Digital Darwin

An anonymous reader writes "Using genetic algorithms to breed strings of computer code graphically, this week's Nature magazine describes results from Caltech and Michigan State. Their program is Avida. While they mainly mimic mutation, not genetic cross-over [or inheritance (thus wiping away much memory of initial conditions)], their simulations show how a short-term backward step in survival strategies can generate innovative advances. It is not unlike running a maze which necessarily involves testing alot of dead-ends, and thus shares the graphical look of Conway's classic Game of Life." Here's a National Geographic story about this as well, or see their press release.

Comments

How can a man evolve code...

[JohnnySkidmarks]

I thought only god could do that?

I've used genetic algorithms

[sstory]

And I wish everyone could see them at work. It's really kind of breathtaking how stumbling around in the parameter space, and filtering the bad missteps, can mimic the results of engineering. I think the minor problem of the small number of noisy anti-evolutionists would become even more minor. I mean, it's kind of hard to say that an algorithm doesn't work when you can compile a few thousand lines of c and then watch it work.

Re:I've used genetic algorithms

[Anonymous Coward]

LOL! Yes, I have sometimes wondered too how the heck you're supposed to prevent evolution on a hospitable planet hanging around a stable sun for billions of years.

Re:I've used genetic algorithms

[jdevers77]

That makes the assumption that the anti-evolutionists are logical people. I would say that the many thousands of undisputable cases of evolution around us every day would also make them shut up, but it doesn't. Maybe when they are infected with antibiotic resistant Staph they will think about it from a different perspective...

Re:I've used genetic algorithms

[AndroidCat]

small number of noisy anti-evolutionists

For what value of small?

Re: I've used genetic algorithms

[Black Parrot]

> I think the minor problem of the small number of noisy anti-evolutionists would become even more minor. I mean, it's kind of hard to say that an algorithm doesn't work when you can compile a few thousand lines of c and then watch it work.

Yeah, as soon as I saw the article I thought, "How many evolution deniers will we dredge up this time?".

It would be nice if someone had an on-line hub linking to all the GAs that are free and source-available, so that people could download one and try it themselves, look at the code if they suspected the answer was cheated in, and maybe tweak some parameters to see that both mutation and selection are actually needed for such systems to work. (The evolution deniers on talk.origins are fond of attacking mutation and selection independently, as if one or the other should be sufficient according to the theory of evolution.)

Of course, some puppies would deny peeing on the floor even as you rubbed their nose in it, but we might as well inform those who are informable on matters of science.

Re: I've used genetic algorithms

[aborchers]

I enter the fray reluctantly.

The first thought I had when I saw the article (presented on Space.com as "Darwin Proved Right ...") was that simulating something in a computer does not necessarily prove anything about the physical world. We can synthesize all sorts of things that have no analogy in nature. EA, AI, are fascinating fields inspired by evolutionary theory, but I fail to see how executing a computer program that assumes evolution in its infrastructure proves anything but that modelling evolution in software works.

For the record, I am not anti-evolution, though I may occassionally be noisy...

Re:I've used genetic algorithms

[Anonymous Coward]

Maybe when they are infected with antibiotic resistant Staph they will think about it from a different perspective...

Yes, but God moves in mysterious ways ... (is the pithy response of the christian when anything shitty happens to them/family/friend etc)

Re:I've used genetic algorithms

[b-baggins]

All this program does is take an existing gene pool, introduce random mutation, and stress it.

This has only been going on for, let me see, since mankind first bred cows to increase their milk production?

Here's what this and all genetic algrorithms do NOT address:

Getting the genetic code initially from a bunch of extremely unstable chemicals that do NOT want to combine naturally.

Louis Pasteur demonstrated a couple of centuries ago that spontaneous generation was junk science. Maybe someday evolutionists will finally take a look at his work.

Re:I've used genetic algorithms

[drooling-dog]

Indeed. Given the way that genetic inheritance works -- e.g., with mutation, crossover recombination, etc. -- you could argue that evolution is a matter of mathematical necessity. But faith always trumps reason with the creationists, and so it's usually an exercise in exasperation to debate the issue, no matter how solid your arguments are. They will refuse to comprehend them as a point of principle.

I've done some GA work myself, and it is quite fascinating. E.g., too high a mutation rate and the system destabilizes, but too low a rate and it never (or very slowly) finds its optimum fitness. Throw in some genetic recombination (simulating sexual reproduction) and evolution to higher mean levels of fitness accelerates considerably as useful "genes" are conserved while others quickly disappear. It's very cool.

Modern creationists are in the same place that official Christiandom was in the time of Galileo, I think. If you're religious, nothing in modern biology (which largely is evolution) really denies a role for a deity in kickstarting the whole shebang. Setting up the system to run itself unattended, in fact, would have been the smart way to do it. Those who insist that God would create a system far inferior to this -- i.e., that requires endless hand-tweaking of every minute detail -- are really delivering Him a kind of insult, aren't they?

Re: I've used genetic algorithms

[Black Parrot]

> The first thought I had when I saw the article (presented on Space.com as "Darwin Proved Right ...") was that simulating something in a computer does not necessarily prove anything about the physical world. We can synthesize all sorts of things that have no analogy in nature. EA, AI, are fascinating fields inspired by evolutionary theory, but I fail to see how executing a computer program that assumes evolution in its infrastructure proves anything but that modelling evolution in software works.

Yes, they shouldn't say "Darwin Proved Right" (for several reasons).

However, a simple genetic algorithm instantly refutes many of the most popular claims current in evolution-denial circles, and thus this kind of thing should serve well for informing the public on those claims. (And also inform the public about how uninformed the people making those claims are.)

Re:I've used genetic algorithms

[johnsoda2010]

Hmm...
How does starting with
- 'a few thousand lines of c',
- a well-defined 'parameter space',
- 'filtering the bad missteps'

compare with the real world, where we started with absolutely nothing?

In the real world, where did the c code come from? What about the filtering rules?

The reason evolutionists have to keep coming up with new proofs of their theory is that the old ones keep getting disproved! Wait until one has lasted a few decades, and then we'll talk.

Re:I've used genetic algorithms

[AccUser]

So how many lines of code are you compiled from?

Re:I've used genetic algorithms

[Anonymous Coward]

Louis Pasteur demonstrated a couple of centuries ago that spontaneous generation was junk science. Maybe someday evolutionists will finally take a look at his work.

You're kinda right and kinda wrong. Spontaneous generation as an explanation of how, for example, maggots come to inhabit meat left in the sun, has been comprehensively disproven.

However, none of the methods and experiments used to disprove it apply to the first emergence of life, for the simple reason that all these arguments and experiments took place in a world packed with life, whereas the first emergence of life from simpler chemical processes necessarily happened in a world devoid of life.

The theory of evolution does not attempt to address the first emergence of life; Darwin and all his followers to the modern day write about that specifically as a seperate problem. It's a difficult one --- and one in which a "final answer" as to "how it actually must have happened" is almost impossible to arrive at scientifically due to the difficult nature of experiments and the fact that the first emergence of life was a "one-time" event that cannot by its nature be re-run --- but lots of progress has been made. Look into complexity theory for an example of today's hypotheses.

Re: I've used genetic algorithms

[Black Parrot]

> Here's what this and all genetic algrorithms do NOT address: Getting the genetic code initially from a bunch of extremely unstable chemicals that do NOT want to combine naturally.

a) That's called abiogenesis, and the theory of evolution doesn't say anything about it.

b) To the extent that chemicals "want" to do anything, the chemicals used in life are in fact very eager to combine. Or do you suggest a miracle for every chemical reaction that happens in your body over the course of your life?

> Louis Pasteur demonstrated a couple of centuries ago that spontaneous generation was junk science. Maybe someday evolutionists will finally take a look at his work.

Actually, Pasteur merely demolished folk notions of flies arising spontaneously in meat and mice arising spontaneously in grain. He did not refute chemistry. And all a planet needs for chemical life to get started is for some sort of chemical self-replicator to form. If the self-replication is imperfect and the environment is rich, evolution can bootstrap the wonders of biology from there.

What the computer simulations show is that Darwin not only thought up one of the best ideas in the history of biology, but that he actually thought up a "law of imperfect replicators" that transcends biological history.

Re:I've used genetic algorithms

[greg_barton]

How does starting with
- 'a few thousand lines of c',
- a well-defined 'parameter space',
- 'filtering the bad missteps'

compare with the real world, where we started with absolutely nothing?

How about starting with
- 'the entire universe',
- 'all possible paramater spaces' (see above)
- 'filtering the bad missteps'

We didn't start with "absolutely nothing" as you assert. We started with absolutely everything.

Re:I've used genetic algorithms

[Anonymous Coward]

The reason evolutionists have to keep coming up with new proofs of their theory is that the old ones keep getting disproved!

Nope: the central proofs in Origin Of Species still hold.

Re: I've used genetic algorithms

[aborchers]

Yes, they shouldn't say "Darwin Proved Right" (for several reasons).

Well said, and I assume you would put "irreducible complexity" cheif among them.

It's ridiculous that in the 21st century we have to tread so carefully over the biases, misconceptions, and agendas in presenting science.

Re:I've used genetic algorithms

[Anonymous Coward]

Argh, left my password at home, must post AC, and can't reply to the two (likely to be more) messages directly...

You're absolutely right, evolution (as common descent) says nothing about how the "unstable molecules" ended up forming genes, and life forms that reproduce and mutate and all that.[1] That isn't, however, a weakness of evolution, as it makes no claims to describe the origin of life, just the origin of species once life is already up and kicking. Attacking it on that point is like attacking the Church-Turing thesis on the grounds that it doesn't explain the behavior of semiconductors.

[1] I've read an interesting book putting forward a theory of the origin of life, based on the dissolution/precipitation equlibrium of clay crystals in soils. It described that equilibrium in terms of crystal "reproduction", "death", and "mutation", establishing the necessary preconditions of evolution without there being any life at all. However, that is a theory tangential to what's being discussed.

Re:I've used genetic algorithms

[greg_barton]

That makes the assumption that the anti-evolutionists are logical people.

Very true. And, in the case of using genetic algorithms as a point of evidence in an argument, this assumption works against you. For many people computers are a black box. If you say, "I have a computer program that models mysterious process X" it's just replacing something mysterious with something incomprehensible.

And, before you do that, you have to assume that arguing is a productive activity in the first place. With many evolution deniers, it is not. But since they've wandered into my cave (the realm of logical, rational thought) I find it's my duty to eat them alive. :)

Re: I've used genetic algorithms

[Black Parrot]

> > Yes, they shouldn't say "Darwin Proved Right" (for several reasons).

> Well said, and I assume you would put "irreducible complexity" cheif among them.

No, "irreducible complexity" is utter bunkum made up by Behe to give a pseudo-scientific veneer to his underlying "I don't see how it could happen" argument.

If you want to know how many times the IC argument against biological evolution has been refuted, ask about it on talk.origins. The only interesting research question that IC gives rise to is whether Behe continues to promote it out of idiocy or dishonesty. (Given the number of time it has been debunked, I suspect the latter. But I'm not a mindreader, so maybe I'm wrong about that.)

Re: I've used genetic algorithms

[schon]

That's called abiogenesis

Really? I thought abiogenesis was the R&D of Sony's robotic dog.

