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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: PatrickHenry
Your sources are incomplete - I remembered another blue food. Neither of them make reference to the blue corn being grown nowadays, which at least a few snack companies have used to produce blue tortilla chips...


1,061 posted on 05/10/2003 10:15:20 AM PDT by general_re (Ask me about my vow of silence!)
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To: donh
I personally find it comforting that machines don't feel emotions such as greed, jealousy, rage, overweening pride or vindictiveness. Yikes! And I truly truly hope they never develop a sense of superiority to humans! Double yikes!

Oh, and then there's insanity. Isn't it a Good Thing that machines don't suffer from depression, schizophrenia, paranoia, or psychosis?
1,062 posted on 05/10/2003 10:23:01 AM PDT by CobaltBlue
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To: CobaltBlue
Creation types never actually talk about what they believe, personally, they just try to shoot holes in what evolutionists say.

You've noticed that, have you? That's because there's this sort of implicit assumption on the other side of the aisle that there are precisely two possible explanations for the origin of life - Biblical special creation, and evolution via natural selection. Therefore, the idea is that by poking enough holes in evolutionary theory, Biblical special creation becomes the default explanation. The fact that this is a false dichotomy and the fact that there is no such thing as a default explanation in science does not enter into the thought process, apparently. Theories are evaluated in light of one another, and not strictly on their own merits - the accepted theory is the theory that explains the facts better than all the rest, but obviously creationists are not particularly prepared to put their pet theory side-by-side with evolutionary theory, so that we can evaluate which one is really the stronger theory - I suspect that they know in their hearts that creationism could never survive such a comparison, and so they forswear an honest and fair fight between the two theories in favor of what can reasonably be described as a series of drive-by shootings.

That being said, Andrew is much too clever to be boxed into Biblical literalism in creation, or any other variety of universal special creation theory, which, if you drag his counter-theory out of him, I think you will see. For reasons that are largely opaque to everyone else, however, he likes to give aid and comfort to Biblical literalists and their ilk, despite not actually believing in that sort of thing himself.

1,063 posted on 05/10/2003 10:37:07 AM PDT by general_re (Ask me about my vow of silence!)
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To: AndrewC
Courtesy ping to my last post - feel free to revise or amplify as you see fit. ;)
1,064 posted on 05/10/2003 10:39:10 AM PDT by general_re (Ask me about my vow of silence!)
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To: PatrickHenry
Rainbow-skipping placemarker
1,065 posted on 05/10/2003 10:57:38 AM PDT by longshadow
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To: general_re
Returning to the subject of green mammals, it is a little-known fact that Bigfoot is covered with green fur, which explains his elusiveness.
1,066 posted on 05/10/2003 11:04:04 AM PDT by PatrickHenry (Felix, qui potuit rerum cognoscere causas.)
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To: CobaltBlue
Oh, and then there's insanity. Isn't it a Good Thing that machines don't suffer from depression, schizophrenia, paranoia, or psychosis?

Well, I'd say it would be a good thing, if, in fact, they didn't. I'm inclined to think that a good general characterization of the things you are describing is reduction to machine-like behavior of humans, who, when they are up to snuff, know better.

1,067 posted on 05/10/2003 11:17:16 AM PDT by donh
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To: PatrickHenry
There's a green(ish) polar bear at the zoo here - I think the heat is promoting chameleonism in the mammals. That's my theory, but they won't let me in there to tranquilize the animal and take samples...
1,068 posted on 05/10/2003 11:24:34 AM PDT by general_re (Ask me about my vow of silence!)
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To: CobaltBlue
Nothing substantive, just constant nibbling.

I assume that you've never really taken the trouble to learn about the fossil record because you think it's irrelevant, but you're too proud to admit it.

CB, this thread is about programming. No one is even talking about the actual source of this thread. I commented on what one of the principles of the article stated and was leventually ed to a "circuit challenge". These thread are put up for comment and they have a theme. I am now engaged in a discussion about a peripheral yet closely related item. If you don't like it then I suggest you don't participate.

1,069 posted on 05/10/2003 11:31:50 AM PDT by AndrewC
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To: PatrickHenry
First of all you read that which with you agree. You search out material to help your argument. Typical of those with agendas.

I look at more than one source of information. I do not take one's opinion as fact. The Hiesenberg Principle should always be followed.

My teachers have failed me?

First of all, I live and learn through life. Certain principles are not as "teachers" say. Math is a constant. Language has rules. Science is not absolute. The Hiesenberg Principle once again.

And it is not my opinion of the appearence of modern man. It is being debated by the science community right now. Because it goes against what they have been saying.

