antibiotics, its pumps probably did a poor job of getting rid of them. But on rare occasion the genes for the pumps mutated. A mutant microbe might pump out antibiotics a little faster than others. Before modern medicine, such mutants wouldn’t have been any better at reproducing than other bacteria. Their mutations might even have been downright harmful. But once they began to face antibiotics on a regular basis, the mutants had an evolutionary edge.

  That edge may have been razor thin at first. Only a few of the resistant mutants might have survived a dose of antibiotics, but that was better than getting exterminated. Over time, resistant mutants became more common in populations of E. coli. Their descendants acquired new mutations that made them even more resistant. In 1986, scientists discovered strains of E. coli that made an enzyme able to destroy a group of antibiotics called aminoglycosides. In 2003, another team discovered E. coli carrying a new version of the gene. It had two new mutations that made it resistant not just to aminoglycosides but also to a completely different antibiotic, called ciprofloxacin.

  Even within a single person, E. coli can evolve to dangerous extremes. In August 1990, a nineteen-month-old girl was admitted to an Atlanta hospital with a fever. Doctors discovered that E. coli had infected her blood, probably through an ulcer in her intestines. Tests on the bacteria revealed that they were already resistant to two common antibiotics, ampicillin and cephalosporin. Her doctors gave her other antibiotics, each more potent than the last. Instead of wiping out her E. coli, however, they made it stronger. It acquired new resistance genes, and the ones it already had continued to evolve. After five months and ten different antibiotics, the child died.