Digital Life and Evolution

mrivorey writes "Discover Magazine has a story about The Digital Evolution Lab at Michigan State University. Scientists there have created virus-like computer programs that replicate, mutate randomly, and compete with each other... in other words, they evolve. Among such feats as learning to add and compare numbers, these digital life forms also once avoided scientists attempts at "killing" them, by playing dead. You can download the project yourself from SourceForge." We first mentioned this in early 2003, but it appears to have developed a good deal since then.

Comments

Re:Article Text from TFA (oops..with formatting)

[kaedemichi255]

TESTING DARWIN
DISCOV ER, FEBRUARY 2005 (Cover story)If you want to find alien life-forms, hold off on booking that trip to the moons of Saturn. You may only need to catch a plane to East Lansing, Michigan.

The aliens of East Lansing are not made of carbon and water. They have no DNA. Billions of them are quietly colonizing a cluster of 200computers in the basement of the Plant and Soil Sciences building at Michigan State University. To peer into their world, however, you have to walk a few blocks west on Wilson Road to the engineering department and visit the Digital Evolution Laboratory. Here you'll find a crew of computer scientists, biologists, and even a philosopher or two gazing at computer monitors, watching the evolution of bizarre new life-forms.

These are digital organisms-strings of commands-akin to computer viruses. Each organism can produce tens of thousands of copies of itself within a matter of minutes. Unlike computer viruses, however, they are made up of digital bits that can mutate in much the same way DNA mutates. A software program called Avida allows researchers to track the birth, life, and death of generation after generation of the digital organisms by scanning columns of numbers that pour down a computer screen like waterfalls.

After more than a decade of development, Avida's digital organisms are now getting close to fulfilling the definition of biological life. "More and more of the features that biologists have said were necessary for life we can check off," says Robert Pennock, a philosopher at Michigan State and a member of the Avida team. "Does this, does that, does this. Metabolism? Maybe not quite yet, but getting pretty close."

One thing the digital organisms do particularly well is evolve." Avida is not a simulation of evolution; it is an instance of it," Pennock says. "All the core parts of the Darwinian process are there. These things replicate, they mutate, they are competing with one another. The very process of natural selection is happening there. If that's central to the definition of life, then these things count."

It may seem strange to talk about a chunk of computer code in the same way you talk about a cherry tree or a dolphin. But the more biologists think about life, the more compelling the equation becomes. Computer programs and DNA are both sets of instructions. Computer programs tell a computer how to process information, while DNA instructs a cell how to assemble proteins.

The ultimate goal of the instructions in DNA is to make new organisms that contain the same genetic instructions. "You could consider a living organism as nothing more than an information channel, where it's transmitting its genome to its offspring," says Charles Ofria, director of the Digital Evolution Laboratory. "And the information stored in the channel is how to build a new channel." So a computer program that contains instructions for making new copies of itself has taken a significant step toward life.

A cherry tree absorbs raw materials and turns them into useful things. In goes carbon dioxide, water, and nutrients. Out comes wood, cherries, and toxins to ward off insects. A computer program works the same way. Consider a program that adds two numbers. The numbers go in like carbon dioxide and water, and the sum comes out like a cherry tree.

In the late 1990s Ofria's former adviser, physicist Chris Adami of Caltech, set out to create the conditions in which a computer program could evolve the ability to do addition. He created some primitive digital organisms and at regular intervals presented numbers to them. At first they could do nothing. But each time a digital organism replicated, there was a small chance that one of its command lines might mutate. On a rare occasion, these mutations allowed an organism to process one of the numbers in a simple way. An organism might acquire the ability simply to read a number, for example, and then produce an identical output.

Adami rewarded the digital organ

Re:QUESTION #4: WHY SEX?

[brightboy]

Why sex? Meiotic recombination! It's all about avoiding that monoculture...

Neuromancer

[Scrameustache]

Dan Simmons included this idea in his Hyperion book series, where evolving digital life spead into the "infosphere" and became artifically intelligent.

*cough*Wintermute*cough*

This sounds familiar...

[Mister Transistor]

This has been done before, it's been around since at least the mid 1980's possibly earlier - it was caleld Core Wars. This evolved into another similar more advanced version called CRobots... Short programs are written to "attack" the other by overwriting the other's memory space. They must alternate between "defending" their own space and "attacking" the other guys's... First to blow stack loses!

Here's some links:

Corewars:

Home Page

Source Forge Page

CRobots:

CRobots Home Page

GOLEM Project a lot more interesting

[QuantumG]

http://demo.cs.brandeis.edu/golem/

Re:GOLEM Project a lot more interesting

[Quixote]

From their download page:
NOTE: The golem@Home project has concluded. After accumulating several Million CPU hours on this project and reviewing many evolved creatures we have concluded that merely more CPU is not sufficient to evolve complexity: The evolutionary process appears to be hitting a complexity barrier that is not traversable using direct mutation-selection processes, due to the exponential nature of the problem.

Re:QUESTION #4: WHY SEX?

[KinkifyTheNation]

I believe they are trying to let them run on their own, without such code editing.

Re:QUESTION #4: WHY SEX?

[mercere99]

Its generally clear that sexual reproduction has long term benefits that will help a species... genetic exchange allows multiple benefical mutations to recombine into a single organism rather than competing with each other.

