Avida in Discover Magazine

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Our congratulations go out to Carl Zimmer. Discover magazine published one of Carl Zimmer’s articles as a cover article. The article was titled “Testing Darwin” (Published in Discover Magazine Feb 2005)

Zimmer explores the relevance of work on Avida to evolution

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.”

The work based on Avida is not well received by creationists who argue that Darwinian theory cannot explain the complexity of life. Although others have already shown that complexity and information in the genome can increase under the processes of variation and selection., Avida has recently been used to address the concept of irreducible complexity. (Note: Mark Perakh has addressed some the ever changing definitions of irreducible complexity in ID’s irreducible inconsistency revisited)

When the Avida team published their first results on the evolution of complexity in 2003, they were inundated with e-mails from creationists. Their work hit a nerve in the antievolution movement and hit it hard. A popular claim of creationists is that life shows signs of intelligent design, especially in its complexity. They argue that complex things could never have evolved, because they don’t work unless all their parts are in place. But as Adami points out, if creationists were right, then Avida wouldn’t be able to produce complex digital organisms. A digital organism may use 19 or more simple routines in order to carry out the equals operation. If you delete any of the routines, it can’t do the job. “What we show is that there are irreducibly complex things and they can evolve,” says Adami.

The Avida team makes their software freely available on the Internet, and creationists have downloaded it over and over again in hopes of finding a fatal flaw. While they’ve uncovered a few minor glitches, Ofria says they have yet to find anything serious. “We literally have an army of thousands of unpaid bug testers,” he says. “What more could you want?”

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Computer Life from Rite Wing Technopagan on February 5, 2005 9:16 PM

More on computer life forms (HT: The Panda's Thumb 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. Read More

152 Comments

How delicious:  creationism, slain by an example of evolution which can be demonstrated convincingly by anyone who can play the Sims.  It won’t be long (in generational terms) before there is nothing left of it.

The real problem for the supporters of creationism is that they need the origin tale as one of the supports of their traditions and morality.  Problem for them and us is that the morality may be justifiable even if the creation myth is bogus.  It would be a pity to lose that baby with the bathwater.

Perhaps it’s time to work on evolutionary models of morality.

I had a Thumb posting on the Avida simulations here last year. It ain’t a bad introduction, if I do say it meself.

RBH

Syntax Error: not well-formed (invalid token) at line 9, column 60, byte 1402 at /usr/local/lib/perl5/site_perl/5.12.3/mach/XML/Parser.pm line 187

Charlie, Charlie, Charlie. Has it ever occurred to you that your ‘argument’ could benefit from some… uh … logic or supporting evidence. In fact Avida contains many of the essential aspects of evolution such as limited resources, fitness, variation. Until you familiarize yourself with evolutionary theory, please try to refrain from sounding a bit silly. Most creationists who oppose Avida, try to reject it on far better ‘reasons’ that Charlie. Come on Charlie, provide at least a challenging review of the article and Avida beyond your usual rejection without much reasoning?

‘it stands to reason’, ‘it seems self evident’, ‘it just seems so incredibly simple to me’ do not bode well in any discussion.

Sigh… If your next posting does not clean up its act, it will be removed to a more fitting place on the bathroom wall of PT.

Charlie,

“It seems self-evident to me, and it should to all other observers that living organisms are far more technologically advanced and organized than any machine that humans can build. It stands to reason that an intelligence greater than human intelligence was required to construct them.”

You seem like a scratched record stuck in a time warp. Over and over, you offer the same unsupported opinion and demand that others bow to your incredulity - or is it arrogance.

What seems self-evident to you obviously doesn’t seem self-evident to most of the rest of us. It does not stand to reason that “an intelligence greater than human intelligence was required to construct them.”

I tried to explain to you at least once before that Nelson’s Law proves that humans designed biological organisms. You still haven’t accepted that.

Pulling the plug on Avida certainly places this evolutionary simulation in a thermodynamically unfavorable position.

The most well-known intersection of evolutionary biology with computer science is the genetic algorithm or its many variants (genetic programming, evolutionary strategies, and so on). All these variants boil down to the same basic recipe: (1) create random potential solutions, (2) evaluate each solution assigning it a fitness value to represent its quality, (3) select a subset of solutions using fitness as a key criterion, (4) vary these solutions by making random changes or recombining portions of them, (5) repeat from step 2 until you find a solution that is sufficiently good.

