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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: AndrewC
Also, as technologically savy as you are, I assumed you had a really old machine.

;^)
741 posted on 05/09/2003 9:32:25 AM PDT by null and void
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To: AndrewC
Indeed, but it had been patented in 2000, and there have been more patents pending since then.

This must be a real disapointment to you....

Wow, it could actually change an entire worldview, what a concept.

Doesn't hurt mine though, my faith is not based on a neverchanging outlook on life.
742 posted on 05/09/2003 9:32:59 AM PDT by Aric2000 (Are you on Grampa Dave's team? I am!! $5 a month is all it takes, come join!!!)
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To: null and void
I think you just proved my point.

What point. Cost was not part of the design, compactness was. 9 is less than 17. 17 is less than 55,000,000. Gee isn't that easy.

743 posted on 05/09/2003 9:34:05 AM PDT by AndrewC
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To: AndrewC
I see. In your world a coma "," is not compact, but a period "." is...
744 posted on 05/09/2003 9:36:52 AM PDT by null and void
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To: Aric2000
Indeed, but it had been patented in 2000, and there have been more patents pending since then.

No it hadn't!! The article was written in Feb 2003. The quote was in the article. I saw no evidence of a granted patent for the tuning algorithms or topology.

745 posted on 05/09/2003 9:37:45 AM PDT by AndrewC
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To: null and void
I see. In your world a coma "," is not compact, but a period "." is...

Red Herring. Comma and period both are a single character.

746 posted on 05/09/2003 9:40:28 AM PDT by AndrewC
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To: f.Christian
Elements and atoms are NOT science. The study of them is.

Prove to me that the study of elements and atoms has not changed.
747 posted on 05/09/2003 9:40:35 AM PDT by Quick1
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To: PatrickHenry
So, the first troll got things rolling downhill and the old trolls keep it rolling. The more things change, the more they stay the same.
748 posted on 05/09/2003 9:46:15 AM PDT by balrog666 (When in doubt, tell the truth. - Mark Twain)
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To: Right Wing Professor
No one really knows who wrote much of the New Testament.

Now there's a universal you'd have some difficulty supporting.

I take it you're not a scholar of koine Greek? Fine, neither am I.

A scholar, no. I can read it and understand it which I suspect is something you are unable to do.

Let's stick to the plain English meaning. And in English, a matter that is proven by the preponderance of evidence does not require faith.

??!!!??? That only works if you define faith to suit your own bias. Perhaps those who saw Christ's miracles no longer could have faith in Him. Did Thomas lose his faith when he touched Christ's wounds? No! He had absolute proof and his response was, "My Lord and my God!"

Bottom line: Your definition of faith doesn't square with the Bible. Since we all know who the Author of faith is, it only makes sense to apply the meaning He intends rather than an unbeliever's personal fancy.

If the universe were inanimate, the question would be 'how', not 'why'. Stipulating that this has nothing to do with evolution. I think the best answer which is in accordance with modern physical theory would be that the vacuum is unstable with respect to non-vacuum. A vacuum is the most symmetric possible state; but universally in the physical sciences we see phenomena where more symmetric systems spontaneously break symmetry and become less symmetric.

Nice swing-and-miss. Materialistic cosmology denies the existence of said vacuum before the BB. So where did the vacuum come from?

There is no satisfactory alternative to Creation.

749 posted on 05/09/2003 9:53:17 AM PDT by Dataman
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To: js1138
I'm sure that any Freeper practicing engineer will correct me if I'm wrong, but I suspect that most circuits are up and running long before anyone writes a verbal description. That would be done by a technical writer, who might be a lawyer or work under the supervision of a lawyer.

I've seen a large number of patents (and patent applications) in the electronics field. The one quoted in this thread is typical in its detail and style. The patent lawyers I've known are indeed engineers (who for one reason or another went on to law school). It's nerd city, usually, with pocket protectors, and probably a youth spent wearing propeller beanies, but they're amazingly bright. They are quite capable of writing such descriptions after briefly consulting with the inventors. It's the drawings, in my experience, that are done by a specialized technical person.

