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."

[Aric2000]

Beat you on this one too....

Ahh, that's no fair, you probably went to bed...

No fun in that, what's the fun of competing when there is no competition?

[donh]

A simulation does not walk in a real physical environment. Programs are concepts as demonstrated in all of the virtual creatures that were "created" in the link you cited. IOW nothing that you presented as evidence was a material object.

A successful demonstration in a simulation, however, demonstrates that the possibility exists.

[Nataku X]

Thank you for your response.

First of all, your claim that the patent has only 5 transistors is wrong. If you actually read through the patent, it refers to transistors Q1-Q8, and refers to a diagrams. It has at least 8 transistors, and probably 9.

Second of all, genetic algorithms are by no means deterministic. We can assume that there is a potentially infinite number of circuits will outperform these patents, and this GA discovered one of htem. You do not have to publish every single little result--that is the major reason why I told you to e-mail the author for the details. However, a GA constructing a circuit outperforming a patent in a few dozen generations is impressive, and would most likely be published. That does not mean that the 17-transistor circuit is the -only- circuit discovered by GP performing similarly to the patent.

Your argument about simulations is an uncharacterstically silly one. Think about the moon landings for example. For something as "simple" as a circuit, theoretically, our ability to make simulations would be perfected. However, the feasibility for mass-production, harsh real-world environments, etc., are not determined.

As a serious question, why are you so quick to put down evolutionary programming? It certainly has its uses. When I took AI, we were shown a video taken at a nearby university.

Basically, they had this robot arm that would throw a tennis ball. Their ultimate goal was to have the robot throw the tennis ball wherever it was told to. Fairly hard to do... sure, you can calculate the ball's path from an initial velocity from a cannon, but you don't really have initimate knowledge of the strength of a robot's arm. They used a genetic algorithm on this robot to make it "learn" how to throw, and pretty soon it was throwing balls very accurately at whatever they told it to throw.

There is nothing religious about genetic algorithms... it's simply one of many useful programming techniques out there that does *very* well in a certain range of tasks, and it would have been invented (albeit with different terminology) even if 6-day creationism was universally accepted as scientific fact.

[f.Christian]

Don't you think the admonition 'know thyself' is good ?


To: PatrickHenry

Do evolutionists like you ...

even examine philosophically the difference between ---

subjective -- bias reasoning ...

and objectivity -- reality ---

your answer all the time -- NO (( "anything mental is not science" )) !


Main Entry: ad·mo·ni·tion
Pronunciation: "ad-m&-'ni-sh&n
Function: noun
Etymology: Middle English amonicioun, from Middle French amonition, from Latin admonition-, admonitio, from admonEre
Date: 14th century
1 : gentle or friendly reproof
2 : counsel or warning against fault or oversight

[Ichneumon]

What science has found is relevant. It has found that over 40 new animal phyla arose during the Cambrian

You're really off to a bad start. "40 new animal phyla"? Time for you to publish your discoveries, because "science has found" only thirty or so animal phyla. Which rock did you find the other 8-10 under, and what are they?

As for "arose during the Cambrian", you might want to show your research on *that* one, too, since the time of the "rise" of many animal phyla is still a subject of debate. The earliest known fossil representation of each phyla certainly doesn't all fall in the Cambrian, for example:

Furthermore, you'll note that phyla Cnidaria most certainly arose *before* the Cambrian. So if you're aware of any evidence that *all* phyla demonstrably arose *during* the Cambrian, feel free to present it now. Or retract your bogus unsupported assertion.

in a matter of a few million years at most.

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.

I also note you carefully left ambiguous what timespan you're referring to when you say "a few million years". After all, half a billion years is "a few million years", if you want to be vague enough.

Hint for those who don't get all their "science knowledge" from creationist sources: Undeformed Cambrian and pre-Cambrian strata which are reachable from the surface are far and few between. The older a rock strata, the more likely it is to be buried under thousands of feet of more rock, or eroded away at some point in the past to sand and dust, or so crushed and deformed or damaged by force and heat, or lost to subduction, that few fossils would remain intact (and fossilation is a rare enough process anyway, requiring special conditions to occur). And Cambrian (or older) strata are *VERY* old (540 million years and up). So there are only about a dozen known Cambrian or pre-Cambrian fossil beds of good quality anywhere in the world, period. To fill in the admittedly large gaps in our knowledge of this period in the Earth's history, we'll have to wait until we make more lucky finds of fossil beds of that great age.

