Artificial Life Experiments Show How Complex Functions Can Evolve

NSF ^ | May 8, 2003 | Staff

[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."

[Doctor Stochastic]

The old Philco 2000 (circa 1955) has asynchronous units. Mulit-functional unit computers such as the big Crays also worked asynchronously.

[Gee Wally]

Thank you for that explanation. I do understand that the computer can generate, for practical purposes, a random number. That really wasn't my question. This program is generating random mutations. Mustn't it have a mutation that corresponds to the randomly generated number? If it does have such a database of mutations, then wouldn't that be a finite list supplied by the programmers? In that case, I don't see how it can be called random, since all outcomes are limited to a pool of results foreseen by the programmers. If it is truly a random outcome, I'd be interested in knowing how they accomplished that.

[f.Christian]

FR thanks to evolutionists -- anarcho-loons ...

is becoming the demacrat overdrive -- ground !

[AmericanAge]

Since when is FreeRepublic a site where people are asked to disprove God??? That's about as Liberal as it gets. No, I guess you could be asking me to disprove God for the sake of Communism, that would be a bit more Liberal, but seriously....

[longshadow]

We don't need atheists like you here.

Dear 5-month FR newbie;

who died and put you in charge of who is, and isn't, "needed" on FR?

Yours truly,

the 405th Freeper

[elbucko]

This idea was debunked several years ago due to dis-similar traits in the supposed progression of the animals..

It was my understanding that it was back in fashion, again. More equine fossils were found since the Chicago museum.

[AmericanAge]

If you can't *read* - and there's many translations of the bible out there - that's your problem. And the Pope's, too.

Oh, and if you hark on the Pope's every word, the Pope adimantly opposed the war on Iraq. He even sent a Cardinal over to Iraq to try and help deter the war. What kind of example is he, supporting a brutal tyrant like Saddam?

[Aric2000]

Sorry, I tossed that little ball in your court.

What moral story did Genesis give? what was it's point, besides being a creation story.

I can tell you all kinds of creation stories, some are VERY similar to the genesis account, and you know what you would tell me, that those stories are myth, and are wishing to provide a lesson in morality. BUT, when it comes to the story in your bible, you are unwilling to look at it that way.

And I was making a joke to js1138, it had nothing to do with you. and no, I am not saying that you believe the earth is flat.

I don't think that even you would go that far.

[donh]

This idea was debunked several years ago due to dis-similar traits in the supposed progression of the animals. Not sure if the Chicago museum still has their exhibit on display, though.

Hogwash. The eohippus-horse progression gets better established with each passing decade's new finds. You are no doubt reporting a minor early mis-apprehension in the ordering of the fossils--the sort of adjustment that is made all the time as new evidence comes in, and in more fields of science than just paleontology. Anyone with access to a natural history museum can verify that this progression has not been "debunked" except to the satisfaction of the "scientists" at the Creationist Institute.

[f.Christian]

eb ...

Both you, f. Christian and "AmericanAge" would have made excellent "inquisitors" in Spain.

fC ...

state science (( Atheism // evolution )) 2003 America ---

you are the inquisition attacking theism // GOD !

[whattajoke]

just skimmed the thread and I refuse to believe AmericanAge is legit. The first 100 posts I thought were totally sarcastic, now they are just silly. He is very most likely an atheist himself trying to get YEC's here to say their typical dumb stuff to cut and paste and show his dorky buddies.

I smell a rat.

[BMCDA]

Cool article
Bookmarked ;)

[stanz]

Great line. Hope I can remember it.

[CobaltBlue]

>>Please, present your evidence that the earth is so old.<<

It's called "the earth."

Get out there and take a look at it. Look at the geological record. Look at the fossil record. It's right in front of your eyes.

[PatrickHenry]

Again, you just tried to demonize creationists again

And you don't try to demonize evolution? Of courst not. You wouldn't be so slimy. You wouldn't claim that all evolutionists are atheists, or leftists. You wouldn't be that ignorant and dishonest. Not you.

[f.Christian]

Science has't changed since it existed -- was created ...

people thanks to evolution like you ---

are getting dumber --- WHACKIER !

[AmericanAge]

I believe in the Bible. I think you'll find that not only the vast majority of people on FreeRepublic.com, but also in the US as a whole, feel exactly the same way. And about half of America believes in Creationism, despite your control of the schools. And let me tell you, most of them are *not* liberals. We're largely silent on the political front, but we're here, and we exist because we believe in the Bible, in Jesus Christ, and in the word of God, as written in the Bible. If you don't, again, it's surprising that you consider yourself conservative.

[Dimensio]

Since when is FreeRepublic a site where people are asked to disprove God???

You are either incredibly stupid or you're a very persistent troll. I suspect the latter, judging from some earlier comments.

I never asked you nor anyone else to disprove God. I asked for a means by which God could, if this God does not exist, be falsified. That is, a test that would, given certain results, disprove the existence of God. This does not mean that those results would ever come about -- in fact, if God exists, then those results would never come about, but the criteria must be defined. If not, then God cannot be addressed in any way, shape or form by science.

Again, I am not asking for a test to prove that God does not exist. I am asking for a test that would, if God does not exist, show as much. If this God does exist, then this test could be performed over and over and the 'disprove' results would never come about.

[AmericanAge]

A lot of evoltuionists are atheists, most are leaning in that direction, and, notably, most ARE leftists. Very, very few creationists are flat-earthers.

[stanz]

Another great line. Must remember that one, too.