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]

However, sometimes it's really hard to tell a troll from a creationist.

To be fair, I've known of Creationists who do not live under bridges, even in Madison County.

[Doctor Stochastic]

Now that I've read the paper I can comment. It's rather nice. They emulate DNA functionality better than my simulations. I liked the was that sub-optimal forms are generated naturally and that one may have to retirer pour mieux sauter (I don't remember where the diacriticals go). I suggested some time ago (in analogy with the Metropolis algorithm) that one might acquire several neutral or even slightly disadvantageous mutations before the combination gave a great leap forward. The paper suggest that this happens.

I did not check the dynamics of their simulation. What I found in mine was that randomly driven (Brownian motion) mutations causes the genotypes to vary at a Sqrt(N) rate for N time steps but the selection worked proportional to N. (I should develop a real study of this after I retire and get some time.)

Thanks for the article. It was fun to read.

[js1138]

Just remember, koalas need an entire forest. Single plants are not sufficient.

And what about the passenger pigeon? Even a thousand individuals could not revive that species.

[Aric2000]

Maybe it's absurd to you, but you're not the one with DR in front of your name either.

I think he probably knows more about what he is talking about then you do.

Also, evolutionary programs have actually created circuits that work BETTER then human designed ones, and we can't figure out how they work. All we know is that they DO work, and many have been patented.

Evolutionary science is going WAY beyond biological and paleantology science now, it is going into the realm of electronics and software. Programs that are allowed to evolve on their own to become something that no human could have programmed.

Evolution works, and it's being PROVEN EVERY day.

What a disappointment for you, huh Andrew?

[f.Christian]

Technology (( science )) works, and it's being PROVEN EVERY day ...

evolution (( mind disease )) has nothing to do with it !

[js1138]

When is it right to murder in a relativist world?

In any world, murder is by definition wrong. To accuse somone of moral relativism is nothing more than to assert that you differ about the role of motive. In every case it is motive rather than action that defines the wrongness.

[Aric2000]

Poor FC, you really are deluded aren't you, well, every website needs a jester, ours is just a little stranger then most.

f.Christian, our new official Freeerepublic website jester.

[f.Christian]

Haven't you made a distinction of your desires and reality yet ?

[Aric2000]

All of my desires are realistic, I'm just not sure that yours are.

Make sure your meds are at the right level there FC, we don't want you wandering off in a stupor.

[f.Christian]

Maybe your desires are personal and reality is objective !

[Doctor Stochastic]

Good point. I forgot about the passenger pigeons.

[Aric2000]

Boy, aren't we just philisophical tonight, tell your nurse that your meds are perfect right now and to keep them there.

Objective or subjective, what an interesting philisophical question.

I'll have to think of a REALLY good response for that.

[Ichneumon]

[Evolutionary design," says Pennock, "can often solve problems better than we can using our own intelligence."]

Absurd! Even leaving out the often does not make the statement much more believable.

You remind me of the guy in "The Princess Bride" who kept declaring, "inconceivable!" whenever something happened that he hadn't thought to take into account. Rather than go "oops", or stop to figure out where his mistake was, he just declared it preposterous.

"You keep using that word. I do not think it means what you think it means." -- Inigo Montoya

Your personal astonishment is hardly a valid rebuttal to Pennock's statement. Furthermore, I believe I've seen you on threads where the following was already posted:

Evolution *can* and indeed *does* produce results which exceed those of "our own intelligence". Deal with it. In this case, it made a cubic function generator circuit which outperforms the best that all electronic engineers were capable of producing in all the history of electronics.

The circuit at the top was patented in 2000, and is the current state of the art. The circuit at the bottom was produced by pure unaided evolution, and outperforms the human version. It's also complex enough that no one's figured out how it works yet...

[Aric2000]

Thank you, I need to save that picture and keep it for future posts, when it is said that evolution can't work.

[null and void]

And science has discovered quite a few species that went extinct about 11,500 years ago, including: Mammoth, Sabre tooth tiger, european rhinocerous.

Goodness. About the time the last ice age ended. The glaciers melted. Sea level rose 200'. (Did you know that 85% of the world's population lives within 200' of sea level today? Imagine the stories our decendants would hear - the sea rose and covered EVERYTHING!)

[null and void]

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

Actually, Asian Indians are caucasian...

[RadioAstronomer]

Bump for later read :-)

[null and void]

Humm? Why did 503 get pulled? Did somebody object to the word "idiot"?

Dunno. I missed the darn thing. (Musta been good - FReep mail it to me???)

[null and void]

The Devil has free will, as do we all. The Devil is not working God's will. That's heresy.

Is it?

[Aric2000]

Keep reading her posts, she was HOT this afternoon, she had poor AA freaking. It was GREAT!!