What is known at this point is that by the early Cambrian period, there were many diverse life forms already in existence (although by today's standards they were all *extremely* primitive, and many downright "alien"). And that the few known fossil beds from 10-20 million years earlier show only considerably simpler life forms (gee, just as you'd expect from evolution, hmmm...) From this, some people have concluded that there was a large burst of evolution which took place within that relatively (but not unreasonably) short geological time period, dramatically changing the biological landscape in what would have been one of the more abrupt evolutionary diversifications in history.

As you'll note from his subsequent rantings, Gore3000 tries to claim that this was "impossibly" fast. Nowhere does he provide any *support* for his claim that this amount of evolution couldn't occur that quickly under the right conditions, you'll note. Actually, people who study evolution for a living generally agree that while the so-called "Cambrian explosion", if it actually occurred (and its occurrence is only implied) would likely rise only to the level of "surprisingly" fast, not "impossibly" so.

However, the Cambrian "explosion" may only be an apparent, and not a real, sudden proliferation. What Gore3000 "forgets" to mention (along with his creationist buddies who similarly like to sieze on the sudden Cambrian appearance of diverse life forms -- despite the fact that it causes far more problems for their *own* theory than for evolution) is the fact that there are certainly entirely other explanations for the apparent "explosion".

One of the more plausible, and in fact the one I personally think is extremely likely, is the idea that there were separate seas in those days, cut off from each other for many millions of years. Continental drift caused the continent(s) to be configured very differently in those days, and it's quite possible that for many tens or hundreds of millions of years, a portion of the ocean was landlocked with respect to the other oceans of the time. Evolution taking place in this isolated sea could have had a biological breakthrough of some sort which over, say, 100 million years led to the diversification we eventually see in the Cambrian period. And yet, fossil beds from the oceans *outside* the landlocked ocean would show relative evolutionary stagnation during this entire period.

Finally, when continental drift spread the landmasses apart and "broke open" the landlocked ocean, the "advanced" life forms it contained would quickly (geologically speaking) spread throughout the rest of the world's oceans, making for a "sudden" appearance in the fossil record from those regions of "new" lifeforms which appeared "suddenly", supplanting the more primitive life which had until recently lived in those oceans.

Arguments for this hypothesis:

1. The Cambrian period is *known* to be the time that most of the world's continents, until then all jammed together, began to move apart from each other and break up the "supercontinent". This would be the time you would *expect* any landlocked seas to "spill open".

2. In the fossil record there appears to be a wave of extinction, with most of the known pre-Cambrian life forms vanishing and being supplanted by the Cambrian life forms.

3. DNA analysis of modern phyla indicate a divergence point for most to be long before the Cambrian -- up to 400 million years earlier. Such "molecular clock" techniques are sometimes controversial (mostly with respect to the question of how "constant" the "clock" may run), but barring some better explanation, the best research currently indicates a much longer run of pre-Cambrian evolution than could justfiably be called a short-term "explosion".

If the above scenario is correct, then someday we ought to discover a pre-Cambrian fossil bed (i.e., from a region which was within the landlocked ocean) which contains a fossil history of life from at least 700MyA to 540Mya that is much richer than that currently discovered for the same period (which so far presumably are from outside the landlocked pre-Cambrian "cradle of life").

In short, creationists like Gore3000 presume that if a pre-Cambrian fossil bed from *one location* shows a certain collection of life forms at a certain point in time, then the *whole world* must have been like that at that time. Next, he'll likely be telling us that kangaroos can be found worldwide...

It has found no possible ancestors for the vast majority of these phyla.

Your wording reveals that you're aware that there *are* ancestors for *some* of the phyla. For example, there are pre-Cambrian fossils that are clearly soft-bodied ancestors to trilobites, despite the fact that all Cambrian-and-later trilobites are armored:

In addition, no new animal phyla have arisen since that time.

Again with the psychic pronouncements, eh? Prove it. For example, please demonstrate your evidence which shows that, say, the Nematoda phyla did not arise after The Cambrian. We'll wait.

