If you want to find alien life-forms, hold off on
booking that trip to the moons of Saturn. You may only need to catch a plane
to East Lansing, Michigan.
The aliens of East Lansing are not made of carbon and water. They have no DNA.
Billions of them are quietly colonizing a cluster of 200computers in the
basement of the Plant and Soil Sciences building at Michigan State University.
To peer into their world, however, you have to walk a few blocks west on
Wilson Road to the engineering department and visit the Digital Evolution
Laboratory. Here you'll find a crew of computer scientists, biologists, and
even a philosopher or two gazing at computer monitors, watching the evolution
of bizarre new life-forms.
These are digital organisms-strings of commands-akin to computer viruses. Each
organism can produce tens of thousands of copies of itself within a matter of
minutes. Unlike computer viruses, however, they are made up of digital bits
that can mutate in much the same way DNA mutates. A software program called
Avida allows researchers to track the birth, life, and death of generation
after generation of the digital organisms by scanning columns of numbers that
pour down a computer screen like waterfalls.
After more than a decade of development, Avida's digital organisms are now
getting close to fulfilling the definition of biological life. “More and
more of the features that biologists have said were necessary for life we can
check off,” says Robert Pennock, a philosopher at Michigan State and a
member of the Avida team. “Does this, does that, does this. Metabolism?
Maybe not quite yet, but getting pretty close.”
One thing the digital organisms do particularly well is evolve.“ Avida is
not a simulation of evolution; it is an instance of it,” Pennock says.
“All the core parts of the Darwinian process are there. These things
replicate, they mutate, they are competing with one another. The very process
of natural selection is happening there. If that's central to the definition
of life, then these things count.”
It may seem strange to talk about a chunk of computer code in the same way you
talk about a cherry tree or a dolphin. But the more biologists think about
life, the more compelling the equation becomes. Computer programs and DNA are
both sets of instructions. Computer programs tell a computer how to process
information, while DNA instructs a cell how to assemble proteins.
The ultimate goal of the instructions in DNA is to make new organisms that
contain the same genetic instructions. “You could consider a living organism
as nothing more than an information channel, where it's transmitting its
genome to its offspring,” says Charles Ofria, director of the Digital
Evolution Laboratory. “And the information stored in the channel is how to
build a new channel.” So a computer program that contains instructions for
making new copies of itself has taken a significant step toward life.
A cherry tree absorbs raw materials and turns them into useful things. In goes
carbon dioxide, water, and nutrients. Out comes wood, cherries, and toxins to
ward off insects. A computer program works the same way. Consider a program
that adds two numbers. The numbers go in like carbon dioxide and water, and
the sum comes out like a cherry tree.
In the late 1990s Ofria's former adviser, physicist Chris Adami of Caltech,
set out to create the conditions in which a computer program could evolve the
ability to do addition. He created some primitive digital organisms and at
regular intervals presented numbers to them. At first they could do nothing.
But each time a digital organism replicated, there was a small chance that one
of its command lines might mutate. On a rare occasion, these mutations allowed
an organism to process one of the numbers in a simple way. An organism might
acquire the ability simply to read a number, for example, and then produce an
Adami rewarded the digital organisms by speeding up the time it took them to
reproduce. If an organism could read two numbers at once, he would speed up
its reproduction even more. And if they could add the numbers, he would give
them an even bigger reward. Within six months, Adami's organisms were addition
whizzes. “We were able to get them to evolve without fail,” he says. But
when he stopped to look at exactly how the organisms were adding numbers, he
was more surprised. “Some of the ways were obvious, but with others I'd say,
'What the hell is happening?' It seemed completely insane.”
On a trip to Michigan State, Adami met microbiologist Richard Lenski, who
studies the evolution of bacteria. Adami later sent Lenski a copy of the Avida
software so he could try it out for himself. On a Friday, Lenski loaded the
program into his computer and began to create digital worlds. By Monday he was
tempted to shut down his lab and dedicate himself to Avida. “It just had the
smell of life,” says Lenski.
