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."

[AndrewC]

So there you have it.

Well let's see the real data.

[AndrewC]

the same stat sheet you referred to earlier showed a chart of its frequency response, and it was shown as still pretty linear up into the gigahertz range.

h_fe of 0db at 600 Mhz is not response in the gigahertz range.

[AndrewC]

Before I get accused of anything 0db is unity gain thus the transistor is not amplifying.

[Ichneumon]

[You're really off to a bad start. "40 new animal phyla"?]

You want to play the numbers game?

No, I'd rather you didn't "play games" of any sort. But I see I'm about to be disappointed.

Well at least I have facts to suppor it:

Astute readers will note that Gore3000 claims to have "facts" to support his claim. In his original post he said that "Science has found" his assertion "over 40 new animal phyla arose during the Cambrian". "Facts", he says. "Science has found", he says. Now look at what he waves around as support: Compared with the 30 or so extant phyla, some people estimate that the Cambrian explosion may have generated as many as 100.

Hmm... "Some people estimate", do they? Where are the promised "facts"? Where is the docmentation that "science has found" what he says? Instead, we get speculation by unnamed "some people". That's quite a bit... less than he promised, isn't it?

G3K, you really need to learn the difference between "facts" and speculation. You make that same mistake over and over again (usually in the context of mistaking your *own* speculation for "facts").

The important point is that there were a lot.

Oh, well then, ok. "a lot", and that's imporant.

Even more important, there have not been any new animal phyla since the Cambrian (the last missing phyla known at present, vertebrates, were recently found. A fish, with eyes and very much looking like any fish around nowadays).

Please try to make some sense... Since when were vertebrates a "missing phyla" at all (hell, *we're* vertebrates, and I don't think we've ever been "missing", and so were all those dinosaur fossils, so you can't be talking about missing fossils either), much less "the last missing" phyla? And what precisely is a "missing phyla"? What is this, Voodoo Taxonomy?

[As for "arose during the Cambrian", you might want to show your research on *that*]

Now you are really going off the deep end. Aside from sponges and perhaps worms there were no other multi-cellular animals before the Cambrian.

Well first, the point is that neither you nor anyone else has been able to pin down the fossil origins of about a dozen different extant phyla (see the chart I posted), so there's no way to prove *when* they arose. For all we know those originated in the Devonian or later. More to the point, you're just making things up as you go along when you claim to *know* that they originated IN THE CAMBRIAN as opposed to, say, some later era.

And speaking of "going off the deep end", I find it... interesting that you would assert that there were no pre-Cambrian multi-cellular animals "aside from sponges and perhaps worms". Oh, really? How about Cyclomedusa? Neither a worm nor a sponge. How about Eoporpita? Pteridinium? Arkarua? Kimberella? Or good old Spriggina:

Which is that, G3K, a "worm" or a "sponge"? All of the above are precambrian.

In a mere period of less than 10 million years a multitude of completely new life forms appeared

Yes, "appeared" in the current fossil record we have managed to recover. Don't make the mistake of thinking that they necessarily "appeared" on Earth that quickly, for reasons I explained earlier.

Taxa recognized as orders during the (Precambrian-Cambrian) transition chiefly appear without connection to an ancestral clade via a fossil intermediate.

Note the careful scientific wording: "Appear", not "arose" -- the distinction is made between what the few fossils we have *show*, versus any claim that they necessarily *happened* that quickly. Furthermore, the statement is not made that there *is* no intermediate, but only that there is no [currently known] *fossil* intermediate. Don't make the mistake of reading more into that than the author intended.

I did say that no new animal phyla have arisen after the Cambrian

which is yet again a statement of presumption, not fact, as I already pointed out. It's true that we don't *know* that any phyla arose for sure post-Cambrian, but the point is that there are at least a dozen phyla for which we don't know when they arose AT ALL. So your claim that "no" new animal phyla arose in post-Cambrian eras is simply an unsupported, and at the point unsupportable, presumption on your part.

Don't claim to have more knowledge than you actually have.

and that there is no way that evolutionary ancestors can even be postulated for the vast majority of them.

What are you, daft? Of course evolutionary ancestors can be "postulated". Are you sure you understand what the word means?

The most you could possibly support is the statement that for those phyla which *are* known to exist in Cambrian times (which is *not* all of them, contrary to your claim), most of them (*not* all, contrary to your implication) have no obvious ancestor in the *currently known* pre-Cambrian fossil record (which at this time is *extremely* few and far between). So your conclusion from that limited data set would be... what?

