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

Dr Liddle You have publicly claimed that I have deeply misunderstood Lewontin and the elites who generally agree with him. That is a very serious thing to say and in my view -- with reasons given in summary above, it is in gross error. Kindly substantiate that claim, if you can. Or else, kindly EXPLICITLY retract it. And, a non materialistic cause can be easily tested, just stop imposing materialistic a prioris on science. Then, you can see clearly to test for natural causes tracing to chance and/or necessity, or to intelligent causes acting through ART and leaving empirical signs that can be evaluated for reliability. As we have highlighted and explained to you over and over for months now. Start with the equation: Chi_500 - I*S - 500, bits beyond the solar system threshold. And for inference to a definitively non materialistic cause, I suggest you examine -- say, starting here and footnoted linked discussions from there -- the evidence pointing even through the multiverse speculations to the intelligent design of a fine tuned observed cosmos set to an operating point that facilitates C-chemistry cell based life. (In short the material universe is credibly contingent and so is not its own causal explanation. It points beyond itself to an ontologically necessary being as root cause. And such a being has no beginning and is causeless.) I beg to remind you -- again -- that ever since Thaxton et al in TMLO, 1984, design thinkers have consistently held that the design of life does not by itself imply a designer necessarily within or beyond the cosmos. Observe my repeated notes on how a lab a few generations beyond Venter's could do it. Venter has given proof of concept of the possibility for the design of cell based life. GEM of TKIkairosfocus_{October 16, 2011
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KH: You are resorting to some very outrageous strawman tactics. Before taking you on, I ask you to re-read yourself, and then correct yourself. And BTW, on the design of life, I am on repeated record that the design inference is incapable of identifying the nature of the designer of life as within or beyond the cosmos, which is exactly what has been publicly on the table ever since the first technical design theory work, TMLO in 1984. (Recall, my remarks about Venter and nanotech labs, in a current thread where you have been corrected?) Whatever Ms Forrest or Ms Scott et al may say to the contrary, ID is not Creationism in a cheap tuxedo. the design inference is about natural causes tracing to chance and or necessity and intelligent causes acting by art, and leaving empirically detectable traces. Since you seem to have conceived a patent personal animosity and contempt to me or what I say, I direct you to the NWE article on ID, which is far better than the notorious hatchet job at Wikipedia. Please read it. Please also read the Weak Argument Correctives, in the Resources tab top of this and every UD page. You are taking talking points of objectors who habitually misrepresent as though they were well established fact. They are not. Indeed, sadly, in some cases, we are looking at ideologically motivated willful and continued misrepresentations in the teeth of duties of care to fairness and accuracy. GEM of TKIkairosfocus_{October 16, 2011
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"I’d argue that it allows us to know God better, not worse." To know God, the only thing that is necessary is a pure heart, nothing else.Eugene S_{October 16, 2011
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kf: there is no "a priori materialist censorship on science", whatever Lewontin is saying. I don't think he's saying that, but if he is, he's wrong. What there is is a method that by its very nature precludes non-material explanations. To try to break the logjam, kf, let me ask you something: How would you devise a scientific experiment to test a non-materialist hypothesis?Elizabeth Liddle_{October 16, 2011
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Try here for starters.kairosfocus_{October 16, 2011
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And, BTW, please read the weak argument correctives before resorting to the creationists in a cheap tuxedo caricature.kairosfocus_{October 16, 2011
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Material causes as used on our side denotes chance and/or necessity [i.e. nature]. The contrast to such is INTELLIGENT cause [i/e. art]. The process you used to post just now would be an example. And, a tested, reliable sign of such is FSCI, such as in your post. Please do not try to force-fit design thinkers into the STRAWMAN templates set up by the more agenda driven objectors.kairosfocus_{October 16, 2011
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KF, Just for clarity, can you please describe one of these "non-material causes" and how it can be investigated, given that we can only investigate material causes as we are material beings in a material world and I am a material girl (HT Madonna). If you think otherwise, that non-material causes can be investigated by science, please describe to me how I'd go about investigating such a non-material cause. I can't think how I would, but you seem so desperate to get that divine foot in the door you *must* have some idea of what you'd do once it was there! Don't you? Don't tell me it's all been a bluff all along! The "non-material causes bluff" I think I'll call it. Railing against science and it's exclusion of non-material causes but then unable to actually articulate what it is that such an investigation into said non-material causes would consist of when asked.kellyhomes_{October 16, 2011
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KF,
This extends to trying to redefine science and to revisionise its history propagandistically.