It also mirrored Lenski's own research. Since 1988 he has been running the
longest continuous experiment in evolution. He began with a single
bacterium-Escherichia coli-and used its offspring to found 12separate colonies
of bacteria that he nurtured on a meager diet of glucose, which creates a
strong incentive for the evolution of new ways to survive. Over the past
17years, the colonies have passed through35,000 generations. In the process,
they've become one of the clearest demonstrations that natural selection is
real. All 12 colonies have evolved to the point at which the bacteria can
replicate almost twice as fast as their ancestors. At the same time, the
bacterial cells have gotten twice as big. Surprisingly, these changes didn't
unfold in a smooth, linear process. Instead, each colony evolved in sudden
jerks, followed by hundreds of generations of little change, followed by more
Similar patterns occur in the evolution of digital organisms in Avida. So
Lenski set up digital versions of his bacterial colonies and has been studying
them ever since. He still marvels at the flexibility and speed of Avida, which
not only allow him to alter experimental conditions with a few keystrokes but
also to automatically record every mutation in every organism. “In an hour I
can gather more information than we had been able to gather in years of
working on bacteria,” Lenski say.“ Avida just spits data at you.”
With this newfound power, the Avida team is putting Darwin to the test in a
way that was previously unimaginable. Modernevolutionary biologists have a
wealth of fossils to study, and they can compare the biochemistry and genes of
living species. But they can't look at every single generation and every
single gene that separates a bird, for example, from its two-legged dinosaur
ancestors. By contrast, Avida makes it possible to watch the random mutation
and natural selection of digital organisms unfold over millions of
generations. In the process, it is beginning to shed light on some of the
biggest questions of evolution.
QUESTION #1: WHAT GOOD IS HALF AN EYE?
If life today is the result of evolution by natural selection, Darwin
realized, then even the most complex systems in biology must have emerged
gradually from simple precursors, like someone crossing a river using
stepping-stones. But consider the human eye, which is made of many different
parts-lens, iris, jelly, retina, optic nerve-and will not work if even one
part is missing. If the eye evolved in a piecemeal fashion, how was it of any
use to our ancestors? Darwin argued that even a simpler version of today's
eyes could have helped animals survive. Early eyes might have been nothing
more than a patch of photosensitive cells that could tell an animal if it was
in light or shadow. If that patch then evolved into a pit, it might also have
been able to detect the direction of the light. Gradually, the eye could have
taken on new functions, until at last it could produce full-blown images. Even
today, you can find these sorts of proto-eyes in flatworms and other animals.
Darwin declared that the belief that natural selection cannot produce a
complex organ “can hardly be considered real.”
Digital organisms don't have complex organs such as eyes, but they can process
information in complex ways. In order to add two numbers together, for
example, a digital organism needs to carry out a lot of simpler operations,
such as reading the numbers and holding pieces of those numbers in its memory.
Knock out the commands that let a digital organism do one of these simple
operations and it may not be able to add. The Avida team realized that by
watching a complex organism evolve, they might learn some lessons about how
complexity evolves in general.
The researchers set up an experiment to document how one particularly complex
operation evolved. The operation, known as equals, consists of comparing pairs
of binary numbers, bit by bit, and recording whether each pair of digits is
the same. It's a standard operation found in software, but it's not a simple
one. The shortest equals program Ofria could write is 19 lines long. The
chances that random mutations alone could produce it are about one in a
thousand trillion trillion.
To test Darwin's idea that complex systems evolve from simpler precursors, the
Avida team set up rewards for simpler operations and bigger rewards for more
complex ones. The researchers set up an experiment in which organisms
replicate for 16,000generations. They then repeated the experiment 50 times.
Avida beat the odds. In 23 of the 50 trials, evolution produced organisms that
could carry out the equals operation. And when the researchers took away
rewards for simpler operations, the organisms never evolved an equals program.
“When we looked at the 23 tests, they were all done in completely different
ways,” adds Ofria. He was reminded of how Darwin pointed out that many
evolutionary paths can produce the same complex organ. A fly and an octopus
can both produce an image with their eyes, but their eyes are dramatically
different from ours. “Darwin was right on that-there are many different ways
of evolving the same function,” says Ofria.