We make random mutations and then intelligently select those that fit what we’re looking for. The program is intelligently selecting those progams that are more fit according to its fitness value. So, of course, we end up with programs that fulfill exactly what we were looking for. This is like generating programs that produce a random colors and then selecting those programs that generate only blue, and then we turn around and are amazed that we have programs that produce only blue. How exactly does this support evolution?

Jeff: First learn what evolution is, then learn how Avida works. That should answer your question.

Pim: Sysiphus is an old legend. Over time it has been distorted and altered. For instance, in the version we have, it says he was condemned to push a boulder up a hill for eternity. But in the original, it said he was condemned to explain evolution to Charlie Wagner. Basically the same thing.

Charlie writes

It seems self-evident to me, and it should to all other observers that living organisms are far more technologically advanced and organized than any machine that humans can build. It stands to reason that an intelligence greater than human intelligence was required to construct them.

Whoa, it seems to me that your thinking must have “evolved” Charlie. I seem to recall sometime last year arguing with you about whether “ID theory” made any claims about the nature of the designer other than mere “intelligence”.

Now it seems that you have something to say about the intelligence of the designers. Were the mysterious aliens smarter than any human being who ever lived? Or were they just super smart, like Einstein?

Any other insights into the designers that you’ve recently acquired?

As always, I’m not really interested in your answers to these questions.

Charlie Wagner Wrote:

It seems self-evident to me, and it should to all other observers that living organisms are far more technologically advanced and organized than any machine that humans can build.

So far. But given how much more “technologically advanced” these autocatalytic systems we call cells are, one could reasonably expect that, even though they, at a casual glance, and in the ridiculuously short time intervals in which they have been observed by humans, seem to evolve only within poorly defined “kinds,” their long range evolutionary potential is almost boundless.

Charlie said:

“It seems self-evident to me, and it should to all other observers that living organisms are far more technologically advanced and organized than any machine that humans can build.”

Please elaborate on exactly what these “technologically advanced” structures within organisms are. I mean, how are you defining “technology” here? Don’t you need to prove they *are* technologically advanced, or a form of technology, in order to point out where they’re advanced?

Also, “It seems self-evident to me, and it should to all other observers”

- ah, the mating cry of the wandering martyrbird. “I can see it, why can’t anyone else?”

Marcus Good Wrote:

Please elaborate on exactly what these “technologically advanced” structures within organisms are. I mean, how are you defining “technology” here? Don’t you need to prove they *are* technologically advanced, or a form of technology, in order to point out where they’re advanced?

They are more highly organized and they perform more operations, employ more processes and structures, and are integrated together in more complex ways. Take the human brain, for example. It’s far more advanced than any computer that humans have built. Were it not, all of the artificial intelligence people would be folding their tents and going home. They aspire to duplicate what living brains already easily accomplish. Take the cell for another example. It is nothing less than a universal automaton. It’s protein synthetic apparatus can construct any biochemical machine and if given the raw materials, has almost unlimited potential to construct every living thing that ever existed on earth. It can also replicate itself and construct all of its components in a matter of minutes, and a complete organism in a matter of months from a piece of DNA that is millions of times smaller than any functional machine produced by humans.

- ah, the mating cry of the wandering martyrbird. “I can see it, why can’t anyone else?”

Better than the blind followmebird who flies in ever decreasing concentric circles until it disappears up its own a**hole, all the while shrieking “mountain of evidence…mountain of evidence…”

…so, why not refute some of the mountain of evidence? “I think…” doesn’t cut it.

ThisisPainful Wrote:

… so, why not refute some of the mountain of evidence? “I think … “ doesn’t cut it.

When it comes to evidence, I somehow feel like I’m on the Great Plains…

http://www.greydragon.org/trips/Kan[…]yside082.jpg

Charlie Wagner http://enigma.charliewagner.com

Are you saying that picture shows explicit evidence that grass was specially created? Go to talkorigins.org, pick something, and lets discuss your misunderstandings about life.

ThisisPainful Wrote:

Are you saying that picture shows explicit evidence that grass was specially created?

No. It’s a metaphor . The flatness of the plain represents the absence of evidence, just as the mountain represents a large amount of evidence.

Go to talkorigins.org, pick something, and lets discuss your misunderstandings about life.

