Free Republic
Browse · Search
News/Activism
Topics · Post Article

Skip to comments.

Artificial Life Experiments Show How Complex Functions Can Evolve
NSF ^ | May 8, 2003 | Staff

Posted on 05/08/2003 10:11:06 AM PDT by 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."


TOPICS: Culture/Society; Miscellaneous; News/Current Events
KEYWORDS: ai; crevolist
Navigation: use the links below to view more comments.
first previous 1-20 ... 1,361-1,3801,381-1,4001,401-1,420 ... 1,961-1,975 next last
To: gore3000
Evolution teaches ignorant people ...

that they than can be -- do -- believe ---

opposite things at the same time (( abscence of reality // sincereity )) !
1,381 posted on 05/14/2003 7:30:44 PM PDT by f.Christian (( the VERY sick mind - won't recognize facts -- REALITY -- probability anymore ! ))
[ Post Reply | Private Reply | To 1380 | View Replies]

To: Doctor Stochastic
Your beliefs are quite relevant when you make claims that are at variance with generally accepted scientific practice.

The scientific facts about the Cambrian are as I stated them to be. Not a single evolutionist has been able to come up with a legitimate evolutionary explanation that fits the facts. The Cambrian disproves gradual evolution completely. My beliefs (and yours) are irrelevant as to the facts in this matter or any other scientific matter. The facts speak for themselves. What you are trying to do is what the evolutionists here try to do all the time - to change the subject from the facts in the discussion to the person showing up facts against evolution. All you and your friends are doing is showing that my statement is correct - evolution is bunk and the only proof it can provide is: lies, doubletalk and insults.

1,382 posted on 05/14/2003 7:49:31 PM PDT by gore3000
[ Post Reply | Private Reply | To 1366 | View Replies]

To: Ten Megaton Solution
The saying 'the pen is mightier than the sword' ilustrates the complete difference between man and beasts.-me-

Yes, men build pens to keep animals in for later consumption, and use swords on each other.

Well, at least you try to evade the point in a funny way. However, you know quite well what the point is - that man is much more than a beast. He strives for more than to just satisfy his material needs. He seeks to build, to create, to leave a legacy, to make the world better not just for himself but also for others and many other things which beasts do not even dream of. Man is far and away different from the beasts not in degree, but in kind.

1,383 posted on 05/14/2003 7:55:00 PM PDT by gore3000
[ Post Reply | Private Reply | To 1367 | View Replies]

To: Ten Megaton Solution
Art is a "non-material activity", is it? Guess you never considered the reason why artists do their thing.

1) To sell. (ie make money, to buy food, shelter, clothing, time share condos, girlfriends, etc)

2) Social recognition (which is another pathway to food, shelter, girlfriend's pants, etc)

The "artist" that creates, but doesn't show it to anyone, has a mental disorder not conducive to survival.

Well, all the above is disproven by the cave paintings in Northern Spain and Southern France. Who do you sell a cave painting to? The caves were so hidden that it took thousands of years to find them, so who was he showing up for? No one.

Further, many people paint and do artistic things for the pleasure of it. Some women knit, sew, some men do things from wood and other materials. They do it for the pleasure it gives them, not for profit and not to satisfy any material need. Mankind is the only creature that does this.

1,384 posted on 05/14/2003 7:59:54 PM PDT by gore3000
[ Post Reply | Private Reply | To 1368 | View Replies]

To: donh
This does not constitute a claim that I have read the book. No one has read the book--that would be like reading Numbers or the phone book. Like everyone else, except possibly Wolfram, I have scanned it for the meat, and ignored most of the examples and details of implementation.

Oh, I see, you call me ignorant for not having read it, yet you yourself have not read it. You claim it proves that non-living matter can create a turing machine but you cannot back it up. Thanks for showing all of us your mode of discussion is just one bluff after another and that your words should not be taken seriously.

1,385 posted on 05/14/2003 8:02:50 PM PDT by gore3000
[ Post Reply | Private Reply | To 1371 | View Replies]

To: donh
Nobody writ in concrete that fitness test failures are necessary for evolution to take place.

Really? Evolution does not say that natural selection is the agency by which the good and the bad changes in organisms are sifted???????????

The above is the reason why the evolutionists will never state exactly what the theory of evolution is and how it works. As soon as a refutation is given for what it obviously says and for what evolutionists have been saying for 150 years, they say that evolution is not about that. They are thus always saying what evolution is not, but never what evolution is since just about every single statement in it has been totally disproven.

1,386 posted on 05/14/2003 8:07:27 PM PDT by gore3000
[ Post Reply | Private Reply | To 1372 | View Replies]

To: Ichneumon
Yes, they intelligently designed an experiment that tested how complexity can and does arise *without* the intervention of intelligent design.