Which is exactly what you are trying to do yourself! So if you want to redefine science to allow the divine foot in the door you are free to do so. All you have to do is give *a single example* of that explaining something that materialistic science cannot. Then scientists around the world, seeing the fruitfulness of your methodology will copy you and you'll get the worldwide revolution that you want. I don't know if you've noticed but scientists like things that generate results. So generate some results already! It seems to me that when I ask "well, how does ID explain the origin of bodyplans" you say "It was designed, all the signs point to it". So if you allow that divine foot in the door you can then add the detail "It was designed by god". Not much difference really. So, tell me KF, what advantage does allowing the divine foot in the door bring? Give me a *single* example of that advancing the cause of human knowledge? Just a *single* example. Go on, dare you. And if you say that Newton was a creationist and he created the laws of motion because of that then I'll ask you where in his equations he allows a divine foot in the door!kellyhomes_{October 16, 2011
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KF,
we are forced by our a priori adherence to material causes
Ok, let's allow that divine foot in the door. Now what? Where, specifically, do we say "ah, that was God" then? Is the reason why you are so reluctant, going off into multiple diversions, to talk about the actual "design" in "Intelligent design" and how it was done? As you really think it was god but know that saying such makes a mockery of the idea that the designer is not the Christian God? Why do you want to allow the divine foot in the door KF? What advantage does it bring? What can it explain that materialistic science cannot?
while in fact Wernher von Braun, the man who sent the Apollo rocket to the Moon was a Christian and a Creationist.
Perhaps you could show me where in the work of sending Apollo to the moon divine causes were referenced? If you can't what possible relevance does his beliefs have? Sure, if the rocket went wrong they might have cracked open the manual and read "pray" but other then that, what? So, and I don't expect a short answer to this nor an answer actually relevant to the question asked but here goes anyway: What changes once "materalist science" allows "a divine foot in the door"? What will we investigate and say "oh, we can't invesitgate that any more as that's divine"? What specifically do you have in mind? And what relevance does all this (it's one of your favorite subjects judging by the number of times you've re-used that quotemine) have to ID anyway? If the "designer" is simply responsible for the "design" you see in life that does not make it god. So what does it matter to you if science disallows divine causes as ID does not claim that the design of life was a divine event in any case. So what gives KF? Is the designer not study-able because of sciences refusal to allow the divine into science? If so then you've obviously already decided the "designer" is in fact god. When it could well be aliens, remember? Pathetic.kellyhomes_{October 16, 2011
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Ah boy: I missed the correct "Reply" point and so my response to Dr Liddle's claim that I do not correctly understand Lewontin is out of place, here. Pardon.kairosfocus_{October 16, 2011
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Dr Liddle: Please, just READ what is being said. Do you have any phil background, if not just take in here as a background primer. Now, please look at the -- frankly, sophomoric (this generation of scientists is nowhere near as sophisticated that way as the generation of Bohr and Einstein) -- worldview and epistemological-logical assertions and inferences that cannot stand serious scrutiny, noting that this is a report by a member of the elites, on the views of the elites (one backed up here on by no less than three other cites, including by the US NAS and the US NSTA, the American Scientific Academy and the national science teachers body: ______________ >> . . . to put a correct view of the universe [1 --> a claim to holding truth, not just an empirically reliable, provisional account] into people's heads we must first get an incorrect view out [2 --> an open ideological agenda] . . . the problem is to get them to reject irrational and supernatural explanations of the world, the demons that exist only in their imaginations [3 --> a declaration of cultural war], and to accept a social and intellectual apparatus, Science, as the only begetter of truth [ 4 --> this is a knowledge claim about knowledge and its possible sources, i.e. it is a claim in philosophy not science; it is thus self-refuting]. . . . To Sagan, as to all but a few other scientists, it is self-evident [5 --> a self evident claim is that this is true, must be true and its denial is patently absurd. But actually, science and its knowledge claims are plainly not immediately and necessarily true on pain of absurdity, to one who understands them; this is another logical error, begging