I’ve read almost everything in the t.o archive and I’ve been discussing it for over 10 years, having posted thousands of articles. Just Google on my name (I use both Charlie Wagner and Charles Wagner) and read some of them. You can also visit my website at: http://www.charliewagner.com or my blog at: http://enigma.charliewagner.com for more information about me.

Jeff Wrote:

We make random mutations and then intelligently select those that fit what we’re looking for.

Not really. Have you looked at the program? It selects according to fitness

Jeff Wrote:

The program is intelligently selecting those progams that are more fit according to its fitness value. So, of course, we end up with programs that fulfill exactly what we were looking for. This is like generating programs that produce a random colors and then selecting those programs that generate only blue, and then we turn around and are amazed that we have programs that produce only blue. How exactly does this support evolution?

The program’s fitness function is as ‘intelligently’ designed as nature’s fitness function which selects based on ‘what it’s looking for’. Why do you not have a look at the program and how it works and how it was used before making such strawman arguments.

How does the program supports evolution? Because it is an instance of evolution with variation, selection and competition for resources and helps us understand many issues confronting us when it comes to evolution. Such as: Can evolution increase the information/complexity of the genome? The answer is yes (see Adami or Schneider). Can evolution explain irreducibly complex systems? And the answer once again is yes. As such it not only helps reject poorly founded assertions (often found amongst creationists) but it also helps researcher with many other issues such as ‘stasis/punk eek’, speciation, ecology, adaptation, robustness/evolvability, dynamics.

For those who want to familiarize themselves with the program and join the countless creationists who seem to be ‘bug testing’ see Avida homepage

I am sure the researchers are looking forward to a well reasoned discussion. I would… And I still am… but sigh…

For instance: Robustness and evolvability are very interesting concepts. Theoretical research has shown how the ability of evolution to evolve itself (evolvability) is also linked to robustness. And what is essential for evolvability? A level of neutrality… Found in the degeneracy of the genetic code for instance. So in short, what has Avida helped us resolve?

1. Evolution cannot explain the information in the genome. False… 2. Evolution cannot explain the complexity of life such as irreducibly complex systems. False…

Not bad for starters. Even if Avida were limited to disproving creationist assertions, it would have been highly successful.

Charlie. other than mumbling ‘it appears to me that’, ‘it seems self evident that’ has failed to address the issues here. In the thousands of postings on TO, Charlie has not fared much better either.

Pim Wrote:

Charlie. other than mumbling ‘it appears to me that’, ‘it seems self evident that’ has failed to address the issues here. In the thousands of postings on TO, Charlie has not fared much better either.

On the contrary, I have addressed the validity of computer simulations many times. You want more? Here it is: Computer simulation models of evolution are not valid because there is no way to demonstrate that they model what actually happens in nature. They only model your belief about what happens in nature. So trying to find ‘flaws’ is useless because the simulation is not being judged against what actually is happening, it’s being judged against your belief in what’s happening, which can always be ‘adjusted’ to compensate for any problems. In general, the value of computer simulations is heuristic, they strengthen what has already been established through other means. The evolutionary mechanism of mutation and natural selection has not been established as the mechanism of evolution. There has been no empirical support for the notion that changes in gene frequency can result in the emergence of highly organized structures, processes and adaptations without the help of intelligent input, so any simulation models based on this mechanism are fictions, and they can never be a representation of the real world because there may be factors at work of which we are unaware.

Charlie Wagner http://enigma.charliewagner.com

Computer simulation models of evolution are not valid because there is no way to demonstrate that they model what actually happens in nature. They only model your belief about what happens in nature. So trying to find ‘flaws’ is useless because the simulation is not being judged against what actually is happening, it’s being judged against your belief in what’s happening, which can always be ‘adjusted’ to compensate for any problems.

The evolutionary mechanism of mutation and natural selection has not been established as the mechanism of evolution.

FIrst of all we know that mutations happen and that natural selection happen so the next step is to figure out if these mechanisms are of any importance/relevance. Additionally, based on these facts, science can start formulating theoretical foundations and simulations to establish how variation and selection affect the temporal behavior of populations. Computer simulations are not meant to mimick in every detail what happens in nature, they model relevant concepts in nature to see their effect. Such is how science works. If Charlie objects that science is studying evolution because he disagrees with the relevance of variation and selection then fine, let him so argue. But for science, who has found significant evidence supporting their viewpoints, the findings based on Avida help understand in even more intricate detail how evolution has shaped populations. In addition Avida has helped establish that creationist arguments that mutationa and variation cannot explain X, are based on flawed reasoning.

