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."

[Dimensio]

Perhaps he is implying that the observations of the ten different people directly altered the events under observation, which created a quantum fluctuation such that the accident actually did occur in ten different ways simultaneously.

Of course, I think that what's really happened is that you've trapped him but he's too much of a coward to admit that he has no idea what the Uncertainty Principle is or where and how it applies.

[longshadow]

Perhaps he is implying that the observations of the ten different people directly altered the events under observation, which created a quantum fluctuation such that the accident actually did occur in ten different ways simultaneously.

Well, if he had said it was a collision of sub-atomic particles, there might be some merit to the argument. But, as he specified that it was cars, and has further compounded the damage by claiming that observation modifies ALL observed phenomona, this really isn't going to get him out from under the mess he created for himself. Ignorance is a cruel misteress.

[PatrickHenry]

What probably happened is that some creationoid swami told him all scientists are fools, and to back that up, he cited the Uncertainty Principle (of which the swami knows nothing except the phrase), but it's presumably authoritative because ... hee hee ... it comes from a scientist. And our newbie freeper, fresh from a session with the swami, and thus fully charged with a pure load of The Truth! enters our thread and begins spouting his wisdom. So it goes in the wonderful world of "creation science."

[f.Christian]

To: f.Christian

g3 ...

The central point of science is the discovery of causes and effects and materialist evolution denies it. It proposes random events as the engine of the transformation of species.


ag ...


You do realize, I hope, that you're claiming modern physics is also unscientific? Randomness is the basis of quantum mechanics, in essence. We've long since gotten past deterministic cause and effect - we now look at probability as the tool for measuring the physical world. Try again.

Drew Garrett


39 posted on 04/23/2003 3:52 PM PDT by agarrett

fC ...

all SPIN --- flips !

[f.Christian]

evorevulsion !

[AndrewC]

that is the the circuits designed by the computer program have features that could that could not be designed by the people who wrote the program.

No, that has been alleged about those that designed original circuits. It is most readily apparent that the people who wrote the program do not know how the object it produced works. At the moment we have, on this thread, no evidence of the performance of the evolved circuit in question(cubic function generator).

As to perjorative terms, kludge( or kluge if you prefer) is a spot on description of the evolved circuit.

kludge or kluge    ( P )  Pronunciation Key  (klj)
n. Slang

1. A system, especially a computer system, that is constituted of poorly matched elements or of elements originally intended for other applications.
2. A clumsy or inelegant solution to a problem.

That purple transistor in the evolved circuit is a perfect example of inelegant and poorly matched.

[AndrewC]

According to my husband, who has been a patent examiner for 15 years, and is a Primary Examiner, you cannot search applications for pending patents. You can search applications once a patent is granted.

I guess I believe my eyes more than I believe your husbands opinion and experience. Anyone can find something that includes portions like the following/

( 1 of 4 )

---

United States Patent Application	20030055025
Kind Code	A1
Nelson, Mark L. ;   et al.	March 20, 2003

---

7-substituted tetracycline compounds

[AndrewC]

So, given your skepticism, the only way to prove what is claimed is to actually build the thing in question and test it yourself.

As many have already said, write to the inventor, explain your position, and see if he is willing to assist you in your quest for knowledge.

How about just saying that there is no evidence? I am not going to ask the Raelians how they cloned a human and perform an experiment in order to prove that they have only a claim of cloning and have no evidence to back up their claim.

[f.Christian]

hale bopp ... cargoe cult --- evolution !

[Nataku X]

At the moment we have, on this thread, no evidence of the performance of the evolved circuit in question(cubic function generator).

Happy? Lots and lots of papers by these authors are available by inter-library loan, too. This one looks promising... "Routine Duplication of Post-2000 Patented Inventions by Means of Genetic Programming" by Streeter.

Quit playing this vile "Ah, I can't find it on Google, so someone's lying or being fraudalent" game of yours.

[Michael121]

It is precisely the location of the cars as to each of the 10's perspective. Read Dr. Hawkings writings on the Uncertainty Principle.

No one sees the same EVENT the same.

How long will we wait for the definitive answer as to how the Pyramids were built?

How long before we have the answer as to how South American Indians performed surgery on the skulls of people, when there are 2, 3, up to 5 holes in a skull?

Science has the evidence. They create models, have theories and yet they cannot agree. There have been carbon datings done on green leaves that say they are thousands of years old. Science has its failings.