This totally disproves Darwinian evolution

No, it doesn't. You are, however, invited to explain why you believe it does. Be sure to be specific and show all your work. Extra points for neatness.

and is why Gould and Eldredge, both inveterate atheists, broke off with Darwin and proposed a totally new materialistic/atheistic theory

You're delusional again. Gould and Eldredge did not "break with Darwin", as any examination of their writings will amply prove, nor is punctuacted equilibrium "a totally new" theory. It is, in fact, nothing more than Darwinian evolution with the realization that evolution is not always a steady progression, since varying conditions will cause it to speed up and slow down quite a bit -- just as, say, erosion sometimes happens at a snail's pace (in low moisture, low wind conditions), and sometimes proceeds with the speed of a flash flood which washes away millions of cubic feet of material literally overnight.

(based on nothing but wishful thinking).

Where *do* you get this goofiness? Oh, right, creationist sources. Try cracking open a science journal someday, son.

Far from being based on "nothing but wishful thinking", the theory of punctuated equilibrium was based on mathematical models of how evolutionary processes would vary in rate depending upon conditions, and was verified by field studies.

Your batting average isn't real good tonight, is it?

The scientific facts about the Cambrian are as I stated them to be.

*cough*. See above.

Not a single evolutionist has been able to come up with a legitimate evolutionary explanation that fits the facts.

For pete's sake -- just because *you're* blissfully ignorant of them, doesn't mean that there aren't "legitimate evolutionary explanations that fit the facts". There are, in fact, at least a dozen competing explanations (including the one given above, as well as many others which argue that even a 10-20 million year "explosion" of evolution would not be unreasonable at that point in the history of Earth and life as it existed at the time, based on rising oxygen levels, the first development of predation driving evolutionary pressures into high gear, the plasticity of a more simplistic DNA, etc. etc.)

If *you're* not aware of these "evolutionary explanations", it's just because you haven't bothered to look. And you're naive if you think your favorite creationist reading material is going to present them for your education.

What do you expect, for every new idea in evolutionary theory to be personally delivered to your door gift-wrapped? Get thee to a library, son.

The Cambrian disproves gradual evolution completely.

Really? How? You "forgot" to explain your reasoning.

My beliefs (and yours) are irrelevant as to the facts in this matter or any other scientific matter.

And yet, you just expressed your unsupported *belief* in the prior sentence. Contradict yourself much?

The facts speak for themselves.

Yes they do. And when you learn as many of them as the rest of us, you'll make a fool of yourself less often.

evolution is bunk and the only proof it can provide is: lies, doubletalk and insults.

I'm sorry, you seem to have us confused with your own posts.

[donh]

."Faith" is the proud claim that you haven't proved diddly.

You certainly have not. All you do is ask others to prove their point

Gee, you mean I ask for a demonstration of fantastic claims to certainty about the nature of abiogensis--Oh, the horror of it all!

you never prove yours.

Yes...well, but then, I don't make universal claims to certainty, do I? I never claimed I had, needed, cared about, or believed in a proof in any natural science, unlike someone I know, who repeatedly claims to have "proven" that evolution can't have happened.

[Ichneumon]

As a serious question, why are you so quick to put down evolutionary programming?

As he is unlikely to give a straight answer to that question, allow me... He is so quick to put down evolutionary programming because he and most of his fellow creationists have invested a lot of time, emotion, and belief into the claim that evolution (in general) simply *can't* produce complexity, clever solutions, or novel results.

They believe this as an act of faith, because they "know" that only a "Designer" can produce complexity. And conversely, if something appears complex, it "must" be the result of a "Designer".

They even write long essays and books (or buy and read same) which provide armchair philosophical "proofs" for why evolutionary processes simply "can't" produce complex results. (See Behe, Spetner, Dembski, etc.) This gives them comfort for their "complex things *must* be designed" presumption (and the theistic conclusion it "proves").

So, no matter how overwhelming and undeniable the evidence that evolutionary process can, when put into action, produce beautifully elegant and complex results, they're always going to a) reject the obvious, and b) claim that the test must be "rigged" somewhere, even if they can't quite locate the "fix".