As I said, even if we were to limit Avida to disproving the claims of creationists, it has been highly successful but Avida is doing much more than that. That Avida’s simulations end up strengthening the hypothesis that variation and selection are an important evolutionary mechanism should hardly be seen as an objection. That’s how science works.

Pim Wrote:

FIrst of all we know that mutations happen and that natural selection happen so the next step is to figure out if these mechanisms are of any importance/relevance.

I agree. Mutations and natural selection do occur and the goal of evolutionary science is to prove that these effects can result in the emergence of highly organized structures, like the eye and processes like the biochemical pathways in vision, and integrate these into functional, living systems without the help of intelligent input. Therefore, I’m not opposed to using these simulations because I think they can prove that this is not what happens in nature. I could argue that these simulations are not free of intelligent input, but let me put that aside for a moment. I’ll concede for arguments sake that they are. That being the case: 1) is Avida capable of demonstrating that unguided processes of mutation and natural selection can result in greater organization? and 2) has this been accomplished? What exactly does the computer simulation produce when it is run? Obviously, not a three-dimensional entity or a biochemical process. So what evidence has it actually generated? Is this merely an increase in complexity, which I concede can be generated by non-intelligent, random processes or an increase in information, which I also concede can be generated by non-intelligent, random processes, or does it demonstarte an increase in organization, which is essential to the evolution of living organisms?

Charlie Wrote:

Mutations and natural selection do occur and the goal of evolutionary science is to prove that these effects can result in the emergence of highly organized structures, like the eye and processes like the biochemical pathways in vision, and integrate these into functional, living systems without the help of intelligent input. Therefore, I’m not opposed to using these simulations because I think they can prove that this is not what happens in nature.

You are free to think whatever you want Charlie but that’s not relevant to the issue. YOu seem to be intent on moving the discussion towards an irrelevant area namely

1) is Avida capable of demonstrating that unguided processes of mutation and natural selection can result in greater organization? and 2) has this been accomplished?

Describe ‘greater organization’ in a scientific manner that could be tested using Avida.

I am glad that you agree however that creationist claims about information and complexity are misguided and I encourage you to develop your own ideas in a scientific manner. PT has an open submission policy for relevant ideas.

This thread however is about Avida and its relevance. I hope you can accept this and abide by my suggestions to focus on the topic of the thread instead.

Charlie Wrote:

Mutations and natural selection do occur and the goal of evolutionary science is to prove that these effects can result in the emergence of highly organized structures, like the eye and processes like the biochemical pathways in vision, and integrate these into functional, living systems without the help of intelligent input.

We have some pretty good evidence that it can.

When evolution skeptics want to attack Darwin’s theory, they often point to the human eye. How could something so complex, they argue, have developed through random mutations and natural selection, even over millions of years?

read more Here

See also

The eye is too complex to have evolved for more relevant research

Some Avida relevant papers

Chris Adami, Learning and Complexity in Genetic Auto-Adaptive Systems Physica D, volume 80 p154 (PDF)

We describe and investigate the learning capabilities displayed by a population of self-replicating segments of computer code subject to random mutation: the tierra environment. We find that learning is achieved through phase transitions that adapt the population to the environment it encounters, with a learning rate characterized by external parameters such as mutation rate and population size. Our results suggest that most effective learning is achieved close to the transition to disorder, and that learning curves of evolutionary systems are fractal.

Many papers by Chris Adami can be found here and here

Avida’s homepage also has many links as to how Avida has been used in evolutionary research

So you can cope with increased complexity and increased information, but not increased organisation? How do you deal with snowflakes then?

Charlie, even if you don’t accept that it’s a valid simulation of nature, Avida shows that an entirely algorithmic process of mutation, reproduction and selection can evolve “irreducibly complex” operations from simple commands. Given that the central, indeed only, substantial claim of ID is that irreducibly complex things can’t evolve, but must be created fully formed, do you not think that is relevant? And bringing the discussion back to nature simulation, if a system based solely on mutation and selection can create such remarkably “lifelike” products as diversity, complexity, punctuated equilibrium

As I was saying:

… (in Dennett’s synthesis-compatible sense), does this not provide at least circumstantial evidence that a similar process might cause such features in nature?

