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."

[Quick1]

A player? What? A CD player? Yes, I have both a hard drive and a CD player. What's your point?

[Quick1]

What does that have to do with science?

[f.Christian]

Have some orignal thought and just don't give me your brainwashing spiel !

[Quick1]

Let's move back to our original topic. Can you show me that science, as defined by the definition I provided above, has not changed, ever?

For example, the Theory of Gravity. Do you believe that 900 years ago, people understood that two bodies with mass will exert a force on each other?

[Quick1]

What the hell? You asked me a question, dingbat. I answered it. Why did you ask me the question?

[f.Christian]

Do I know the difference ...

between historical fiction (( evolution )) and ---

the Bible (( TRUTH )) ?

Yes !

[freeper4u]

Carl Sims' Virtual Creatures Paper, Siggraph '94 is an earlier computer validation of the theory of evolution.

Programming a robot (or simulation of a robot) to walk in a real physical environment is hard problem. It's difficult enough to compute the set of parameters used to program the joints of a flexible creature with the right pressures and angles to get a creature to stand up and balance itself, let alone figure out the complex interactions required to define it's gait used run, jump, fly, swim, climb, etc.

Using genetic algorithms, however, Carl Sims was able to completely avoid all that complicated design work, and achieve results far better and faster than if he had set out to directly design the motor characteristics of the creatures himself.

Evolution is not simply random changes as creationists tend to think. It also requires a mechanism for selecting good random mutations over bad ones (the environment), and a memory to store a history of good changes (DNA).

Watch the videos on this website. All of the creatures in the paper not only "evolved" from a "single celled" organism, but they also "learned" to walk on their own, using a computer program that puts models of physical creatures' motor characteristics based on a simplified DNA in a real world physical environment.

http://www.genarts.com/karl/evolved-virtual-creatures.html

His famous video is at:

http://alife.ccp14.ac.uk/ftp-mirror/alife/zooland/pub/research/ci/Alife/karl-sims/creatures-demo.mpg

[Ten Megaton Solution]

You said "yes", but the body of your response indicates that "no" would be appropriate.

Historical fiction are literary works weaving tales of fiction in and around the facts of a historical era to promote the author's desires.

The Bible is one particular example of historical fiction.

[CobaltBlue]

Thanks for the silly patents. My husband collects silly patents, I need to make sure he has those.

The one I asked about earlier he says is for a perpetual motion machine, but it's being reviewed.

He says food patents are really hard to do because there are no engineering specialties that are related. A close friend of his did food for years -- she hated it -- as a reward they made her an Administrative Law Judge.

A lot of it has to do with making food different colors. Design patents aren't as hard to get as utility patents.

[PatrickHenry]

We're all making bets on how long it takes you to realize that your dialogue with a certain unnamed person is a worthless effort. (I'm betting it won't go on much longer.)

[f.Christian]

Your mind like a filthy old lady (( dirty old man )) changing her dresses (( shorts )) CHANGES ...

but SCIENCE -- God -- Truth ---


NEVER CHANGES (( impossible )) !

[Quick1]

Nah, I enjoy doing this. I realized it was sa fruitless effort from the start, but I needed to kill some time anyway. :)

[f.Christian]

Evolution is inherently stupid --- impossible !

[Quick1]

So the Theory of Gravity has never changed?

What did asking me about my hard drive have to do with anything?

Has the Bible never changed over time, between different translations?

[whattajoke]

haha, and I thought it was just me. Btw, was it you who posted the link to that old computer program thing that just answers questions with stiled questions back, in regards to our "friend?" (see my post 777 and his post 779) to get what I'm talking about.

thanks.

[CobaltBlue]

>> one billion dollars (( every 12 years ))!<<

I don't know how much money the patent office makes but I do know that it is one of the few government offices that makes more money than it spends. When Clinton shut down the government except for non-essential services, my husband still had to go to work every day.

[whattajoke]

stiled = stilted

[f.Christian]

For example, the Theory of Gravity. Do you believe that 900 years ago, people understood that two bodies with mass will exert a force on each other?


884 posted on 05/09/2003 2:17 PM PDT by Quick1


Very dumb question to prove my pt ...

did gravity pre exist unknown --- secretly ?

Is gravity even in a relative sense really changing ?

[Ten Megaton Solution]

Evolution is inherently stupid --- impossible !

I don't think your personal emotional responses on the matter will alter the truth in any way.

[PatrickHenry]

Btw, was it you who posted the link to that old computer program thing that just answers questions with stiled questions back, in regards to our "friend?"

Nope. Wasn't me.