the question, confused for real self-evidence] that the practices of science provide the surest method of putting us in contact with physical reality [6 --> Science gives reality, reality is naturalistic and material], and that, in contrast, the demon-haunted world rests on a set of beliefs and behaviors that fail every reasonable test [7 --> i.e. an assertion that tellingly reveals a hostile mindset, not a warranted claim: if you reject naturalistic, materialistic evolutionism, you are ignorant, stupid, insane or wicked, by direct implication] . . . . It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world [8 --> redefines science as a material explanation of the observed world], but, on the contrary, that we are forced by our a priori adherence to material causes [9 --> another major begging of the question . . . by imposition of a priori materialism as a worldview that hen goes on to control science as its handmaiden and propaganda arm that claims to be the true prophet of reality, the only begetter of truth] to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. [10 --> In short, even if the result is patently absurd on its face, it is locked in, as materialistic "science" is now our criterion of truth!] Moreover, that materialism is absolute [11 --> i.e. here we see the fallacious, indoctrinated, ideological, closed mind . . . ], for we cannot allow a Divine Foot in the door. [12 --> Hostility to the divine is embedded, from the outset, as per the dismissal of the "supernatural"] The eminent Kant scholar Lewis Beck used to say that anyone who could believe in God could believe in anything. [13 --> a slightly more sophisticated form of Dawkins' ignorant, stupid, insane or wicked, certainly, irrational. This is a declaration of war! Those who believe in God, never mind the record of history, never mind the contributions across the ages, are dismissed as utterly credulous and irrational, dangerous and chaotic] To appeal to an omnipotent deity is to allow that at any moment the regularities of nature may be ruptured, that miracles may happen. [14 --> Perhaps the second saddest thing is that some actually believe that these last three sentences that express hostility to God and then back it up with a loaded strawman caricature of theism and theists JUSTIFY what has gone on before. As a first correction, accurate history -- as opposed to the commonly promoted rationalist myth of the longstanding war of religion against science -- documents (cf. here for a start) that the Judaeo-Christian worldview nurtured and gave crucial impetus to the rise of modern science through its view that God as creator made and sustains an orderly world. Similarly, for miracles -- e.g. the resurrection of Jesus -- to stand out as signs pointing beyond the ordinary course of the world, there must first be such an ordinary course, one plainly amenable to scientific study. The saddest thing is that many are now so blinded and hostile that, having been corrected, they will STILL think that this justifies the above. But, nothing can excuse the imposition of a priori materialist censorship on science, which distorts its ability to seek the empirically warranted truth about our world.] [[From: “Billions and Billions of Demons,” NYRB, January 9, 1997.] >> ____________ Do you see my fourteen main points of concern in the clip? And if you go to the immediately linked, you will see a following note that raises much more, e.g Lewontin's caricature of the woman who thought the TV broadcasts form the moon were fake because she could not get Dallas on her set; while in fact Wernher von Braun, the man who sent the Apollo rocket to the Moon was a Christian and a Creationist. There is even more in the onward linked full article. Read the above, work your way throughte4 fourteen points, then come back to me and show me how I have misunderstood what Lewontin "really" meant. Kindly, do. For, I fear that I have only just begun to understand the full depth of what this notorious article reveals about a hostile agenda that can only be exposed and broken, not reasoned with. In particular, do please explain to me how I am to deal with those who are redefining truth question- beggingly in a way that shows that they do not even understand that a claim to be the provider of knowledge is inevitably a phil claim not a scientific one, the criteria of truth likewise, the nature of science, refuse to be corrected even by reductio ad absurdum, and are openly declaring that people like me are ignorant and/or stupid and/or insane and/or wicked, menaces to reason and to science and to society. If that is not a declaration of cultural war under the false flag of scientific progress, I do not know what more would have to be said to be that. Ten, please go back to the link and read down on Coyne, on the NAS and the NSTA. Then, please come back to me and explain to me how I have profoundly misunderstood what is being said. GEM of TKIkairosfocus_{October 16, 2011
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I would agree with you if I did not know that the founding fathers of European science of modern age all believed in God.
