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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
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1 posted on 05/08/2003 10:11:07 AM PDT by Nebullis
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To: *crevo_list
For all the irreducible complexity fans.
2 posted on 05/08/2003 10:11:56 AM PDT by Nebullis
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To: Nebullis
Anyone can sell their soul to get results out of the ordinary; this is nonsense.

Next this person is going to start using statistics, a "science" long since disproven. Just ignore them.
3 posted on 05/08/2003 10:13:42 AM PDT by AmericanAge
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To: Nebullis
Ohhhh! Thread flambe.
4 posted on 05/08/2003 10:14:38 AM PDT by js1138
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To: Nebullis
Perhaps someone will someday explain how to use ping lists.
5 posted on 05/08/2003 10:17:04 AM PDT by js1138
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To: PatrickHenry
ping the old bulldogs list.
6 posted on 05/08/2003 10:18:56 AM PDT by stanz
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To: Nebullis
If ya can't find the fossils, rig a computer program to "prove" your theory.
7 posted on 05/08/2003 10:19:10 AM PDT by Cedric
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To: Nebullis
Arificial life explains evolution?

Life begets life

Artificial life begets artificial life

Artificail Life begets artificail evolution

Here's Evolution in the making.


8 posted on 05/08/2003 10:20:43 AM PDT by Zavien Doombringer (If I keep my eyes on Jesus, I could walk on water - Audio Adrenaline)
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To: js1138; Junior
Junior has a good list.
9 posted on 05/08/2003 10:20:49 AM PDT by Nebullis
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To: All
It sounds like these *INTELLIGENT* people *DESIGNED* themselves a really nice experiment in a tightly controlled environment.

Semper Fi

10 posted on 05/08/2003 10:21:37 AM PDT by dd5339 (Lookout Texas, here we come!)
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To: Nebullis
Interesting that this is a biological theory which they only seem to be able to demonstrate or produce on computer simulations.
11 posted on 05/08/2003 10:23:58 AM PDT by martianagent
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To: Nebullis
The abstract:

The evolutionary origin of complex features

RE Lenski, C Ofria, RT Pennock, C Adami

A long-standing challenge to evolutionary theory has been whether it can explain the origin of complex organismal features. We examined this issue using digital organisms—computer programs that self-replicate, mutate, compete and evolve. Populations of digital organisms often evolved the ability to perform complex logic functions requiring the coordinated execution of many genomic instructions. Complex functions evolved by building on simpler functions that had evolved earlier, provided that these were also selectively favoured. However, no particular intermediate stage was essential for evolving complex functions. The first genotypes able to perform complex functions differed from their non-performing parents by only one or two mutations, but differed from the ancestor by many mutations that were also crucial to the new functions. In some cases, mutations that were deleterious when they appeared served as stepping-stones in the evolution of complex features. These findings show how complex functions can originate by random mutation and natural selection.

12 posted on 05/08/2003 10:24:21 AM PDT by Nebullis
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To: martianagent
Interesting that this is a biological theory which they only seem to be able to demonstrate or produce on computer simulations.

Perhaps you know of a way to go back in time or speed up the reproduction of organisms?

13 posted on 05/08/2003 10:26:00 AM PDT by Nebullis
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To: Cedric
If ya can't find the fossils, rig a computer program to "prove" your theory.

You will eventually have to explain how a rigged program can design new and useful things that have not been foreseen by humans. It has already happened. A computer program using the technique described in this article has already designed a new, useful and patented electronic circuit.

This ain't a game anymore. And this is just the first few baby steps.

14 posted on 05/08/2003 10:27:20 AM PDT by js1138
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To: Nebullis
Your post is too humorous for words.

Amazing to what lengths athesits, oops evolutionists will go to to bolster their ridiculous theory. Something as sophisticated as the human body, didn't evolve out of nothing. Nothing comes from nothing. That is just OBVIOUS common sense for those who use their God given brains.

15 posted on 05/08/2003 10:29:23 AM PDT by nmh
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To: Nebullis
mr ...

There is a sub-set of lunatic loons who appear to wish the end of American society as we know it. Like the Nazis and the communists in Weimar Germany, they have a great deal in common as ... potential destroyers --- of the social fabric.

I have engaged in several debates in the last few days, and I admire FreeRepublic as a forum for the free expression of ideas, but the overwhelming presence of this bunch of loons is very off-putting.

Lenin is supposed to have said that capitalists would sell him the rope by which they were to be hung. The “anarcho-loons” on this forum would not bother to sell the rope but provide it as a public service.