Oh, no - that would be AIBOgenesis.

My bad :o)

Re: I've used genetic algorithms

[Black Parrot]

> Really? I thought abiogenesis was the R&D of Sony's robotic dog. Oh, no - that would be AIBOgenesis.

AIBOgenesis is the robodogs' myth about where they came from.

Re:I've used genetic algorithms

[Anonymous Coward]

You guys have some serious baggage you need to get over. You look at a very cool experiment in evolution theory and one of the first things that comes to mind is how you can beat anti-evolutionist over the head with it. What's that about?

Neither the "evolution as the creator of all we see" or the "white-haired guy snapping his fingers" approach to creation are truth. They are simply models that help organize and explain experience in very different domains.

Truth does not need fanatics of any kind to beat their chest and point fingers of disparagement at other human beings. Truth isn't that fragile. Truth wins.

Re: I've used genetic algorithms

[Dr. Wonz]

I was looking at GAs for a solution in a n parameter system in chemistry.

Here's a nice collection of links and source codes I found back then: The Genetic Algorithm Archive

Re:I've used genetic algorithms

[gillbates]

Modern creationists are in the same place that official Christiandom was in the time of Galileo, I think. If you're religious, nothing in modern biology (which largely is evolution) really denies a role for a deity in kickstarting the whole shebang. Setting up the system to run itself unattended, in fact, would have been the smart way to do it. Those who insist that God would create a system far inferior to this -- i.e., that requires endless hand-tweaking of every minute detail -- are really delivering Him a kind of insult, aren't they?

A point seemingly lost on a lot of right-wing fundamentalists. When you study religion, you notice certain trends, and one of these trends is that the oldest and most well established religions don't ask their believers to deny their intellectual capacities. The problem with "creation scientists" is the same problem with "evolutionary biologists" - each firmly believes in their position regardless of the weakness of the position or evidence to the contrary.

Weak minds often have a hard time with the intelligent design arguments of creation. While we don't specifically deny evolution, we posit that there was a Creator who started the process, and has and does attend to his creation. When one looks at the complexity of living things compared to that of inanimate objects, one can't help but be struck by the difference in complexity between what merely exists and those things that grow.

Interestingly, while this study can show the merits of evolution, it does more to bolster the intelligent design theory than to destroy it. While the experiment was very interesting, we must remember that the digital organisms did have an intelligent designer - it's not like the programs sprang to life on their own!

Re: I've used genetic algorithms

[VendingMenace]

hmmmm...the chemicals in our body are EAGER to combine?

I think not. Most of the reactions in out body have such a high activation energy that their kenetics are extremely slow. Granted, most of the reactions are thermodynamically favorable. However, in ambeint temp and pressure, you would be hard pressed to measure the rate of many of the reactions that are common within our bodies.

The fact remains that there is just no good explination for how life (and the chemicals of life) arose out of nothing. Most "scientific" expliniations are just half-baked suggestions. To there credit, they are the best that science has come up with, but that does not mean that they are sound theories. THere is just too many crazy things that have to happen, from the formation of the basic chemical to the creation of protiens and DNA sequeces (let alone the protiens that read DNA!) That i think is where many people have their problem, NOT with evlolution.

Now about evolution. By the stict definition of evolution, no one can logically deiny that evolution is happening right now. HOWEVER, speciation, that is another thing entirely. I am not sure that we have ever witnessed specieation, but i could be wrong about this. Please let me know if i am.

SWEET!

Re:I've used genetic algorithms

[fluffy666]

Well, in Europe it's a 'Lunatic fringe' thing, although the American evangalists seem to be trying to export it.

Re: I've used genetic algorithms

[enbody]

I interpret the results differently. Some anti-evolutionists argue that there are certain existing structures which they believe could not have evolved and use that observation to claim that the theory of evolution is wrong. This work demonstrates a mechanism for the evolution of that class of structure. Hence, it removes yet another argument from anti-evolutionists.

In my interpretation of the results, I would argue that while the criticism "all this work does is simulate evolution on a computer" is a correct observation it misses the important result that a mechanism is demonstrated.

Re:I've used genetic algorithms

[Waffle Iron]

While we don't specifically deny evolution, we posit that there was a Creator who started the process, and has and does attend to his creation.

Fine. Now who designed this Creator?

Re:I've used genetic algorithms

[56ksucks]

You would also assume that all creationists are anti-evolutionists. This is not always the case. There are some that believe that Micro-evolution is not only possible but conforms to their sacred writings (the bible). Micro-evolution being that all the different variety of one kind of animal all began with the first ancestor of the same kind, for example, cocker spaniels, poodles and wolves and even foxes all came from a common ancestor, but that common ancestor was in fact a dog. What isn't accepted is Macro-evolution, or that cats, dogs, and lizards, being of a different kind, have a common ancestor. In this way of thinking an antibiotic resistant Staph would be very possible because even though the Staph has now become resistant to modern medicine it is still a Staphylococcus aureus bacteria. We discover a new virus all the time, but one thing remains the same, it's still a virus.

Re:I've used genetic algorithms

[naasking]

What the experiment actually shows is that complexity can evolve from simplicity. Thus, it is one more nail in the coffin of intelligent design since "the difference in complexity between what merely exists and those things that grow" could be merely a consequence of evolution.

Re: I've used genetic algorithms

[aborchers]

I persist because it seems more diligent than to take the easy path that leads me to interpret the results as justifying what I already perceive to be true.

I don't think I missed the result that a mechanism was demonstrated, and I definitely didn't mean to suggest that demonstrating a mechanism was without value. I merely view it as a side show in context of a philosophy of science.

I fail to see how demonstrating a mechanism in simulation (as opposed to in nature) can be used to make any proper claim about the physical universe. Remember the issue I took with the article I read was with the notion that there was a "proof" inherent in this demonstration.

The EA programmers take a hypothesis about how the universe works (a hypothesis that, I stress again, I consider to be effectively "proven" without the assistance of simulations), use it to build a model, and then demonstrate that certain things follow from that model. Where is the philosophical "connective tissue" to the physical world?

I'm perfectly willing to believe that I'm missing one or more details as I'm neither an EA or biology expert (in fact, even my philosophy of science studies are pretty far in the past) but I'd like to be filled in if I am.

My greatest fear is that some anti-evolutionist may seize upon this argument somehow to bolster their claims. Maybe I should shut up now. :-)

Re:I've used genetic algorithms

[drooling-dog]

So... Because something can be successfully modeled and simulated, it's thereby disproven? That's one I've never seen before, even from creationists.

The reason evolutionists have to keep coming up with new proofs of their theory is that the old ones keep getting disproved! Wait until one has lasted a few decades, and then we'll talk.

No, it's because this is science, where truth is subject to quality control through observation. A lot messier than religion, where knowledge is absolute and frozen for all time. Do you reject all scientific knowledge that isn't delineated in the Bible, which after all reflects no more than mankind's understanding of the universe at the times it was written? Do the sun, moon, and the heavens all revolve around the earth at the center of the universe? Why is it only the theory of evolution that so threatens the faith, and not, say, theories of gravity or electromagnetism?

And lastly, could God have given us these wonderful brains and not expected that some of us would use them?

Re: I've used genetic algorithms

[Black Parrot]

> Hmm... How does starting with
- 'a few thousand lines of c',
- a well-defined 'parameter space',
- 'filtering the bad missteps'
compare with the real world, where we started with absolutely nothing?

> In the real world, where did the c code come from? What about the filtering rules?

In the real world, the "c code" is called "chemistry", and it comes from the basic laws of nature. The "well defined parameter space" is called "the universe". The "filtering rules" are the simple fact that with the given "c code" and "parameter space", some organisms are more likely to survive and reproduce than others.

Now as to where chemistry, the universe, and everything came from... biology doesn't pretend to address those answers.

> The reason evolutionists have to keep coming up with new proofs of their theory is that the old ones keep getting disproved! Wait until one has lasted a few decades, and then we'll talk.

I'm curious whether you even know what the current theory that explains evolution is, let alone know how long it has been around.

Re: I've used genetic algorithms

[Noren]

Now about evolution. By the stict definition of evolution, no one can logically deiny that evolution is happening right now. HOWEVER, speciation, that is another thing entirely. I am not sure that we have ever witnessed specieation, but i could be wrong about this. Please let me know if i am.

We've seen speciation lots and lots of times. See the relevant portion of the talk.origins FAQ.

Another set of interesting examples are "ring species"- species where population A can breed with B, B can breed with A or C, and C can breed with B... but A can't breed with C (or produces only infertile offspring.) This can happen when the three populations are semi-isolated but with occasional travel between A and B, and between B and C. By most species definitions A, B and C are one species, as each type can (at least indirectly) share genetic information with the others. The key development which can occur in this situation- if all the B die, there are now two different species A and C. This would be instant speciation.

Re: I've used genetic algorithms

[Black Parrot]

> The problem with "creation scientists" is the same problem with "evolutionary biologists" - each firmly believes in their position regardless of the weakness of the position or evidence to the contrary.

Could I trouble you to summarize the weakness of the position of evolutionary biologists and the contrary evidence? Presumably you have something beyond the same old tripe that has been refuted hundreds of times, or you wouldn't be saying that.

> Weak minds often have a hard time with the intelligent design arguments of creation. While we don't specifically deny evolution, we posit that there was a Creator who started the process, and has and does attend to his creation.

And that position is completely worthless as a way of understanding the universe, because it is compatible with any observation whatsoever.

> When one looks at the complexity of living things compared to that of inanimate objects, one can't help but be struck by the difference in complexity between what merely exists and those things that grow.

What measure of complexity are you using? I'd like to see your calculations showing the complexity of a squirrel and the complexity of the Nile delta.

But maybe before we get into that too deeply... What has complexity got to do with anything? Are you making an underlying claim that complexity can only come about as a result of intelligent design? Is the Nile delta the result of intelligent design? Are intelligent designers the result of intelligent design? (Where did the first intelligent designer come from?)

> Interestingly, while this study can show the merits of evolution, it does more to bolster the intelligent design theory than to destroy it. While the experiment was very interesting, we must remember that the digital organisms did have an intelligent designer - it's not like the programs sprang to life on their own!

Yes, and our simulations of continental drift are written by humans too. Are we to conclude that humans are pushing the continents around?

Study up on the concept of "non sequitur" when you have a little spare time.

Re:I've used genetic algorithms

[NialScorva]

"We discover a new virus all the time, but one thing remains the same, it's still a virus."

Except this is a purely linguistic definition, not corresponding to anything in nature, and explicitely shows the flaw in the majority of creationist thinking: The name *is* the thing. "Kind" is a completely useless word. I've seen it equated to "species", and then I've seen a creatist backed so far into a corner that there was a "bacteria kind", "plant kind", and "fungus kind". The only common definition for "kind" is that humans must occupy an excusive niche, it seems.

There is more diversity in viruses than there is between a human and any other mammal, yet they're all the same "kind" to because it's convenient and removed from daily experience.

Re:I've used genetic algorithms

[BooRadley]

Your ignorance of science and history do not make either any less true. If you were truly interested in the origins of life, you'd google for it:

http://www.geocities.com/CapeCanaveral/Lab/2948/or gel.html

http://www.accessexcellence.org/WN/NM/miller.html

http://www.resa.net/nasa/origins_life.htm

Re: I've used genetic algorithms

[crashfrog]

Where you're wrong is that the program doesn't "assume evolution", it models random mutation and natural selection. We know that random mutation occurs. We know that populations experience selection pressures.

