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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: js1138
I'd read about that. I don't know why it skipped my mind ... I must be getting a bit doddery in my old age.
1,841 posted on 05/22/2003 11:52:15 AM PDT by Junior (Computers make very fast, very accurate mistakes.)
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To: whattajoke
Does anybody know why "Gore" or "3000"?

Is he/she/it a liberal buffoon or a AlGore supporter?

1,842 posted on 05/22/2003 11:52:17 AM PDT by balrog666 (When in doubt, tell the truth. - Mark Twain)
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To: balrog666
It is an "it" -- a very simple computer algorythm (hence the "gore" part).
1,843 posted on 05/22/2003 11:56:35 AM PDT by Junior (Computers make very fast, very accurate mistakes.)
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To: balrog666
I asked that once myself and was lambasted for my supposed inability to discern "sarcasm." I guess that means Gore will run again in the year 3000 because he is a robot or something.

I'm not a dumb guy and I've never understood it... then again, my moniker is stupid, but it's too late to change it now.
1,844 posted on 05/22/2003 12:13:03 PM PDT by whattajoke (Gore3000 and the Amazing Technicolor DreamFont... coming to your town soon!)
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To: All
PLACEMARKER Look, look! He's doing it again!
1,845 posted on 05/22/2003 12:13:53 PM PDT by PatrickHenry (Felix, qui potuit rerum cognoscere causas.)
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To: null and void
My response was more concise...

I concede; you win the "brevity" award.

;-)

1,846 posted on 05/22/2003 12:34:32 PM PDT by longshadow
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To: PatrickHenry
I hear and obey [8-|]
1,847 posted on 05/22/2003 12:42:52 PM PDT by Junior (Computers make very fast, very accurate mistakes.)
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To: js1138
All these lapses of hostility have one thing in common -- the absense of g3k.

Funny how that works..... you win the insightful observation award of the day.

1,848 posted on 05/22/2003 12:47:13 PM PDT by longshadow
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To: PatrickHenry
Slap-ass time again, I see. Cute.
1,849 posted on 05/22/2003 2:38:09 PM PDT by Michael_Michaelangelo
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To: Michael_Michaelangelo
Slap-ass time again, I see. Cute.

Funny, how you always seem to have that on your mind.

1,850 posted on 05/22/2003 2:54:21 PM PDT by balrog666 (When in doubt, tell the truth. - Mark Twain)
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To: balrog666
slap-*ss placemarker
1,851 posted on 05/22/2003 3:21:35 PM PDT by longshadow
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To: longshadow
Non-insulting placemarker.
1,852 posted on 05/22/2003 3:58:15 PM PDT by Lurking Libertarian (Non sub homine, sed sub Deo et lege)
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To: Lurking Libertarian
Innocent placemarker. Important directive from Darwin Central at midnight on MTV. Oook, Oook!
1,853 posted on 05/22/2003 4:17:35 PM PDT by PatrickHenry (Felix, qui potuit rerum cognoscere causas.)
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To: longshadow
I concede; you win the "brevity" award.

*blush* Thank you...

Charm wit and levity
will win you in the start
but in the end it's brevity
that keeps the public's heart...

1,854 posted on 05/22/2003 4:17:59 PM PDT by null and void
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To: gore3000
G3K: "Only in living things. And they do not really self assemble anyway. They follow the program set out by the parents."

Lets see how much of a creationist/evolutionist you are. Since the topic has branched into three parts, I want you to answer with an honest yes or no to each independant argument...

1) The first self-replicating machinery arose due to natural chemcial processes and without the guidance of an intelligent entity.

2) Once the first self-replicating machine was in place, the execution of that machinery required no outside intelligent agent.

3) The improvement of that machinery with respect to its environment occurred by solely by natural evolution.

Do you believe that outside intelligence is required for all three steps? My guess is that you would say No to #1 and #3 -- but will at least concede that there are no little invisible angles moving molecules around once all the machinery needed to execute are in place -- hence "self assembly".

--

freeper4u: "Second, there is no need for anyone to "find all the possible ways" to make a certain sequence to exist in all species. In fact, with evolution you would expect to find common sequences among organisms with common ancestors."

G3K: "Continuing to discuss what is not being discussed and to create confusion. The post is about abiogenesis. It is pretty clear from the post what it is about. You are attempting to refute something to which the post does not apply."

I must have misunderstood the point you were trying to make. Please restate or explain why you think our ability "to find all the possible ways in which 3 different bit pairs... appear in the DNA sequence of all species" proves that "the arrangement [of DNA]" "cannot be due to [natural forces]" and I'd be happy to try again.

--

Bookkeeping: Still waiting for reasons why sexual reproduction prohibits speciation.
1,855 posted on 05/22/2003 4:57:18 PM PDT by freeper4u
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To: PatrickHenry
Ook!
1,856 posted on 05/22/2003 6:03:58 PM PDT by balrog666 (When in doubt, tell the truth. - Mark Twain)
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To: whattajoke
Were/are prokaryotes "designed?"

Of course they were. That is why the atheist/materialist/evolutionists insult me. Because they cannot respond to the question of how life could have arisen from inert matter. Mind you, I am only asking for a theoretical explanation of how it could have happened according to what we scientifically know about life and what it requires. So yes, abiogenesis is impossible and the first life, likely bacteria (prokariotes as you call them in order to seem knowledgeable to lurkers, but really just an attempt to confuse the issue) was designed by our Creator.

1,857 posted on 05/22/2003 7:58:49 PM PDT by gore3000
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To: whattajoke
Were/are prokaryotes "designed?"

Of course they were. That is why the atheist/materialist/evolutionists insult me. Because they cannot respond to the question of how life could have arisen from inert matter. Mind you, I am only asking for a theoretical explanation of how it could have happened according to what we scientifically know about life and what it requires. So yes, abiogenesis is impossible and the first life, likely bacteria (prokariotes as you call them in order to seem knowledgeable to lurkers, but really just an attempt to confuse the issue) was designed by our Creator.

1,858 posted on 05/22/2003 7:59:22 PM PDT by gore3000
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To: PatrickHenry
I have often challenged you to show a single post from you on this thread which is not an insult. A single post from you discussing the subject at hand. There are none such because you do not discuss, you insult and encourage your friends to do the same and turn threads into shouting matches so that they will be pulled. 1,799 posted on 05/21/2003 11:28 PM EDT by gore3000

Yes Patrick, I have asked you and your minions several times on this thread to show a single post where you discuss the subject at hand. All your posts are either nasty placemarkers or insults.

Therefore, since neither you nor your fellow thugs can show a single post where you act like people are supposed to act on a thread, which is discuss the subject, my statement is absolutely true. Now I know the truth hurts, but nevertheless my statement is the truth and not an insult.

1,859 posted on 05/22/2003 8:05:48 PM PDT by gore3000
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To: donh
What you mean to suggest,

No, I say what I mean and I mean what I say. Computer programs cannot approximate reality. They are selective by necessity. This allows the programmer to use the code to promote whatever agenda they wish to promote. The present one, as I have already shown, conveniently fails to punish for useless and non-working functions which should normally be destroyed in real life by 'natural selection'. It is therefore just more evolutionist garbaaaage.

Oh, and (as Columbo would say) just one more thing. If evolution is science, how come evolutionists cannot prove their theory from real life? Science requires observable facts. Therefore evolution cannot be science since it cannot prove itself through observable evidence.

1,860 posted on 05/22/2003 8:13:22 PM PDT by gore3000
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