They are, quite simply, the modern flat-earthers, ready to reject any and all evidence no matter how voluminous or indisputable, until the day they die.

"I know that most men, including those at ease with problems of the greatest complexity, can seldom accept even the simplest and most obvious truth if it be such as would oblige them to admit the falsity of conclusions which they have delighted in explaining to colleagues, which they have proudly taught to others, and which they have woven, thread by thread, into the fabric of their lives."

Leo Tolstoy (1828 - 1910)

[Ichneumon]

Yes...well, but then, I don't make universal claims to certainty, do I? I never claimed I had, needed, cared about, or believed in a proof in any natural science, unlike someone I know, who repeatedly claims to have "proven" that evolution can't have happened.

He makes quite a habit of making wild claims and then running away from challenges that he support them.

[donh]

Don't feed the troll.. It makes him stronger, kinda like popeye and spinach.

Thanks for the advice, but I intend to feed this troll his own detritus every time I find him peeping in public. Creationists who are merely ignorant warrant some slack, perhaps; but this guy is an animate post-bot with apparently no memory, no significant responsiveness, and no apparent argumentative scruples, and egging him into displaying his stuff is maybe the best thing one could do to tip any lurking fence-sitters into the science fold.

[Nataku X]

The explanation's more complicated with that.

Coming from a religious background, I was constantly surrounded by fundamentalist Christian literature and people. There is an unfortunate tendency to mix very highly political "doctors" and professors (e.g., the philosophy professor who said that we have a 20% chance of living in The Matrix) who have controversial, liberal opinions. Chuck Colson, for example, spends many radio broadcasts on silly Feminist-Ecology professors who are truly the "evil atheists" that G3K seeks out so viligantly. (Then he switches tracks and he will talk about evolution.)

You mix scientific doctors/evolution in the bag, and it's easy to make the connection that the peer-review world is nothing but a political sham, and that all university scientists are like that Matrix philosophy professor or feminazi professors.

Then, you have the "Elizabeth Smart" effect--even though the number of kidnappings are historically low, it seemed last year that kidnapping was epidemic because of over-reporting. When the Piltdown fraud, and the Haeckel fraud are repeated over and over, it's easy to believe that peer review is about as solid as a house of cards.

It's impossible to sympathize unless you've grown up in that kind of culture, but the basic point is--I don't blame AndrewC, Gore3000, or any of that crowd in the least bit for being so suspicious.

[f.Christian]

ok wizard ...

the science fold ---

tornado !

[f.Christian]

No one posed the issue more forthrightly than did Isabel Patterson in her book "The God of the Machine," written in 1943: "There can be no greater stretch of arbitrary power than is required to seize children from their parents, teach them whatever the authorities decree they shall be taught, and expropriate from the parents the funds to pay for the procedure." She declared that "every politically controlled education system will inculcate the doctrine of state supremacy, sooner or later. ... A tax-supported compulsory educational system --- is the complete model of the totalitarian state."

Patterson wasn't talking about Cuba, she was talking about America. Her words are prophetic. It is plain to see, for anyone who wishes to see, that the government of the United States has begun the process of usurping parental rights, and dictating what our children may and may not know, believe, think and value.

[donh]

.You will kindly note, from your own evidence here, the phrase "...evolution, which has not been FULLY proved even in the domain of natural sciences..."

Keying on Fully as the evidence that the Church accepts Darwinian evolution? If not, what other evidence do you offer about the Church's acceptance of this as man's origin? I am not aware of any and I have checked extensively since returning to the Church.

Checked where? In a paper bag in the back of your closet? Let me call your attention to the 1996 formal address of the Pope to the Pontifical Academy of Science. I draw your attention to the rather famous 4th numbered paragraph, which, while the first official peep from a pope on the question, does not belay the fact that the jesuits have been teaching evolution since the 50's.

http://www.newadvent.org/docs/jp02tc.htm

I have heard many a lame explanation about how the Pope didn't really mean, it, or the pope wasn't speaking in the FORMAL VOICE OF JESUS at that particular moment--which is a pretty funny one, considering where He Said It.

But, I have never heard anyone say it was too obscure for him to look up. How innovative.

[donh]

ok wizard ...

the science fold ---

tornado !