Because we directly observe these phenomenon in nature, we then model them on the computer. That evolution then occurs is not a result of its assumption in the program but rather because evolution is a natural result of random mutations acted on by natural selection.

No one disputes that natural selection and random mutation are at work in nature, not even young earth creationists. The question has always been "are these sufficient mechanisms for complex function to arise?" According to computer models, the answer is yes.

Re: I've used genetic algorithms

[aborchers]

Thank you. That is exactly the kind of clarification I was hoping for. I had only one course that touched on EA but briefly, so bear with me...

I am curious how the selection is applied. The mutation part is easy enough to understand, but how do you apply selection pressures without making some sort of assumptions up front about what types of organisms deserve to thrive? This is the part that always seemed arbitrary/presumptuous to me.

Re: I've used genetic algorithms

[Allegro]

I'm of the mind that science should view nature in a way that places us inside of it at all times. All we can know is what we can test.

So, there is a line, somewhere, separating what we can know from what we can't know. At what point does one say, "OK, this is how nature seems to me; therefore, I'll view it in light of the way I must treat it"?

That's my argument in the whole creationism versus evolution debate. Creationists seem to have a tendancy to extrapolate outside of their data sets. Scientists do this too, but when was the last time you've encountered a creative creationist that solved major, physical world problems?

Re:I've used genetic algorithms

[Copid]

Not to mention the fact that nobody has really answered the simple question, what prevents lots of microevolution from adding up to macroevolution?

Nobody seems to have come up with a mechanism for that. Since we've observed instances of speciation for at least 100 years, I'm not sure how much further we need to push the issue.

Re: I've used genetic algorithms

[JimDabell]

The first thought I had when I saw the article (presented on Space.com as "Darwin Proved Right ...") was that simulating something in a computer does not necessarily prove anything about the physical world.

I completely agree. However, one of the most popular arguments against evolution is that complex, interdependent traits like the mechanism involved in poisonous snakebites, for example, cannot evolve through random mutation, since two "random" developments need to happen at once in the same individual.

Not only can this be refuted with examples from nature, genetic algorithms also count against this argument, as very complex behaviour can also arise here (and we can examine each step of the way).

Re: I've used genetic algorithms

[NoOneInParticular]

The only general approach I have seen to date to tackle this question is Tom Ray's Tierra program (don't feel like linking, try google: Ray Tierra). Here selection is based on the only resource present in a computer, CPU-time. Very interesting behaviour, and although old (late 1980's) the most convincing experiment in artificial evolution to date.

And yes, genetic algorithms model artificial selection (breeding) more than natural selection (struggle for survival).

Re:I've used genetic algorithms

[Anonymous Coward]

No one designed the Creator - He is self-existent and transcendant.

Those who look for God as if He is a physical entity are not apt to find Him. For if He was merely physical, that is, constrained by the laws of science, then there would be little remarkable about Him...

Re: I've used genetic algorithms

[Anonymous Coward]

> Interestingly, while this study can show the merits of evolution, it does more to bolster the intelligent design theory than to destroy it. While the experiment was very interesting, we must remember that the digital organisms did have an intelligent designer - it's not like the programs sprang to life on their own!

Yes, and our simulations of continental drift are written by humans too. Are we to conclude that humans are pushing the continents around?

Study up on the concept of "non sequitur" when you have a little spare time.

Umm, here's the difference: we can't observe what is going on in the evolution simulations in nature, where we can observe continental drift. A geologist can go and look for evidence that bolsters his theory: he can propose a set of data, which if found, would disprove his theory.

Evolutionary biologists seem to think they're exempt. No matter how much, nor how damning the evidence, they continue to believe theories that are logically suspect. Take, for example, the idea of "survival of the fittest". It sounds good, until one thinks about it. From a logical point of view, evolution should favor the most prolific breeders, but according to evolutionary biologists, it favors the most well adapted. In truth, it matters not the least how well a species is adapted to its environment if it can live long enough to reproduce. Which means that the most highly advanced (or oldest) species should have the shortest reproduction cycles. They don't. In fact, the more complex the animal, the fewer offspring they give birth to. Furthermore, there's another reason why evolution should favor prolific breeders: those who reproduce more often would have a greater chance of having a mutation which better adapted them to their environment. So how does evolution explain humans? We aren't very well adapted to our environment, we reproduce very slowly, and we are very susceptible to disease. We should have become extinct a long time ago.

Re: I've used genetic algorithms

[sstory]

'Irreducible complexity' is crap. What complex structure exists which does not contain any independently-useful substructure? None I've ever seen.

Re: I've used genetic algorithms

[aborchers]

What complex structure exists which does not contain any independently-useful substructure?

Most discussions on slashdot, perhaps? ;-)

Re:I've used genetic algorithms

[j0hnfr0g]

That makes the assumption that the anti-evolutionists are logical people.

This broad generalization is not an accurate statement, assuming you mean "anti-evolutionists" are the same people as "creationists".

I am a creationist, yet I am an electrical engineer working on my thesis and I consider myself *very* logical (too much for my wife sometimes). Yet I also believe that there is evolution since it is obviously apparent (and I am not talking about "theistic evolution" either). But how I can believe both and the implications of this go beyond the scope of this medium.

But please be aware that there are more than two types of people: those who believe in evolution and look down upon creationists, and those who are creationists and believe there is no evolution at all.

Re: I've used genetic algorithms

[Kazoo the Clown]

I fail to see how executing a computer program that assumes evolution in its infrastructure proves anything but that modelling evolution in software works.

Such programs constitute a mathematical proof that random mutation filtered by selection can produce innovations. These programs don't "assume evolution in its infrastructure," they merely mathematically model filtered random mutation, and that is the only claim being made, and the only claim needed to be made to disprove the creationist argument that innovations cannot be produced by unconscious processes.

Re: I've used genetic algorithms

[Anonymous Coward]

why is it that scientists to date have not been able to produce a living organism from dead material

Modern biology has been around for what?? 300? yrs
(say since the sighting of bacteria).. surely since then biology(and science) has contributed TREMENDOUSLY to mankind ?
And in most cases has given ENOUGH proof whenever it asserted something...

Now ASK YOURSELF: What proof has religion produced in 2000 yrs?
about god ? adam & eve ? abraham ? noah ? 12 tribes ?(yet science does not ignore these stories)
What proof from hinduism? islam ? etc..
And WHAT *GOOD* has religion brought mankind ?

And how old is the DNA discovery ? 40 yrs ?
But look HOW MUCH it contributes to mankind..

Ok I know evolution has no conclusive proof.. but science KNOWS THAT .. and things are constantly under review and change..

Are you willing to review and change the bible ??
Accept **one word** is out of place??
When no ones ALL the people who wrote the bible ?

All that the church can do is say "sorry gallileo" after 300 yrs..

Choice is yours..ie you need not wait 300 yrs say sorry...

Re: I've used genetic algorithms

[Kazoo the Clown]

The question has always been "are these sufficient mechanisms for complex function to arise?"

Acutally, an increase in complexity is not an inherent characteristic of evolution, innovation is a better term (though I suppose it may depend on what definition of complexity you choose, an issue which itself is somewhat controversial). While it is true that from an initial self-replicator there is a significant bias towards an increase in complexity (as any decrease would tend to eliminate the ability to self-replicate at that point), it is only an initial bias, at some point increases in complexity will tend to be less viable due to the overhead of sustaining such additional complexity. The important factor in evolution is the production of innovations, NOT the production of increases in complexity (again, depending on how you define it...).

Re: I've used genetic algorithms

[aborchers]

You're the second to rightly call me down for my poor choice of words. What I meant to say was that these programs apply artificial selection by rewarding some sorts of mutation and punishing others. There is not an unconcious process involved because of the programmer's deliberate application of the carrot and stick principle. So far, none of the replies have convinced me of an error in my basic assertion that a simulation is not a proof.

Where does simulation fit in the scientific method? I am assuming that it is in the realm of testing hypotheses. If that is the case, then doesn't the simulation need to exhibit predictive power to be considered to have advanced the cause of proof?

If you trace back to my initial comment, what I winced at was Space.com's headline "Darwin Proved Right by Experiment with 'Alien' Life", which I felt overreached the claims of the work and offered bait for yet another round of creation vs evolution nonsense. I have no interest in disproving creationist arguments (or any other variety of shooting fish in barrels) but I also don't think that "proof" is a concept that should be tossed about lightly.

Re:I've used genetic algorithms

[56ksucks]

"what prevents lots of microevolution from adding up to macroevolution?"

Micro-evolution doesn't produce new organs, make a reptile into a mammal or a fish into an amphibian. It doesn't mean that one day a reptile happen to be born with feathers so it was a bird. It's a small variation of what's already there. A change in color or size perhaps, or for example in turtles, the shape of a water turtles' feet are good for swimming while a land turtle's feet are good for walking.

Micro-evolution doesn't neccisarily mean a genetic change either. Some believe that, for example in dogs, the first dogs in creation had the genetic makeup of all breeds of dog, and that those genetic traits began to pass down and seperate over the generations. This can be represented by a giant punit square, in which a set of original dogs from the beginning of time are the parents, and you can see by making this punit square that the genetic traits of all breeds can be traced back to an original breed of dog, even so much as a fox which can not normally backwards breed with a dog. Were the first dogs big or small? Were the first cats big like lions? probably, But one thing is fairly certain, they were still cats.

This theory easily fits with natural selection, as the cats that were born with stripes could hide in the grass, and easily populate grassy areas, while cats that were born plain aren't suited for such areas and probably died off in such a setting.

What Macro-evolution doesn't explain is species that can not advance without certain features, for example the giraffe. The giraffe has a very long neck, which is designed not only to reach tall trees, but also so that the giraffe can bend down and drink without his brain being gorged with blood and exploding. The giraffe has a very powerful heart for getting blood up its long neck, but when he bends down to drink blood is going very powerfully downhill with the added force of gravity. There is a spongy tissue around his brain that holds blood until he is done drinking, and, valvues in his blood vessles to keep more blood from coming into his head. If these things were not in place in the first species of giraffe at the dawn of time, the first species of giraffe would have died as a result of too much blood going to his head and there would simply be no more giraffes. Yet according to Macro-evolution it took a long amount of time for these complex things to develope. Were there ever short neck giraffes? Could be, but, would they be designed in such a way? These things are specifically designed for an animal with a very long neck. The powerful heart would kill a short neck giraffe. He'd die of high blood preasure, yet if the first long necked giraffe was born without a strong heart, it would have died from not having enough blood to its brain. So how did this complex animal come to be? There are many different species such as this that defy the theory of Macro-evolution, species with features that have to be in place in their full form for the species to simply exist and advance because without them they will simply die.

Re: I've used genetic algorithms

[Anonymous Coward]

What does religion have to do with this?

If one wanted to talk about divine revelation as a source of truth, fine. But not everyone accepts divine revelation. So you are left with science. And the problem with evolution is that it looks more like a psuedo-religion than science, a kind of assertion-by-proxy that God doesn't exist. In short, believing in evolution is not trusting the scientific process. The scientific process has not verified evolution.