Since you admit that only ONE (1) multicellular phyla existed before the Cambrian, my statements are correct by your own admission.

You're hallucinating again, I said nothing of the kind. I *named* one (1) extant pre-Cambrian phyla. I never said there *weren't* any other precambrian animal phyla, and in fact I even posted you a picture of another. Are your glasses fogged up again?

Also let me note here that we are trying to discuss here scientific facts.

Yes we are -- be sure you have some.

This is not a personal issue, it is about the truth and the truth is that the Cambrian is totally unexplainable according to evolutionary theory and totally disproves it.

Don't be a loon. You can't go from the sparseness of the pre-Cambrian fossil record to a claim of "truth" that the "Cambrian is totally unexplainable" (um, *which* facts do you allege "prove" this, and *HOW*?) -- in fact, I specifically gave you a scenario that perfectly fits the known evidence (i.e. facts) and which perfectly *explains* the Cambrian appearance of many new animal forms. Sort of "forgot" to refute it, didn't you?

Plus you really go into crank territory when you further stretch your chain of argument to go flying off into a conclusion that the Cambrian/Vendian fossil record somehow "totally disproves" the "evolutionary theory". Sorry, son, but you're hallucinating again.

[Wow, not only are you the only person on the planet who knows for sure *when* all the animal phyla arose, you know exactly *how quickly* they did so! You must be psychic! Or at least delusional.]

As usual, instead of presenting facts showing me to be wrong, you instead insult.

As usual, you totally ignore the facts I present which *do* show you to be wrong. Have you forgotten that chart again so quickly? It quite clearly shows that one can *NOT* make the certain claim, as you have, that "no" animal phyla arose after the Cambrian. Period. You're lying, and I proved it. Furthermore, I quite clearly presented facts which showed that you were hallucinating when you claimed to have "shown" that there was no scenario by which evolution could explain the Cambrian "explosion". Did you refute my points? No, you didn't even bother, did you? So don't give me that pre-rehearsed speech about how I insult "instead" of proving you wrong. I insult you *because* I prove you wrong. Deal with it.

1. you hope to bluff your way out of a fact that contradicts your theory with bluster.

You haven't given any facts that "contradict my theory". The facts you gave are perfectly consistent with "my" theory, as I explained at length in my post, and which you have utterly failed to even attempt to refute. Nice try.

2. you are too lazy and too lame to look at the facts for yourself.

Troll...... When you grow up, come back and try again.

I am not too lazy or too lame to look up the facts, here is support for my statement from the University of Bristol site:

I'm sorry, where does that "support" your statement again? It simply reiterates the point that multiple animal forms "appeared" in the fossil record in a relatively short period of time. You've got a *LONG* way to go before you can work that up into a "disproof" of evolution, boyo.

Remember what I said about making sure you don't confuse your speculations with facts? Well, there you go again.

You cannot measure a distance when all you know is the end point.

You can when you have *two* endpoints, which is how DNA distance analysis works.

DNA analysis of modern phyla cannot give us any such information because we do not know what the DNA of these organisms was some 500 million years ago.

Actually, to a great extent we do, which is he point you fail to grasp.

This is trying to prove evolution by assuming evolution which is total circular reasoning and total bunk.

No, it's not, but I can see why you wouldn't be able to see why. I'm not going to wear myself out trying to educate you, from previous conversations I know your mind is entirely closed.

As to the rest of your talk about the difficulty of dating strata and so forth,

I said nothing of the kind, troll boy. Try to work on your reading comprehension.

well, it seems to me that evolutionisits always tell us that dating techniques are very specific and can tell us almost what day of the week a new species arose (/sarcasm).

Are you done with your non sequitur troll yet?

The research and dating were done by mostly evolutionist paleontologists (are there any others?) so you cannot give us this dating nonsense as an excuse.

Which is why I didn't. Blather much?

Further, the vast majority of these new phyla, which by themselves represent the greatest example of the Cambrian, the Burgess Shale find, is in one place and all the fossils are close in time. It cannot be denied with your obfuscating tactics.

You are invited to point out where, exactly, you have hallucinated that I denied anything about the strata dates.

As I have said before, the evidence is so strong for the sudden arising of all these phyla,

EEERRRNNTTT! The sudden "appearance" in the few fossil strata we have, thank you very much, which is a very different thing from claiming knowledge about he actual speed of "arising". You really *do* need to work on your reading comprehension.

that the famous atheist/materialist/charlatan of evolution S.J. Gould gave up on Darwinian gradualism because of it.

