From http://www.carlzimmer.com/articles/2005/articles_2005_Avida.html
That's how science works, and hey, isn't it cool to see creationists doing something useful?
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.?
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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 identical output.
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 jerks.
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?"
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That's how science works, and hey, isn't it cool to see creationists doing something useful?
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