I'm not talking about the reproducible aspects of evolutionary biology. The problem with evolution is that in the eyes of the general populace it has gone from a family of theories (some of which were proven, others, merely speculation) to being accepted as fact. People have turned the speculation of evolutionary biologists into their own religion, taking on faith as true something that science hasn't yet accepted.

And that's my problem. Evolution theory is not well thought out. It's a religion, but without the divine revelation. And it is certainly not science - not the way science was intended to be.

Oh, and what good has religion brought to mankind? Well, you could ask survivors of the holocaust, who witnessed firsthand what a society without religion is like. But I digress....

Re:I've used genetic algorithms

[Anonymous Coward]

I would say that the many thousands of undisputable cases of evolution around us every day.

I am curious. Can you please point me to just a couple of these many thousands of indisputable cases? I am trying to justify my faith in the doctrine of Evolution but am having a hard time.

Re:I've used genetic algorithms

[Anonymous Coward]

There is no such thing as "micro" and "macro" evolution. These are the exactly the same process. And they are never know to be "micro evolutionary" or "macro evolutionary" until long after the fact, if ever.

Re: I've used genetic algorithms

[MoxFulder]

Avida's digital organisms compete for CPU time in at least two ways, last time I looked:

• Each organism is allocated a fixed number of CPU cycles to start out, so all other things being equal, more efficient programs (genomes) are better.
• Organisms that learn to perform mathematical operations (such as addition, equality test, etc.) by processing random numbers receive extra CPU time (the actual amount of the reward is adjustable).

So the only resource that Avida organisms require is CPU time, which will allow them to reproduce faster than their neighbors if they are efficient. This is certainly quite simplistic. Nonetheless, I believe that Avidans' and real organisms' resource requirements have similar fundamental value and necessity, although they differ in complexity.

Also, evolving the ability to perform mathematical operations might be compared to "wet" organisms gaining the ability to extract energy from a food source. Adjusting the rewards for various operations over the course of an Avida run would then be analogous to varying the supply of a certain food source.

Re: I've used genetic algorithms

[Anonymous Coward]

Why do these bones in my ear lock every time I am exposed to a loud noise, preventing damage to my cochlea?
Am I supposed to believe that we all evolved next to exploding volcanoes?

What about all those parts of me that are irreducibly complex? Did they just pop out of nothing? (remember an irreducibly complex system cannot, by definition, function with any one part missing, misplaced or malformed).

Re: I've used genetic algorithms

[Anonymous Coward]

"From a logical point of view, evolution should favor the most prolific breeders, but according to evolutionary biologists, it favors the most well adapted."

I'm curious how survival of the fittest favors prolific breeders. Fitter organisms are more likely to live long enough to reproduce, and so forth. The capacity to breed 10x more offspring does no good if the creature in question has some limitation preventing it from reaching sexual maturity.

Re: I've used genetic algorithms

[Kazoo the Clown]

Okay, here's the current evolutionary biology problem set:

If the theory of evolutionary biology is true, then we should see less genetic diversity the farther back in time we go. We should be able to find an ancestor common to all species. We haven't yet.

In general, evolution doesn't predict that genetic diversity should correlate with time-- and also doesn't predict a single common ancestor-- there may have been multiple initial replicators, for example. Genetic diversity can increase, and then decrease, it is not forever on an increase. Genetic diversity can be gained and lost over time. And the fact is, initial replicators will be simple, won't have a skeletal structure that will fossilize, and would have existed one heck of a long time ago, making it pretty unlikely that one can be found. These are not problems in evolution.

There are gaps in the fossil record. Species seem to go from one form to another with no evolutionary steps in between. Evolutionary biologists explain this with the theory of "punctuated equilibrium" - an intellectual kludge at best.

Actually we see such punctuations in the mathematical simulations. When a population is faced with significant selection pressures (generally due to a change in environmental conditions) evolutionary changes can occur relatively quickly. At least one species is even capable of adjusting its mutation rate to aid this process-- some yeasts will switch from sexual to asexual reproduction which makes it less resistant to mutations, therefore increasing the rate at which it can accumulate new variations. And some "gaps" are just gaps in the record, as few organisms fossilize, what we have in the fossil record is a very scattered sampling, not a record of every creature that ever lived.

Fossil dates are notoriously inaccurate. Geologists uses fossils to date strata, and Paleontolists use strata to date fossils. The dating of strata is based on two methods: carbon dating, and the decay of heavy isotopes, both of which make certain assumptions which are not necessarily true. (Carbon dating assumes that the ratio of carbon isotopes in the atmosphere has remained constant over the past 10,000 years, however recent studies have shown this to be false.)

These are completely ignorant statements about dating methods. Carbon dating is calibrated against dendrochronology, not strata. Carbon dating is only good for about the last 50,000 years, it's not used for dating any but the most recent fossils because of that, but in any event, its dates can be correlated with dendrochronological dating (tree rings, ice cores, etc). Carbon dating is therefore not dependent on an assumption of the amount of carbon in the atmosphere, but is merely consistent with such an assumption. Isotope decay dating makes use of multiple isotopes which have different decay rates, and the results are compared so that samples which have been subject to some process over time (such as the incursion of adulterating materials) that would alter the dating will stand out as the different isotope decay curves won't agree on the resultant date (consequently, the sample then can't be dated by such methods). Even if the decay rates of the isotopes has not been constant over time, the decay curves of the different isotopes would not converge on the same date, so isotope dating too, is not dependent on constant decay rates over time, but is merely consistent with them.

Re:I've used genetic algorithms

[Anonymous Coward]

Maybe when they are infected with antibiotic resistant Staph they will think about it from a different perspective...

You have no idea. I've actually heard the argument that the anitbiotic resistant bacteria were always there (right from the beginning), but we just go a long time without discovering them. And that's not even the most rediculous argument I've heard from creationists, either.

Re: I've used genetic algorithms

[Anonymous Coward]

To clarify: it doesn't matter how long you live as long as you reproduce before you die. You can be either better adapted, or a better breeder to survive. The idea that a particular species flourished because it was better adapted to its environment is just as plausible as that of being a better breeder.

The implication of this is that all other things being equal, about half of the species in existence would not be particularly well-suited to their environment, but be prolific breeders, and the other half would be well-suited, but lethargic breeders.

Humans are neither - our reproductive cycles are relatively long, and our ability to survive relatively weak. Think about how long a naked person could live without shelter or tools. According to palentologists, humans didn't begin to use tools until sometime around 10,000 to 50,000 years ago, yet as a species we are supposedly 50 million years old. So what were we doing for the previous 49,990,000 years? We can't live without shelter (need tools, skins), and we can't reproduce fast enough.

It would seem that if "survival of the fittest" was indeed true, humans would not exist.

Re:I've used genetic algorithms

[John Bayko]

Interestingly, while this study can show the merits of evolution, it does more to bolster the intelligent design theory than to destroy it.

That doesn't really follow the argument far enough. A good discussion on this particular point is made as part of Robert J. Sawyer's novel Calculating God, in which alien beings come to earth as part of a scientific expedition to look for evidence of God.

Re: I've used genetic algorithms

[MoxFulder]

Exactly! Creationists seem to get hung up on this all the time.

A creationist (admittedly a fairly foolish one) told me, "Sure, dogs can evolve, but when have you ever seen a dog become something that is not a dog?" Well at what point do you consider it not to be a dog? It's just a convenient term.

What I told the creationist: Suppose a group of isolated dogs evolve genitals that physically don't couple with other "normal" dogs. Sure, we can still call them dogs, but these are clearly different species since there is NO WAY that they can naturally interbreed. If they continue to evolve separately, they may eventually diverge to the point that their common ancestry is unrecognizable.

Re: I've used genetic algorithms

[Eric S. Smith]

Oh, and what good has religion brought to mankind? Well, you could ask survivors of the holocaust, who witnessed firsthand what a society without religion is like.

Myself, I thought that the Nazis' biggest problem was that they were a pack of bigoted, racist murderers. So, while we're at it, why don't we use them as an example of the perils of poor taste in art?

By which I mean to say, your example is beyond poor.

Anyway, it's not as though the Germany from which the Nazis arose was a society without religion.

Re: I've used genetic algorithms

[Kazoo the Clown]

What about all those parts of me that are irreducibly complex? Did they just pop out of nothing? (remember an irreducibly complex system cannot, by definition, function with any one part missing, misplaced or malformed).

Simple-- presuming there even are such parts (which may be questionable), "irreducibly complex" parts would at one time have been some more complex structure that has already lost some of its complexity such that it now no longer can function with further parts removed. One such possible example is a structure that is used as a scaffolding that facilitates the construction of a secondary structure that eventually has no further need for the original scaffolding. Does the fact that the scaffolding used to construct masonry arches (for example) may no longer exist mean that the arch could not have been built a stone at a time?

Re: I've used genetic algorithms

[junkgrep]

Because the major reason people reject the idea is because they simply don't think it's plausible. Models may be simplified: but what they do demonstrate quite handily is the plausibility of some mechanism to accomplish what we suggest it can.

Re: I've used genetic algorithms

[junkgrep]

---Where is the philosophical "connective tissue" to the physical world?---

Logical possibility, coupled with modeling that tries to mirror certain key features of the physical world. It can certainly be argued that a ey feature was left out: something that would alter the results. But that's what we should be arguing about when we argue about specific models: simplicity is not an argument against the very idea of using models at all to learn about the world.

Re:I've used genetic algorithms

[drooling-dog]

No one designed the Creator - He is self-existent and transcendant.

And so it goes...

Re: I've used genetic algorithms

[junkgrep]

---There are gaps in the fossil record. Species seem to go from one form to another with no evolutionary steps in between. Evolutionary biologists explain this with the theory of "punctuated equilibrium" - an intellectual kludge at best.---

Eh? No.
The fossil record, in Darwin's day was far far far more incomplete. In fact, no one expected it to get any better. So when the theory was first widely accepted among scientists, it was WITHOUT the confirmation of the sort of fossil evidence: the gaps in the record were MUCH MUCH bigger than they are today. So, if this wasn't a big problem back, then, how can it be now that we have a much better and more complete record today? If you think about it, ANY new fossil found multiplies the number of "gaps" that there are, but this is progress, not regress, towards a more complete reocrd.

Likewise, the idea that biologists respond with PE is nonsense. First of all, outside of Gould's circle, radical PE is not taken all that seriously as a new or important idea. But secondly, the major reason for gaps in the record isn't because of PE, it's simple random distribution. Fossilization IS fairly rare, and we would expect that the record would be incomplete. There's nothing kludgy about this: we've known it for centuries.

Re: I've used genetic algorithms

[junkgrep]

---The fact remains that there is just no good explination for how life (and the chemicals of life) arose out of nothing. Most "scientific" expliniations are just half-baked suggestions.---

I'm not sure I see your problem here. The various proposals for theories of abiogenesis are NOT accepted in the same way that evolution is. Their own authors state that they are speculative. So... what's your problem? Science is full of unanswered questions.

Re: I've used genetic algorithms

[Black Parrot]

> Okay, here's the current evolutionary biology problem set:

I'm passing that part because Kazoo has already addressed your three points very well...

> So call me a skeptic. Faith is something that should exist in religion, not science

It sure has gotten popular over the past few years to dis evolution by calling it a faith. Is that perhaps because evolution deniers aren't making any progress at refuting it on the facts?