You seem to have missed my point entirely, Eugene. Yes, they probably did. Many scientists today also believe in God. That does not mean they will let the Divine Foot in the door of science. If you do, it ceases to work. Science is all about abstracting regularities, not irregularities. By definition, the supernatural is an irregularity.
I think it is fair to say that the likes of Pascal or Newton or Kepler understood more about science than either you or I do.
Depends what you mean. In some senses they did. In some senses both you and I know more science than they did. A lot more.
It is their interpretations of what science can or cannot, should or should not do, I am ready to take as first-hand scientific knowledge, not a materialistic ideology in the cloak of science.
There is no "materialistic ideology" in science. There is a method. That method deals with the material, or, at least, the natural. It cannot deal with the supernatural. Newton made his biggest mistakes when he tried to write God into his orbital equations.
You seem to be saying things that are 95% correct (I do not mean your evolutionary stand, which is another matter), but this 5% is what makes it all miss the target. In my opinion, science without God is like a 2D black and white picture in comparison with a 3D full colour model. Science without God is incapable of delivering really deep insights. By itself, science is incomplete. If everything happens by fluke, then why bother finding out how?
Because "happens by fluke" is a complete misrepresentation of the scientific model! On the contrary, as Lewontin says, if we allow the Divine Foot in the door of science, anything can happen - predictability goes out of the window. Science, on the other hand, is all about predicting what will happen, not by "fluke" but the opposite - by natural law. I don't know where this weird idea came from that somehow scientists think that the world happens "by chance". It's a meaningless statement anyway, but it appears to be presented as the only alternative to: happens "on purpose". There is a vast excluded middle there! Yes, one thing we have discovered in the last century is that there is (or appears to be) a fundamentally stochastic element to the universe. Indeed, it is gpuccio's position that this stochastic "window" is the access point for divine influence. But the goal of the scientific model is to find out why things happen, which is not the same as asking "for what purpose" they happen, but nor is it the same as claiming that they happen "by fluke"! Quite the opposite.
All materialist motivations for science are aimed at building an “earthly heaven” without God.
This is a completely unsupported and unwarranted assertion, Eugene. I do not know of a single scientist whose motivation is "building an "earthly Heaven" without God". Sure, many scientists are motivated by the desire to make the world a better place - and so they should be. Others are motivated primarily by sheer curiosity. Nothing to do with "without God" whatsoever.
In the best case, the proposed motivation is to help people in their daily lives. That would be fine, if materialists did not want to make a religion out of science.
Who does? None of my acquaintance.
Science by itself has no more right to become a philosophical foundation for our life than a sledge hammer or a screw driver has.
Well, no. This is apples and oranges. Actually science is a pretty good philosophical foundation for life. Rational, evidence-based decisions uninfluenced by superstition or irrational behavioural precepts (stoning adulterers; covering women's faces; forcing celibacy on gays) seem pretty sound to me. But a scientific philosophical foundation does not preclude belief in God. I'd argue that it allows us to know God better, not worse. After all, if God made the universe, wouldn't understanding how it works increase our understanding of its Maker?
