Posted on 05/08/2003 10:11:06 AM PDT by Nebullis
Arlington, Va.—If the evolution of complex organisms were a road trip, then the simple country drives are what get you there. And sometimes even potholes along the way are important.
An interdisciplinary team of scientists at Michigan State University and the California Institute of Technology, with the help of powerful computers, has used a kind of artificial life, or ALife, to create a road map detailing the evolution of complex organisms, an old problem in biology.
In an article in the May 8 issue of the international journal Nature, Richard Lenski, Charles Ofria, Robert Pennock, and Christoph Adami report that the path to complex organisms is paved with a long series of simple functions, each unremarkable if viewed in isolation. "This project addresses a fundamental criticism of the theory of evolution, how complex functions arise from mutation and natural selection," said Sam Scheiner, program director in the division of environmental biology at the National Science Foundation (NSF), which funded the research through its Biocomplexity in the Environment initiative. "These simulations will help direct research on living systems and will provide understanding of the origins of biocomplexity."
Some mutations that cause damage in the short term ultimately become a positive force in the genetic pedigree of a complex organism. "The little things, they definitely count," said Lenski of Michigan State, the paper's lead author. "Our work allowed us to see how the most complex functions are built up from simpler and simpler functions. We also saw that some mutations looked like bad events when they happened, but turned out to be really important for the evolution of the population over a long period of time."
In the key phrase, "a long period of time," lies the magic of ALife. Lenski teamed up with Adami, a scientist at Caltech's Jet Propulsion Laboratory and Ofria, a Michigan State computer scientist, to further explore ALife.
Pennock, a Michigan State philosopher, joined the team to study an artificial world inside a computer, a world in which computer programs take the place of living organisms. These computer programs go forth and multiply, they mutate and they adapt by natural selection.
The program, called Avida, is an artificial petri dish in which organisms not only reproduce, but also perform mathematical calculations to obtain rewards. Their reward is more computer time that they can use for making copies of themselves. Avida randomly adds mutations to the copies, thus spurring natural selection and evolution. The research team watched how these "bugs" adapted and evolved in different environments inside their artificial world.
Avida is the biologist's race car - a really souped up one. To watch the evolution of most living organisms would require thousands of years – without blinking. The digital bugs evolve at lightening speed, and they leave tracks for scientists to study.
"The cool thing is that we can trace the line of descent," Lenski said. "Out of a big population of organisms you can work back to see the pivotal mutations that really mattered during the evolutionary history of the population. The human mind can't sort through so much data, but we developed a tool to find these pivotal events."
There are no missing links with this technology.
Evolutionary theory sometimes struggles to explain the most complex features of organisms. Lenski uses the human eye as an example. It's obviously used for seeing, and it has all sorts of parts - like a lens that can be focused at different distances - that make it well suited for that use. But how did something so complicated as the eye come to be?
Since Charles Darwin, biologists have concluded that such features must have arisen through lots of intermediates and, moreover, that these intermediate structures may once have served different functions from what we see today. The crystalline proteins that make up the lens of the eye, for example, are related to those that serve enzymatic functions unrelated to vision. So, the theory goes, evolution borrowed an existing protein and used it for a new function.
"Over time," Lenski said, "an old structure could be tweaked here and there to improve it for its new function, and that's a lot easier than inventing something entirely new."
That's where ALife sheds light.
"Darwinian evolution is a process that doesn't specify exactly how the evolving information is coded," says Adami, who leads the Digital Life Laboratory at Caltech. "It affects DNA and computer code in much the same way, which allows us to study evolution in this electronic medium."
Many computer scientists and engineers are now using processes based on principles of genetics and evolution to solve complex problems, design working robots, and more. Ofria says that "we can then apply these concepts when trying to decide how best to solve computational problems."
"Evolutionary design," says Pennock, "can often solve problems better than we can using our own intelligence."
But then you wouldn't need a mountain, would you? Same for you x-ray vision wackos. Nope, it's flat, always has been, and it's turtles all the way down.
Why, the same way *YOU* rationalize about the Sikhs, the Jans, the Hindus, the Buddhists, the Moslems, the Shintoists, the Voodooisants, the Wiccans, the shamanists, the Last Thursdayists, and the just-plain-crazies and all their special, little, obscure, and equally-holy books and beliefs.
So you are the gatekeeper who gets to say which parts of the bible are literal and which parts are metaphore?
Arg, got me! I guess I jsut haven't spent as much time studying such absurdities.
I'll "evolve" to that! Cheers!
Given time, materials, and gravity, you can form a sun and planet systems out of Hydrogen. How is this any different?
Depending on how good your microscope is, they all operate on a random clock cycle.
There are some partially async computers around. There are some truly async, clockless analog computers operating on factory floors.
Wouldn't the function yielding the random mutation have to be checked at the regular clock cycle of the computer system or some timer interval dependent upon the computer's clock cycle? Wouldn't that function have to have been programmed by somebody?
I would say this speculation is correct, but largely irrelevant. A computer simulation on an ordinary computer is going to be code-constrained by a clock. Whether this code constraint manifests itself materially in the data (the display or other consumption of the simulation) will depend on what the programmers decide to do. The random function they used is, I highly suspect, random enough for our purposes. You can find whole computer science books on this subject. We're pretty good now at for-all-practical-purposes random number generation--it's tricky, but it's not that tricky.
Isn't the "random" function, in fact, not random, but dependent upon the computer's clock cycle and the program itself? Just wondering.
Not usually. Beginners often try to generate random numbers that are, in fact, rendered non-random by the clock, in some devious manner, but by the time you are actually doing commercial work, you've figured out how not to do that.
huh?
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