> and in light of these problems, I'm not convinced that evolution was responsible for the beginning of life.

Neither am I. Evolution doesn't have anything to do with the beginning of life; it's what happens to imperfect replicators after they come in to being.

BTW, evolution is compatible with special creation, as much as it is compatible with non-magical notions of abiogenesis or the transport of life to earth from elsewhere.

> Ask yourself this: if evolution as we understand it can really bring about living beings, why is it that scientists to date have not been able to produce a living organism from dead material? No other legitimate science would accept something as truth if the results could not be reproduced

Now that is just plain silly. Can astronomers make black holes? Can geologists cause continental drift? Can meteorologists create hurricanes? Can archaeologists make prehistory repeat iself?

> and until such happens, evolution is still just a theory.

And it would still be "just a theory" if we did create life too. "Theory" is as good as it gets in the empirical sciences, which is why we have "atomic theory" and "theory of relativity" and all that other good stuff, in addition to the "theory of evolution".

A theory, for scientists, is just a well-founded explanation of some class of phenomena.

Re: I've used genetic algorithms

[sstory]

HA! But they aren't complex enough to qualify.

Re: I've used genetic algorithms

[Finuvir]

It is a point not often made that given heredity and mutation, logic leads undeniably to evolution. These two bases do not simply make evolution possible, they make it unavoidable (at least in the presence of selection pressures). Evidence, though abundant, isn't even strictly necessary. If there was none, we should ask why not.

Re: I've used genetic algorithms

[jonabbey]

And the problem with evolution is that it looks more like a psuedo-religion than science, a kind of assertion-by-proxy that God doesn't exist. In short, believing in evolution is not trusting the scientific process. The scientific process has not verified evolution.

Of course it has. We observe evolution all throughout nature, in the laboratory, in computer simulations, everywhere. What the scientific process has not done is to disprove the existence of God.

Given the paucity of evidence FOR the existence of God, that's not such a big deal. Evolution merely provides an explanatory mechanism for the development of life on Earth once a primordial chemical replicator was created.

God (oh, sorry, 'a designer') may well have created that original replicator, and while that is again a thesis without much objective evidence in support of it, is fully compatible with evolutionary theory.

Re: I've used genetic algorithms

[Nucleon500]

The hypothesis is: If I write a program thusly, based on simple rules, with mutation and selection, then complex patterns will emerge. The first few thousand times you try the program, it doesn't work, so you tweak your hypothesis and test again. And it eventually worked.

Re:I've used genetic algorithms

[kirkjobsluder]

Micro-evolution doesn't produce new organs, make a reptile into a mammal or a fish into an amphibian. It doesn't mean that one day a reptile happen to be born with feathers so it was a bird. It's a small variation of what's already there. A change in color or size perhaps, or for example in turtles, the shape of a water turtles' feet are good for swimming while a land turtle's feet are good for walking.

I don't know why I bother because this is too easy. One of the facts that best support evolution is that there are no truely new organs. A brain is just overgrown ganglia. A scale is just a slightly modified form of skin. A feather and hair are just slightly modified scales. mammary glands are slightly modified sweat glands. In fact, the development of a truely different, truely new organ with no developmental ties to other previously existing organ systems would be clear evidence of design. So far, all the evidence is that if there is a designer, it works in ways that produce effects identical to evolution.

But what is amazing is that we have examples of such transformations forwards and backwards. We have arthropods that became land animals and later, insects that recolonized the water. We have amphibians that came to shore and reptiles, mammals and birds that went back to sea.

What Macro-evolution doesn't explain is species that can not advance without certain features, for example the giraffe. The giraffe has a very long neck, which is designed not only to reach tall trees, but also so that the giraffe can bend down and drink without his brain being gorged with blood and exploding. The giraffe has a very powerful heart for getting blood up its long neck, but when he bends down to drink blood is going very powerfully downhill with the added force of gravity. There is a spongy tissue around his brain that holds blood until he is done drinking, and, valvues in his blood vessles to keep more blood from coming into his head. If these things were not in place in the first species of giraffe at the dawn of time, the first species of giraffe would have died as a result of too much blood going to his head and there would simply be no more giraffes. Yet according to Macro-evolution it took a long amount of time for these complex things to develope. Were there ever short neck giraffes? Could be, but, would they be designed in such a way? These things are specifically designed for an animal with a very long neck. The powerful heart would kill a short neck giraffe. He'd die of high blood preasure, yet if the first long necked giraffe was born without a strong heart, it would have died from not having enough blood to its brain. So how did this complex animal come to be? There are many different species such as this that defy the theory of Macro-evolution, species with features that have to be in place in their full form for the species to simply exist and advance because without them they will simply die.

Of course, knowing a bit about what you are talking about would help quite a bit. The question to be thrown back is why can't these features develop in tandem through gradual incremental changes? Like most people who don't know a lick about evolution, you assume that one characteristic must have appeared first suddenly, leaving the other characteristics to radically catch up. This view is perhaps the fault of biology educators who over-emphasize the role of mutation in evolution and under-emphasize the role of diversity within populations. For a start while the problem of blood pressure regulation is more accute for giraffes, it is not unique to giraffes. Most of the features cited as essential to girafes are present to some degree in all mammals (the basic creationist problem of no original organs again). And in fact, we have short-necked giraffes (Okapi) in the present day that, amazingly enough show many of the adaptations cited as unique for giraffes.

But there are many other features of giraffes that make them bad candidates for design. For example, giraf

Re:I've used genetic algorithms

[Alsee]

assuming you mean "anti-evolutionists" are the same people as "creationists"

Why assume that? Your entire post complains/explains that he used the correct term.

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Re:I've used genetic algorithms

[Alsee]

I am trying to justify my faith in the doctrine of Evolution but am having a hard time.

Ah, the old "science is just another religion" meme.

Logic and rational arguments are worthless in an argument between "religions". No one calling science a religion is not going to pay any attention to logic and reason.

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Re: I've used genetic algorithms

[fluffy666]

To clarify: it doesn't matter how long you live as long as you reproduce before you die. You can be either better adapted, or a better breeder to survive. The idea that a particular species flourished because it was better adapted to its environment is just as plausible as that of being a better breeder.

The better an individual is adapted to it's environment, the more offspring it will produce.. 'Better adapted' and 'Better breeder' are part of the same thing!

According to palentologists, humans didn't begin to use tools until sometime around 10,000 to 50,000 years ago

Perhaps you should learn to use Google before posting something so incorrect.. the first homonid tool use dates back to 2.6 or so Million years ago.

yet as a species we are supposedly 50 million years old

Again, this takes just seconds to check; the Genus Homo is around 2.3-2.5 million years old. The species Homo Sapiens is much younger than this. A cynic might suggest that you were just making up numbers to suit your argument and hoping no one would check them.

Re: I've used genetic algorithms

[Alsee]

how do you apply selection pressures without making some sort of assumptions up front about what types of organisms deserve to thrive? This is the part that always seemed arbitrary/presumptuous to me.

The real point is that it doesn't matter what the selection criteria is. All that matters is that the individual's genes affect that individual's number of descendants in some manner, and that the descendants' genes are similar but not identical to the parent's genes. In that case evolution will always occur.

In the "real world" the selection criteria is extremely complicated and is affected my a million factors, but it all boils down to how many decendants you have. You are selecting for disease resistance, food gathering, predator avoidance, enviornmental tolerance, and mate attaction all at the same time. A computer simulation can select for any of those things, or entirely different things like the fuel efficency of a jet engine design. It's still evolution, just with different pressures.

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Re: I've used genetic algorithms

[Alsee]

Creationists seem to have a tendancy to extrapolate outside of their data sets.

LOL. The Creationism "result" is predefined by religion. Data and facts are merely obstacles to getting the answer they want. That's why Creationism isn't science.

Scientists are constantly challenging relativity, the laws of gravity, evolution, quantum mecanics, etc. Any scientist who succeeds in disproving any of those things would be hailed as a genius.

When was the last time anyone saw a creationist try to disprove creationism?

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Re: I've used genetic algorithms

[Alsee]

Other people have countered your other points quite well, but I want to comment on this one:

why is it that scientists to date have not been able to produce a living organism from dead material?

Actually they are currently working on doing exactly that. Just give it a couple more years.

When life first appeared on earth the "lab" was the entire planet and it had hundreds of millions of years to arise at random. We have no idea what the first replicator looked like, but I'm sure it was far simpler than the simplest cell. That is what we plan to build from scratch - a simple cell.

If you go back not so many years, scientists were unable to make diamonds. Was that somehow evidence that diamonds could only have been created by god?

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Re: I've used genetic algorithms

[Anonymous Coward]

The Communists are a better example.

Re: I've used genetic algorithms

[Alsee]

Anonymous idiot, but you did raise an interesting, if flawed point.

From a logical point of view, evolution should favor the most prolific breeders

Yes, that is a factor, but it is highly simplistic to assume that would be an overriding factor. Being "highly prolific" can hae a variety of negative consequenses. For one thing it tends to lead to a population boom and bust. The species will rapidly overload it's ecological niche, potentially leading to extinction. Having many offspring also means those offspring will compete with each other.

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Re:I've used genetic algorithms

[56ksucks]

We agree on some things. Adaptation and variety does happen and that doesn't rely on mutation. Mutation is usually harmful. Also there are many features in lifeforms that are very similar and are modified versions of the other, such as skin,feathers,scales etc. A creationist would say that simply means they were made from the same general template. I suppose evolutionists would say the same. As for the way things are designed being flawed, well things now are obviously not the way they were originally designed. I could go on and on about that but Slashdot is hardly the place. As for other species that have no basis for evolution, there are plenty. I suggest that if you would like to conitinue the discussion further you give me permission to visit your site and send you an email.

Re:I've used genetic algorithms

[junkgrep]

Yeah. Please guys: don't continue a discusion in these forums! These forums are for posting jpegs of naked celebrities only!

Re:I've used genetic algorithms

[junkgrep]

I sure wish he'd move his mysteriously fat ass off the couch and do some dishes for once.

Re: I've used genetic algorithms

[crashfrog]

That's very true. Evolution does not itself demand an increase in complexity. it's just that complexity is commonly used as a criteria for the necessity of design so that's what I picked as an example.

So, yeah, I agree with you. Generally complexity is an advantage although there's plenty of situations where that won't be true. It would probably be best to say that evolution favors survival but that's almost tautological.

Tierra, Avida, MS - a short story

[freality]

Tierra was by Tom Ray, a pioneer in the AL field. It was a great idea, but failed to turn around with interesting biodiversity. You'd create creatures, they'd optimize themselves, some variants and parasites would evolve, but then things would simmer down within a few hours and you'd be in a steady state for ever.

Network Tierra was Ray's response to this. It was supposed to allow a "Cambrian explosion" of biodiversity, by providing tons of (networked computer) space for the little creatures to explode into, and then specialize, in. This led to interesting migration behavior, and one of my all-time favorite web-pages, but it too failed to spark that je ne sais quois, that spark of life.

Anyways, it did spark Avida and the Digital Life Lab at Cal Tech. Avida is essentially a deeper look at the fundamentals behind AL. In Tierra, I think the design philosophy was something like "make it look a lot like a living ecological system and the life-force will appear out of the ether", and actually, Tierra was a great leap forward beyond more mundane genetic programming a la John Koza.