The Avida team then traced the genealogy leading from the first organism to
each one that had evolved the equals routine. “The beauty of digital life is
that you can watch it happen step by step,” says Adami. “In every step you
would ordinarily never see there is a goal you're going toward.” Indeed, the
ancestors of the successful organisms sometimes suffered harmful mutations
that made them reproduce at a slower rate. But mutations a few generations
later sped them up again.
When the Avida team published their first results on the evolution of
complexity in 2003, they were inundated with e-mails from creationists. Their
work hit a nerve in the antievolution movement and hit it hard. A popular
claim of creationists is that life shows signs of intelligent design,
especially in its complexity. They argue that complex things could never have
evolved, because they don't work unless all their parts are in place. But as
Adami points out, if creationists were right, then Avida wouldn't be able to
produce complex digital organisms. A digital organism may use 19 or more
simple routines in order to carry out the equals operation. If you delete any
of the routines, it can't do the job. “What we show is that there are
irreducibly complex things and they can evolve,” says Adami.
The Avida team makes their software freely available on the Internet, and
creationists have downloaded it over and over again in hopes of finding a
fatal flaw. While they've uncovered a few minor glitches, Ofria says they have
yet to find anything serious. “We literally have an army of thousands of
unpaid bug testers,” he says. “What more could you want?”
QUESTION #2: WHY DOES A FOREST HAVE MORE THAN ONE KIND OF PLANT?
When you walk into a forest, the first thing you see is diversity. Trees tower
high overhead, ferns lurk down below, vines wander here and there like tangled
snakes. Yet these trees, ferns, and vines are all plants, and as such, they
all make a living in the same way, by catching sunlight. If one species was
better than all the rest at catching sunlight, then you might expect it to
outcompete the other plants and take over the forest. But it's clear that
evolution has taken a different course.
Figuring out why is a full-time job for a small army of biologists. A number
of them seek enlightenment by comparing places that are rich and poor in
species and trying to figure out the other things that make them different.
One intriguing pattern has to do with food. Ecologists have found that the
more energy a habitat can provide organisms, the more species it can support.
But a habitat can get too productive. Then it supports fewer species. This
pattern has emerged time and again in studies on ecosystems ranging from
grasslands to Arctic tundra.
Until recently, a typical Avida experiment would end up with a single dominant
organism. The Avida researchers suspected that was the result of providing an
endless supply of food-in this case, numbers. Perhaps, they reasoned, if they
put their digital organisms on a diet, they might evolve into different
forms-just as it happens in nature. So the Avida team retooled their software
to limit the supply of numbers flowing into their digital worlds. Then they
made the numbers even more scarce by splitting them up into smaller supplies,
each of which could be used only for a particular operation, such as adding
two numbers. As the organisms used the numbers at a faster rate, they got a
smaller benefit. And if too many organisms gorged themselves on one supply of
numbers, they would stop replicating altogether.
The Avida team subsequently flooded some digital worlds with numbers and
limited others to a scant supply, and the same pattern of diversity found in
global ecosystems emerged. When the number supply was low, only one type of
organism could survive. At intermediate levels, three or four different types
emerged and coexisted. Each type evolved into a specialist atone or a few
kinds of operations. But when the number supply got too abundant, diversity
dropped to a single species again.
Bringing diversity into Avida has brought more bad news for those who think
complexity cannot evolve. Ofria decided to run the complexity experiment over
again, this time with a limit on the supply of numbers. “It just floored
me,” he says. “I went back and checked this so many ways.” In the
original experiment, the organisms evolved the equals routine in 23 out of 50
trials. But when the experiment was run with a limited supply of numbers, all
the trials produced organisms that could carry out the equals routine. What's
more, they needed only a fifth of the time to do it.
Ofria suspects that the difference comes from the fact that several species
are now evolving in the experiment rather than just one. More species mean
more opportunities for success.
QUESTION #3: WHY BE NICE?
Human society depends on countless acts of cooperation and personal sacrifice.
But that doesn't make us unique. Consider Myxococcus xanthus, a species of
bacteria that Lenski and his colleagues study. Myxococcus travels in giant
swarms 100,000strong, hunting down E. coli and other bacteria like wolves
chasing moose. They kill their prey by spitting out antibiotics, then spit out
digestive enzymes that make the E. coli burst open. The swarm then feasts
together on the remains. If the Myxococcus swarm senses that they've run out
of prey to hunt, they gather together to form a stalk. The bacteria at the
very top of the stalk turn into spores, which can be carried away by wind or
water to another spot where they can start a new pack. Meanwhile, the
individuals that formed the stalk die.
