Computer Simulations and Darwinism

_{Gil Dodgen

October 1, 2011

Intelligent Design}

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Okay dudes, no more talk about my abandonment of atheism. Here’s some science and engineering talk.

I know something about computer simulations. In fact, I know a lot about them, and their limitations.

Search algorithms (and especially AI-related search algorithms) are a specialty of mine, as is combinatorial mathematics.

The branching factor (the average number of moves per side) in chess yields approximately 10^120 possible outcomes, but the number of legally achievable positions is approximately 10^80 — the estimated number of elementary particles (protons and neutrons) in the entire known universe. Compare this to the branching factor of nucleotide sequences in the DNA molecule. Do the math.

Finite element analysis (FEA) of nonlinear, transient, dynamic systems, with the use of the most sophisticated, powerful computer program ever devised for such purposes (LS-DYNA, originally conceived at Lawrence Livermore National Laboratory in the mid-1970s for the development of variable-yield nuclear weapons) is another of my computer-simulation specialties.

Dyna has been used heavily in the automotive industry for simulating car crashes, so that cars can be designed to produce the least damage to occupants.

In these simulations everything is precisely known and empirically quantified (the material properties of the components — modulus of elasticity, mass density, shear modulus, precisely calibrated failure modes, etc.).

In addition, the explicit FEA time step (the minimal integration time step determined by the software based on the speed on sound in the smallest finite element and its mass density, which is required to avoid numerical instability) is critical. In my simulations the time step is approximately a ten-millionth of second, during which partial differential equations, based on the laws of physics (F=ma in particular) are solved to compute the physical distortion of the system and the propagation of the forces throughout the system in question.

One learns very quickly with FEA simulations that even with all of this knowledge and sophistication one must empirically justify the results of the simulation incrementally by comparing the results with the reality it attempts to simulate.

One false assumption about a material property or any of the other aspects of a simulation can completely invalidate it. Worse yet, it can produce results that seem reasonable, but are completely wrong.

So, the next time someone tries to convince you that a computer simulation has validated the creative power of the Darwinian mechanism of random errors filtered by natural selection in biology, you should tell them to go back to school and learn something about legitimate computer simulations, and how difficult it is to produce reliable results, even when the details are well known.