Avida, on the other hand, is much more systematic in exploring the parameter space (which is large and sensitive) for setting up an AL system. This turned out to be fruitful, as Adami found that only when certain, very narrow, environmental conditions were met would the little creatures start outsmarting that Creationist boogeyman, the Second Law of Thermodynamics.

Turns out that Tierra didn't have spatiality (needed to be more restrictive on who could sleep with who) and mutation rates (some power law math that's way over my head) set right.

But the real punch-line to this whole story is that the direct beneficiary of these insights in Microsoft! Hah!

Microsoft was funding Adami's work because Windoze crashed too much. They were searching for a way of programming - in this case using closed instruction sets like Avida's (another deep topic) - that would be inherently robust to problems like seg faults and illegal instructions.... e.g. Adami's instruction set was engineered so that little programs (creatures) couldn't crash the Avida VM when they mutated into new, unknown programs.. or in Windoze's case, when a coder did something stoopid. It's funny that MS was researching this, since releatively low-tech solutions such as protected memory and QA take care of this. (not to mention Java ;)

Re:Tierra, Avida, MS - a short story

[Anonymous Coward]

As someone who was actually working on Avida at the time and visited Microsoft Research in Redmond with
Charles and Chris (Ofria and Adami respectively). I just thought I'd say a few things.

MS (through the head of University Relations at the time) did give a no-strings-attached gift (and a computer for my desk) because they thought it was neat research. The same head of Univ Relations at MS actually did a great deal of coding on avida to port it to Windows. I don't think they really thought that Alife or GP or GA or AI would be useful in any products anytime in the forseable future, but they did to seem to think it was cool and maybe important someday. I'd also like to point out that MS Research had two theoretical physicists on staff that did theoretical physics (with no obvious connection to any potential products).

We did visit MS Research, and it was way cool. Sat around talking with lots of really smart people about various random ideas. I don't think we really had anything to contribute to their work an at all direct manner, but everyone we spoke with was really smart and seemed pretty interested in Alife.
I want to point out a very important observation here since this is /. after all. MS Research is not MS Marketing. The culture, motiviations, and average intellegence levels are way different. Also, at the time, MS Research wasn't under much pressure to do anything useful in the short term. Sadly, I've been told by friends there that this has changed and it has become a much less fun place to work.

About the paper... I didn't write it or even get an opportunity to read it (sniff), but I did chat about it with the authors when it was being worked on, and their intention was to write a paper that showed how "Irreducable Complex Structures" can arise from very basic mutation/selection. The point was to pop the "Intelligent Design" creationists bubble that they seem to have regarding the scientific basis of their claims.

Pennock wrote "Tower of Babel: The Evidence against the New Creationism" and "Intelligent Design Creationism and Its Critics: Philosophical, Theological, and Scientific Perspectives".
Lenski is a brilliant Microbiologist (bacteria, viruses, and such).
Ofria is a Computer Scientist with a background in Alife (and a friend of mine).
Adami's background is from Quantum Physics (where he has made important contributions), but has been one of the stong voices for doing real science using alife (trying to understand how evolution actually works) instead of just making pretty pictures with dots.

Interesting

[Anonymous Coward]

...their simulations show how a short-term backward step in survival strategies can generate innovative advances.

Sounds similar to what brought the great amount of development power to the Free Software movement. When people are stuck with something as uninnovative as Windows for so long, nature will eventually devise a workaround to the previous lack of competition to stimulate the industry.

Re:Interesting

[Anonymous Coward]

There is no future in evolution. If you survive today and long enough to breed, that's about it. Your Free Software flamebait is just as likely to evolve Windows mimics that can survive hidden in a herd of MS users.

Interesting but sort of scary

[PotatoHead]

technique that has always made me think.

I read a magazine article about this a while back. (probably Sci Am.)

One researcher setup a problem to be solved with an analog circut. The problem was to distinguish between the words yes and no.

Nobody can explain how the circut that evolved actually works. Like us, there were parts of the circut that seemed redundant or unnecessary. Sort of like the appendix.

This whole thing makes me wonder just what we don't know that we think we do.

Re:Interesting but sort of scary

[Davak]

Nobody can explain how the circut that evolved actually works. Like us, there were parts of the circut that seemed redundant or unnecessary. Sort of like the appendix.

The appendix isn't unnecessary! There would be starving families of general surgeons everywhere without this wonderful organ.

Ooohhhh... my abdomen hurts.

Davak

Re:Interesting but sort of scary

[Anonymous Coward]

Yeah, it was Scientific American.

The 'appendix' was a blind capactitor in the circuit that looked like this:

_
|....|
|..---
|..---
|__|
|
|
O -- connected to the rest of the circuit here

. = filler to get by the white-space filter

Re:Interesting but sort of scary

[PotatoHead]

That's it!

Seeing that was spooky for sure. It would be interesting to sort through all the 'wanna be' circuts to understand a little about how that thing ended up in there.

What I cannot remember is whether or not the circut worked without it.

Scientific American

[Anne_Nonymous]

had a nice article about this recently (pp. 52-59 of the Feb 2003 issue). They showed evolutionary design examples primarily in the electronics field, and included an E.D. circuit that was an improvement over existing technology.

Good Intro Resources on ALife/Complexity

[sbot5000]

1) Thomas S. Ray is a great starting point

Especially: Evolution, Ecology and Optimization of Digital Organisms and Zen and the Art of Creating Life

2)The Santa Fe Institute

3)Kevin Kelly's Out of Control: The New Biology of Machines, Social Systems and the Economic World

Re:Good Intro Resources on ALife/Complexity

[acidwizard]

A really good book on the subject is Stephen Levy's Artificial Life. It's done from a somewhat historical perspective - includes work done by Von Neuman up to more modern stuff like Tierra. Very accessible to the lay person, fun for a biologist/computer scientist as well.

Thank god for super computers...

[LilGuy]

"Our work allowed us to see how the most complex functions are built up from simpler and simpler functions."

Um... wtf everyone knows this already... you don't need a computer 'simulation' to tell you this. It's been known for years that each complex function is made possible by the perfectly working, ultra-simple functions underneath. I'm not even into biology or anything either...

ai is the devil.

[m1chael]

if intelligence is intelligence then why is artifical intelligence artificial intelligence? we are starting of in this field all wrong because its name implies a lower class of entity. when robots become sentient will we treat them as animals because we are used to thinking this way? will we be the masters of our own destuction? i dont know, why dont you brood over it a little while. anyway i dont care much for ai, i would rather humans become insanely intelligent.

Computer Evolution

[jefu]

I've worked with various kinds of things related to genetic algorithms and its a wonderful field and very interesting to work in.

Its wonderful how these things can find odd and interesting solutions to problems in some cases and completely miss them in others.

One of the things that anyone learns who has tried this kind of method is that you can't hurry things to a result - that you often need to actively intervene to slow the evolutionary march, or even back it up (as in the article) or the system can easily get stuck exploring an area with a local optimimum extensively and miss a better one thats just a ways away.

Wonderfully fun stuff though and well worth investigating.

Brain vs genetic alogrithms

[ProfitElijah]

their simulations show how a short-term backward step in survival strategies can generate innovative advances.

This isn't really a challenging assertion, and is well discusssed in evolutionary psychological circles. Consider any given genetic setback. In order for the organism suffering this set back not to be disadvantaged, it must develop a mechanism which compensates for the setback at least as much as the organism is disadvantaged. Simple statistics will show that any solution which is at least as good as another solution is probably better. Because unless it is exactly as good, it is better, and the range of better solutions is much wider than the range of exactly as good solutions. So you don't need this study to show you that, you just need your highly genetically evolved brain.

forget the anti-evolution argument

[gol]

having just successfully completed an undergraduate project in which i have used genetic algorithms to achieve full adaptive image compression, i have learnt rather a lot about these curious beasts that is seldom mentioned in modern text. the use of genetic algorithms in a computer does in no way prove or disprove any evloution/anti-evolution argument. these algorithms do not magically evolve new creatures, or new solutions. they just search the solution space in a highly parallel manner, and they surprise people because they come up with solutions they did not consider. the solution is there waiting in solution space - but you can't find it because your brain is not capapble, you don't spend enough time on it... whatever. this is not new, its not intelligent, its not the creation of a new species. think of genetic algorithms as exploiting adaptive characteristics, simple as that, i.e. skin colour changing due to intensity of sunlight. of course... there are fields of research that involve using one class of genetic algorithms to derive the schemata (structure) of another class, but the research has come up with nothing to date.

Re:forget the anti-evolution argument

[djeaux]

having just successfully completed an undergraduate project in which i have used genetic algorithms to achieve full adaptive image compression

The real twist is that genetics in the context of evolution doesn't strive to "achieve" anything other than survival of the gene. It simply puts out a product & natural selection determines if it works & survives.

This is, IMO, the big difference between so-called "genetic" computer algorithms & biological evolution. Evolution doesn't have an end in mind. And the results can be very novel. You might "want" adaptive image compression & wind up with code for controlling sequential port fuel injectors.

Applying the general principles to a system where we expect a particular result just ain't the same thing.

As far as creating a system that mutates a sequence of 12-bit code (which is what I think a codon would be), probably a good many /.istas could kludge that in an afternoon. Do I smell a grant application brewing?

Re:forget the anti-evolution argument

[gol]

"natural selection determines if it works & survives" indeed it does. how do we model natural selection in a computer system? via a fitness function that determines that population member's ability to perform the desired task. for humans this could have once been hunting, hut building or being an attractive mate. for adaptive compression you have to tell you population members how they're doing, which ones are closer to the source than others. the fitness function essentially shapes the population, it is the "natural selection that determines if it works and survives". without this you get a bunch of crap, or maybe strike lucky. of course, just mutating things and seeing if they get better is pretty crude, and pretty far from biology. more sophisticated methods exist such as selection & crossover to repopulate your test population. also remember that you don't have to use GAs to create code... they are equally adept at manipulating schemas. so in short... if you're applying a GA, you're applying it for a purpose. you check that it tends towards its purpose by way of a selection of appropriate fitness/selection/crossover functions. it would of course be amazing if we could just throw these things out in the wild and see if they work, but we have to model the survival too. oh, an no, there's no grant involved. i'm moving into parallel computation architectures, GAs give me a headache now :-)

Re:forget the anti-evolution argument

[Nucleon500]

they just search the solution space in a highly parallel manner, and they surprise people because they come up with solutions they did not consider.

[Evolution] just search[s] the solution space [of things that survive] in a highly parallel manner [throughout the universe], and [it] surprise[s] people because [it] comes up with solutions [Creationists] did not consider [and thus attribute to God.]

Re:forget the anti-evolution argument

[wct]

I think you've hit the nail on the head. A lot of people without a biology background get excited about the parallels between evolutionary algorithms and the process of evolution. Unfortunately it is rarely stated that evolutionary algorithms are just a model of how evolution works. A good comparison is the simplified perceptron model of the neuron used in neural networks. The actual mechanism by which genetic algorithms work is really close to a gradient descent search. And almost all evolutionary algorithms require some kind of manual design to initiate or further the progress of the computation.

Frank and Stein

[Tablizer]

It's alive, IT'S ALIVE!.....damn, it chewed up my paycheck.

