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."

[Grando Calrissian]

BOWLING FOR BLADDER INFECTIONS

[Dataman]

In this respect, you're not a very good Christian.

A little judgemental, aren't we? After all, theology isn't your long suit.

I hope you read your students' papers more closely than you read my posts:

The Fathers of the Church, from Paul to Martin Luther, have repeatedly stressed that Christianity is a matter of faith. Luther went so far as to state that the statements of the devil are fully in accord with reason, whereas faith is not. One does not need to have faith in what can be proven (c.f. Hebrews 11:1) .

Your faulty conclusion lies in

1)the thing you imagine to be faith. Faith to you materialists seems to be the mere antithesis of fact,

2) what you imagine to be proof. Proof to crush your will is not possible (it is not possible to crush a resolute will with reason) but proof beyond a reasonable doubt is.

That is, in part, why faith is required. If faith and reason are antithetical, Moses would have lost his faith when he saw the burning bush. Abraham would have had less faith after the Theophany, and the soldier at the foot of the cross would not have said, "Truly this man was the Son of God."

[MEGoody]

Fill a page with suppositions and fantasies and call it 'science'.

[MEGoody]

"I know some REAL Christians, and if they saw what the 2 of you were writing, they would be praying for you, hard."

Wouldn't surprise me if they wouldn't have started 'praying hard' for Jesus after He drove the money changers out of the temple or called the Pharisees vipers and dogs.

[Grando Calrissian]

"If all the world was made of granite, I'd eat the granite. If all the world was made of salt, I'd eat the salt. But, if all the world was made of lemon, it would probably collapse upon itself and cease to exist."

- Sir Barry Peters XIV, 1956 from "The Illiterate Cowboy From South Africa Returns"

[balrog666]

Do you mock Ponch -- His existence ?

You are one funny poster!

[Aric2000]

I see, so arrogance is good?

I get it.

I wish you christians would make up your fricking minds.

First it has to be taken literally, then no, it doesn't have to be taken literally, as long as I ask AA first, and he will tell me what is supposed to be what.

Now it's Christians should be humble, but now it's Christians should be arrogant and destory or demonize anything that disagrees to questions the literal meaning of the bible.

You guys really scare me sometimes, I don't know if your just different faiths, or just plain out of you minds.

[balrog666]

One who needs proof that religion exists first needs critical thinking skills.

Your critical reading skills need to be upgraded to, at least, 3rd grade level before you even think of responding again.

[f.Christian]

anarcho-loon alert !

[RightWhale]

Complexity is entirely natural; it's the simple, canonical forms that get our attention, that we call beautiful. Wolfram says the entire universe might be generated from 5 lines of code. From this point of view, it might be so. We like complexity in literature, which we create, and simplicity in our mathematical forms, which we believe somehow describe nature. Take natural complexity as a given, it's hard to avoid, even for theorists such as Dirac. Find simplicity in the program, complexity in the result--the other way around would be absurd.

[MEGoody]

"I see, so arrogance is good?"

Why do you view it as arrogance and not just passion? Please be specific. After all, I'm sure Jesus was viewed by some as 'arrogant' and 'self-righteous' when He did the things I mentioned in my previous post.

[merak]

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.

Steve and George (Spielberg and Lucas) can make pretty much any sort of thing happen in computer simulations these days. Are you going to call this the Hollywood version of evolution?

[f.Christian]

"Would you appoint some flowers to reign
In matchless beauty on the plain
The rose (mankind will all agree)
The rose, the queen of flowers should be."
By Sappho, 600 B.C.

Throughout time, "the queen of flowers" has become the flower of kings, queens and sweethearts. There are more than 30,000 varieties of roses.

Historically, roses have been used in extravagant ways. Cleopatra once received Mark Anthony in a room knee deep in rose petals. There are some 4,000 songs about roses. And, of course, just down the road is the annual "Rose Parade."

Roses, you see, are symbols of love, beauty, war and politics, and you’ve all heard of England’s "the war of the roses."