401 posted on 05/06/2003 5:54 PM PDT by moneyrunner (I have not flattered its rank breath, nor bowed to its idolatries a patient knee.)

16 posted on 05/08/2003 10:29:30 AM PDT by f.Christian (( Marching orders: comfort the afflicted // afflict the comfortable ! ! ))
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To: Nebullis
Artificial life is not LIFE.
Evolution is a discredited religion.
Unfortunately, its adherents refuse to give up their faith.

17 posted on 05/08/2003 10:29:35 AM PDT by ppaul
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Comment #18 Removed by Moderator

To: nmh
Amen! Nothing comes from nothing.

Except God.
19 posted on 05/08/2003 10:31:20 AM PDT by AmericanAge
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To: dd5339
It sounds like these *INTELLIGENT* people *DESIGNED* themselves a really nice experiment in a tightly controlled environment.

I usually don't get involved in these threads, but that was my first thought. From a distant lens, they've done the following:

1. Created the world.
2. Created the rules.
3. Created the initial organisms.
4. Kickstarted execution.
5. Prompted evolution by introducing mutation external to the organisms.
6. Set the organisms loose on each other.

I played this game in the early '90's - it was called Unnatural Selection. Cool game.

20 posted on 05/08/2003 10:31:56 AM PDT by vollmond (And I don't even do drugs!)
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To: Cedric
"If ya can't find the fossils, rig a computer program to "prove" your theory."

You've got it! Rigging is the ONLY way this theory could continue to evolve. Honestly, it's scary to know that some really buy into evolution. Then again, what else is there for an atheist to belive in? Nothing but godless evolution with absolutely NO evidence to support it. Fossils don't show ANY transitional species but maybe this computer program with fix that too.

21 posted on 05/08/2003 10:33:21 AM PDT by nmh
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To: nmh
Ever been to talkorigins.org? All of those godless atheists over there have spent a long time putting together documents trying to explain their "theory" of evolution. To be fair, they are pretty good at filtering out the hoaxes.

There's a pretty good debate forum too, and some people who've gone to college for years on this stuff are there, and met with the people who know better, at about a 50/50 mix.
22 posted on 05/08/2003 10:35:57 AM PDT by AmericanAge
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To: ppaul
Nebullis doesn't care to hear or acknowledge the word "artificial" since it would destroy his fantasy of evolution. For him, an atheist, evolution must be true, despite NO evidence to support it, since it is godless.
23 posted on 05/08/2003 10:36:09 AM PDT by nmh
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To: Nebullis
Can someone point me to a scientific article that attempts to explain how Sexual reproduction (as opposed to asexual) evolved and why?

24 posted on 05/08/2003 10:37:43 AM PDT by Carlucci (Liberalism is the triumph of Emotion over Reason.)
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To: nmh; FactQuest
To: f.Christian

I've struggled with this for years. First being fully indoctrinated on young earth creationism (before it had that name), then being fully indoctrinated with evolutionary naturalism.

Never have fully sorted it out, but I have reached a few conclusions.

I. The Bible is open to some limited interpretation. Day-age, for starters. Which hebrew words are used for "made"? For that matter, look at what leading Jewish theologians say about it, its vastly different that what they teach in mainstream protestant sunday school.

II. Science itself is not anti-God. It is a study of that which God has made, and can provide a multitude of lessons about the nature of God.

III. Science is limited to naturalistic assumptions. Meaning, being based on repeatable experiments, it [i]a priori[/i] excludes the miraculous. Some misunderstand this and conclude miracles are impossible. No, they are just not subject to investigation by science, because they are by their very nature non-natural, non-repeatable.

IV. The Theory of Evolution is a mixture of good and bad science, and advocated zealously by the naturalists. The naturalists seem to think that the T-of-E removes the need for a God. Ignoring the whole question of where did the universe come from in the first place.

V. The two single biggest problems for the T-of-E are macroevolution and abiogenesis.

A) Abiogenesis, that life arose from inorganic material, is, scientifically, a discipline in shambles. A lot of time and energy spent, a lot of speculations made, and so far, nothing but some impossible speculations to show for it.

Oddly ... the impossibilities are suppressed --- the cleverness of the speculation trumpeted, and in some quarters people think its already proven.

B) Macro-evolution - perhaps a bad term. I mean to say, descent with change is proven - children differ from their parents, over time this can lead to changes in a species.

But, the assumption or speculation that this accounts for the grand diveristy of all life on the planet has not been proven, and in fact, scientifically, is a huge and largely unsupported leap. Put another way: the fossil record supports this theory very poorly.

