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Wesley R. Elsberry



Posts: 4523
Joined: May 2002

(Permalink) Posted: Dec. 09 2007,12:12   

Rob Pennock's testimony in KvD included discussion of Avida [The court reporter doesn't know how to spell "Avida"].

 
Quote

[86]Q. Have you done any scientific research on the subject of evolution?

[87]A. Yes. Some of my current research is on testing evolutionary hypotheses making use of evolving computer organisms.

[88]Q. Can you describe in general terms what that research is?

[89]A. Sure. The idea is to make use of a system that essentially is an evolutionary system whereby the Darwinian mechanism is implemented in the computer and using that to form experiments to test evolutionary hypotheses. Essentially one is able to watch evolution happen and in replicable controlled experiments test particular evolutionary hypotheses.

[90]Q. Has this research been published in a peer reviewed scientific journal?

[91]A. Yes, in Nature.

[92]Q. Matt, could you pull up Exhibit P-330? Is this the first page of that article in Nature?

[93]A. Yes, that's right.

[94]Q. And Ken Miller plugged Nature repeatedly in his testimony, but I'll give you the chance as well. Is Nature one of the more prestigious scientific journals?

[95]A. Nature, together with Science and PNAS, Proceedings of the National Academy of Science are really considered the top three journals within science.

[96]Q. And obviously peer reviewed?

[97]A. Peer reviewed journals, that's right.

[98]Q. You didn't write this article by yourself?

[99]A. This was a collaborative project. My collaborators in this case were two of my colleagues at Michigan State, Richard Lenski, who is an evolutionary biologist. He's most known for his work on experimental evolution using bacteria. He's had lines of bacteria evolving for the last fifteen years that allows one to do experiments to test evolutionary hypotheses in that kind of system.

He got very excited about this new system that allows one to test evolutionary hypotheses in a way where things are even faster. Charles Ofria is another colleague at Michigan State. He's in the department of computer science, and he together with Christoph Adami, the last name there, are the two originators of the platform known at Evita.  Adami is a theoretical physicist. He's most known currently for his work solving a problem that Steven Hawkings was trying to work on regarding black holes, but he works in this area as well. He at the time was at Tech.

[100]Q. At where?

[101]A. At Tech Research Institute out in California.

[102]Q. I'm going to ask you the same question here that I have asked you in our private meetings, which is these are computer organisms.  They're not biological organisms. What can they possibly show about biological evolution?

[103]A. They show us how the Darwinian mechanism works. The key thing about them is that it's a model where you have the laws that Darwin discovered, the mechanism of random variation that's heritable, that then can be naturally selected, can be seen, manipulated, experimented with in just the same way, it works in just the same way that it works in the biological case. These organisms, computer viruses if you will, evolve. And so one can set up experiments to watch them evolve and test hypotheses about how the Darwinian mechanism works.

[104]Q. Now, these organisms, computer organisms, they didn't arise by themselves, correct? There was a programmer involved?

[105]A. Yes. That would have been Charles Ofria particularly, writing we called the Ancestor Program. The Ancestor is simply a self-replicator, an organism that has instructions to allow it to replicate itself, but otherwise is just a series of blank instructions. That's the basic part that, was hand coded.

[106]Q. So with that, you know, fact of a human designer, a programmer, how can this teach us anything about evolution in the natural world?

[107]A. Our investigations are not about the origin of life. Like Darwin we're not really interested in that particular question. We're interested in as Darwin said the origin of species, the origin of complexity, the origin of adaptations, and what we're able to do in this system is examine essentially what Darwin examined. We're not investigating how life began itself. We're investigating how once that happens, things evolve, evolve complex traits.

[108]Q. So just to make sure I understand, this research wouldn't be valuable in any way to coming up with a natural explanation for how the first biological life arose?

[109]A. No. It's not at all aimed at that.

[110]Q. Does the designer, the programmer, play any role in the development of these computer organisms, like their evolution after that?

[111]A. The wonderful thing about this is that we can essentially sit back and watch evolution happen. We'll set up an environment, set up a system, put in place the Ancestor, put in place the original organism, and then within the experimental set-up, depending on what one wants to investigate you'll set it up differently, but essentially at that point we're not going to go in and hand code anything. We're not going to manipulate the code. What happens at the end, if they've evolve some new functional trait, that something that happens by virtue of the Darwinian mechanism. They randomly evolve, they randomly vary, that variation is inherited, and the natural selection then does its work.

[112]Q. What advantages does this computer model have over doing research on the subject of evolution with biological organisms?

[113]A. It has the advantage of speed primarily, and precision. It allows us to do what you really can do with natural organisms.  Lenski's work with E. coli lets one do experimental evolution so one can test hypotheses in that way. It's taken fifteen years, E. coli are pretty fast replicators, but even so, four generations or so a day still is a long time, and your graduate students would never get out and get jobs if you had to wait for that whole process to go through, and what this does is let one watch it happen much more quickly, and then set up very controlled circumstances so that you can really do replications. A controlled experiment is now possible in a way that allows very precise comparison of groups and then statistically significant results.

