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."

[PatrickHenry]

PatrickHenry: an Equal Opportunity Evolutionist, defending freedom, truth, reason, capitalism, the American Consitution, and Western civilization against the ever-present evils of socialism, theocracy, all other irrational belief systems, and plain old ignorance, regardless of your age, race, religion, national origin, physical handicap, marital status, intellectual capacity, or the configuration of your genitalia.

[Rightwing Conspiratr1]

It sounds like these *INTELLIGENT* people *DESIGNED* themselves a really nice experiment in a tightly controlled environment.

Grin. Exactly.

[Ichneumon]

[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 evolved circuit has 17 transistors while the patented circuit has 9, and the electronic engineers could undoubtedly produce better control with nearly a doubling of the number of transistors.

Wow, what a lame dodge. Then why haven't they?

Look, if you don't have any proper response to the point made by the fact that evolution can out-perform human design, just admit it.

Notice the word compact.

What, another lame excuse? 17 transistors is still "compact" any way you cut it. You *are* aware that modern transistors are only 180 nanometers in size, aren't you? See the tiny chip on the technician's finger in the following photo? It's a Pentium 4 processor die, which contains FIFTY FIVE MILLION transistors on a square the size of your thumbnail. So yes, 17 transistors is still "compact" -- in fact, they'll fit on a VLSI die (or subregion of a larger high-level chip) 0.005 millimeters on a side, which means that they'll be microscopic; a 100x microscope would still only make the 17-transistor circuit appear about the size of the period at the end of this sentence. Is that "compact" enough for you?

[Ichneumon]

[It sounds like these *INTELLIGENT* people *DESIGNED* themselves a really nice experiment in a tightly controlled environment.]

Grin. Exactly

Yes they did -- and they did it to discover whether *non-intelligent* processes *without* design could achieve results that the creationists believe could only happen via intelligent design. And it turns out that yes, indeed they can -- the creationists are wrong on that point.

Now, does it really console you in any way to snicker about how the experiment itself was conducted by intelligent beings, when the results undercut the creationist presumptions?

Have you ever heard the phrase, "whistling past the graveyard"?

[Ichneumon]

His preoccupation with you, borders on the psychotic.>

...so says the guy who just made three almost identical responses to PatrickHenry within 60 seconds...

[Rightwing Conspiratr1]

So you're saying God writes computer programs. Sure I'll buy that.

[<1/1,000,000th%]

No, I am not.

Yes. You are wrong. I am a Christian first. However, evolution is still the only viable scientific explanation for the existing evidence.

Your approach to this issue helps explain why there are over 250 separate Christian Churches in the US alone. We're too busy nitpicking each other to death over trivia.

Christian Churchgoers in the US make up approx. 73% of the population and still we can't even vote together to allow Bible study in the public skools.

Not good.

[AndrewC]

Why not, Dan? It pointed out his preoccupation.

[AndrewC]

Wow, what a lame dodge. Then why haven't they?

Dan, why don't you back up your assertions instead of red herring distraction. Put up or shut up!

[Ten Megaton Solution]

There are many folk who are totally unsociable and like to live by themselves.

I've Fallen And Can't Get Up!

There are many folk who are totally unsociable and like to live by themselves. If it were an instinct it should be universal amongst mankind.

Yes, this statement is clearly true. Everybody has brown skin and blue eyes, red hair and is six feet eight inches tall. There's no genetic variation at all between different people. (Sarcasm off)

Secondly, the point of the reference was that religion is good for the health of people.

The point of reference was that attending church was good. I explained why.

the well proven point that the will to live leads to longer life.

Yes, suicide tends to shorten the life span, agreed.

[Ichneumon]

Why not, Dan? It pointed out his preoccupation.

And I pointed out the irony of you accusing someone of having a "preoccupation" with someone else "bordering on the psychotic" shortly after you yourself were reduced to repeatedly pestering *him* with several almost identical posts.

That's why not.

[Ichneumon]

[Wow, what a lame dodge. Then why haven't they?]

Dan, why don't you back up your assertions

I did. Why don't you answer the question?

instead of red herring distraction.

You mean, red herrings like your "I know you are but what am I?" dodge above? Come on, answer the question, don't play games.

Put up or shut up!

I do "put up" on a regular basis. May you someday start to do the same, instead of playing word games in a transparent attempt to distract attention from the fact that you can't/won't deal squarely with rebuttals and questions.

[Ichneumon]

So you're saying God writes computer programs.

No, I'm not saying that. Which part of my post had words too big for you?

Sure I'll buy that.

You'll buy quite a lot of things, apparently.

If you're under the impression that you're being clever, I regret to inform you that you're mistaken.

Now, would you like to deal with what I actually wrote, or are you going to posture and giggle some more? If the latter, there are more thoughtful people with whom I could be spending my time conversing.

If you're playing games, I'm not in the mood. If you think you had a real point here, try again, or give it up. For starters, try rereading my post until you understand what my actual point was, if you're able.

[gore3000]

Yes they did -- and they did it to discover whether *non-intelligent* processes *without* design

Nonsense, the program was designed by intelligent designers the product of it is therefore the product of intelligent designers.

As I said before, the interesting thing about this article is the admission that evolutionists cannot give proof for their theory from real life. HOw can evolution be science if it cannot back it up with real life facts?

[gore3000]

PatrickHenry:

Nope, just a stalking slimer that contributes nothing to discussion except disruption.

[AndrewC]

I did. Why don't you answer the question?

You have not provided the evidence for the assertion that the evolved circuit performs better than the patented circuit even in its modified form. Not one measurement, not one graph, not one number.

[AndrewC]

And I pointed out the irony of you accusing someone of having a "preoccupation" with someone else "bordering on the psychotic" shortly after you yourself were reduced to repeatedly pestering *him* with several almost identical posts.

Yes, I accused him. I directed my comment towards him, not as he does, "hiding in the shadows", like a stalker. He never directs his worthless comments towards his target in these cases. I'd say it again under the same circumstances, and "to his face" not as he does to others.

[PatrickHenry]

Hee hee. See what happens when you don't post to people for a year, notwithstanding virtually continuous posts addressed to me from them? Such non-posting is called stalking!

[null and void]

IMHO, he is being "deliberately dense".

No-one who can function in society is really that stupid...

[Lurking Libertarian]

1300.