This sort of cooperation poses a major puzzle because it could be undermined
by the evolution of cheaters. Some bacteria might feast on the prey killed by
their swarm mates and avoid wasting their own energy making antibiotics or
enzymes. Others might evolve ways of ensuring that they always end up becoming
spores and never get left behind in the dead stalk. Such cheaters are not
theoretical: Lenski and his colleagues have evolved them in their lab.
The Avida team is now trying to address the mystery of cooperation by creating
new commands that will let organisms exchange packages of information. “Once
we get them to communicate, can we get them to work together to solve a
problem?” asks Ofria. “You can set up an information economy, where one
organism can pay another one to do a computation for it.”
If digital organisms cooperate, Ofria thinks it may be possible to get them
working together to solve real-world computing problems in the same way
Myxococcus swarms attack their prey. “I think we'll be able to solve much
more complex problems, because we won't have to know how to break them down.
The organisms will have to figure it out for themselves,” says Ofria. “We
could really change the face of a lot of computing.”
QUESTION #4: WHY SEX?
Birds do it, bees do it, and even fleas do it-but why they all do it is
another matter. Reproduction is possible without sex. Bacteria and protozoa
simply split in two. Some trees send shoots into the ground that sprout up as
new trees. There are even lizard species that are all female. Their eggs don't
need sperm to start developing into healthy baby female lizards.
“One of the biggest questions in evolution is, why aren't all organisms
asexual?” says Adami. Given the obvious inefficiency of sex, evolutionary
biologists suspect that it must confer some powerful advantage that makes it
so common. But they have yet to come to a consensus about what that advantage
So Dusan Misevic, a biologist at Michigan State, has spent the past couple of
years introducing sex into Avida. While digital sex may lack romance, it
features the most important element from an evolutionary point of view: the
genetic material from two parents gets mixed together in a child. When a
digital organism makes a copy of itself, the copy doesn't immediately take its
own place in Avida and start reproducing. Instead, chunks of its code are
swapped with the copy of another new organism. Only after this exchange do the
two creatures start to reproduce.
In 1964 the German biologist H. J. Muller proposed that sex allows organisms
to mix their genomes together in combinations that can overcome the effects of
harmful mutations. Asexual organisms, on the other hand, are stuck with all
the mutations their ancestors pass down to them. Over time, Muller argued,
they can't reproduce as quickly as their sexual competitors. Misevic designed
an experiment to put Muller's hypothesis to the test.” It's a classic
explanation, so it seemed like a good place to start,” he says.
Misevic created two kinds of worlds: one full of sexual digital organisms and
the other full of asexuals. After they had evolved for tens of thousands of
generations, he measured how fast they could replicate. “The overall
conclusion we got was that, yes, there are some situations where sex is
beneficial,” says Misevic. But there were surprises. Sex is good mainly as a
way to escape annihilation from lethal mutations. But in Avida, sexual
organisms had to pay a price for that insurance-they carried more nonlethal
yet harmful mutations than the asexual organisms.
“We must look to other explanations to help explain sex in general,” says
QUESTION #5: WHAT DOES LIFE ON OTHER PLANETS LOOK LIKE?
Life on Earth is based on DNA. But we can't exclude the possibility that life
could evolve from a completely different system of molecules. And that raises
some worrying questions about the work going on these days to find signs of
extraterrestrial life. NASA is funding a wide range of life-detecting
instruments, from rovers that prowl across Mars to telescopes that will gaze
at distant solar systems. They are looking for the signs of life that are
produced on Earth. Some are looking for high levels of oxygen in the
atmospheres of other planets. Others are looking for bits of DNA or fragments
of cell walls. But if there's non-DNA-based life out there, we might overlook
it because it doesn't fit our preconceptions.
“We can look at how known life-forms leave marks on their environment,”
says Evan Dorn, a member of Chris Adami's lab at Caltech, “but we can never
make universal statements about them because we have only one example.”