[114]MR. ROTHSCHILD: Your Honor, at this time I'd like to move qualify Dr. Pennock as an expert in the philosophy of science, in the history of science, in intelligent design, the subject of intelligent design, and in his research on the evolution of computer generated organisms.


 
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[193]Q. Are irreducible complexity and specified complexity associated with particular individuals in the intelligent design movement?

[194]A. Irreducible complexity is most associated with Michael Behe.  Specified complexity is most associated with William Dembski. These are interrelated concepts though. Specified complexity is the more general form. Dembski directly though says that irreducible complexity is a type of, a case of specified complexity.

[195]Q. Does your work on computer organisms address these arguments of irreducible complexity and specified complexity?

[196]A. Yes, it does.

[197]Q. Can you just describe for us briefly how it does that?

[198]A. Sure. The claims that are made with regard to these two concepts are as follows. Systems that exhibit or that purportedly exhibit irreducible complexity or specified complexity, actually at this point let me just focus on irreducible complexity, because since it's an example of specified complexity, any conclusion that we can get with regard to irreducible complexity would also deal with specified complexity. So we can just focus on that.

So the claim is any system, Behe's example is a mouse trap, so it doesn't have to be a specifically biological system, just a very general argument, any system that is irreducibly complex, thus to say has interacting parts that are well matched to introduce a function, such that if you remove any of those parts, it breaks, stops functioning, doesn't produce that basic function, is an irreducibly complex system, and such systems the claim is couldn't have been evolved through a Darwinian mechanism.

What our system shows is that's just wrong. We can observe digital organisms evolving by the Darwinian mechanism, starting with an organism that cannot produce some effect, cannot fulfill a function, doesn't have this possibility, and later on evolve to the point where it can, some complex trait that we can then examine. The nice thing about this system is it lets one look at it very precisely, we can look inside and see does it fulfill the definition?

In fact, it does. We can test to see, remove the parts, does it break?  In fact, it does. And we can say here at the end we have an irreducibly complex system, a little organism this can produce this complex function. But the nice thing about the system is that we can look back and see in fact it did evolve. We can watch it happen. So it's a direct refutation of that challenge to evolution.

[199]Q. Is that point addressed, put forward in the Nature paper?

[200]A. It's not. The Nature paper itself is meant just to be a test of a general evolutionary hypothesis, examining how it is that complex features arise. Darwin had specific things to say about that. What we were doing was simply looking into that, testing it in a way. It just turns out that it also applies to this case.


Cross-examination:

 
Quote

[205]Q. I want to ask you a few questions about your work in the computer science area and Evita. You testified that in your opinion that Evita is an artificial life system designed to test evolutionary hypotheses, correct?

[206]A. That's correct.

[207]Q. And that's the scope of your testimony here today. You said the same thing, correct?

[208]A. That's correct.

[209]Q. And you said today and I believe in your opinion that it's designed to instantiate Darwin's law, correct?

[210]A. That's correct. By instantiate, just so that I this kind of explain this sort of philosophical term, the difference here is between a simulation of something and an actual instance of it. That's to say a realization of it. In the Evita system we're not simulating evolution. Evolution is actually happening. It's the very mechanisms of evolution itself as Darwin discovered them. The organisms actually do self replicate. They do randomly vary the code changes. The mutations happen at random. There is competition and actual natural selection. So these are not being simulated. Those processes are actually happening. So that's the sense in which it's an instance of evolution, not just a simulation.

[211]Q. And to make sure I understand, it seems you're saying that the instantiation makes it a more perfect model of Darwinian law of natural selection, is that correct?

[212]A. What I'm saying is it's an actual example of it, that what we have in the system our organisms, Evitians, have the very properties that the Darwinian mechanism discusses. So it's not a simulation of replication. They are actually self replicating. It's not a simulation of a random mutation. That's what's going on with the code. It's not a simulation of natural selection. They do compete and are naturally selected, without intervention, without design.

[213]Q. And Mr. Rothschild asked you and I believe you testified that the program doesn't address the question of origins, but rather the process of Darwin's law, it's working out in the computer program organisms, correct?

[214]A. It doesn't deal with the origins of life. It deals with the evolution of complexity of adaptations. So origins can sometimes be used in both ways. So what's relevant here is it's not about the origin of life. It's about the origin of complex traits.

[215]Q. And I believe you said that the overall purpose of the project is to test how evolution actually works, is that correct?

[216]A. That's right. What we're able to do in the system is put forward an evolutionary hypothesis and then set up a controlled experiment and let the system evolve with replications, as many are as needed, and in some cases you might have fifty different populations replicating in a controlled situation, fifty in an experimental situation, so that you can then watch what happens in each case and observe evolution, the Darwinian process, do its stuff.

[217]Q. Now, if someone looked at a computer program, I think you have said that it was written by a particular individual called the, what did you call it, the genesis program or the --

[218]A. No, the Ancestor.

[219]Q. Ancestor program, forgive me. They would look at that and immediately know that was done by a computer programmer, correct?