7 posted on 04/28/2003 8:03 AM PDT by FactQuest

25 posted on 05/08/2003 10:39:40 AM PDT by f.Christian (( Marching orders: comfort the afflicted // afflict the comfortable ! ! ))
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To: VadeRetro; jennyp; Junior; longshadow; *crevo_list; RadioAstronomer; Scully; Piltdown_Woman; ...
Ping.

[This ping list is for the evolution -- not creationism -- side of evolution threads, and sometimes for other science topics. To be added (or dropped), let me know via freepmail.]

26 posted on 05/08/2003 10:40:58 AM PDT by PatrickHenry (Felix, qui potuit rerum cognoscere causas.)
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To: Nebullis
I guess we won't have to worry about coming up with new uses for more and more powerful computers.
27 posted on 05/08/2003 10:41:13 AM PDT by Moonman62
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To: nmh
Common sense says the earth is flat and the stars are holes in the sky. Common sense says that living things too small to see can't possibly cause widespread death and destruction. What does common sense have to do with the object of this discussion?
28 posted on 05/08/2003 10:43:41 AM PDT by js1138
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To: Carlucci
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.
29 posted on 05/08/2003 10:45:45 AM PDT by AmericanAge
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To: Nebullis
Of course if one designs a sufficiently rich digital environment, with a designed in notion of "fitness" one can use stochastic processes to evolve more fit digital configurations from less fit ones. The process can surely be modeled by a classical dynamical system in which 'more fit' is embodied as minimizing free energy, in which case this is no more surprising that that random perterbations will cause a book standing on end in the middle of a table to fall over. (Of course, the book was purposefully placed there to demonstrate the effect. . .)

If evolutionary biology really embraces these computer models and manages to shape itself into a more predictive theory as a result, the result will be a stronger scientific theory, but one far less apt as a iron with which atheistic polemeicists can brand theists as obscurantist, retrograde and anti-scientific. After all the computer runs take place inside one of the most magnificent artifacts of human craft: a computer!

30 posted on 05/08/2003 10:46:44 AM PDT by The_Reader_David
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To: Carlucci
Can someone point me to a scientific article that attempts to explain how Sexual reproduction (as opposed to asexual) evolved and why?

Don't touch that dial. I can't, but it has been done many times on these threads. I might add that there are many intermediate modes of reproduction that are neither completely sexual or completly asexual.

31 posted on 05/08/2003 10:46:47 AM PDT by js1138
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To: js1138; gore3000
g3 ...

evolution, as I have said many times is ANTI-SCIENCE.

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.

This is totally unscientific, it is an attack on science which in order to expand human knowledge and human health and living standards needs to find the causes and effects of how our Universe functions.

Randomness answers nothing and leads to no discoveries.

In fact it opposes scientific inquiry and is a philosophical know-nothingism.

That is why evolution has been popular with the masses and virtually ignored by scientists.

It is ... pseudo-science (( link // source )) --- for morons.

With a few words such as 'survival of the fittest' and 'natural selection' it seeks to make idiots think they are knowledgeable.

We see the idiocy of evolution and evolutionists daily on these threads. That is why they all repeat the same stock phrases, throw a few links (because they cannot even understand the concepts being discussed), but never give any facts showing their theory to be what they claim it is - the center of science. If it was, they should have no problem doing so. It is not, that's why they cannot.

sop ...

The theory of evolution is just that - a theory.

g3 ...

It may be a theory, but it is not a scientifically supported theory which is what evolutionists claim it to be. Anybody can have a theory about anything. It is whether a theory is valid that is the point. So you have not given any evidence for your side. All you have done is indulge in rhetoric, but you have not shown that evolution is science or have in any way refuted my statement that evolution cannot in fact be science because of its central proposition that 'evolution just happens'. Such is not science.

539 posted on 03/13/2003 8:59 PM PST by gore3000

32 posted on 05/08/2003 10:47:33 AM PDT by f.Christian (( Marching orders: comfort the afflicted // afflict the comfortable ! ! ))
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To: AmericanAge
statistics, a "science" long since disproven.

Really? You know where I can find this proof?

33 posted on 05/08/2003 10:47:48 AM PDT by donh
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To: f.Christian
1. Why should we trust them? They're not Christian. They're more our allies than, say, the Muslims, but they don't believe in the saving love of Jesus Christ.

2. Science *Is* anti-God. It seeks to disprove His existance every day!

3. See 2.

4. There is nothing good about evolution. Nothing evolves - period. Even diseases. It's all nonsense, as I just mentioned.