Scripture speaks of ... the Ultimate Rose --– the Rose of Sharon (Song of Solomon, 2:1).

Religious historian, Dr. William Smith states that "the Rose of Sharon," in Eastern tradition, is generally believed to be the sweet scented narcissus, but in Western thought, the Rose of Sharon is the Hibiscus syriacus which especially attracts hummingbirds because of its sweetness. "The Rose of Sharon" demonstrates an interesting phenomenon – it does not bloom until late spring causing many gardeners to believe that it has died; but, to their astonishment, it suddenly resurrects. Considering the legacy of "the Rose of Sharon" in 1922, Ida A. Guirey wrote the song "Jesus, Rose of Sharon."

Jesus, Rose of Sharon, bloom within my heart;
Beauties of thy truth and holiness impart,
That where’er I go, my life may shed abroad
Fragrance of the knowledge of the love of God.
Jesus, Rose of Sharon, sweeter far to see
Than the fairest flowers of earth could ever be

Fill my life completely, adding more each day
Of thy grace divine and purity, I pray.
Jesus, Rose of Sharon, bloom forevermore;
Be thy glory seen on earth from shore to shore,
Till the nations own thy sovereignty complete,
Lay their honors down and worship at thy feet.

Chorus:

Jesus, blessed Jesus, Rose of Sharon, Rose of Sharon,
Bloom in radiance and in love within my heart.

[balrog666]

Why do you view it as arrogance and not just passion?

Who cares? A cow pat by any other name would stink as badly.

[cookcounty]

Were these point mutations? Did they occur (as "normal" in nature), in groups? Was there lethality involved in any of them? ...some of them? ....most of them? How did they mimic interdependent systems? What happened when a necessary substructure was eliminated? ...damaged?

Hopefully all these questions are answered in the longer report....otherwise these people should be fired for incompetence.

[Grando Calrissian]

"Ah man, the Doobie Brothers broke up. Sh!t"

- Michael Douglas, 1984 from "Romancing The Stone"

[balrog666]

Dust in the wind
All we are is dust in the wind
Dust in the wind
All we are is dust in the wind

I close my eyes
Only for a moment, then the moment's gone
All my dreams
Pass before my eyes, a curiosity
Dust in the wind
All we are is dust in the wind

It's the same old song
We're just a drop of water, in an endless sea
All we do
Just crumbles to the ground, though we refuse to see
Dust in the wind
All we are is dust in the wind

Life's too short brothers and sisters
Dust in the wind
All we are is dust in the wind

Don't hang on
Nothing lasts forever, but the earth and sky
It's there always
And all your money won't another minute buy
Dust. . . all we are is dust in the wind
Life's too short brothers and sisters
Dust. . . all we are is dust in the wind

Open your eyes you've acquired quite a bit
Keep your balance don't you slip
It could all end instantly as you will see
Time waits for no one, it just moves on
There is a white one
Who won't accept the black one
Who won't accept the yellow one
Who can't accept the white. . .

When will we learn
That all we are is dust in the wind
Time for the healing to begin
All we is are dust in the wind
Time for the healing to begin
All we are is dust in the wind
Everything is dust in the wind!

[Grando Calrissian]

gracias

[Dataman]

The force that causes objects to fall to the ground is defined as gravity (again, a definition, not an explanation), kind of how like we define water falling from the sky as 'rain'. That objects have been falling on earth for millenia is certain, though while evidence strongly suggests it it is not 100% certain that things will continue doing that in the instant future.

I think this is degenerating to semantics. If you're asserting that the inductive method only gives probability rather than certainty, correct. Little to nothing in evolution is established by the inductive method. If any aspect of evo can be reasonably certain through inductive logic, that falls short of factual. Most of evolution doesn't rise above speculaton. And if, as you say, things are not 100% certain, then how can you rule out miracles?

[Grando Calrissian]

That is some of the deepest wisdom I've ever seen in my life. Did you write that yourself?