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Artificial Life Experiments Show How Complex Functions Can Evolve
NSF ^
| May 8, 2003
| Staff
Posted on 05/08/2003 10:11:06 AM PDT by Nebullis
Artificial Life Experiments Show How Complex Functions Can Evolve
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."
TOPICS: Culture/Society; Miscellaneous; News/Current Events
KEYWORDS: ai; crevolist
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To: All
So I just got my new computer evolution kit. Its basically a 4-bit instruction processor with program counter, address decoder and sufficient RAM to store a set of microinstructions and do something worth doing. You get 8-10 discrete integrated circuits plus assorted resistors, capacitors and LEDs.
Note: If you would like to make your own, all the supplies are available at a nearby Radio Shack store or from mail order dealers like Digi-Key.
I thought the computer was going to be designed randomly and over a period of time but when I read the instructions well, I was surprised:
For best results, follow meticulously the precise design and careful assembly
Placing the components in a container and shaking them randomly for an extended time will only damage them.
It goes on to say:
Once the computer is fully developed (meaning you have bought all the other accessories and incorporated them per the intended design), all new evolutionary changes take place according with the preinstalled program and plug and play components
mutations are known as bugs that should be removed immediately
beneficial changes exist in the software and hardware provided
Oh well, I guess we cant design things as well as nature
(/sarcasm)
To: Doctor Stochastic
I suggested some time ago (in analogy with the Metropolis algorithm) that one might acquire several neutral or even slightly disadvantageous mutations before the combination gave a great leap forward.This is behind the idea of cooption.
I have some unforseen obligations to attend to but I'll try to comment more, later. I appreciate your comments!
To: js1138; Aric2000
True... My man James Randi makes it a personal mission of his to ferret out the bogus patents that are granted (free energy type stuff usually). I believe he secured a patent on the pb&j sandwich as a way of showing the absurdities of the US Patent office. May be Urban Legend, I'm not sure and don't feel like checking right now!
To: whattajoke
I used to marvel at the seemingly endless list of patents printed on each and every pack of Polaroid film. Seemed like overkill. But you don't see many Kodak instant cameras on store shelves. At least not anymore...
804
posted on
05/09/2003 12:26:24 PM PDT
by
js1138
To: Dataman
Don't pretend the naturalistic origin of the universe has nothing to do with evolution.
Evolution is a theory of biology. It has nothing to do with universe origins. That evolution is an attempt to remove God from every aspect of human life is a creationist strawman. It is a lie, not a true reflection of the theory. Demanding that evolution explain aspects outside of its scope just because you cannot comprehend that evolutionary biologists really aren't trying to destroy religion from people's minds doesn't count as a legitimate criticism of the theory.
805
posted on
05/09/2003 12:29:47 PM PDT
by
Dimensio
(Sometimes I doubt your committment to Sparkle Motion!)
To: jwalsh07
So to be clear, your view is that moral absolutes such as murder are not absolutes at all but murder, like a choice between the Mets and Yankees, is relative to who murders whom?
I've seen no reason to assume any attributes to murder other than it just 'is' (though I'd hardly call it similar to a choice between the Mets and the Yankees...I don't really understand the comparison). It isn't 'wrong' in any universal sense, just a relative sense when someone with some intelligence defines it as much. As such, I don't see reason to believe that there is an inherent 'law' coded in the universe regarding murder.
If that is correct your views are antithetical to theism which necessarilly makes you an anti-theist.
Well, if all theists believe otherwise, then yes, but I'd hardly claim that as evidence that I have 'disdain' for all theism.
806
posted on
05/09/2003 12:33:01 PM PDT
by
Dimensio
(Sometimes I doubt your committment to Sparkle Motion!)
To: whattajoke
True... My man James Randi makes it a personal mission of his to ferret out the bogus patents that are granted (free energy type stuff usually). I believe he secured a patent on the pb&j sandwich as a way of showing the absurdities of the US Patent office. May be Urban Legend, I'm not sure and don't feel like checking right now! Long live The Amazing Randi!
807
posted on
05/09/2003 12:35:26 PM PDT
by
balrog666
(When in doubt, tell the truth. - Mark Twain)
To: Dimensio
Evolution is a theory of biology. It has nothing to do with universe origins. How many times will we have to repeat this? Forever, I suppose.
808
posted on
05/09/2003 12:35:36 PM PDT
by
PatrickHenry
(Felix, qui potuit rerum cognoscere causas.)
To: AmericanAge
So, if these things evolve, though, why didn't this one?
I just explained it. No selective pressure. No selective pressure means no natural selection which means that the population remains relatively unchanged.