34 posted on 05/08/2003 10:48:26 AM PDT by AmericanAge
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To: donh
Yeah, look at how accurate polls are, for one.
35 posted on 05/08/2003 10:48:59 AM PDT by AmericanAge
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To: AmericanAge
Nothing evolves - period. Even diseases. It's all nonsense, as I just mentioned.

I think your reality check just bounced...

36 posted on 05/08/2003 10:53:29 AM PDT by null and void
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To: Nebullis
I have a question. Is there a conservative position on evolution?
37 posted on 05/08/2003 10:53:34 AM PDT by RonF
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To: nmh
I'd love to watch a discussion divided into three discreet segments:

1. First segment, where YECs get to propound their principles of cosmology, universal age, and the size of the universe without resorting to any scripture, and without making any any attempt to specifically discredit evolution (and if they are offering up principles which require changing constants such as a shifting speed of light, clearly stating the scientific principles which buttress that belief, the amount of change, and the names and credentials of the scientists who postulate it).

2. Second segment, where YECs detail their criticisms of evolutionary theory, without resorting to scripture.

3. Third, YECS will get to defend their beliefs in an inerrant and short timeline of scripture by offering up their absolute proof of the events referenced in the books of Genesis and Exodus.

38 posted on 05/08/2003 10:54:32 AM PDT by Chancellor Palpatine
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To: AmericanAge; Carlucci
Most of those atheists over there on talkorigins say that it's related to the dual-helix nature of DNA

hmm. Where do most of them say this? Fungi have a multitude of perverse sexual practices, including up to 19, at last count, observed genders with distinct roles in a single species. Ameba can be observed having three way sex, and more, and there is a regular saturday night party where various species of microorganisms have been observed to pass around usefully altered DNA so everyone can take a toke.

Bi-sexuality is just one hugely successful variation from a population of competing DNA-exchange schemes. Think of it as a living fossil.

39 posted on 05/08/2003 10:55:09 AM PDT by donh
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To: AmericanAge
Next this person is going to start using statistics, a "science" long since disproven.

Oh boy, just what we need, some more idiocy posted with complete assurance.

40 posted on 05/08/2003 10:56:28 AM PDT by Right Wing Professor
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To: donh
Check their forums; it's been a while since I've been over there. I don't think they have a document on it, though.

Just because they do it doesn't mean that they evolved to do so. We don't need atheists like you here.
41 posted on 05/08/2003 10:57:47 AM PDT by AmericanAge
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To: RonF
I have a question. Is there a conservative position on evolution?

If you follow these threads, you will see that there are quite a few of them.

42 posted on 05/08/2003 10:58:50 AM PDT by Lurking Libertarian (Non sub homine, sed sub Deo et lege)
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To: AmericanAge
aa ...

4. There is nothing good about evolution. Nothing evolves - period. Even diseases. It's all nonsense, as I just mentioned.





34 posted on 05/08/2003 10:48 AM PDT by AmericanAge


fC ...

What is really strange in our society and the FR ...

this gypsy cult of thieves have the reign of the store and shop too !
43 posted on 05/08/2003 10:58:51 AM PDT by f.Christian (( Marching orders: comfort the afflicted // afflict the comfortable ! ! ))
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To: AmericanAge
Yeah, look at how accurate polls are, for one.

Polls are raw data, not statistics. Statistics is a formal mathematical discipline not normally considered in the least questionable. Algebra can't vouch for the data it is applied to, and neither can statistics.

44 posted on 05/08/2003 10:59:51 AM PDT by donh
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To: null and void
What, are you going to side with all of the God-haters too?
45 posted on 05/08/2003 11:00:07 AM PDT by AmericanAge
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To: AmericanAge
"We don't need atheists like you here."

FR is a discussion place of ideas for EVERYONE to amiably explore concepts. Keep your exclusionary comments to yourself.
46 posted on 05/08/2003 11:00:10 AM PDT by webstersII
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To: Nebullis
I'm printing the paper now. Will comment late this afternoon or tonight after reading.
47 posted on 05/08/2003 11:00:49 AM PDT by Doctor Stochastic (Vegetabilisch = chaotisch is der Charakter der Modernen. - Friedrich Schlegel)
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To: nmh
Fossils don't show ANY transitional species but maybe this computer program with fix that too.

Same old threads, same old lies.

48 posted on 05/08/2003 11:01:00 AM PDT by Right Wing Professor
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To: webstersII
Fair enough.

But its surprising to see the number of atheists today.
49 posted on 05/08/2003 11:01:26 AM PDT by AmericanAge
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To: AmericanAge
We don't need atheists like you here.

Get lost, newbie.

50 posted on 05/08/2003 11:01:56 AM PDT by Right Wing Professor
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