Comments

Thornton demonstrated an historical example of an IC system evolving. the debate with Behe continues: http://blogs.discovermagazine.com/loom/2009/10/15/the-blind-locksmith-continued-an-update-from-joe-thornton/Petrushka_{October 10, 2011
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12 isolated populations, after 5*10^4 + generations, all mutations that could have mutated, mutated (numbers in the millions according to lenski), and every population lands at exactly 15 +-5 fixed beneficial mutations. Where is the tail liz? That seems like a flat distribution to me. Data comes from: wiki+lenski+e-coli.junkdnaforlife_{October 9, 2011
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What "flat distribution rates"? I'm not even sure what you mean by this term. Can explain, and give a citation?Elizabeth Liddle_{October 9, 2011
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Yes, of course I would. I am sure that some systems are out of reach of Darwinian evolution. Centaurs, for instance. Indeed it is the absence of such things that is one of the evidence for Darwinian evolution - there really are limits to evolution and those limits are evident in the distribution of observed features, namely the nested hierarchies that Linnaeus delineated. But here we have a One Black Swan situation. If it can be shown (as AVIDA shows) that complex features can in fact evolve via deeply IC pathways, and do so regularly and reproducibly, the argument that any observed complex feature for which only deeply IC pathways can be postulated cannot have evolved is refuted.Elizabeth Liddle_{October 9, 2011
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Thanks :) I'm going to be busy myself for the next few days, but I'll check back later. cheers LizzieElizabeth Liddle_{October 9, 2011
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You don't need a computer sim for this, we can simply look at the flat distribution rates of the fixed beneficial mutations along with the flat distributions of neutral "drift" mutations from the 12 isolated e-coli Lenski colonies and compare to simulated results. I wager they will not support one another, just as Gil has said over an over concerning the problems of sim vs field.junkdnaforlife_{October 8, 2011
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Oh, in the meantime, if you could respond to the following question, I think it would help a lot in focusing our attention on the key issues: If I were to write a computer program based on the idea that some biological systems are irreducibly complex and that a Darwinian pathway would not be able to achieve them, and after running the program, sure enough, the Darwinian approach did not achieve them, would you be willing to publicly acknowledge that Behe's irreducible complexity is a real principle in biology and that some systems are simply out of reach of Darwinian evolution? If not, why not?Eric Anderson_{October 8, 2011
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Elizabeth, thank you for taking time to look through my essay of a few years ago. I probably won't have time to respond to your critique tomorrow, but hopefully in the next day or two I can give you a worthy response.Eric Anderson_{October 8, 2011
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Eric, I have just read your paper, linked to by Gil. Let me point out what I think are your fundamental errors. You go through the "assumptions" you think the AVIDA designers make. First you say:
Avida was programmed so that a slight, successive cumulative pathway to the ultimate complex function existed. In other words, the researchers assumed that the ultimate complex feature was not irreducibly complex, and wrote their program in such a way as to guarantee that it would not be irreducibly complex, before they even ran the very first simulation.
This is an error. AVIDA was not "programmed so that a slight, successive cumulative pathway to the ultimate complex function existed". AVIDA was programmed so that the virtual organisms (I will stick with the standard terminology) were subject to slight random variation in their genomes. This means that any change, whether in the direction of either greater or decreased fitness, was incremental. Therefore all pathways in AVIDA are incremental (slight, successive). And that, clearly, by definition, includes any pathways that might exist to the various rewarded functions. Equally it includes any pathways to non-rewarded states. So there is no bias there. Far more importantly, far from "assum[ing] that the ultimate complex feature was not irreducibly complex" they deliberately ensured that all their complex features were irreducibly complex, in that none could be achieved by a series of advantageous mutations from the initial state. And it turns out that EQU, the most complex function, was not only irreducibly complex (would not function if any parts were removed) but that its necessary precursors included changes that were actually substantially deleterious. So you have simply misunderstood this, and it is absolutely critical. Lenski et al set out to show that IC functions could evolve. To do this, they set up an algorithm in which all rewarded functions were IC. All evolved.
Relatively few changes are required to get from the initial organism to the complex feature
Yes, it's a model, written to establish a principle, that IC functions can evolve. Pathways to EQU ranged from 51 to 721 steps,over many thousand generations, although in principle (if intelligently directed!) it could have been done in 16 mutations. That should be indication in itself that no direction was provided.
There are regular and closely spaced fitness plateaus in proceeding from one function to the next.
This claim is quite bizarre. You later say, in support, that:
The Avida researchers initially approach the intermediate functions as though there were a beneficial continuum from one function to the next, although it is far from clear that this would be the case in the real world. A large part of evolutionary critics’ argument from irreducible complexity is that there is unlikely to be a functional advantage for intermediate steps. What good is a cornea without a lens? What good are a cornea and a lens without the retina? And what good are all of these without an exceedingly complex and interconnected nervous system to carry the information to the brain? This is in fact one of the key areas in question in the debate over irreducible complexity, but the Avida authors simply assume it away.
No they do not! I'm not even sure what you mean by "the Avida researchers initially approach the intermediate functions....". They certainly do not provide (let alone assume) "a beneficial continuum from one function to the next". On the contrary, they took pains to ensure there was not. Indeed, they designed their fitness landscape to reflect precisely what "evolutionary critics" assume, that there is unlikely to be a functional advantage for intermediate steps. And, indeed, if you follow their case study, you will read, explicitly, that a great many non-functional intermediate steps were taken along the path, including some very deleterious ones. So not only is it not true that "the Avida authors simply assume it away" but the deliberately make sure that the pathways to the rewarded functions require unrewarded steps. Bizarrely you then say:
In other words, Avida’s cumulative pathway to EQU was elastic enough to allow an unrewarded function to be preserved until the organism got lucky enough to mutuate a further rewarded function and get back on track to its EQU goal.
So it isn't as though you haven't noticed that the pathways include neutral steps! The "elasticity" you mention isn't some cheat algorithm that the authors somehow smuggled in - it's evidence to support their prediction - that even with neutral - and deleterious - steps, in other words even along IC pathways, complex functions can evolve! Then you say: <blockquote? Certainly, there is some possibility that neutral mutations in nature could hang around pending final assembly of a complex feature, but such an approach takes us completely out of the slight-successive-mutations-preserved-by-natural-selection mode and back into a reliance on pure chance. Exactly. Which Behe claims won't work. And Lenski shows does. Although, as you yourself noted earlier, if there are no rewarded steps, then EQU won't evolve. The point is that they can be quite sparse, and separated not just by "plateaux" but by quite deep troughs.
Thus, this finding is not supportive of the authors’ attempt to demonstrate a cumulative pathway, and is not further addressed in the Avida article.
And here is a clue as to where your misunderstanding comes from. You seem to be conflating "cumulative" in the sense of "a sequence of advantageous mutations that lead to a function" with "cumulative" in the sense of "a sequence of any mutations, advantageous, neutral or disadvantageous that are necessary on the pathway to a function". The authors did not set out to demonstrate the first, which would indeed have been circular - to set up a functional feature that could be easily reached via a series of advantageous steps (like Weasel, in fact) and then claim that it proved that all functional feature could be reached by a series of advantageous steps (which Dawkins did not, of course, claim about Weasel). They set out to demonstrate that even if a functional feature could only be reached via necessary neutral and disadvantageous steps, it could still evolve. And succeeded, thus refuting Behe's argument that IC functions cannot evolve by incremental steps.
Each functional advantage is promptly rewarded.
Yes, this ignores stochastic aspects of selection that we find in nature. It could easily be included though. But under the same heading you say:
It is entirely an open question whether a particular functional advantage in isolation would be able to integrate successfully into the organismic whole.
But the AVIDA fitness function required this. Each organism was only rewarded for one performance of each function, and so a function that knocked out another function couldn't compensate by performing the other function more often. So integration was required, and was accomplished.
“The benefits increased exponentially with the approximate difficulty of each function.” In other words, each step closer to the complexity goal (wait a minute, what is that word “goal” doing in an alleged evolutionary mechanism!) is rewarded in a way that makes that step more advantageous vis-à-vis previous steps.
Ahem. The word "goal" does not appear anywhere in the paper! There is, of course, no "goal" (apart from the researcher's goal of demonstrating that complex IC functions can evolve, contrary to Behe's claim), so this is a straw man. The "other words" are yours, and are not what the authors either said, or meant. What they meant is what they said - more complex functions reap bigger rewards (you can run it yourself with different reward schedules). But remember, the organism doesn't get the reward until it performs the function, and the mutations are blind, so the rewards do not act as an "incentive". "Benefits" would have been a better word. All that is happening is that some mutations are "beneficial" just as in nature. But the beneficial mutations, in this case, require non-beneficial precursors, and even some deleterious ones. You say:
What the Avida authors have done is slip a goal, a design if you will, in through the back door. Rather than turning the organisms loose to stumble upon the ultimate complex system in a realistic environment, the researchers have carefully established a specific pre-determined goal and then incessantly flogged the population up the back of Mount Improbable.