Charlie,

Isn’t a logical conclusion of ID that something must have created the intelligence that created us? And so on?

Further, you stated:

> and they can never be a representation of the real world because there may be factors at work of which we are unaware.

This may be true but surely the same argument can be applied to so-called irreducible complexity. As the demolishing of the mousetrap example has shown, just because you cannot conceive something doesn’t mean that it cannot be conceived or implemented. The factors of which “we are unaware” might, quite literally, be factors of which the ID people are unaware because they are seeking evidence for what is, to them, a foregone conclusion.

Put differently, if we are here because invisible pink unicorns that live on Pluto created us then no simulation can ever capture that. However, to the extent that Avida has predictive power than to that extent it is a valid simulation. It is no different than using a computer to predict weather, orbits of planets or through the use of genetic algorithms to design things (circuits, antennas etc) which are not the direct result of traditional “logical” design.

Essentially ID has zero predictive power whereas evolution has - e.g., it predicts that diseases will become resistant to anti-biotics etc. Evolution is not here because it exists to make the point that God does not exist or that God did not craete us. It is here and important because it is actually a useful concept as opposed to ID.

Charlie - do you actually want medical research to proceed based on the notion that we were created and that evolution is wrong?

Fred

How does the program supports evolution? Because it is an instance of evolution with variation, selection and competition for resources and helps us understand many issues confronting us when it comes to evolution. Such as: Can evolution increase the information/complexity of the genome? The answer is yes (see Adami or Schneider). Can evolution explain irreducibly complex systems? And the answer once again is yes.

actually, my favorite implication of the examples in the article would be: Can evolution explain how competing species in a world of limited resources achieve an equilibrium of existence, rather than the most adaptable species taking over the entire system? To which, the answer is yes.

its not a common discussion now, but when Darwin first published, the assumption up to that point was that God created the animals specifically to fit their niches in the balance we see them as. Of course, such a balance couldn’t explain away “casual” extinction (which also happened, and more often than catastrophic (asteroid) or man-induced extinctions).

Misinterpreted, natural selection, and the social-darwinistic attitudes that came from it, implied that one species must reign supreme. Avida shows otherwise, as does Darwin and most post-Darwin evolutionary research.

Pardon me, but I do believe these digital organisms were created by an intelligent agent called a “computer software engineer”.

I’d also remind you that the universe hosting these digital organisms was also created by an intellegent agent called a “computer hardware engineer”.

Let me know when you boys get some organisms going that do not require an intelligent agent to get the ball rolling in the first place.

Thanks in advance.

“Let me know when you boys get some organisms going that do not require an intelligent agent to get the ball rolling in the first place.”

Spot the logical error in this sentence.

You’re missing the point here, DaveScot. Although the program and computer were created by humans, the individual organisms weren’t. Moreover, genetic algorithms frequently lead to solutions that are extremely hard to grasp with human understanding, as they don’t follow rules we usually use when designing something (like having a hiearchy of units and tasks). This would translate into “impotent God”, one who doesn’t understand his creation in full, who can’t predict what effects his miracles would have, and who therefore prefers to sit watching the world in wonder of its marvels.

In other words, the part of “creator” in Avida is limited to creating the universe and its rules and letting it run its course. But this is NOT contrary to evolution! An evolutionist can accept such view of his own universe (and indeed, many Christian evolutionists did), since evolution is not an universal theory - it doesn’t deal with origin of life, it deals with its diversity.

Avida contradicts special creation and ID in that it shows that evolution mechanisms WORK and CAN produce complexity those theories claim it can’t. It won’t contradict theistic evolution or Christianity or most of reasonable religious systems.

I asked Bob a question and I would appreciate an answer.

John A. Davison,

If you are using MicroSoft’s Internet Explorer, there’s no call to talk of special attention being made to cause you problems; you have voluntarily taken on problems. You can try using the “Refresh” button to get the page again, but your time is probably better spent downloading and installing the Firefox browser.

http://www.pandasthumb.org/pt-archi[…]/000654.html

That “Bathroom Wall” contains comments from http://www.pandasthumb.org/pt-archi[…].html#c11589 to http://www.pandasthumb.org/pt-archi[…].html#c16584

The specific comment requested is at http://www.pandasthumb.org/pt-archi[…].html#c16114

Loads fine for me. I’d suggest a change of browser, or better yet, load a Knoppix bootable CD and browse from that.

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