After comparing the DNA from different anole lizard species in the Caribbean, scientists found predictable patterns in their evolution.
Michael Lässig can be certain that if he steps out of his home in Cologne, Germany, on the night of Jan. 19, 2030 — assuming he’s still alive and the sky is clear — he will see a full moon.
Lässig’s confidence doesn’t come from psychic messages he’s receiving from the future. He knows the moon will be full because physics tells him so. “The whole of physics is about prediction, and we’ve gotten quite good at it,” said Lässig, a physicist at the University of Cologne. “When we know where the moon is today, we can tell where the moon is tomorrow. We can even tell where it will be in a thousand years.”
Early in his career, Lässig made predictions about quantum particles, but in the 1990s, he turned to biology, exploring how genes evolved. In his research, Lässig was looking back in time, reconstructing evolutionary history. Looking ahead to evolution’s future was not something that biologists bothered doing. It might be possible to predict the motion of the moon, but biology was so complex that trying to predict its evolution seemed a fool’s errand.
But lately, evolution is starting to look surprisingly predictable. Lässig believes that soon it may even be possible to make evolutionary forecasts. Scientists may not be able to predict what life will be like 100 million years from now, but they may be able to make short-term forecasts for the next few months or years. And if they’re making predictions about viruses or other health threats, they might be able to save some lives in the process.
“As we collect a few examples of predictability, it changes the whole goal of evolutionary biology,” Lässig said.
Replaying the Tape of Life
The book is ostensibly about the Cambrian explosion, a flurry of evolutionary innovation that took place more than 500 million years ago. The oldest known fossils of many of today’s major animal groups date to that time. Our own lineage, the vertebrates, first made an appearance in the Cambrian explosion, for example.
But Gould had a deeper question in mind as he wrote his book. If you knew everything about life on Earth half a billion years ago, could you predict that humans would eventually evolve?
Gould thought not. He even doubted that scientists could safely predict that any vertebrates would still be on the planet today. How could they, he argued, when life is constantly buffeted by random evolutionary gusts? Natural selection depends on unpredictable mutations, and once a species emerges, its fate can be influenced by all sorts of forces, from viral outbreaks to continental drift, volcanic eruptions and asteroid impacts. Our continued existence, Gould wrote, is the result of a thousand happy accidents.
To illustrate his argument, Gould had his readers imagine an experiment he called “replaying life’s tape.” “You press the rewind button and, making sure you thoroughly erase everything that actually happened, go back to any time and place in the past,” he wrote. “Then let the tape run again and see if the repetition looks at all like the original.” Gould wagered that it wouldn’t.
Although Gould only offered it as a thought experiment, the notion of replaying the tape of life has endured. That’s because nature sometimes runs experiments that capture the spirit of his proposal.
For an experiment to be predictable, it has to be repeatable. If the initial conditions are the same, the final conditions should also be the same. For example, a marble placed at the edge of a bowl and released will end up at the bottom of the bowl no matter how many times the action is repeated.
Biologists have found cases in which evolution has, in effect, run the same experiment several times over. And in some cases the results of those natural experiments have turned out very similar each time. In other words, evolution has been predictable.
One of the most striking cases of repeated evolution has occurred in the Caribbean. The islands there are home to a vast number of native species of anole lizards, which come in a staggering variety. The lizards live in the treetops, on forest floors and in open grassland. They come in a riot of colors and shapes. Some are blue, some are green and some are gray. Some are huge and bold while others are small and shy.
To understand how this diversity evolved, Jonathan Losos of Harvard University and his students gathered DNA from the animals. After they compared the genetic material from different species, the scientists drew an evolutionary tree, with a branch for every lizard species.
When immigrant lizards arrived on a new island, Losos found, their descendants could evolve into new species. It was as if the lizard tape of life was rewound to the same moment and then played again.
If Gould were right, the pattern of evolution on each island would look nothing like the pattern on the other islands. If evolution were more predictable, however, the lizards would tend to repeat the same patterns.
Losos and his students have found that evolution did sometimes veer off in odd directions. On Cuba, for example, a species of lizard adapted to spending a lot of time in the water. It dives for fish and can even sprint across the surface of a stream. You won’t find a fishing lizard on any other Caribbean island.
For the most part, though, lizard evolution followed predictable patterns. Each time lizards colonized an island, they evolved into many of the same forms. On each island, some lizards adapted to living high in trees, evolving pads on their feet for gripping surfaces, along with long legs and a stocky body. Other lizards adapted to life among the thin branches lower down on the trees, evolving short legs that help them hug their narrow perches. Still other lizards adapted to living in grass and shrubs, evolving long tails and slender trunks. On island after island, the same kinds of lizards have evolved.
“I think the tide is running against Gould,” Losos said. Other researchers are also finding cases in which evolution is repeating itself. When cichlid fish colonize lakes in Africa, for example, they diversify into the same range of forms again and again.
“But the question is: What’s the overall picture?” Losos asked. “Are we cherry-picking the examples that work against him, or are we going to find that most of life is deterministic? No one is going to say Gould is completely wrong. But they’re not going to say he’s completely right either.”