This is quite false. As I've said, now, several times, not only is the population not rewarded for steps it takes up Mount Improbable, several of those steps are actually penalised. Only very few steps are "rewarded" on the way, and some of these are actually reversed before the most advantageous function is reached. I think your metaphors have misled you. Something has, anyway. This paragraph is the exact reverse of the truth. The organisms were, in fact, contrary to your assertion, "turned loose" in the environment, and the fact that it took them from between 51 and 721 mutations on the path to EQU, even though 16 mutations would have done it, is pretty good evidence of their "stumbling". The were helped on the way by only 8 rewarded steps, which tended to occur earlier than EQU, not surprisingly, given that they were simpler. Remember that the vast majority of mutations were either neutral or deleterious. Not surprising that they stumbled a bit. Nonetheless they made it, even though all the beneficial functions were IC.
It is the result of assuming that each step along the way toward the goal has an increased advantage.
No. They neither assumed it, nor built it in. Each step along the way did NOT have an increased advantage, as should be clear to you by now. Many necessary steps were neutral, and some were deleterious. That will do. I think I have demonstrated that your critique is absolutely flawed; you seem to have fundamentally misunderstood AVIDA, and Lenski et al's finding. Oddly, you seem also to have fundamentally misunderstood the claim (Behe's: that some functions are IC, therefore cannot have evolved by incremental steps) that the paper soundly refutes. I rest my case :)Elizabeth Liddle_{October 7, 2011
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Only in biology does it equal ability to reproduce.
Perhaps you can supply an example of self-reproduction from outside biology.Petrushka_{October 7, 2011
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I hope I've addressed this in my other response to you, but let me make a couple of points here:
NormO, the reason for bringing Weasel into the discussion is that I’m trying to get everyone back to basics and on the same page so that we can have a rational discussion about Avida. People tend to swoon when they see a slightly complicated program that affirms their beliefs, so thus (on this thread, for example) we’ve seen nothing but absolute praise for Avida from the Darwinists, without so much as a hint of willingness to even consider the possibility that Avida might have serious problems.
Possibly because there aren't any? As for me, I'm perfectly willing, but all the problems that have been pointed out seem to be based on a misunderstanding of it.
With Weasel, it is simple enough to see that it has problems, so that was a start. But even there I was able to ascertain that not everyone was thinking about the key issues. For example, Elizabeth thought the problem with Weasel was that it has a single solution.
I don't think it's "the problem" with weasel. But that feature renders it misleading when you generalise to algorithms where the problem, solution are not identical. As a result, many people seem to have conflated the desired output of the evolving organisms with the organisms as output. The first is coded in (as the fitness function) but the second is not (and is what evolves).
As a result, she thinks that Avida, with more than one solution, doesn’t suffer from some of the same issues as Weasel.
Well, it doesn't, but not simply because there are multiple solutions. The much more important difference is that there is a distinction between the organism's output and the organism as output. In Weasel, they are coterminous.
Had she correctly understood that the circularity problem with Weasel has absolutely nothing to do with a single solution and everything to do with the fact that there is an initial target built in and that the program is set up to converge on the solution, then we might have been able to take the discussion and apply it to Avida.
There is no circularity problem with Weasel.
Yes, Weasel is a joke, but sometimes we have to go back to the basics and regroup.
So much of a joke that there were vigorous arguments at one stage that it could only work because it "latched". It need not, and does not latch, and, by not latching, demonstrated that latching is not required for Weasel to evolve. It was a small point, but an important one. Even jokes have their uses.Elizabeth Liddle_{October 7, 2011
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Elizabeth, let’s parse the wording, and we will see that either (1) you have misunderstood, or (2) you are purposely trying to hide the issues.
The last is certainly not the case. The first is possible. There is a third, which is that you have misunderstood the issue. I will not give a fourth ;)
You quote Lenski et al. as saying the following: “The evolution of a complex feature, such as EQU, is not always an inexorably upward climb toward a fitness peak, but instead may involve sideways and even backward steps, some of which are important.” Do you see that word “always”? Do you see the term “upward climb”? The only thing Lenski is saying is that the pathway toward EQU might not be a straight line. Behe never claimed there had to be a straight line, and I certainly didn’t either. Let’s look at what Lenski actually say:
Yes, Lenski is saying that the pathway toward EQU is often not a straight line, by which he means there are necessary steps that involve no increase, or a decrease, in fitness. This is exactly what Behe means by "Irreducibly complex". He did not say "there had to be a straight line" - what he said was that if there is NOT a "straight line" (i.e. if necessary precursors are non-advantageous or deleterious) then the thing can't have evolved by Darwinian processes. His poster child analogy is the mousetrap. His case for the bacterial flagellum is that it could not have evolved by Darwinian processes because its necessary precursors are non-advantageous or deleterious. I think you have misunderstood. As for the word "always" - there may well be a straight path to EQU, I don't know (I don't think I've seen one demonstrated). That doesn't matter. The point is that EQU can, and does, evolve by paths that are IC. Therefore things can evolve by paths that are IC. Therefore Behe is wrong.