Expecting a comprehensible answer ---

looked in vain ...

fooled again! ---

[donh]

A tax-supported compulsory educational system --- is the complete model of the totalitarian state."

The one creationist theory with which I can agree. Proving the adage that even a broken clock can be right twice a day.

[Celtic Conservative]

"lecher christian"? who mentioned "mutiny on the bounty"?

---

Slainte,

CC

[f.Christian]

There are many conclusions and ideas that can be drawn from these passages. Here is mine, for the benefit of the remnant, whoever and wherever you are:It requires soul-deep faith to stand strong and hold your place ... when raging winds --- are uprooting and scattering everything around you. If there is a temptation to cease the struggle and give way, keep in mind that the threatening winds may have been sent by a God who is about the business of separating the wheat from the chaff.

Linda Bowles ... memorium (( FR thread ))!

[Ichneumon]

The bad news is that:

It is all simulated

Not necessarily. I see no indication in the paper that they didn't breadboard their best result in order to verify it in the "real world". You're jumping to conclusions.

But even if they didn't and it was "all simulated", so what? Are you not aware that using circuit simulators like SPICE is how *human* designers formulate their designs as well? Are you under the impression that electronic devices like transistors and resistors somehow aren't so well understood and predictable that circuit simulators *aren't* highly accurate? If transistors et all were as unpredictable as you imply, they couldn't even be used to make reliable circuits at all.

Finally, even if evolved circuits allegedly outperform human-designed circuits "on the simulator" (a trivial point, since the behavior of an electronic circuit is just as complex on the simulator as it is in "real life", even if it's allegedly "off" by a few percent), how does that somehow invalidate the point being made, that evolution can outdo human-designed efforts, in whatever realm? The arena is irrelevant when the rules are applied equally to both competitors.

In short, you're really splitting hairs again.

The evolved circuit in the paper has 18 transistors not 17 as in the SciAm article(it is not the same circuit)

True, it's not the same circuit. The researchers appear to have topped their prior "personal best" and produced an even better circuit, which they presented in their later paper. Your point?

The patented circuit has 5 transistors and 4 diodes not 9 transistors(pointed out previously)

Oh, puh-leaze... If you know this little about circuit design, maybe you shouldn't be trying to critique it.

Hint for the newbies: If you wire the base and collector of a transistor together, it acts as a diode.

Now, how many transistors in the Scientific American picture are wired this way. Four, right? How many diodes are in the Patent application Figure 6. Four you say? This leaves 9-4=5 transistors operating as 3-lead transistors, right? How many transistors are there in Figure 6 of the patent application? Can you say 5? I knew you could.

Bigger hint: Replace the input-looped transistors in the Sci.Am. article with diodes, and *ta daa*, you get exactly the circuit in Figure 6 of the patent application.

Thus endeth Circuit Design For Dummies.

The evolved circuit has a larger maximum error

Whoop de do. It's only on the very top end, for a tiny fraction of the domain, and it's 1.3% deviation versus 0.87% deviation for the patented circuit. At almost all other portions of the domain it has significantly less error than the patented circuit, including during the critical first 90%. Furthermore, the patented circuit shows some real ugly deviation from 75% upwards, while the evolved circuit only starts going into significant deviation upwards of 95+%.

You're grasping at straws again. For any real application I'd choose the evolved circuit over the patented one any day.

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.

And since the patent *did* "call for a different model" by specifying a frequency domain up into the gigahertz range, your point is moot, isn't it?

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.

And your belief that circuit simulation (a process so well refined due to the inherent physical predictiability of electronic components that human designers consistently rely upon it when doing *their* designs) is somehow a huge departure from actual performance is based on... what?

Again, you're grasping at any straw you can find to try to avoid having to deal with the undeniable fact that despite creationist "proofs" that evolution can't produce any solution of complexity or "increasing information content" or at a level to compete with "intelligent design", when evolution is actually put to work, time and time again it *does*.

Deal with it squarely, and stop squirming.

[js1138]

Flecher Christian

[PatrickHenry]

Beat you on this one too.... Ahh, that's no fair, you probably went to bed... No fun in that, what's the fun of competing when there is no competition?

Winning is what it's all about. Don't worry about fighting fair.