Book about Avida and theory of Alife

[plastik55]

Those interested in playing with Avida and seeing how evolution can be modeled using computation, thermodynamics, and information theory should get a copy of Cristoph Adami's book, Introduction to Artificial Life

I had the fortune to take Dr. Adami's class on the subject. It was an eye-opener to say the least. I think I remember more about statistical physics from his brief overview than I do from any other classes I took on the subject.

I've posted this link before but...

[pyr0]

I've posted this link before on /., but I figure a story like this is going to stir up a great number of people that would both strongly agree and disagree. So, here it is.

evolution is dumb

[Anonymous Coward]

There is really nothing particularly amazing about evolutionary or genetic algorithms. They just try a bunch of stuff until they find something that works. In general, they are terribly inefficient algorithms.

The only reason evolution has been able to come up with amazing results like human life is the immense computing capability of the natural world. One gram of hydrogen has 6.02 x 10^23 atoms. Even if you could represent each of those atoms with one bit of information, we are nowhere near being able to track all of those atoms on a computer. Even a Terabyte of memory is less than 10^13 bits. This doesn't even begin to consider the 36 x 10^46 pairwise forces between the atoms. The computing power of the earth is immensely more than anything that we will ever attain in von neumann style computers.

When you start to consider the astronomical number of chemical reactions that occur continously on the earth, it makes sense that even a dumb algorithm like evolution could come up with some pretty amazing stuff. Add to this the multitude of other planets in the universe and intelligent life almost seems inevitable. Assume the universe is infinite, and intelligent life _is_ inevitable (every configuration of matter occurs with probability 1).

Evolution : no longer a theory -- it's technology

[Thud457]

"It's really kind of breathtaking how stumbling around in the parameter space, and filtering the bad missteps, can mimic the results of engineering.

A lot of "engineers" work that way -- particularly "software engineers".

Re:If you could ask Darwin

[JimFromJersey]

You are such a loser, can you not make any sort of rational arguement? Or must just fall back "you're going to hell"? Do you not have a brain? Who are you, mere mortal, mere worm, to pass judgement on anyone? You know the will of God, do you? You are a hate filled leper, passing your disease from one generation to the next, filling minds with fear, anger, and hate. YOU are the sinner.

outdated...

[lauterm]

I realize the articles might be new, but the last code release was 9-29-2000. There is a message at the top of the page from Sept 2002 promising new code soon. This probably would have been even more impressive over 2.5 years ago.

Re:outdated...

[IdahoEv]

Yeah, I'd been lazy about getting the new stuff on the site. The new site was 95% done in a different directory this morning when I saw the posting.

Check back now.

Re:outdated...

[lauterm]

Looks good...Thanks for taking the time to inform. I wasn't trying to crack on your site, but rather the news media that didn't bother to cover the topic until now.

Damn arrogant AMA butchers!

[Thud457]

They took my appendix out, now I can't frixnab anymore. YOU BASTARDS!

Society Devolution

[Anonymous Coward]

> their simulations show how a short-term backward
> step in survival strategies can generate
> innovative advances

Considering how human society is beginning to prevent evolution in our species, I'm looking forward to some innovations!

Darwin t-shirts

[Anonymous Coward]

Get your Darwin t-shirts!

http://www.cafeshops.com/darwinman/

Re:Darwin t-shirts

[ikewillis]

Oh wow, that's certain to offend any Christians in the audience...

Future

[eventhorizon5]

Of course this will probably increase the acceptance of Darwin's own ideas, some of which are here:

"It might also naturally be inquired whether man, like so many other animals, has given rise to varieties and sub-races, differing but slightly from each other, or to races differing so much that they must be classed as doubtful species..."

"At some future period, not very distant as measured by centuries, the civilized races of man will almost certainly exterminate, and replace, the savage races throughout the world. At the same time the anthropomorphous apes, as Professor Schaaffhausen as remarked, will no doubt be exterminated. The break between man and his nearest allies will then be wider, for it will intervene between man in a more civilized state, as we may hope, even that the Caucasian, and some ape as low as a baboon, instead of as now between the Negro or Australian and the gorilla." (Quoted from Decent of Man, Chapter Six: On the Affinities and Genealogy of Man, on the Birthplace and Antiquity of Man)

"...Do the races or species of men, whichever term may be applied, encroach on and replace one another, so that some finally become extinct? ...We shall see that all these questions, as indeed as obvious in respect to most of them, must be answered in the affirmative, in the same manner as with the lower animals."

Darwinism sounds like blatant racism to me...

Re:Future

[X-rated Ouroboros]

Darwinism sounds like blatant racism to me...

Darwin sounds like a blatant racist, which wouldn't really be particularly surprising considering when and where he was living. Of course, Darwinism has very little to do with Darwin, though, so this wouldn't be a problem, even if you hadn't taken these quotes out of context.

Re:Future

[hexxx]

Sure those quotes seem a bit harsh, but keep in mind that Decent of Man for example was written in 1871.

Darwin was fairly advanced for his time. Just to show the man wasn't all bad:

"On the 19th of August we finally left the shores of Brazil. I thank God, I shall never again visit a slave-country. "

"Those who look tenderly at the slave-owner, and with a cold heart at the slave, never seem to put themselves into the position of the latter;--what a cheerless prospect, with not even a hope of change! picture to yourself the chance, ever hanging over you, of your wife and your little children--those objects which nature urges even the slave to call his own--being torn from you and sold like beasts to the first bidder!"

Both of the quotes are from The Voyage of the Beagle (probably written in 1839, I don't feel like googling around for that info. Sorry)

I however agree that Darwin nor Darwinism are God and I'm sure Darwin wouldn't have wanted us to think so either.

My Informed Thoughts

[SEGV]

I've done work (including professional) with genetic algorithms. I wouldn't say I'm an expert, but I do have a number of books on the subject.

They really are very keen, GAs. Amazing to see work.

It's funny, because typically crossover (and inheritance) are the big operators, not mutation. But it is helpful to study each operator individually, even though they work best together.

And the word for the day is...

[djeaux]

... teleology .

This may come as a shock to readers who aren't trained in biological sciences, but we presume that nature does not "begin with the end in mind." Thus, a "genetic" algorithm only loosely follows genetics, because there is some assumption about "fitness" (i.e., a particular purpose for the alogorithm) that nature never makes about a biological system.

I'm not sure what the correct semantics might be -- "self modifying algorithm" or "self evaluating, self modifying algorithm" or whatever -- but "genetic" ain't it.

Note that in his later works (e.g., "Descent of Man"), Darwin floated the concept of sexual selection, aka "survival of the sexiest." Simply put, no matter how cool & useful your new mutation may be, if you don't breed, ultimately you die & your mutation vanishes. Applying this concept to fitness-testing a "genetic" algorithm might be pretty interesting...

I think that's the missing ingredient in "genetic" algorithms -- if the algo does what it (teleologically) is supposed to do it survives, whether or not it attracts a cute algo of the opposite gender & begets a litter of fuzzy logic.

Huh?

[SEGV]

First of all, selection (inheritance, reproduction) is one of the three operators of GAs. If you are not selected for reproduction, you do not reproduce.

Secondly, that answers your fitness question. In a GA, the fitness function is used to determine who reproduces. This is the same as in nature, where some complex fitness criterion determines who gets to reproduce and who does not. That fitness criterion is unknown, but that doesn't mean it doesn't exist.

Re:Huh?

[djeaux]

Simple survival does not ensure that an organism will breed. Simply having a good feeding strategy or whatever doesn't ensure that an organism will breed. In fact, many species have evolved methods (colors, crests, behaviors) for attracting mates that run 100% counter to best interests of the organism's individual survival. A field trip to any singles bar will prove this point.

Are GA's set up to reproduce if they're elegantly coded? Or colorful? Or large-breasted? Is reproductive selection contingent on some random & unpredictable event in another algorithm's "life?"

You are correct that "the fitness criterion is unknown, but that doesn't mean it doesn't exist". However, you have no way to predict with any accuracy whatsoever what that fitness criterion may be. In fact, it is unknowable, except ex post facto.

As I mentioned elsewhere in this topic, I can't imagine any software developer being satisfied with the outcome if s/he started out to develop an adaptive image compression algorithm but came out with a control system for a fuel injector.

Re:Huh?

[SEGV]

You are missing the point.

By definition, fitness is breeding. Because nature rewards breeding, and activities that lead to breeding (even if they also lead to dying).

In software, fitness also is breeding, and whatever else we choose to reward. We define the world. In our world, perhaps ability to compress images determines breeding power.

Just because we define our fitness function to be image compression, and nature defines it to be strong, able to find shelter, procure food, and obtain a mate, doesn't mean they aren't both doing the same thing. Both systems have a fitness function that results in breeding.

Surely you can see that?

Re:Huh?

[gol]

That was put far more elegantly to djeaux then i was able to in my earlier thread. :-)
I do agree, just because we're not including some all-encopassing immesely complex fitness function that would allow possible reverse traits to become manifest in the population does not mean that this is not a genetic method, nor that what we are doing is not a simulation of nature.

Re:Huh?

[djeaux]

OK.

I think I've picturing GA's as being handled in a fashion more like selective livestock breeding than "evolution in the wild." And that would make sense from an economic/production standpoint, too.

P.S. Also a relief to have a couple of follow-up posters who have brains & don't live under bridges! :-D

Re:Huh?

[gol]

agreed
a compromise
nice to hear from somebody with a biological background to this problem :-)

Re:Huh?

[SEGV]

That's how they work in practice for solving practical problems.

But for research, many researchers run GAs that do indeed try to simulate nature. They even simulate a little world with little creatures with those genes, living their little lives with food and predators and mating. You can make such a simulation as detailed as you care to.

In that case, it is the creatures' ability to survive (and mate) in that world that dictates their fitness. This is an extrinsic fitness criterion, just like the natural world.

Genetic Images: Evolvo; Sims SIGGRAPH 10 years ago

[JacobKreutzfeld]

Evolvo is a cool program which does genetic images: http://sourceforge.net/projects/evolvo/

It's based on Karl Sims work, which I saw presented about 10 years ago at SIGGRAPH. His page is at http://www.genarts.com/karl/

I tried implementing something in LISP then C based on Sims' work way back but got stuck; I'm glad evolvo has emerged so I can actually play with it.

Where to get Avida

[IdahoEv]

For the record, I'm one of Dr. Adami's grad students in (The Digital Life Lab) at Caltech. Most of the programming is done at our sister lab in Michigan.

We recently released Avida version 2.0, with a new GUI and complete with god mode where you can inspect and edit the genome of any organism at any point.

We encourage you to play with Avida yourself. You can get information and a Mac OS X binary at:

Avida's Hompeage. Older versions for linux and windows are available there as well.

The intrepid can build the current version for OS X or Linux from source, please see Avida's Sourceforge Project. If you want the nice GUI, you'll need QT.

Other information about Avida, our lab's research, and artificial life in general can be found at:

The Digital Life Lab Homepage

Our sister lab at MSU, run by Professors Charles Ofria and Richard Lenski.