“The benefit increased exponentially with the approximate difficulty of each function.” “The most complex function, EQU, evolved only when several simpler functions were also useful.” “At the other extreme, 50 populations evolved in an environment where only EQU was rewarded, and no simpler function yielded energy. We expected that EQU would evolve much less often because selection could not preserve the simpler functions that provide foundations to build more complex features. Indeed, none of these populations evolved EQU, a highly significant difference from the fraction that did so in the reward-all environment.” The last quote is the real lesson from the “experiment” and is an excellent support of Behe’s point.
Not at all. Nobody is claiming that stepwise evolution of complex features can occur without some selected precursor steps. This is a straw man, and Behe is too smart to attack it. What Behe argues, indeed it's his whole IC concept, and one I've frequently seen here, is that some functions are on "islands" that cannot be reached by a series of advantageous steps. AVIDA shows that these "islands" can indeed by reached - that the intervening steps can be both neutral and deleterious.
It is amazing to me that you are defending Avida tooth and nail without even demonstrating a willingness to consider the possibility that the program is flawed. Can you even stop for a moment and consider that Avida might not be the knock-down proof of Darwinian evolution you think it is?
Certainly I could. But I'm not seeing that it isn't, and your counter argument seems to be based on a) a misreading of Behe and b) a misunderstanding of what evolutionary theory claims.
You seem very impressed with the idea that there is a set of possible solutions, rather than one solution. I hope, based on what I wrote in my other response to you yesterday, you now realize that is not the issue.
It's an issue when talking about Weasel. But as Weasel is irrelevant, I'm happy to leave it to one side.
Do you deny that there was a step-by-step process to get to EQU? Do you deny that there were regular rewards along the way? Do you deny that the program was written in such a way to move the populations toward EQU?
Of course there was a step-by-step process!!!! The point is not whether there were steps (we all think that there were steps) but that not all the steps were advantageous, even when they were necessary, and that some were quite seriously deleterious, i.e. EQU is IC!!!!! And yes, I "deny that the program was written in such a way to move the population towards EQU" except in the sense that it was written to demonstrate that even IC functions would evolve as long as some steps are rewarded. Not a single step in AVIDA is "designed to move the population towards EQU" and the vast majority of steps are neutral (don't move at all) or deleterious (make the individual less likely to breed). The only "moving" is done by the fitness landscape, just as in the natural world. But far from designing a landscape in which EQU would evolve easily, it was deliberately designed to be extremely rugged, with all rewarded functions IC, and EQU very IC. Yet all regularly evolved, thus refuting Behe.
Avida demonstrates that even in an extremely simple context (17 steps to EQU) populations won’t get to a complex function without regular rewards along the way. That is precisely Behe’s point and it stands. Avida most certainly did not refute Behe. Any statement to that effect is either clueless or purposely deceptive.
No, it is not Behe's point. If that were Behe's point he'd be part of the evolutionary establishment, because that's what everyone thinks. What Behe's point is is that you won't get to a complex function by an incremental process if the complex function is IC, i.e. requires precursor steps that are neutral or deleterious. That's the definition of IC (if you take any part away, it doesn't function, therefore many neutral or deleterious steps are required for it to evolve, which won't therefore happen). AVIDA shows that even when many neutral or deleterious steps are required, when you have a function that requires many non-advantageous parts to function at all, it nonetheless evolves. I am not deceptive (and get pretty cross when people suggest I am) nor am I clueless, as I hope is now clear to you. You yourself have made an error. IMO that doesn't make you "clueless", but it does make you wrong.Elizabeth Liddle_{October 7, 2011
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Elizabeth, let's parse the wording, and we will see that either (1) you have misunderstood, or (2) you are purposely trying to hide the issues. You quote Lenski et al. as saying the following: "The evolution of a complex feature, such as EQU, is not always an inexorably upward climb toward a fitness peak, but instead may involve sideways and even backward steps, some of which are important." Do you see that word "always"? Do you see the term "upward climb"? The only thing Lenski is saying is that the pathway toward EQU might not be a straight line. Behe never claimed there had to be a straight line, and I certainly didn't either. Let's look at what Lenski actually say: "The benefit increased exponentially with the approximate difficulty of each function." "The most complex function, EQU, evolved only when several simpler functions were also useful." "At the other extreme, 50 populations evolved in an environment where only EQU was rewarded, and no simpler function yielded energy. We expected that EQU would evolve much less often because selection could not preserve the simpler functions that provide foundations to build more complex features. Indeed, none of these populations evolved EQU, a highly significant difference from the fraction that did so in the reward-all environment." The last quote is the real lesson from the "experiment" and is an excellent support of Behe's point. It is amazing to me that you are defending Avida tooth and nail without even demonstrating a willingness to consider the possibility that the program is flawed. Can you even stop for a moment and consider that Avida might not be the knock-down proof of Darwinian evolution you think it is? You seem very impressed with the idea that there is a set of possible solutions, rather than one solution. I hope, based on what I wrote in my other response to you yesterday, you now realize that is not the issue. Do you deny that there was a step-by-step process to get to EQU? Do you deny that there were regular rewards along the way? Do you deny that the program was written in such a way to move the populations toward EQU? Avida demonstrates that even in an extremely simple context (17 steps to EQU) populations won't get to a complex function without regular rewards along the way. That is precisely Behe's point and it stands. Avida most certainly did not refute Behe. Any statement to that effect is either clueless or purposely deceptive.Eric Anderson_{October 7, 2011