Again, evolution rests on the concepts that if it doesn't evolve, it perishes.
No, evolution rests on the concept that alelle frequencies change over time. Natural selection rests on the concept that if a genetic subset of a population is at a survival advantage over other members of the population that they will eventually thrive and overtake and become the rule rather than the exception and that environmental changes can trigger a sudden shift in the balance of natural selection. If the environment never lends itself to such changes, then the populations won't change.
So, if they put it in an environment where it was competeing with the bacteria that infect us, it would die off, would it not?
Quite likely. Fortunatley for the mold, it manages to survive without any complications despite the fact that some strains of bacteria are resistent to it. Apparently this mold can feed from plenty of other sources and the fact that some strains of bacteria are now no longer an option hasn't affected its chances to survive.
809
posted on
05/09/2003 12:37:00 PM PDT
by
Dimensio
(Sometimes I doubt your committment to Sparkle Motion!)
To: PatrickHenry; js1138; Nebullis; Dimensio; balrog666
Artifical Life
artist's conception
810
posted on
05/09/2003 12:39:14 PM PDT
by
unspun
(Please help us find Merchant Seaman - do your part.)
To: Dimensio
It isn't 'wrong' in any universal sense, just a relative sense when someone with some intelligence defines it as much. Interesting. The power to define right and wrong is relegated to the intelligent with the power to enforce same.
I take it unalienable rights are also antithetical to your world view?
To: AmericanAge
A = without.
Theism = belief in a god or gods.
Atheism = without belief in a god or gods.
If someone expresses a belief in any gods of any kind, then they are not an atheist. There is no specific "God" for which lack of belief defines an atheist, so someone whom you beleive acknowledges the "wrong" god is still not an atheist.
812
posted on
05/09/2003 12:39:35 PM PDT
by
Dimensio
(Sometimes I doubt your committment to Sparkle Motion!)
To: Dataman
A vacuum is something.
Uh, no, a vacuum is the absence of 'something'. Specifically it is the abscence of matter, which would allow for it to contain light, but it does not contain light by definition, so a vacuum could very well be 'nothing'.
...unless you are speaking of a vacuum cleaner, which isn't quite the same thing.
813
posted on
05/09/2003 12:42:13 PM PDT
by
Dimensio
(Sometimes I doubt your committment to Sparkle Motion!)
To: Aric2000
I'd rather know God personally than all the bs$$$$ in the world ... too ! !
814
posted on
05/09/2003 12:42:17 PM PDT
by
f.Christian
(( Marching orders: comfort the afflicted // afflict the comfortable ! ! ))
To: AmericanAge
We don't need atheists like you here.Of course you do. Somone has to do the thinking, don't we?
To: jwalsh07
Interesting. The power to define right and wrong is relegated to the intelligent with the power to enforce same.
'Power' implies some kind of privledge or empowerment. I think of it more as ability. It's just what happens, people define things as 'right' and 'wrong'.
I take it unalienable rights are also antithetical to your world view?
From where would these 'unalienable' rights originate? If you can identify a source from which to derive them, I'm willing to explore the possibility.
816
posted on
05/09/2003 12:43:50 PM PDT
by
Dimensio
(Sometimes I doubt your committment to Sparkle Motion!)
To: AndrewC
"Evolutionary design," says Pennock, "can often solve problems better than we can using our own intelligence." Absurd! Even leaving out the often does not make the statement much more believable.
Artificial evolution, in the form of genetic programming, is employed quite regularly now to solve problems better than humans have been able to. I worked on one to do optimal cuts in lumber mills a few years back. Human brains have pretty tightly constrained upper limits in regard to problem-solving capacity. Humans can handle linear problems with up to about 7 variables, with practice. Ie, toy problems in artificially simplified domains.
817
posted on
05/09/2003 12:44:35 PM PDT
by
donh
To: Nebullis
I'm waiting for the day -- and I don't think it's too far away -- that one of these cellular automatas or other simulations of life get complex enough to ask, "What created me?"
We were created in God's image. We replicate the creative aspect of God by creating our own universes of life.
To: Aric2000
Actually I think I'm happy to be on his ignore list.
Willful ignorance bores me. I don't think he misunderstands what I'm saying, but simply refuses to "get it"...
819
posted on
05/09/2003 12:47:22 PM PDT
by
null and void
(Either that or he really is too stupid to function. I don't think he is...)
To: Dimensio
Agnostic = without belief in a god or gods.
Atheism = with hate belief against God // Truth // science !
820
posted on
05/09/2003 12:49:21 PM PDT
by
f.Christian
(( Marching orders: comfort the afflicted // afflict the comfortable ! ! ))
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