Nonsense. They concocted a program that would do what they wanted to do. Anyone can do that. A program can only be called a valid simulation if it behaves in the same way that the thing being simulated does AND takes into consideration all the relevant factors of the situation.

This program fails as a simulation on two counts:

1. It is totally impossible to simulate all the factors involved in living things and their environment. The program must therefore had to have been selective in what it chose to simulate. Therefore it is not a simulation of real life.

2. As I already pointed out, by evolutionist's own admission:

It's a truism of entomology (been demonstrated in sealed mason jars thousands of times) that when two nearly identical species occupy nearly the same contained biological nitche, one or the other will eventually prevail entirely, no matter how tiny its differential advantage.
1,012 posted on 05/09/2003 9:59 PM PDT by donh ).


that fitness cost is very important to evolution. The program did not exact a fitness cost for non-working functions. This makes the program total bunk.

Furthermore, as I have said, with so many experiments going on all the time, so much money poured into biology not just by the US Government, but by private foundations, medical firms, drug firms, hospitals in the US and throughout the world - why is there a need for a program to prove that evolution is science? If it were science the proof would be coming out on a daily basis from all the scientific research going on.

1,387 posted on 05/14/2003 8:22:02 PM PDT by gore3000
[ Post Reply | Private Reply | To 1374 | View Replies]

To: gore3000
My beliefs are irrelevant to the discussion.

Finally, something we can both agree on wholeheartedly.

1,388 posted on 05/14/2003 8:27:26 PM PDT by Ichneumon
[ Post Reply | Private Reply | To 1362 | View Replies]

To: gore3000
I have read the book. Wolfram does show that one can get a universal Turing machine in the way described. (The politics behind this theorem are amusing.)
1,389 posted on 05/14/2003 8:40:43 PM PDT by Doctor Stochastic (Vegetabilisch = chaotisch is der Charakter der Modernen. - Friedrich Schlegel)
[ Post Reply | Private Reply | To 1385 | View Replies]

To: Ichneumon
he must be making his way through all the primary colors or something.

OK, we'll call this the primary color skipping placemarker.

Can you believe this G3K, the {place your antievolutionist, fundamentalist without a clue, favorite term here} from hell.
1,390 posted on 05/14/2003 8:41:00 PM PDT by Aric2000 (Are you on Grampa Dave's team? I am!! $5 a month is all it takes, come join!!!)
[ Post Reply | Private Reply | To 1388 | View Replies]

To: gore3000
Oh, I see, you call me ignorant for not having read it,

Where did I call you ignorant for not having read it?

If you were ignorant, at least there'd be an anemic excuse for your creative approach to generating data.

yet you yourself have not read it. You claim it proves that non-living matter can create a turing machine but you cannot back it up.

I never read the bible. That doesn't mean there's a law against me quoting from it, now does it? I never finished Euclid. Does that mean I can't provide a geometric proof out of Euclid's geometry? As usual, you are making up laws and data as you go along.

Thanks for showing all of us your mode of discussion is just one bluff after another and that your words should not be taken seriously.

Thanks for showing us once again what an opportunistic, self-aggradizing lightweight dissembler you are.

1,391 posted on 05/14/2003 10:08:09 PM PDT by donh (u)
[ Post Reply | Private Reply | To 1385 | View Replies]

To: gore3000
Really? Evolution does not say that natural selection is the agency by which the good and the bad changes in organisms are sifted???????????

The theory of evolution is about prokariotes or better, as you know. The theory of evolution is mute about what might have happened before we got to prokariotes. As you know, on those rare occasions when you aren't deliberately misrepresenting what claims science makes.

The above is the reason why the evolutionists will never state exactly what the theory of evolution is and how it works. As soon as a refutation is given for what it obviously says and for what evolutionists have been saying for 150 years, they say that evolution is not about that. They are thus always saying what evolution is not, but never what evolution is since just about every single statement in it has been totally disproven.

As usual, you do not give the appearance of person with the slightest notion of what a proof is. And as usual, every claim you've made here is totally irrelevant, to anyone that's been to a natural history museum in the last 20 years or so, with his brights turned on. It is not science's job to jump through any hoops any lame idiot with a bee in his bonnet raises for it to jump through. The basic laws of physics aren't the same as they were 100 years ago, and I don't see you complaining about that. Science changes as we learn more. This is not, contrary to your nonsensical skreed, a jailable offense.

