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."

[AmericanAge]

You mentioned a single sentence, often used figuratively. And then tried to compare it to an entire chapter of Genesis. And you act like there's no difference? That's like saying there's no difference between War And Peace and Where's Waldo.

[CobaltBlue]

I sent my comment to you by mistake - meant it for Dataman - did I misunderstand the point?

Lenny Bruce complained that so-called Christians persecuted him in a way that was not consistent with Christ's teachings. In other words, they were not only hypocrites, they were exactly the type of hypocrite that Christ himself denounced as "whited sepulchers."

[balrog666]

Oops, that's what I get for not reading ahead!

[RightWingNilla]

"The Bible never says anything about dinosaurs. You can't say there were dinosaurs when you never saw them. Someone actually saw Adam and Eve. No one ever saw a Tyrannosaurus rex." What about dinosaur bones? "Made by man," he says.

LOL. Just when I thought my opinion of this guy couldnt get any lower. He was a real dog on my rotisserie team last year.

[Aric2000]

Where does it say that?

You are making assumptions based on no evidence at all.

Did eve and adam have more children or didn't they? The bible doesn't tell us, so how do you know for sure?

Because it just makes sense?

But, that's you're argument against evolution, that it's based on no evidence and we are jumping to conclusions.

OK for you, not OK for us.

You have an interesting worldview.

By the way, that in no way says that I believe that evolution jumps to conclusions, because it does not.

I am just repeating what you are saying and trying to make sense out of it.

Logic just doesn't seem to be working though.

[AmericanAge]

"Where did he get them from?"

Right where he lived. The Lord will provide. For all we know, they could have been expansive before the flood. A worldwide flood would do amazing things to global geography, fossil arrangements, strata, etc.

[balrog666]

How did the koalas survive on the ark?

Hoisted on my on petard once again for not reading ahead! Oh, well, great minds think alike and all that.

[AmericanAge]

You act like a couple having more children is some sort of a shock, or a real stretch of the imagination. From a couple who broke the sole cardinal rule that they had been given, the act of reproducing would be nothing to them.

[balrog666]

Lenny Bruce complained that so-called Christians persecuted him in a way that was not consistent with Christ's teachings. In other words, they were not only hypocrites, they were exactly the type of hypocrite that Christ himself denounced as "whited sepulchers."

Yep. The difference between words and deeds doth make a hypocrite of most of them. See AA or DM or G3k.

[Aric2000]

Yeah, I know people like you, they show up at my doorstep at 8:00 in the morning on a Saturday.

My 7 year old answers the door and tells them that Mommy and Daddy are sleeping.

Then they come back at noon, and I have to chase them off with a broom.

I need an insecticide or something for you people.

And by the way, who's truth?

Your truth, Datamans truth, Brigham Youngs truth, the Pope's truth.

Who's truth? Because if you're all true, then we have a problem in the translation.

By the way, if the truth is the one who has the most believers, then you aren't the truth, that would belong to the Hindus. There are more Hindus then any other religion on earth.

[balrog666]

Right where he lived. The Lord will provide. For all we know, they could have been expansive before the flood. A worldwide flood would do amazing things to global geography, fossil arrangements, strata, etc.

What kind of idiot troll are you? We do know and that's crap - just like most of your arguments here.

[Lurking Libertarian]

Did eve and adam have more children or didn't they? The bible doesn't tell us, so how do you know for sure?

I don't believe that Genesis is meant to be taken as literal history or science, or that it contradicts evolution, but, in fairness, the Bible does say that Adam and Eve had other children. Genesis 5:4.

[Aric2000]

But you are assuming, you have NO proof for your assertions.

You say that we can't, and that we don't and then you do it yourself.

Fascinating worldview, just fascinating.

[forsnax5]

eventually this thread will get pulled after people start rolling in the dirt biting each others' ears off.

LOL! The best characterization of this thread so far!

[djf]

The story of a man in a boat with animals, and worldwide catastrophe, is cited throughout so many religions and cultures that it simply cannot be deemed apochryphal. And science has discovered quite a few species that went extinct about 11,500 years ago, including: Mammoth, Sabre tooth tiger, european rhinocerous.

[Aric2000]

I know that, darnit Lurking, you ruined my game here, and I was having so much fun too.

[Grando Calrissian]

He's tearing it up this year. That probably hurts even more.

[balrog666]

Hey, dumbass, koalas didn't go extinct 11,500 years ago and Australia wasn't flooded. You got another guess coming (hopefully from a non-Middle Eastern perspective).

[Grando Calrissian]

By the way, if the truth is the one who has the most believers, then you aren't the truth, that would belong to the Hindus. There are more Hindus then any other religion on earth.

Actually, the truth is the one who has the most white believers.

[AmericanAge]

Actually, that is not correct. There are 1.5 billion Christians in the world. 1.1 billion Muslims. Hinduism has 750 million, and is more of a cultural faith than a religion. Buddhism has slightly less than 350 million. It goes down from there.