However, science was turned into an ideology. And this is exactly where Darwinism and Communism have a lot in common, in my opinion.
I find this assertion unsupported and unwarranted.Elizabeth Liddle_{October 16, 2011
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23.2.2.2.6 Elizabeth, I would agree with you if I did not know that the founding fathers of European science of modern age all believed in God. I think it is fair to say that the likes of Pascal or Newton or Kepler understood more about science than either you or I do. It is their interpretations of what science can or cannot, should or should not do, I am ready to take as first-hand scientific knowledge, not a materialistic ideology in the cloak of science. You seem to be saying things that are 95% correct (I do not mean your evolutionary stand, which is another matter), but this 5% is what makes it all miss the target. In my opinion, science without God is like a 2D black and white picture in comparison with a 3D full colour model. Science without God is incapable of delivering really deep insights. By itself, science is incomplete. If everything happens by fluke, then why bother finding out how? All materialist motivations for science are aimed at building an "earthly heaven" without God. In the best case, the proposed motivation is to help people in their daily lives. That would be fine, if materialists did not want to make a religion out of science. Science by itself has no more right to become a philosophical foundation for our life than a sledge hammer or a screw driver has. However, science was turned into an ideology. And this is exactly where Darwinism and Communism have a lot in common, in my opinion.Eugene S_{October 16, 2011
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Thanks for the background, kf, and perhaps I can now understand why that passage has made such an extraordinarily deep impression on you. But, as I have said several times, I don't think it means what you think it means. In fact I'm sure you are misinterpreting it. What Lewontin clearly means (and he says so explicitly) is that the entire scientific method is predicated on the assumption that the universe is predictable. That doesn't mean it is but that science can only proceed on that assumption. There is no indoctination here - because no doctrine. Science does not teach the doctrine that there is "no Divine Foot". What it teaches is that scientific methology must exclude that possiblity because otherwise the entire system collapses. To be specific: science proceeds via hypothesis testing, as I am sure you will agree. To test a hypothesis, you make a prediction. Then you collect appropriate data and see whether your prediction is confirmed. If it is, your hypothesis is supported. If it is not, you retain the null. If we "allow a Divine Foot in the door" we are unable to test our hypotheses, because all bets are off. Sure, we might get data that support our hypothesis, but how could we tell that it wasn't just the Divine playing Footsie with us? We couldn't. Ditto if our hypothesis is not supported. Does that mean we are off on the wrong tack? Who knows! Perhaps the Divine Foot kicked the data into touch whilst we weren't looking! That's why we keep the Divine Foot out. Not because we have to believe there is no God, but because the possiblity that God interferes with our data makes a nonsense of the entire project. And the project itself is extraordinarily successful. Perhaps, nonetheless, God does intervene from time to time, to add a flagellum to a bacteria, or raise someone from the dead, or make the sun wobble in the sky. But we are unable to take that into account in our scientific methodology.Elizabeth Liddle_{October 16, 2011
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PS: I know both relativity and gravitation. Darwinism is very different, and the sort of a prioris just mentioned are pervasive, usually implicit but sometimes explicit. This extends to trying to redefine science and to revisionise its history propagandistically.kairosfocus_{October 16, 2011
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Dr Liddle: I went to a marxism-dominated 3rd world university. I saw marxist indoctrination in action formally and as subtly pervading the general environment. What I have seen in the five or six years since I first took up discussing ID in online fora as a thought exercise [and then saw that it had something serious in it], is all too familiar, and it fits in with what ES saw. If you doubt the ideological framing, cf Lewontin et al. Try here on. Think about ideas like a priori, seeming self-evident, only beggetter of truth, and absolute commitment. All of this is ever so familiar to me. And to ES. We've both seen it before. GEM of TKIkairosfocus_{October 16, 2011