Twaddle. Feel free to quote him to that effect. Oh, wait, you can't, can you? Troll much?

For a thorough and up to date discussion on the Cambrian those interested might check out The Cambrian Explosion - Biology's Big Bang.

AAAAAHHAHAHAHAHA! A creationist screed. I'm sorry, I thought you were going to stick to *science. Sorry, but that work is full of dishonest "pay no attention to that man behind the curtain" evasions, all designed to falsely "eliminate" all alternatives but, "God decided to create worms and other primitive stuff half a billion years ago, and then *they* evolved into humans and things".

Are you sure you want to stick with that theory?

Furthermore, it dishonestly "eliminates" the incompleteness of the fossil record by (laughably) presuming that the pre-Cambrian biota were uniformly distributed across the entire globe (false for reasons I gave in my prior post), and that all fossils found so far are a random sample of them (false on its face, we have fossils from only a handful of regions). This is so stupid it hurts. It also (again, dishonestly) fails to address "evolved one place, radiated elsewhere" scenarios of any sort, like the kind I described in detail in my prior post (and which Gore3000 himself dared not address either).

Creationists are *such* poor players at the game of "I've demolished all your arguments (except for all the ones I'll pretend you didn't make)".

They get caught at it every time, I don't know whom they think they're fooling. Themselves, perhaps.

[Ichneumon]

You have not done much of "anyting"[sic] but blather on about trolling.

Quite the contrary, Andrew, I have repeatedly tried to get you to just stop dancing and discuss the implications of the fact that evolutionary processes can produce complex solutions to non-trivial problems, as shown by the generation of the evolved circuits previously mentioned, and other examples.

Instead, you nitpick and bitch and moan about trivialities like whether substituting a transistor for a diode (in a perfectly accepted method) is enough of an excuse for you to avoid talking about the REAL issues.

So I started documenting all of your silly side trips and red herrings, in an attempt to shame you into dropping the dance and talking about the central topic. It turns out that such an approach won't work because you have no shame.

That's when I declared that you had lost the discussion, as indeed you have. Playing "how long can I nitpick" ad absurdum just demonstrates your intellectual cowardice in a manner that isn't fooling anyone.

(Just out of curiosity -- if I get annoyed enough at your antics to cut to the chase and actually breadboard the circuits in question, test them, will *that* finally be good enough to end your digressions, or will you pull a whole new list of excuses out of your hat for putting off dealing with the obvious?)

Now -- are you finally going to discuss the implications of the results, (yes, SIMULATED or otherwise, Herring Boy), or are you going to raise more useless side issues like "well, unterminated leads can *possibly* cause interference, and even though I haven't the slightest idea whether the purple transistor in this case *will* cause any interference bigger than a mosquito fart, by gosh it's a good enough excuse for denouncing the whole thing as unsupported lies by those damned evilutionists, I'm such a clever guy!!"

You've lost. You lost a dozen posts ago, at least. Dig yourself deeper if you choose, it's your own hole and welcome to it.

[AndrewC]

You are blathering again.

Breadboard it, evidently it has not been done.

[Ichneumon]

You are blathering again.

Readers are capable of making up their own minds on that matter, trying to lead them won't change it.

Breadboard it, evidently it has not been done.

Answer the question first; I want to make sure it's not a waste of my time. You'll find the highly relevant question in the part you tried to write off as "blathering".

[AndrewC]

Answer the question first; I want to make sure it's not a waste of my time

That is what I asked with my initial post. All of this since then has been to get you to produce real evidence to back up your assertions. But remember the circuit must operate at 1Ghz and 2 volts as stipulated in the patent. And use diodes for the patented circuit. If the evolved circuit is the one SciAm, you are going to need the schematic. The SciAm circuit does not indicate which transistors are NPN or PNP. It also seems to be missing the 2V connection for the voltage to current input source.

The other stipulation is that the patented circuit as modeled in the SciAm article has a very important resistor. It is the resistor that provides a "reference" current into the patented circuit(I_out = I_in³ / I_c² It provides the I_c). We don't want to select it so as to handicap the patented circuit.

[gore3000]

Here ya go, *two* of them:

All you are showing is two circuits. There are millions of circuits out there. What you have to show is that any circuit evolved from another without human intervention. Did they breed? Did they solder themselves? Did they pick pieces out of the stock bin without human aid?