750 posted on 05/09/2003 10:04:42 AM PDT by PatrickHenry (Felix, qui potuit rerum cognoscere causas.)
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To: AndrewC
According to my husband, what is required in a patent application is that the device be described with sufficient certainty that it can be constructed by someone who is learned in the art.

Upstream somebody said that a computer program has designed a circuit and that the device in question has been built but the engineers are not really sure how it works.

If they built it, they can certainly describe how they built it with sufficient certainty that a replica can be constructed by someone who is learned in the art.

751 posted on 05/09/2003 10:06:56 AM PDT by CobaltBlue
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To: Quick1
Aren't you confusing learning -- perception -- symbols with subject // object ...

two sometimes opposite things ---

has physics // mathematics ever changed ?

"such knowledge or such a system of knowledge concerned with the physical world and its phenomena" ...

does that change ---

physical world ?

phenomena ... things we see --- don't understand ?


The definition I work by ... in a positive science you don't interject your value system or your bias --- those change all the time --- not science !
752 posted on 05/09/2003 10:09:10 AM PDT by f.Christian (( Marching orders: comfort the afflicted // afflict the comfortable ! ! ))
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To: Dataman
There is no satisfactory alternative to Creation.

does your assertion therefore allow for different "creations?" Cause even you must be aware that there are countless creation myths, right? There are entire religions/cultures that don't pay head to the Genesis account. Which Creation?

Ooooooooooooooooooooohhhhhhhh, you mean the Fundamentalist christian version of things! Your failure to see the silliness of your assertion speaks volumes.
753 posted on 05/09/2003 10:10:04 AM PDT by whattajoke
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To: whattajoke
"head" = "heed."
754 posted on 05/09/2003 10:11:19 AM PDT by whattajoke
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To: Dataman
Evolutionists don't ignore the questions involving the origin of the Universe and the origin of life, but it's a philosophical question, not a scientific question.

I think what you're doing is ignoring the questions of how God created the universe and life on earth. You really can't know that by reading the Bible, because it doesn't really explain it.

The Bible says God did it in 6 days, but it doesn't say how long a day is to God.

755 posted on 05/09/2003 10:15:11 AM PDT by CobaltBlue
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To: whattajoke
Placemarker.
756 posted on 05/09/2003 10:15:20 AM PDT by Lurking Libertarian (Non sub homine, sed sub Deo et lege)
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To: AndrewC
A coma is bigger than a period. A 17 transistor circuit is bigger than a 9 transistor circuit, yet you describe one as being compact, and the other as not being compact.

I'm trying to determine where in your pea brain something is no longer compact.

Is it 100 square microns? 200? 300?

For scale, a hair has a cross section of about 5000 sqµ...

757 posted on 05/09/2003 10:15:43 AM PDT by null and void
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To: Ichneumon
My husband wants to know if the circuit you are talking about is this one:
http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO1&Sect2=HITOFF&d=PALL&p=1&u=/netahtml/srchnum.htm&r=1&f=G&l=50&s1=6362718.WKU.&OS=PN/6362718&RS=PN/6362718
758 posted on 05/09/2003 10:21:41 AM PDT by CobaltBlue
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To: AndrewC
Sorry, information overload, you're right, it wasn't explained in this article. My apologies.

I have read elsewhere, that this device had been patented in 2000 and since then there have been a number of others that have been submitted.

Hence the term, Patent Pending.

Sorry, but NOT all of my information comes from this forum, but then again, I should have been more succinct, you can't seem to handle the fact that evolution does INDEED work, and is proven EVERY day.

Yep, must be tough for you guys, but then again, galileo made it awfully tough for the church too, but they finally came around.
759 posted on 05/09/2003 10:32:02 AM PDT by Aric2000 (Are you on Grampa Dave's team? I am!! $5 a month is all it takes, come join!!!)
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To: null and void
"Not true" ...

most patents are not in reality --- they are supposed to be !

Patent examiners are like traffic cops and mayors court --- moneymakers !
760 posted on 05/09/2003 10:35:18 AM PDT by f.Christian (( Marching orders: comfort the afflicted // afflict the comfortable ! ! ))
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