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everything to do with the fact that there is an initial target built in and that the program is set up to converge on the solution, then we might have been able to take the discussion and apply it to Avida.
It is quite easy to build a GA that doesn't converge on a target. In fact, I've done it, and I have rather limited programming skills. You can start with the same seed and it will produce different output every time, even though the fitness landscape remains unchanged. Run a travelling salesman GA and you will get different results every time. In fact, there is no way to know the best solution if you use enough stops. The point is that there are open ended landscapes that cannot be explored except by GAs. Landscapes having 10^150 points or more.Petrushka_{October 7, 2011
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Yes, I know it is, Joseph. But, it turns out Behe is wrong. And so are you. AVIDA demonstrates that even blind and undirected process can result in the evolution of IC functions. In AVIDA, the evolution is both blind (no variant is selected for what it might be useful for later, merely for what it is currently useful for) and undirected (the variants are complete random; they are not biased in the direction of usefulness - most are either neutral or deleterious, and only a very small fraction advantageous). And all the functions that evolve in AVIDA are IC, EQU being, additionally, complex, and, apparently requiring necessary deleterious precursors. Behe's claim is that only systems with foresight can evolve IC functions. In AVIDA, without using foresight, IC functions evolve. Therefore AVIDA refutes Behe.Elizabeth Liddle_{October 7, 2011
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NormO, the reason for bringing Weasel into the discussion is that I'm trying to get everyone back to basics and on the same page so that we can have a rational discussion about Avida. People tend to swoon when they see a slightly complicated program that affirms their beliefs, so thus (on this thread, for example) we've seen nothing but absolute praise for Avida from the Darwinists, without so much as a hint of willingness to even consider the possibility that Avida might have serious problems. With Weasel, it is simple enough to see that it has problems, so that was a start. But even there I was able to ascertain that not everyone was thinking about the key issues. For example, Elizabeth thought the problem with Weasel was that it has a single solution. As a result, she thinks that Avida, with more than one solution, doesn't suffer from some of the same issues as Weasel. Had she correctly understood that the circularity problem with Weasel has absolutely nothing to do with a single solution and everything to do with the fact that there is an initial target built in and that the program is set up to converge on the solution, then we might have been able to take the discussion and apply it to Avida. Yes, Weasel is a joke, but sometimes we have to go back to the basics and regroup.Eric Anderson_{October 7, 2011
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Actually, what Behe says is right here: http://www.evolutionnews.org/2011/10/wheel_of_fortune_new_work_by_t051621.html And Elizabeth's summary is accurate. It's not about whether the direction is blind. It's about whether evolution can reach a state that requires neutral or deleterious intermediate steps.Petrushka_{October 7, 2011
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But anyway you still have issues with the fact that ID is not anti-evolution and things that are designed to evolve. evolve by design are in no way connected to darwinism
I look forward to the day when you flesh out that statement. It makes no sense to me. Perhaps you could start a thread on the topic.Petrushka_{October 7, 2011
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Umm Behe's IC argument is that blind and undirected chemical/ physical processes cannot produce it. And AVIDA does not simulate blind and undirected processes. Buy a vowel...Joseph_{October 7, 2011
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Elizabeth:
When you set up an evolutionary algorithm, it has several components, including a virtual environment and a starting population of virtual organisms that replicate with variance, some of which results in variable reproductive success within that virtual environment. This whole set up is designed so as to allow the population of virtual organisms to evolve.
Evoled by design/ designed to evolve- same thing. Thanks.
These later members are not “designed” – they evolved within a designed system, but nobody designed them.
The original population was designed to evolve and evolved by design. Umm GA = genetic algorithm and those are designed. The final thing was designed by the program.
Right, but not by the designer of the program.
I never said nor implied the designer of the program designed the final population- not necessary. But anyway you still have issues with the fact that ID is not anti-evolution and things that are designed to evolve. evolve by design are in no way connected to darwinismJoseph_{October 7, 2011