Your whole statement (and apparently the statements of unScientific American) are utterly ridiculous. You atheist/materialists are really going off the deep end.

[gore3000]

Like, for example, when you yourself dump a great load of inflammatory and transparently false nonsense such as:-icneumon-

Now it seems to me that it is the evolutionists, who insult in every post,-me-

Amazing! You call my statement about evolutionists insulting at every post false and inflammatory right after starting the post with:

[Trollish Behavior #9:]

Clearly you are just blathering on without the slightest regard to honesty or what you have just said.

[null and void]

Interesting that these threads usually die out early. But here, where there is actual proof that an evolutionary process works, It's deny reality city.

If the facts do not fit the theory theology, they must be disposed of...

[f.Christian]

g3 ...

You atheist/materialists are really going off the deep end.


1,509 posted on 05/16/2003 4:57 AM PDT by gore3000


fC ...

uri geller anarcho loon mind benders alert !

[PatrickHenry]

PLACEMARKER

[Lurking Libertarian]

Blather-resistant placemarker.

[donh]

Then how about giving us an example of a circuit that was not humanly designed? How about giving us an example of a circuit that assembled itself?

Are you not paying attention to the rest of this thread? I guess that wouldn't be much of a surprise, would it?

How about showing us how a pile of garbage organized itself into a tv set, a car, an airplane?

Since, unlike you, I don't take seriously the notion that prokariotes organized spontaneously out of pile of junk, this isn't my problem, now is it?

Your materialist dreams are not evidence, facts, real life examples are what counts.

As you know, I am not a materialist, and, as you know, you have no scientifically valid everyday examples of abiogenesis of prokariotes from junk to offer up to support your thesis, so, naturally, you have to resort to these apposite irrelevancies.

[Ichneumon]

Amazing! You call my statement about evolutionists insulting at every post false and inflammatory

Okay, I'm open to being shown I'm wrong. Feel free to demonstrate that "every" (you did say "EVERY") post by evolutionists contains an insult. Remember, if you find a *single* post by an evolutionist which does not contain an insult, then your statement is indeed false.

Run along now.

[gore3000]

Are you not paying attention to the rest of this thread? I guess that wouldn't be much of a surprise, would it?

Yes, and what I see is a bunch of evolutionists manipulating programs and circuits BY DESIGN and calling it evolution. Now evolutionists claim that it occurs without design as a result of a stochastic process. The materialists/atheists even go so far as claiming that matter can assemble itself. So the question I am asking is perfectly legitimate and cuts to the bone of the whole discussion:

WHERE ARE THE EXAMPLES OF MATTER ASSEMBLING ITSELF WITHOUT HUMAN INTERVENTION????

We know quite well that humans can make a program do anything they feel like such as push 'white' and show 'black'. So programs which are humanly designed do not and cannot ever prove stochastic evolution.

The evolutionists here have also not dealt with the question I have been asking for some 300 posts:

If evolution is science, then evolution must be discernible in real life. How come there is any need to write a program to 'prove' evolution when examples from real life should be everywhere to be seen?????????

[gore3000]

Since, unlike you, I don't take seriously the notion that prokariotes organized spontaneously out of pile of junk, this isn't my problem, now is it?

Lying about my statements. It is your friend donh that supports abiogenesis, not me. Clearly you have not been reading my statements. I am completely against the belief that life can come from non-life. I am glad at least that you agree with me on this one point.

[gore3000]

, I am not a materialist,

You are not only according to your totally contorted definition. According to normal English speech you are.

[gore3000]

You want to play the numbers game? -me-

No, I'd rather you didn't "play games" of any sort.

You certainly are since I already backed up my statement about there being at least 40 new phyla in the Cambrian in the post you just responded to (post# 1489):

Described recently as "the most important evolutionary event during the entire history of the Metazoa," the Cambrian explosion established virtually all the major animal body forms -- Bauplane or phyla -- that would exist thereafter, including many that were 'weeded out' and became extinct. Compared with the 30 or so extant phyla, some people estimate that the Cambrian explosion may have generated as many as 100. The evolutionary innovation of the Precambrian/Cambrian boundary had clearly been extremely broad: "unprecedented and unsurpassed," as James Valentine of the University of California, Santa Barbara, recently put it (Lewin, 1988).

So in a sense you really are not playing games, you are just plain lying.