But this benefit is only in the *long term*. What would allow sex to be around long enough in the first place to allow this to come into play? Any individual subgroup is likely to be more successful if they don't have to (1) find mates, (2) maintain all of the extra mechanisms to facilitate recombination, or (3) have only half of their population (the males) actually producing offspring.

There are many alternative hypotheses about how sex could get started (and in what situations it would have short-term benefits) and we're trying to explore these one-by-one in Avida.

Charles Ofria
Director, MSU Digital Evolution Lab

Similar to Gaia

[bcnstony]

This reminded me of James Lovelock's book Gaia, which explained his Gaia theory, also reviewed here.

Lovelock was hired by NASA in the 60's to begin the process of looking for life on Mars. He concluded that a lifeless planet would have a static environment in equilibrium (or chemical equilibrium), unlike a planet with life which would neither be static or have chemical equilibrium. This seemed to dovetail with the article's " QUESTION #5:WHAT DOES LIFE ONOTHER PLANETS LOOK LIKE?". Readers of evolutionary biology and people who study game theory in economics will probably find much theory in common with the Zimmer article.

Re:virus?

[mercere99]

Fortunately, I think that it'll be somewhat difficult to create a true computer virus based on this code. The Avida organisms are written in a virtual assembly language that is quite different from real-world assembly languages. The commands are simplified and designed to do *something* reasonable in just about any situation.

We've done some experiments with more complex genetic languages, but in all cases they just didn't evolve as well without very specialized mutation types.

I can think of a number of ways that it would be possible to design an evolving computer virus, but I hope they're all non-intuitive enough that we have some time before anyone manages to get one working well. I've often though about trying to extend this work into the security arena -- if I didn't have so many projects going at once right now, I'd seriously consider that.

Dr. Charles Ofria
Director, MSU Digital Evolution Lab

Re:Not "virus like"

[mercere99]

This is a very good point. Computer viruses actually have the computer as a "host" and hence fit the definition well. We tend to compare the digital organisms to computer viruses as a way of explaining them to people, but you are right that they're not the same thing.

We are, however, doing some research on viruses within Avida. Specifically, we allow organisms to inject small snippets of code into each other. Sometimes these code segments could have the ability to take over the replication mechanisms inside of the digital organisms host and force them to use up their resources to make more copies of the snippet. These are much closer to the classical definition of a virus.

Dr. Charles Ofria
Director, MSU Digital Evolution Lab

Re:Great, now all we need

[mercere99]

All that really says is that is possible for intelligent beings to start up the evolutionary process, not that this is the only way it could happen.

In Avida, we are often examining issues of how it is possible for evolution to produce organisms of greater and greater complexity. We're interested in the generic process of evolution, not necessarily bound to a specific substrate. While the system we are examining was initially designed by a human, the complexity itself is generated by the basic rules of heritable variation and selection, without a human futher interfering.

Dr. Charles Ofria
Director, MSU Digital Evolution Lab

Intelligent Design vs Darwinism? Or both?

[rinkjustice]

Reminds me of Intelligent Design versus Darwinism. Allow me to yammer on for a bit and I'll explain why:

Evolution did occur (scientific findings are in the latest issue of "Duh" magazine), but the question is how it occured. Darwinism doesn't explain everything as tidily as some may think. ID defender and Associate Professor of Biochemistry at Lehigh University Michael Behe posturises biochemistry reveals a cellular world of such astonishing complexity and molecules so "precisely tailored" as to make inexplicable by gradual evolution. Only by an intelligent designer, i.e., God could much of this be plausibly explained. Behe goes on to say some systems can't be produced by natural selection because "any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional." Heavy stuff, but relative to this virus-like digital life. This is a good example of how God could've started the evolutionary ball rolling.

Darwinism and Creationism are not mutually exclusive. Our Heavenly Father could very well have used the evolutionary mechanism to bring about ideal living conditions for Adam and Eve, as well as help them and their offspring be fruitful and multiply (Genesis 1:28), or, as Slashdot puts it, "replicate, mutate randomly, and compete with each other".

Re:QUESTION #4: WHY SEX?

[Linuxathome]

Philip Gerrish and Richard Lenski (investigators at MSU) published this paper in 1998 and its abstract gives a hint to why sex:

In sexual populations, beneficial mutations that occur in different lineages may be recombined into a single lineage.

Re:Tierra

[Evil Pete]

The reality is that attacking Creationists is so much fun. Their comically stupid in the way they repeat their arguments ad infinitum, yet it stimulates you to read stuff you don't normally read. However, it does radicalise you too much. Which is why I stopped. But lots of fun. And yeah at the end of it you just can't treat them seriously, they don't even pass the Turing Test as far as I can see they are so mechanical in their thought processes. Sad but true.

Another related project

[Eythian]

The Tierra project has been around for many years, but seems to be pretty slow moving. It works in a somewhat similar fashion, but has its issues, such as only really optimising for reproduction speed (which is correlated with small size), and so you miss some potentially interesting results as the system tends away from complexity.

A friend and I have been talking about writing something that will use some of the ideas from this system, and a bunch of our own, but haven't really gotten very far yet, aside from writing some notes and some prototype code.

Treaten?

[Zentac]

I don't think it will have the capability of emotional joy in threatening you, so it will just kill you I guess.