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Yes it is bogus - do you have a dictionary? Look up the word "fitness". Only in biology does it equal ability to reproduce. I also see you failed to respond to my reasoning of why the biological definition is bogus- very telling, that...Joseph_{October 7, 2011
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No, it's not "bogus", Joseph - it's what the word means. If you want to critique evolution, you really have to understand what the theory is!Elizabeth Liddle_{October 7, 2011
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Elizabeth:
Designed to evolve is not the same as “evolved by design”.
What is teh difference? Please be specific.
I've already been specific. When you set up an evolutionary algorithm, it has several components, including a virtual environment and a starting population of virtual organisms that replicate with variance, some of which results in variable reproductive success within that virtual environment. This whole set up is designed so as to allow the population of virtual organisms to evolve. And they do. In the end, the population of virtual organisms is quite different from the starting population, and its members can perform functions that none of the members of the starting population could perform. These later members are not "designed" - they evolved within a designed system, but nobody designed them. And the designs are often extremely surprising to the people who designed the environment in which they evolved.
Obviously the virtual organisms in a GA are “designed to evolve” – what is designed are the conditions under which this will happen.
You say things yet you never support them. Strange.
I do, did, and have, again.
But the final GAs are not “designed” The GA creator does not even know what they will look like.
Umm GA = genetic algorithm and those are designed. The final thing was designed by the program.
Right, but not by the designer of the program. The designer of the program simulates a starting population in a virtual environment. Within that environment, the population evolves - acquire function that maximise its reproductive success within that environment. What its evolved members will look like is completely unknown in advance by the designer of the environment. Indeed, sometimes the virtual organisms do something quite unintended by the designer of the environment - they "cheat" in other words. A bit like harmless snakes that evolve to look like poisonous ones, without having to go to the bother of evolving venom :)Elizabeth Liddle_{October 7, 2011
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Elizabeth:
OK, so you accept that natural selection (i.e. heritable variation in reproductive success) results in adaptation, but you argue that the variance must be directed?
Natural selection is 1- an oxymoron as nature does not select and 2- a result of three processes. Adaptaion? Anything is possible.
And I’m defining “fitness” as “reproductive success within the current environment”.
And that is still the most bogus definition, perhaps ever. I say that because it is all AFTER-THE-FACT- you cannot tell which individuals will outreproduce the others in any given population in which all can mate. In real-life the "reward" is mere survival. That said if there is a target then it is directed evolution, period, end of story. The antenna example is a perfect illustration of that. And AVIDA has been laid bare by many others.Joseph_{October 7, 2011
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Elizabeth:
Designed to evolve is not the same as “evolved by design”.
What is teh difference? Please be specific.
Obviously the virtual organisms in a GA are “designed to evolve” – what is designed are the conditions under which this will happen.
You say things yet you never support them. Strange.
But the final GAs are not “designed” The GA creator does not even know what they will look like.
Umm GA = genetic algorithm and those are designed. The final thing was designed by the program.Joseph_{October 7, 2011
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Continuing:
*All* of the key questions about what would make a Darwinian process actually work in the real world were *assumed* in the Avida program, not demonstrated by it. Simple fitness landscape, easy to traverse from one point to the next, regular rewards along the way, increasing rewards the closer you get to the goal, short pathway to a complex function, and on and on. There is a real, genuine, scientific, observational question about whether these things are true in the real world of biology. Avida simply assumes them all.
No, it does not. The fitness landscape is not "easy to traverse", and the rewards along the way are not only sporadic, but are interspersed, often, with severe penalties. There is no "short pathway" to a complex function; there isn't even a "short pathway" to a simple function: even the simplest function is "irreducibly complex" in that several unrewarded steps are required before it is achieved. I think you may have seriously misread the paper!
People are easily impressed because it is a “program” and gee, it seems to work kind of automatically once you finish writing all the details and press “start”. But we have to remember, anything a program can do, we can do with paper and pen.
Well, yes. You could, in principle, given the lifespan of Methusalah, render AVIDA in hand written binary symbols, or even black and white stones, but the medium is irrelevant. What matters is the execution of the program logic.
And what would that pen-and-paper description look like? Well, if we assume all the key points in question, then our theory will work.
Well, if the theory is right, the program will work. But that isn't circular, it's a test of the theory. If Lenski et al had been wrong, and irreducibly complex functions can't evolve, then EQU wouldn't have evolved, because it turns out to be irreducibly complex.
Sure. Of course. But that is *not a demonstration of the efficacy of our theory,* it is simply a restatement of it, in computer format, rather than with pen on paper. Avida is entirely circular.