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Dr Liddle, please read the four clips here on, with particular reference to Lewontin's "all but a few" [recognising, he speaks of the reigning elites]. As one from the UK, you may not be aware of surveys of the NAS and of evolutionary biologists and the like vs the bulk of working grunts. Toss in the medically trained and the disjoint between the elites and ordinary scientifically trained people becomes even more clear; to the point where suspicions of glass ceilings etc are warranted, in light of some recent incidents of career busting even at STUDENT level. Joseph is correct about the reigning elites, their party-line, and their promoters.kairosfocus_{October 16, 2011
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Elizabeth, Thank you for taking time to review my short essay from several years ago and providing your feedback. We may be talking past each other a bit with terminology, so I will endeavor to do a better job on that front. Let me point out, however, why I think your defense of Avida as a refutation of irreducible complexity is misplaced and why the main points of my original critique stand. Programmed for Success I have argued that Avida was “programmed so that a slight, successive cumulative pathway” to the ultimate function existed. You have responded that all the changes were incremental (whether rewarded or not) “so there is no bias there.” The question is not one of bias toward functional states (which is a separate point I’ll discuss below). The question is whether a cumulative pathway exists. A large part of Behe’s point is that a cumulative pathway to a complex integrated system, such as a cilium, the bacterial flagellum, or the vertebrate eye, may not exist. Despite your protestations to the contrary, Avida does have a cumulative pathway built into the system, which may or may not reflect the real world. The word “programmed” does not necessarily mean that the virtual organisms were caused to go from x to y at a particular point in time with a specific command line (although that would be one way of programming). “Programming” can also mean setting up conditions within the virtual world (in other words, within the program), whether those conditions attain inevitably or stochastically, for the population to get there. Why you don’t acknowledge that this pathway is included in Avida is strange, as the authors themselves acknowledge it: “Some readers might suggest that we ‘stacked the deck’ by studying the evolution of a complex feature that could be built on simpler functions that were also useful.” If the word “programmed” is problematic, then we can think of “established parameters” or some other term you find more appropriate. The bottom line is that the cumulative pathway is there; it exists within the virtual Avida world. So the authors are clearly aware that the program contains a cumulative pathway to the complex feature that can be built on simpler useful functions. Why would they be concerned that some readers would believe the deck was stacked? Because whether or not such cumulative pathways to complex systems exist in the real world is precisely the point in question. What is the authors’ response? “However, that is precisely what evolutionary theory requires . . .” We know what evolutionary theory requires. That is not at issue. What is at issue is whether the conditions evolutionary theory requires in fact attain in the real world. Using the authors’ logic, I can prove anything. This is very significant. I can come up with any theory, based on whatever wild or illogical parameters I want, and then write a program that “proves” my theory. All I have to do is include the parameters that my “theory requires.” Again, on such logic, nothing is out of bounds; I can prove literally anything. Whether or not evolutionary theory (in the sense of the Darwinian mechanisms we are discussing) is true is precisely the point at issue. We cannot write a program that includes – as the authors acknowledge – the parameters that are needed for the theory to be true, and then turn around later and pretend that the program has demonstrated the truth of the theory. It is entirely circular. It may be true that there is a cumulative pathway to complex features in the real world, but Avida cannot demonstrate it. In fairness, let us pause at this point and consider the other side of the coin. As I said in my essay, “if a program were written that had no possible cumulative pathway, then the writers of that program could be fairly accused of assuming up front that the complex feature was irreducibly complex [note here that I am talking about IC in the sense of “per se irreducible complexity,” as mentioned in my paper]. Thus, evolutionary algorithms seem to be between a rock and a hard spot: assume a cumulative pathway and then you are unable to challenge irreducible complexity; assume there is no cumulative pathway and then you are unable to support irreducible complexity. And herein lies the crux of the matter. Evolutionary algorithms that assume a cumulative or non-cumulative pathway at the outset simply cannot, by definition, demonstrate whether the complex system is irreducibly complex. Such algorithms define themselves into irrelevance.” As a separate