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

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

[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

[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

[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

[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

[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

[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.

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 ;)

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

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.

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