Testing Darwin
Discover Magazine's latest issue chronicles the adventures of the Digital Evolution Laboratory of Michigan State University and their Avida evolution software. If you buy into evolution -- like most sane people do -- what the folks are doing at the lab is downright fascinating. If you don't buy into evolution, you will come up with a new set of crackpot ideas for disproving their work. At the lab, the researchers use Avida to produce digital organisms, capable of replicating themselves tens of thousands of times in minutes, with code that can randomly mutate, just like DNA, with each replication. The researchers can track birth, life, death and mutations across generations of digital organisms. It's evolution at warp speed -- no intelligent designer required!
Avida is important because it's not a simulation of evolution. It's actually an instance of evolution. Code is created, replicated, and mutated -- natural selection is happening within the computer, based on the researchers playing god with the digital organisms environment. Not much different from DNA -- where code is created, replicated and mutated. Along the way, the researchers are finding some surprises in the way evolution works -- such as organisms evolved to add numbers do so, but in some really crazy ways; or that evolution isn't a smooth linear process, but rather a process regularly punctuated with spurts of change. With Avida, researchers can observe millions of generations of random mutation and natural selection, and they're making tremendous progress in understanding how evolution works.
One of the things that creationists (especially the unintelligent 'intelligent design' crazies) love to dangle in front of sane scientists is that they refuse to believe that complex systems could have evolved. They stress that complex biological systems aren't just the sum of their parts -- taking a part away renders the whole non-functioning. What Avida has shown however, is that the complex systems could evolve from simple precursors -- and the simple precursors were useful in the primitive organisms. In the evolved complex organism however, taking away the simple precursor renders the whole non-functioning. As well, Avida has shown, as Darwin had believed, that there are many different paths to produce the same complex system.
On the subject of diversity, Avida has also shed some light. The diversity that is found in global ecosystems is also generated by Avida when food supply is balanced (not too much, not too little). The organisms that evolve also specialize, and tend to evolve much faster than when the food supply was great. It appears that diversity increases the chances of the entire ecosystem surviving and succeeding. Which begs us to question what we're doing to the global diversity of life.
Cooperation -- it's a foundation of human society, but it's not unique to humans. The article tells the story of the bacteria Myxococcus xanthus, that travel in swarms of 100,000, hunting down, killing and devouring E. coli and other bacteria. When run out of prey, they gather together to form a stalk, with the bacteria at the top forming spores that are carried away to a new location to begin again. The bacteria that's left behind, dies. Why the cooperation? Why didn't cheaters evolve? This is something that the researchers are still pondering. If their digital organisms evolve to cooperate, they could suddenly be harvested to solve real world problems.
Why sex? Asexual reproduction works, yet sexual reproduction dominates the higher species. Sex has been introduced to the digital organisms, but the outcome is far from conclusive. Sex allows organisms to share code, and is a way of avoiding annihilation from lethal mutations -- yet, because code is shared, mutations are shared, and sexual organisms carry more mutations than asexual organisms. Why did sexual reproduction dominate our global ecosystem?
It's a fascinating subject -- one that creationists aren't entirely happy with. The Avida program is available for download for anyone who wishes to create their own universe of digital organisms, and many creationists have downloaded it in hopes of finding a flaw. So far, nothing.
Avida is important because it's not a simulation of evolution. It's actually an instance of evolution. Code is created, replicated, and mutated -- natural selection is happening within the computer, based on the researchers playing god with the digital organisms environment. Not much different from DNA -- where code is created, replicated and mutated. Along the way, the researchers are finding some surprises in the way evolution works -- such as organisms evolved to add numbers do so, but in some really crazy ways; or that evolution isn't a smooth linear process, but rather a process regularly punctuated with spurts of change. With Avida, researchers can observe millions of generations of random mutation and natural selection, and they're making tremendous progress in understanding how evolution works.
One of the things that creationists (especially the unintelligent 'intelligent design' crazies) love to dangle in front of sane scientists is that they refuse to believe that complex systems could have evolved. They stress that complex biological systems aren't just the sum of their parts -- taking a part away renders the whole non-functioning. What Avida has shown however, is that the complex systems could evolve from simple precursors -- and the simple precursors were useful in the primitive organisms. In the evolved complex organism however, taking away the simple precursor renders the whole non-functioning. As well, Avida has shown, as Darwin had believed, that there are many different paths to produce the same complex system.
On the subject of diversity, Avida has also shed some light. The diversity that is found in global ecosystems is also generated by Avida when food supply is balanced (not too much, not too little). The organisms that evolve also specialize, and tend to evolve much faster than when the food supply was great. It appears that diversity increases the chances of the entire ecosystem surviving and succeeding. Which begs us to question what we're doing to the global diversity of life.
Cooperation -- it's a foundation of human society, but it's not unique to humans. The article tells the story of the bacteria Myxococcus xanthus, that travel in swarms of 100,000, hunting down, killing and devouring E. coli and other bacteria. When run out of prey, they gather together to form a stalk, with the bacteria at the top forming spores that are carried away to a new location to begin again. The bacteria that's left behind, dies. Why the cooperation? Why didn't cheaters evolve? This is something that the researchers are still pondering. If their digital organisms evolve to cooperate, they could suddenly be harvested to solve real world problems.
Why sex? Asexual reproduction works, yet sexual reproduction dominates the higher species. Sex has been introduced to the digital organisms, but the outcome is far from conclusive. Sex allows organisms to share code, and is a way of avoiding annihilation from lethal mutations -- yet, because code is shared, mutations are shared, and sexual organisms carry more mutations than asexual organisms. Why did sexual reproduction dominate our global ecosystem?
It's a fascinating subject -- one that creationists aren't entirely happy with. The Avida program is available for download for anyone who wishes to create their own universe of digital organisms, and many creationists have downloaded it in hopes of finding a flaw. So far, nothing.
Testing Darwin [PDF] -- Discover's cover article is also available in PDF format. Caltech's Digital Life Laboratory Download Avida at SourceForge. Evolutionary Learning in the 2D Artificial Life System "Avida" [PDF] Avida: A software platform for research in computational evolutionary biology [PDF] Ab Initio Modeling of Ecosystems with Artificial Life [PDF]
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