[220]A. Not necessarily at all. In fact, one can look at these things and not know which things were coded by a programmer and which things were evolved. We know because we put them in there this was the one that we coded, but if one were to just look at them, you wouldn't necessarily be able to tell at all.

[221]Q. So is it your testimony that if someone happened to cross that computer program, they wouldn't know that someone had designed it?

[222]A. That's right. You would not be able to pick out the ones that were evolved from those that Charles Ofria hand coded as the Ancestor.  As I said, what the Ancestor does is simply replicate it. It's a very basic program. Most of it is just blank code, and as the organisms evolve it can actually turn out that they lose the ability to replicate. Some mutations are harmful.

Many are. Most are, or neutral. It might make no difference. Some mutations can actually make them better replicators, and if it turns out that random mutations replicates better than another organism, that means that in the competition, in the digital environment, those will be naturally selected. So what you'll have over time is the evolution of for example faster replicators. That is they figure out a way to replicate faster than the original programmer programmed in.

Or it could turn out that they'll be worse, and those will then lose out in the competition. So what you see is the evolutionary process, random mutations to the code, being naturally selected for and generation after generation organisms evolving, in this case better replication ability. Or, and this is the other thing that's characteristic about Evita, it can evolve the ability to perform complex logical operations, and in this case again it's not something that was programmed in at all.

The original Ancestor could do none of that, but what one sees at the end are organisms that have evolved these complex abilities. The code has changed. It's acquired an ability that it did not have before. And that's what we're able to see, something we know that was designed at the beginning but couldn't do any of this stuff to something at the end that has evolved so it's quite complex.

The set of instructions has to be executed in a specific order to produce a particular function. That's something we can look at and say how did it do it, and often they're very clever, they evolve things where the programmer would think why, I would never have thought even to do it that way. And that's what allows this to be a nice model for examining how evolution can produce complex functional adaptations.

[223]Q. Sure.

[224]A. If you have it, and the other thing about it is -- sorry, I get excited about this. We can trace, we can keep track of the full evolutionary history. So we have a complete fossil record if you will.  So after we've see that it's evolved something we can look back and look, it's a mutation by random mutation of how that evolved.

[225]Q. Sure, and forgive me if my question was imprecise. I didn't want to cut you off, but my question is a little different than one you've answered at least as I see it, not technical, which is this.  I'm not asking about the difference between the organisms you're looking at. I'm saying if someone came across that computer program, the Ancestor program, wouldn't they believe it was designed?

[226]A. And my answer is that you really can't say that. You might believe it and you'd be wrong. You can't tell the difference between the one that was encoded and one that was evolved later on.

[227]Q. So it's your testimony that someone could believe the computer program was not designed?

[228]A. You're asking a psychological question about what someone could believe, is that right? In that case they could believe all sorts of things, but the question has to do with can you look at them and tell this was one that was designed, and the answer there is no, not necessarily.

[229]Q. Let's use your definition and let's constrict causality to the natural world and I'll ask you the question again. If someone like myself wandered down to Michigan State University and came across your computer system generating this pattern that you have described in great detail which is designed to substantiate Darwinian mechanism, is it your testimony or do you have an opinion concerning whether someone like me would think that was designed or not?

[230]A. Someone might think it was. You might look at it and you might say wow, that looks pretty complicated, how could that have happened.  You might think this is so amazingly functional and interrelated, it's irreducibly complex, it had to have been designed by someone, and you'd be wrong.

[231]Q. So I would be wrong if I inferred that that computer program has been designed by a computer programmer?

[232]A. That's right. You'd be wrong about that. The ones that emerged at the end of the evolutionary process have specific code that lets them do specific adaptive functions, and that was not programmed in.

[233]Q. Would I be wrong if I inferred that the computer program had been created by a supernatural force?

[234]A. If you were to conclude this just as a theological position or as a scientific position?

[235]Q. If I were to conclude it in any way.

[236]A. So again, and this is a nice example to sort of show the difference between thinking about this as a scientist under methodological naturalism versus the intelligent design notion of opening our minds to the possibility, what I have said here is that the organisms at the end weren't designed. We didn't have a hand in doing that. They evolved. Someone who says well, we have to consider the possibility of supernatural interventions might say well, you know, God was in there or some supernatural designer was in there changing the bits inside the computer.

Well, you know, we don't know if that's true, and no scientist can ever know if that's true. That's not a testable proposition. So in that sense we can never rule that out. That's part of what it means to be a methodological naturalist. So we're neutral with regard to that.  Our conclusion that there was no design is one based upon methodological naturalism, namely we're assuming that this is working through ordinary laws, that there aren't any interventions that breaking laws. We know that we didn't do it, and that's what we can say as scientists. If God or some supernatural being is in there fiddling with the gates, the logic gates such that there really was design, we don't have any way of testing that.


I have no idea how they would propose to "overturn" the demonstrable claims Pennock made in KvD with respect to Avida. I think they must be delusional on that point. I guess we'll see whether the EIL improves any on the already-poor track record that the virtual lab has established.

Edited by Wesley R. Elsberry on Dec. 09 2007,12:13

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
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