[xm177e2]

Most of those atheists over there on talkorigins say that it's related to the dual-helix nature of DNA which as a somewhat fragile molecule that has long been observed in bacteria to occasionally absorb DNA fragments from destroyed organisms (in the way that some diseases can get a resistance to a drug from another disease) simply proceeding through a more orderly path.

Can you believe that??!? What nonsense.

You are being sarcastic, right? Just crack open a biology textbook and you'll see how bacteria use their pili to link up and exchance plasmids (loose pieces of DNA), which gives them a tremendous evolutionary advantage: bacteria--they don't even have to be of the same species--can exchange plasmids containing things like antibiotic resistance.

That's the bacterial equivalent of sexual reproduction. Sexual reproduction is so useful to critters because it's the primary way the best genes are spread around and are able to rise to the top. No creature could reasonably evolve into something greater without sexual reproduction. The critters able to reproduce sexually out-evolved the ones without this ability.

It's that simple.

[AndrewC]

The best-of-run circuit (figure 10) for the problem of designing a cubing circuit has 30 transistors, five diodes, and 21 resistors.

The circuit we are talking about has 17 transistors. Try again.

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

Ah, but did you hear that, or just read it? ;)

LOL! OK. I read it.

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

No. I keep dredging it up for an example because I had a friend when I was young who was slowly eaten up by polio. One wierd disease.

Sorry to hear that. Polio is bad.

[longshadow]

It is precisely the location of the cars as to each of the 10's perspective.

Your response appears to have been garbled in transmission, and came through hopelessly incoherent. Please retransmit.

Read Dr. Hawkings writings on the Uncertainty Principle.

Why don't you share with us what you think the Lucasian Professor wrote, and how it applies to what 10 people see when the watch cars collide?

No one sees the same EVENT the same.

Assuming this were true (with respect to an automobile collision), how does this relate to Heisenberg's Uncertainty Principle?

How long will we wait for the definitive answer as to how the Pyramids were built?

How long before we have the answer as to how South American Indians performed surgery on the skulls of people, when there are 2, 3, up to 5 holes in a skull?

Damned if I know. Since I've not commented on those subjects, I have no reason to respond to your unilateral out-of-place demand for an answer. Your feeble attempts to change the subject from your misuse of Heisenberg to something else, on which I didn't even comment, do not obligate me to respond.

Science has the evidence. They create models, have theories and yet they cannot agree. There have been carbon datings done on green leaves that say they are thousands of years old. Science has its failings.

And these statements are connected how to Heisenberg's Uncertainty Principle?

[PatrickHenry]

And these statements are connected how to Heisenberg's Uncertainty Principle?

How terrible of you, trying to keep the newbie on track, and insisting that he explain his prior posting. Doncha know? We're supposed to let these creationoids tap-dance all around every topic, tossing out wild and unsupportable claims, ducking all serious questions, until we grow weary and just give up. It's the technique they learn by watching the master creationists debate. (But somehow, it doesn't work when it's all in writing and there are no time limits.)

[Nataku X]

You said: At the moment we have, on this thread, no evidence of the performance of the evolved circuit in question(cubic function generator). You also drew an implied parallel between these scientists and those UFO-cultists. who's doing the sliming here?

I am not "trying again". I showed evidence of a cubic function generator by these authors almost from scratch (rather than using a patent) using genetic algorithms, which disproves your implied claim that someone's committing fraud here. Haul yourself to the university library and do some research. (I found only one related paper on Google which is what I gave you, BTW, but over a dozen on genetic programming & circuits available by interlibrary loan.) E-mail the professors. Come back when you have actual evidence of a fraud.

Might I ask: what do you want to prove here? That there is rampant fraud and lying in this article, and that it is typical of the scientific world as a whole?

[longshadow]

*****Read Dr. Hawkings writings on the Uncertainty Principle.*****

I have an even better idea: YOU read it and quote for us what you think makes the Uncertainty Principle relevant to anything other than Quantum Mechanics. Show us how it applies to car accidents, looking at Niagra Falls, etc.:

Here you go: Hawking on the Uncertainty Principle

http://www.thegeekgirl.net/Library/science/a%20brief%20history%20of%20time/chapter%204%20-%20the%20uncertainty%20principle.htm

[PatrickHenry]

Weird, low-grade form of pointless disruption. Easily identified. Easily ignored.