No, it is not. If every step required on the pathway to EQU was rewarded, it would have demonstrated that natural selection can work if all steps are rewarded. But every step was not rewarded, and some steps were penalised. And in fact, EQU emerged many times, from many lineages, all of which involved many neutral and some deleterious steps. That means that natural selection works even if the function in question is irreducibly complex.
Indeed, the primary lesson of the Avida progam was that even with a simple function and an easy landscape, the program couldn’t get to the complex function without regular rewards along the way. That is precisely what Behe said!
Except that that is not what Lenski et al found. They found that the program could get to the complex function despite many unrewarded, but necessary, steps, and some penalised, but necessary, steps. Which is the exact opposite of what Behe said!
Avida is a toy, just as Weasel is.
It is indeed. All models are "toys" - that's why we call them "models". They aren't The Thing Itself. But if they fit the data, or emulate the data, then we can infer that they are good models of The Thing Itself.
Oh, it has a few more steps and a few nuances that have to be parsed through to see what is actually going on. And some people who have an a priori inclination to accept the result without asking the hard questions about how the result came about are easily impressed by the smoke and mirrors.
I have "asked the hard questions" and received very satisfactory answers, mostly simply by reading the paper itself. I have also played with AVIDA, and also taken part in a fascinating thread on IIDB, in which Richard Hoppe conducted his own case study, and posted the results as he went along. He confirmed the findings of the paper, which is that EQU regularly evolves but seems to require substantial sequences of unrewarded and even substantially deleterious steps. He also confirmed the obvious, which is that if there are no rewards along the way (no simpler functions that enhance reproduction) that EQU will not evolve. But no-one is claiming this - Darwin's theory was that, given rewards for slight variants, adaptation will occur. Behe's point that some things appear to have necessary but non-advantageous precursors, and therefore could not have evolved by Darwinian processes. AVIDA shows that even functions with necessary but non-advantageous precursors do evolve by Darwinian processes, as long as at least some of the steps are rewarded.
But it is a toy, no more relevant to biology than Weasel and no more able to demonstrate the efficacy of the Darwinian creation theory.
On the contrary, it is a model of evolution that simulates a natural fitness landscape (by rewarding phenotypic functions with "energy" to breed, just as a biological phenotype that is able to exploit an environmental resource gains energy to breed), and it demonstrates that Darwin was wrong, in a sense, and so was Behe: that the incremental necessary changes on the pathway to a complex function do not have to all be beneficial; even when neutral and deleterious changes are necessary precursors, the complex function can still evolve.Elizabeth Liddle_{October 7, 2011
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To be specific: you claim that:
Lenski et al. say: “No! Behe is wrong! If there is a step-by-step incremental pathway with regular fitness rewards along the way, Darwinian processes might produce such a system.”
In fact, Lenski et al say the exact opposite:
The evolution of a complex feature, such as EQU, is not always an inexorably upward climb toward a fitness peak, but instead may involve sideways and even backward steps, some of which are important.
In other words that rewards are not required at every step, and that in some cases, deleterious steps are important. Unless your claim is merely that there have to be some rewards along the way, which is of course true. But Behe's "irreducible complexity" argument is that any non-advantageous step to a function renders the thing is "irreducibly complex" and and thus on an "island" that cannot be reached by evolutionary processes (hence the mousetrap argument). He did at one point talk about "degrees of" irreducible complexity, depending on the number of non-advantegous steps in the lineage, but many EQU-performing organisms in AVIDA have high degrees of irreducible complexity (many steps that are non-advantageous, including deleterious steps) in their lineage. And, in any case, he seems to have reverted now back to his mousetrap case. So AVIDA does indeed refute Behe's core claim, and you seem to have misunderstood Lenski's :)Elizabeth Liddle_{October 7, 2011
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Where do Lenski et al say such a thing? What AVIDA, interestingly, shows is advantageous functions may be reached by way of many neutral, even deleterious, steps. In other words, EQU for example, is "irreducibly complex" in that it doesn't work if you take away any part, and, moreoever, we can check back and show that it was actually reached by paths that included neutral and deleterious steps. So it refutes Behe not by claiming that nothing is "Irreducibly complex" but by demonstrating the irreducible complexity is not a bar to evolution.Elizabeth Liddle_{October 7, 2011
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I mean the final GA virtual organisms - it is important to distinguish between the virtual organisms within a GA and the GA itself, which is the setup in which the virtual organisms can evolveElizabeth Liddle_{October 7, 2011
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Designed to evolve is not the same as "evolved by design". Obviously the virtual organisms in a GA are "designed to evolve" - what is designed are the conditions under which this will happen. But the final GAs are not "designed" The GA creator does not even know what they will look like.Elizabeth Liddle_{October 7, 2011
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