1,392 posted on 05/14/2003 10:19:37 PM PDT by donh (u)
[ Post Reply | Private Reply | To 1386 | View Replies]

To: Nakatu X
AndrewC, I should not have done this, but my desire to defend those in my own profession is so great that I went and answered your challenge anyway (I pulled it off using my university library privileges).
The 9-transistor cubic function generator, results and all, are all right here:

Thanks for your effort. Here is your good news. The paper has a genetically programmed virtual circuit that has an simulated performance edge over another virtual circuit in an average consisting of 4 fitness cases.
The bad news is that:

  1. It is all simulated
  2. The evolved circuit in the paper has 18 transistors not 17 as in the SciAm article(it is not the same circuit)
  3. The patented circuit has 5 transistors and 4 diodes not 9 transistors(pointed out previously)
  4. The evolved circuit has a larger maximum error
  5. There is no evidence that the evolved circuit will operate suitably even in simulation at 1Ghz. This is especially suspected since the paper states -- We used the commercially common 2N3904 (npn) and 2N3906 (pnp) transistor modlels unless the patent document called for a different model. This is from the specs for 2N3904 The useful dynamic range extends to 100 mA as a switch and to 100 MHz as an amplifier.. The 2N3906 has similar characteristics.
Also previously noted --> I suspect that the performance edge is a paper product. Something that the emulating program has produced. Why do I surmise that? Because in evolving the circuit I doubt that each individual circuit was constructed in order to measure its performance of the cubic function. That would be impractical.

So what is to be gathered from this? Well, there is evidence that a genetically developed simulated circuit can, on paper, outperform a human designed simulated circuit in some specific data points, but the patented circuit still remains unchallenged when it comes to a non-simulated circuit operating in the frequency ranges for which it was designed. More to the point, the following assertions still hang.

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.

1,393 posted on 05/14/2003 10:21:15 PM PDT by AndrewC
[ Post Reply | Private Reply | To 1373 | View Replies]

To: gore3000
The basic laws of physics aren't the same as they were 100 years ago, and I don't see you complaining about that. Science changes as we learn more.

uri geller now!

1,394 posted on 05/14/2003 10:23:43 PM PDT by f.Christian (( the VERY sick mind - won't recognize facts -- REALITY -- probability anymore ! ))
[ Post Reply | Private Reply | To 1387 | View Replies]

To: f.Christian
uri geller now!

So...(I should know better than to ask) you think the basic laws of physics haven't changed in the last 100 years?

1,395 posted on 05/14/2003 10:27:48 PM PDT by donh (u)
[ Post Reply | Private Reply | To 1394 | View Replies]

To: donh
Truce (( peace -- consideration -- respect )) ...

on another thread this was debated rather extensively ---

science (( no change )) vs the study of science (( change )) !
1,396 posted on 05/14/2003 10:30:59 PM PDT by f.Christian (( the VERY sick mind - won't recognize facts -- REALITY -- probability anymore ! ))
[ Post Reply | Private Reply | To 1395 | View Replies]

To: AndrewC
Thanks for your effort. Here is your good news. The paper has a genetically programmed virtual circuit that has an simulated performance edge over another virtual circuit in an average consisting of 4 fitness cases.

Which, of course, makes the case under discussion, whether or not your deponent's representation of it was overblown.

1,397 posted on 05/14/2003 10:31:16 PM PDT by donh (u)
[ Post Reply | Private Reply | To 1393 | View Replies]

To: f.Christian
science (( no change )) vs the study of science (( change )) !

That's a silly quibble. The universe does whatever it damn well pleases, and hasn't the slightest demonstrated notion of what a law is to constrain it. Insofar as what is demonstrable, natural laws are human inventions to help us think more effectively about nature. The claim that they are objectively existing things in and of themselves, is unproven and probably unprovable--as is likewise the claim that there is such a thing as "science" which exists independently of "the study of science".

1,398 posted on 05/14/2003 10:36:46 PM PDT by donh (u)
[ Post Reply | Private Reply | To 1396 | View Replies]

To: gore3000
The scientific facts about the Cambrian are as I stated them to be. Not a single evolutionist has been able to come up with a legitimate evolutionary explanation that fits the facts.

Do tell.

1,399 posted on 05/14/2003 10:40:31 PM PDT by donh (u)
[ Post Reply | Private Reply | To 1382 | View Replies]

To: donh
Don't feed the troll.. It makes him stronger, kinda like popeye and spinach.
1,400 posted on 05/14/2003 10:41:44 PM PDT by Aric2000 (Are you on Grampa Dave's team? I am!! $5 a month is all it takes, come join!!!)
[ Post Reply | Private Reply | To 1398 | View Replies]


Navigation: use the links below to view more comments.
first previous 1-20 ... 1,361-1,3801,381-1,4001,401-1,420 ... 1,961-1,975 next last

Disclaimer: Opinions posted on Free Republic are those of the individual posters and do not necessarily represent the opinion of Free Republic or its management. All materials posted herein are protected by copyright law and the exemption for fair use of copyrighted works.

Free Republic
Browse · Search
News/Activism
Topics · Post Article

FreeRepublic, LLC, PO BOX 9771, FRESNO, CA 93794
FreeRepublic.com is powered by software copyright 2000-2008 John Robinson