Fossil records??? You mean like A T-Rex standing tall which these scientists agreed years ago. But today they can say it would break its back. You mean like the Brontosoras that they put together wrong. You mean like about 10 years ago a science confirmed a fossil of a new beast and that was a HOAX?

Like the science books saying that the earth would be covered by water 5 MILES deep if the Ice Caps melted? So far you footing is on soft sand.
1,070 posted on 05/10/2003 11:35:02 AM PDT by Michael121
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To: AndrewC
If you can tell me what you're trying to prove, I'd appreaciate it.

However, don't think you can say that the world of GAs is nothing because you can just wave a hand and say nothing useful has come out of random processes. You said that they had "nothing" and tried to C/P a "For Further Reading" list (for the laymen, even) to back up your assertions that they had "nothing".

You can track down the original authors, the original peer-reviewed articles, and so on to get the full story and to learn about GAs and about the 9-transistor circuit versus the patent you're talking about.

You did not bear good witness. You called their work nothing and cited deliberately misleading information in favor of your position. And then, using that list of references which you perfectly well knew was meant to be for further reading for interested laymen, not the original peer-review articles, you tried to smear some good computer scientists, and all evolutionists by extension.

I'm not going to play more of the "Since they won't show me their research, I'm going to sit here and call them frauds until they, or other Freepers, give me their research" game, you may have the final word in our debate.

Have a nice weekend; seeya.
1,071 posted on 05/10/2003 11:37:27 AM PDT by Nataku X (Never give Bush any power you wouldn't want to give to Hillary.)
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To: Michael121
Science has't changed since it existed -- was created ...

people thanks to evolution // drugs ---

are getting dumber !
1,072 posted on 05/10/2003 11:37:27 AM PDT by f.Christian (( Marching orders: comfort the afflicted // afflict the comfortable ! ! ))
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To: f.Christian
Out of curiousity, is Hawaii worth moving to or does the economy stink down there? How's the IT employment down there? Taxes?
1,073 posted on 05/10/2003 11:43:57 AM PDT by Nataku X (Never give Bush any power you wouldn't want to give to Hillary.)
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To: Michael121
First of all you read that which with you agree. You search out material to help your argument. Typical of those with agendas. I look at more than one source of information. I do not take one's opinion as fact. The Hiesenberg Principle should always be followed.

You said there were no "in-betweens" so I offered you a link that indicates there are many. You have no response to this, yet you accuse me of selective reading. I assume that you will continue to read your favorite sources which claim there are no "in-betweens." No selectivity there.

My teachers have failed me?

Yes. In any event, welcome to FreeRepublic.

1,074 posted on 05/10/2003 11:49:19 AM PDT by PatrickHenry (Felix, qui potuit rerum cognoscere causas.)
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To: general_re
Courtesy ping to my last post - feel free to revise or amplify as you see fit. ;)

You are correct. I am not a literalist in relation to portions of the Holy Bible.

1,075 posted on 05/10/2003 11:54:12 AM PDT by AndrewC
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To: Michael121
The Hiesenberg Principle should always be followed.

Indeed, and don't ever let me catch you asserting that you know both the position and momentum of a particle to the same degree of precision ;)

1,076 posted on 05/10/2003 11:56:37 AM PDT by general_re (Ask me about my vow of silence!)
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To: Nakatu X
Hawaii is moon gravity (( time )) ...

you need a good hobby (( surfin // biking )) to survive ---

everything is ageless (( all the younger woman are attracted to older guys )) ...

rough !
1,077 posted on 05/10/2003 11:58:20 AM PDT by f.Christian (( Marching orders: comfort the afflicted // afflict the comfortable ! ! ))
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To: AndrewC
That much is readily inferrable, but beyond your apparent fondness for Shapiro's work, it's not at all clear what you would propose to replace those portions of current theory that you seem to object to. And I point this out in the spirit of honest inquiry - unlike some others, I can at least imagine you being persuaded to change your mind ;)
1,078 posted on 05/10/2003 12:00:18 PM PDT by general_re (Ask me about my vow of silence!)
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To: f.Christian
That's a shame... lived there 20 years ago & wouldn't mind going back.

all the younger woman are attracted to older guys

Money, property, cars, dontcha know... the eternal female catnip! :o)
1,079 posted on 05/10/2003 12:09:26 PM PDT by Nataku X (Never give Bush any power you wouldn't want to give to Hillary.)
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To: CobaltBlue
...Creation types never actually talk about what they believe...

Perhaps that's because thay have no beliefs? We have been trying to get some of the Creationists to just state simple things such as: how old do they believe the earth to be. The Kefauver Committee got more responses.

1,080 posted on 05/10/2003 12:14:37 PM PDT by Doctor Stochastic (Vegetabilisch = chaotisch is der Charakter der Modernen. - Friedrich Schlegel)
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