Evolution in a Test Tube
Natural experiments can be revealing, but artificial experiments can be precise. Scientists can put organisms in exactly the same conditions and then watch evolution unfold. Microbes work best for this kind of research because scientists can rear billions of them in a single flask and the microbes can go through several generations in a single day. The most spectacular of these experiments has been going on for 26 years — and more than 60,000 generations — in the lab of Richard Lenski at Michigan State University.
Lenski launched the experiment with a single E. coli microbe. He let it divide into a dozen genetically identical clones that he then placed in a dozen separate flasks. Each flask contained a medium — a cocktail of chemicals mixed into water — that Lenski created especially for the experiment. Among other ingredients, it contained glucose for the bacteria to feed on. But it was a meager supply, which ran out after just a few hours. The bacteria then had to eke out their existence until the next morning, when Lenski or his students transferred a little of the microbe-laced fluid into a fresh flask. With a new supply of glucose, they could grow for a few more hours. Lenski and his students at Michigan State have been repeating this chore every day since.
Lenski thought the tape of life would replay differently with each rewind. But that’s not what happened.
At the outset, Lenski wasn’t sure what would happen, but he had his suspicions. He expected mutations to arise randomly in each line of bacteria. Some would help the microbes reproduce faster while others would be neutral or even harmful. “I imagined they’d be running off in one direction or another,” Lenski said.
In other words, Lenski thought the tape of life would replay differently with each rewind. But that’s not what happened. What Lenski witnessed was strikingly similar to the evolution that Jonathan Losos has documented in the Caribbean.
Lenski and his students have witnessed evolutionary oddities arise in their experiment — microbial versions of the Cuban fishing lizards, if you will. In 2003, Lenski’s team noticed that one line of bacteria had abruptly switched from feeding on glucose to feeding on a compound called citrate. The medium contains citrate to keep iron in a form that the bacteria can absorb. Normally, however, the bacteria don’t feed on the citrate itself. In fact, the inability to feed on citrate in the presence of oxygen is one of the defining features of E. coli as a species.
But Lenski has also observed evolution repeat itself many times over in his experiment. All 12 lines have evolved to grow faster on their meager diet of glucose. That improvement has continued to this day in the 11 lines that didn’t shift to citrate. Their doubling time — the time it takes for them to double their population — has sped up 70 percent. And when Lenski and his students have pinpointed the genes that have mutated to produce this improvement, they are often the same from one line to the next.
“That’s not at all what I expected when I started the experiment,” Lenski said. “I evidently was wrong-headed.”
Getting Complex Without Getting Random
Lenski’s results have inspired other scientists to set up more complex experiments.Michael Doebeli, a mathematical biologist at the University of British Columbia, wondered how E. coli would evolve if it had two kinds of food instead of just one. In the mid-2000s, he ran an experiment in which he provided glucose — the sole staple of Lenski’s experiment — and another compound E. coli can grow on, known as acetate.
Doebeli chose the two compounds because he knew that E. coli treats them very differently. When given a choice between the two, it will devour all the glucose before switching on the molecular machinery for feeding on acetate. That’s because glucose is a better source of energy. Feeding on acetate, by contrast, E. coli can only grow slowly.
Something remarkable happened in Doebeli’s experiment — and it happened over and over again. The bacteria split into two kinds, each specialized for a different way of feeding. One population became better adapted to growing on glucose. These glucose-specialists fed on the sugar until it ran out and then slowly switched over to feeding on acetate. The other population became acetate-specialists; they evolved to switch over to feeding on acetate even before the glucose supply ran out and could grow fairly quickly on acetate.
When two different kinds of organisms are competing for the same food, it’s common for one to outcompete the other. But in Doebeli’s experiment, the two kinds of bacteria developed a stable coexistence. That’s because both strategies, while good, are not perfect. The glucose-specialists start out growing quickly, but once the glucose runs out, they slow down drastically. The acetate-specialists, on the other hand, don’t get as much benefit from the glucose. But they’re able to grow faster than their rivals once the glucose runs out.
Doebeli’s bacteria echoed the evolution of lizards in the Caribbean. Each time the lizards arrived on an island, they diversified into many of the same forms, each with its own set of adaptations. Doebeli’s bacteria diversified as well — and did so in flask after flask.
To get a deeper understanding of this predictable evolution, Doebeli and his postdoctoral researcher, Matthew Herron, sequenced the genomes of some of the bacteria from these experiments. In three separate populations they discovered that the bacteria had evolved in remarkable parallel. In every case, many of the same genes had mutated.
Although Doebeli’s experiments are more complex than Lenski’s, they’re still simple compared with what E. coli encounters in real life. E. coli is a resident of the gut, where it feeds on dozens of compounds, where it coexists with hundreds of other species, where it must survive changing levels of oxygen and pH, and where it must negotiate an uneasy truce with our immune system. Even if E. coli’s evolution might be predictable in a flask of glucose and acetate, it would be difficult to predict how the bacteria would evolve in the jungle of our digestive system.