Dorn says Avida is example number two. By finding patterns that are shared by
life on Earth and life in Avida, he thinks he will be able to offer some ideas
about how to look for life that the universe might be harboring.
Some researchers have suggested the best way to look for signs of life is to
look for weird chemistry. Take the building blocks of proteins-amino
acids-which are found on meteorites and can also be created in the lab simply
by running an electric current through ammonia and other compounds. In a
lifeless setting, the most common amino acid that results is the simplest:
glycine. Some slightly less simple amino acids are also common, but all the
larger ones make up only a trace or are missing altogether. That's because it
takes a lot of energy to make those big amino acids. “There's a limited
repertoire of chemistry in the absence of life,” says Dorn.
If you analyze a scoop of soil or pond water, however, you'll find a
completely different profile of amino acids. Life has evolved ways of building
certain big amino acids, and when organisms die, those big amino acids float
around in the environment.
What if life on another planet made compounds that were radically different
from amino acids? Would it alter its planet's chemistry in some similar way?
To test this idea, Dorn created a world devoid of life. Instead of containing
a self-replicating program, each cell contained random assortment of commands.
All of the commands in the Avida language were present at equal levels. Here
was the signature of a lifeless planet.
Then Dorn began dropping organisms into this world, like spores falling to
Earth. At the beginning of the experiment, he set the mutation rate so high
that no spore could replicate very long on the planet. (Think of Mars, where
ultraviolet rays pelt the surface.) Gradually, he lowered the mutation rate
until life could survive. “As soon as the environment was habitable, the
organism took over and dominated the environment,” Dorn says.
As the digital organisms evolved to adapt to the world, Dorn found that some
commands became rare and others became far more common. This distinctive
signature stayed stable as long as life could survive on the planet. And no
matter how many times Dorn repeated the experiment, the same signature of life
appeared. Whether manipulating amino acids or computer commands, life does
seem to leave the same mark. “It gives us a pretty strong indication that
this process is universal,” says Dorn.
If Dorn is right, discovery of non-DNA life would become a little less
spectacular because it would mean that we have already stumbled across it here
on Earth-in East Lansing, Michigan.
QUESTION #6: WHAT WILL LIFE ON EARTH LOOK LIKE IN THE FUTURE?
One of the hallmarks of life is its ability to evolve around our best efforts
to control it. Antibiotics, for example, were once considered a magic bullet
that would eradicate infectious diseases. In just a few decades, bacteria have
evolved an arsenal of defenses that make many antibiotics useless.
Ofria has been finding that digital organisms have a way of outwitting him as
well. Not long ago, he decided to see what would happen if he stopped digital
organisms from adapting. Whenever an organism mutated, he would run it through
a special test to see whether the mutation was beneficial. If it was, he
killed the organism off. “You'd think that would turn off any further
adaptation,” he says. Instead, the digital organisms kept evolving. They
learned to process information in new ways and were able to replicate faster.
It took a while for Ofria to realize that they had tricked him. They had
evolved a way to tell when Ofria was testing them by looking at the numbers he
fed them. As soon as they recognized they were being tested, they stopped
processing numbers. “If it was a test environment, they said, 'Let's play
dead,' ” says Ofria. “There's this thing coming to kill them, and so they
avoid it and go on with their lives.”
When Ofria describes these evolutionary surprises, admiration and ruefulness
mix in is voice. “Here I am touting Avida as a wonderful system where you
have full knowledge of everything and can control anything you want-except I
can't get them to stop adapting. Life will always find a way.”
Thinking about such adaptable creatures lurking on the Michigan State campus,
furiously feeding on data, can be unsettling. Should the Avida team be working
in quarantine? Lenski argues that Avida itself acts as a quarantine, because
its organisms can exist only in its computer language. “They're living in an
alien world,” Lenski says. “They may be nasty predators from Mars, but
they'd drop dead here.”
Still, Ofria acknowledges that harmful computer viruses may eventually evolve
like his caged digital organisms. “Some day it's going to happen, and it's
going to be scary,” Ofria says. “Better to study them now so we know how
to deal with them.”
Copyright 2004 Carl Zimmer