The Int'l Society For Artificial Life

Re:Where to get Avida

[mercere99]

To add one more comment to this (from the Michigan lab mentioned above) we'll have a Windows version of the software out "real soon now". Just this past week we've gotten everything compiled under Visual C++, and are hammering out the last few major bugs. We'll put up a beta as soon as its reasonably solid.

yeah

[sstory]

Speaking of this topic, my favorite anti-evolutionist thing is the 'analogy' of evolution to a tornado in a junkyard putting together a plane. What a piece of junk that argument is. I think you have to laugh about anti-evolution things, or you'll just get depressed about humanity.

regarding idiocy vs dishonesty,

[sstory]

I can't be sure it's dishonesty--I've known people who forced themselves to believe some creationism stuff in order to remain christians. There's an old creationism case, Edwards v Aguillard, which went to the supreme court. A 'friend of the court' brief was filed arguing that creationism was not science. It was signed by, among others, 72 Nobel Laureates.

When 72 Nobel Laureates say your 'science' isn't science, your boat is sinking.

What's new

[rpg25]

Can someone who really dug into this explain what's new about this work?

I'm not saying that nothing is new --- just that all the links seem to point to stuff that's so vague, it could describe any work in Artificial Life. And the notion that the path to a global maximum leads through some steps down seems like no biggie, either --- it's well known that for any interesting search problem hill-climbing isn't enough.

So.... what's new? I'm sure there's something or these folks wouldn't have gotten an Nature paper.

Re:The result was the programmed result.

[bloggins02]

The code IS published on their website, and if you are so confident in your conclusions why don't you analyze the code yourself and give us a full report of your findings.

The article fails at validating evolution...

[let_freedom_ring]

The article's primary goal was to establish an example of how evolution can generate complex functionality that didn't exist before.

From the article ... "biologists have concluded that such features [for the eye] must have arisen through lots of intermediates and, moreover, that these intermediate structures may once have served different functions from what we see today."

In other words a cell might have been part of the immune system but suddenly it was discovered to be usefull for vision. But then they devise a test where they start out with programs that already do a mathematical calculation then after a simulated millions of yr's of evolution they end up with ... (drum roll please) programs that do the same math calculations a little bit faster. Note, they didn't end up doing different math calculations or anything other than the original functionality.
They started with human produced programs.
They only improved the speed of those programs they didn't produce any other type of output.
They didn't bother documenting how much they improved the calculation speed. Did it approach a limit where improvements stopped?

Re:The article fails at validating evolution...

[mercere99]

Actually, this is incorrect. We started with simple digital organisms that were only capable of self-replication, and put them in an environment where they would get more CPU time (basically have their priority increased) if they performed certain mathematical computations, in this case bitwise boolean logic operations.

The organisms were only given a nand instruction to work with, and combinations of nands (linked together carefully with proper juggling of data) could be used to create any of the others. The equals operation (returns 1 where bits in the two sequences are the same, 0 where they differ) seems to require at least 19 instructions to perform. Its important to note that we did not reward partials solutions -- they either got the correct answer of they didn't.

For those interested, we also have a lot of our data related to the paper on our servers, http://myxo.css.msu.edu/papers/nature2003

Charles Ofria (Second author of the paper, and primary author of the software)

Re:The article fails at validating evolution...

[let_freedom_ring]

Thanks granting access to these articles. I only read the 'executive overview' from the original slashdot post since the nature article required a paid subscription.

Re:The result was the programmed result.

[IdahoEv]

Having, in fact, read the code myself, and worked with it for three straight years, I can tell you that you are dead wrong.

These little programs do things we never, ever expected. And some things we don't even know how to control. They cheat! They take advantage of every element of the system that's possible in ways we sometimes don't even understand.

And they write their own code in ways no human ever could. I've had experiences where it takes upwards of an hour to understand a 20-instruction-long digital organism because the code is so twisted. Stuff no programmer could ever have written, not even the obfuscated code gurus.

Like any evolving organism, they'll do whatever it takes to get ahead.

where can i see a fosil of a transitional species?

[MoronBob]

When do we get to see the "Proof" of evolution? Where are all of the missing links. There must be millions of them somewhere because we have the "results" all around us. It's this one minor glich that causes me to question evolutionists claims. I can't prove creation and you can't prove evolution.

My 2 cents

[MoxFulder]

Even a clear case of synchronically irreducible complexity, should one ever be found, is not sufficient to disprove evolution.

Consider the (silly) example of a creature whose head attaches to its body via a three-prong connector and socket, so that its head would literally fall off if either were not exactly the way it is. Assume the connector and socket to be irreducible.

One might claim that it is unlikely that this creature could have evolved because both the socket and the connector mutation would have had to appear simultaneously. But this is wrong: perhaps an earlier form of the organism had a different way to hold its head onto its body. Then the three prong connector appeared on the creature's neck due to a mutation, and proved beneficial because it allowed the creature to recharge from a wall socket. :-) Much later, the socket appeared at the top of the abdomen and the organisms were able to plug their heads into their abdomens! Then the old head-attachment mechanism was no longer needed, and gradually disappeared over many generations.

It sounds dumb, but I think similar arguments have been used to argue that the anatomy of a whale couldn't have evolved naturally, ignoring the fact that many of a whale ancestor's parts served different functions when they lived on land.

Re:The result was the programmed result.

[corsec67]

Do you have an example of some of this code generated by an organism?

Evolution and Avida (from one of the authors)

[mercere99]

The parts of working on this that have amazed me most are when the evolution doesn't go as I've planned. In particular, when writing Avida, the best debugging technique I have is to just run it, and then see how some of the evolved organisms work. If I made any mistakes, they will find a way to exploit my errors.

One key thing about Avida is that its not exactly a genetic algorithm. The digital organisms must self-replicate. No matter how skilled they are at performing any of the rewarded computations, if they can't also copy themselves their genetic material will not make it into the next generation. Some people may consider this a minor difference, but it causes certain side effects, such as an evolution toward being more robust to mutations (See this previous space.com article), and in general helps prevent the population from running into a complexity barrier.

Now, back to the organisms exploiting any mistakes I've made. The story that convices most biologists that these organisms can, in some sense be considered alive is this. I was working on a project where I didn't want any more beneficial mutations to be able to occur, so that I might be able to study more ecological effects. Since I'm using a computer system, I actually have the ability to fully analyze every mutation as it happens -- I can take the resulting organism, start up a new population, and run it for a while to see how it does. Now obviously this will slow down an experiment tremendously, but if I'm willing to take such a time hit, it will work. I can then take any mutation that would be beneficial, kill off those organisms (or even just revert that mutation). I implemented it and set it up to do.

What happened? Well, I watched the run as it was going (looking particularly at these test environments), and was surprized to see the fitness of the organisms appeared to be dropping. I couldn't understand it; just because there would be no mutations to improve their ability to survive, it still shouldn't drop. So I looked more carefull in the population itself, and there the fitness appeared to continue to rise. In enither case did I see the stasis that I expected.

Upon further investigation, it turned out that the organisms had evolved a way to distinguish between the test environments and the real one. I had made a slight difference on how I gave them the input numbers to the computations they needed to be able to perform, thinking it would really matter in the end. But from the organisms persepective they were able to use this -- if the inputs looked like those from a test environment, the organisms would purposfully not perform any tasks, while if they were from a real population they would do all of the rewarded tasks they could and continue to adapt to perform more.

It shocked me that they were able to figure this out so easily. A biologist friend of mine equated it to predator avoidance -- if they showed a particular behavior they would be killed for it, so they were careful how they did it. Kind of like if a squirral wasn't careful collecting nuts, a bird might swoop down and get it. Even being careful there is an occasional problem, but they can do quite well for themselves.

I went in and fixed it: I made both the real population and the test environment as random as possible, and started my runs up again.

Did this work? Of course not. What they started to do now was just play a probability game. They would ususally do all of their tasks, but sometimes they would do none of them. If an otherwise beneficial mutation happened to occur when they weren't doing tasks, it would slip through and get into the population, never to be checked again. This really slowed down the rate of evolution (most beneficial mutations were purged), but enough still slipped though.

I am actually at a loss on how to get rid of them all! Here I have this system that should make experimental evolution all the easier because I have "complete control" over it, when in truth life does always seem to find a way.

Charles Ofria

Re:where can i see a fosil of a transitional speci

[Nucleon500]

I can't disprove creationism, but you could disprove evolution. That's what makes it a testable hypothesis. If evolution can't explain something, it might be able to in a modified form, or with more data.

Creationism can explain everything. That makes it just as worthless as something that can explain nothing.

a practical application - antenna design

[drwho]

A couple of years ago, Richard Formato (WW1RF) released Yagi Genetic Optimizer, the third edition of his software for using genetic algorithms for antenna design. This stuff does really work, and is useful. It's freeware, but for ms-dos, here

Re:where can i see a fosil of a transitional speci

[Alsee]

Where are all of the missing links.

By definition they are all missing. Every time we discover a "missing link" it's no longer missing, is it? And we've discovered tons of them.

The NON-missing links are all around us. We've found millions of fossils, and they are virtually all a "link" between some other pair of animals or fossils. The 7 Archaeopteryx fossils are a perfect link between reptiles and birds. Virtually every living thing is a "link" between some other pair of living things. Land mammals are a link between whales and fish.

There have been billions of years, with millions of species at any given time. There will always be "missing links" unless we could somehow see them all.

We have a few million fossils, but really really old fossils are rare. Some species leave tons of fossils and some some species leave almost none. So we have a picture with lots of "holes", but all the peices we have and all the pieces we find in the fully linked evolutionary picture.

We've got a trillion piece jigsaw puzzle and we have a few million pieces in place. It's enough to say it is a picture of a tree and we can describe the shape of various pieces of the tree.

Evolution is science because every time we find a new piece it can either be evidence supporting evolution or it can be evidence evolution is wrong. When we find a new piece and it fits in the picture and the tree becomes more clear. Evolution can be disproven if we find pieces that don't fit the tree picture. That is why it is science. Every new piece we find that does fit the picture is more proof.

There is tons of evidence for evolution. I guess you never studied evolution if you don't think there's tons of evidence. As if the biological, chemical, and fossil evidence weren't enough there's mathmatical analysis of the power of the evolutionary process and I've personally run evolutionary computer programs. Mutation is a bit of a red herring, it is the weakest process going on. It is the genetic recombination where the real power lies. Recombination is almost infinitely more powerful than mutation. I've seen it in action.

Even if you could prove life on earth isn't explained by evolution, evolution would still be a powerful and important discovery. It will start becoming more common in the computer field. Even if evolution didn't create humans, it is powerful enough to have done so.

Arguing against evolution is almost like arguing against the laws of gravity. They are both useful. They both explain all available evidence. Many smart people have worked really hard to prove each of them wrong and always failed. If you doubt evolution (or the laws of gravity) then you are perfectly free to look for evidence proving it wrong. If you manage to prove evolution (or the laws of gravity) are wrong then I promise you will become quite famous.

Creationism isn't science because no matter how many pieces of the picture we find and no matter what they look like they can never "disprove" creationism, and therefore new pieces are never support for creationism either. Someone can talk about creation-scients till they are blue in the face, it doesn't make it science.

-

Evolving plants with PlantStudio

[Anonymous Coward]

Take a look at: PlantStudio (freeware for windows).

"You can design, animate and breed a wide variety of plants. By using the "evolutionary arts" of variation and selection in the plant breeder, you can quickly and easily create whole families of unique plants for your 3D scenes."