question, I posed to you the above hypothetical and asked whether such a program with no Darwinian pathway would invalidate the Darwinian hypothesis. You responded: “Well, no. All you would be able to conclude is that, given the parameters of your model, the thing is very unlikely to evolve. That conclusion is only as good as your model. The better (more realistic) your model, the more confident you might be that the thing in question really was unevolvable, but we can never rule out a missing parameter.” I am wholeheartedly in agreement that any “conclusion is only as good as your model.” What we need to refute Behe’s claim – the only thing that is adequate – is a faithful representation of what actually exists in the real world. And on that score, Avida leaves much to be desired. Steps and Stumbling I argue that “relatively few changes are required to get from the initial organism to the complex feature.” You responded that: “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.” Well, Avida may establish a principle. Unfortunately, it is not at all clear that the principle has any relevance to biotic reality. In addition, you seem to think that the “stumbling” is evidence that no direction was provided. “. . . 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[y] 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.” Rather than being a vindication of the Darwinian mechanism, the real lesson from all this stumbling is that even with an easy function and a relatively short pathway to get there, the Darwinian mechanism is quite poor. The skeptic might therefore be forgiven for asking whether the stumbling might not in fact overwhelm the available resources, when translated to the real world, with functions much more difficult to achieve and pathways that may or may not exist. Function and Integration Another key problem with treating Avida as a refutation of Behe’s concept of irreducible complexity is that the Avida functions are too easy to attain. Behe highlights complex, integrated biological systems, like the bacterial flagellum, the cilium, the vertebrate eye. Each of these systems requires numerous proteins acting in concert, and that is ignoring the construction process itself, which is an astounding coordinated orchestra of chemical processes. The Avida authors indicate that: “A single mutation distinguished the pivotal genotype from its parent in 19 populations, whereas four involved double mutations. The pivotal mutations included point mutations, insertions, a small duplication and even deletions.” Further, as you note, and as the authors describe: “The phylogenetic depth at which EQU first appeared ranged from 51 to 721 steps. In principle, 16 mutations, coupled with three instructions already present in the ancestor, could have produced an EQU-performing organism. The actual paths were much longer and highly variable, indicating the circuitousness and unpredictability of evolution leading to this complex feature.” Might the skeptic be permitted to ask whether this “complex feature” is even of the same order of magnitude as what we find in the real world? How many “point mutations, insertions, small duplications and deletions” would be required to produce the systems Behe points to, which contain anywhere from dozens to hundreds of proteins acting in concert? Even assuming relatively simple proteins, we are talking about a minimum of hundreds, and likely many thousands, of “point mutations, insertions, small duplications and deletions”. Yet the ultimate Avida function, EQU, can be built with 16 mutations. Avida thus ignores one of the key difficulties facing any Darwinian scenario: the difficulty of obtaining function. By making the process orders of magnitude easier than in the real world, Avida unfortunately fails to replicate one of the key questions dogging Darwinian theory: whether chance processes would be able to stumble upon intermediate functions (or constituent parts of larger machines) in the first place. Yet there remains an equally problematic issue: that of integration. Another key question is whether constituent parts, once they exist, can be successfully integrated into the whole. Avida completely assumes away this issue, effectively granting the organisms successful integration as soon as they come up with a successful operation. Think of it this way. Bacterium A somehow gets a new DNA sequence that codes for a functional protein (let’s assume, just so it is more believable to everyone, that this gene came from horizontal gene transfer from another bacterium, rather than arising through point mutations, replication errors or the like). Let’s further assume that the cellular machinery recognizes this gene as a legitimate gene (which is not as straight forward and certain as we have perhaps been inclined to believe in the past), translates the code and expresses the protein. Great, our cell has a new protein floating around. Now what? In the real world it is not at all clear that the protein would perform a useful function in Bacterium A. Even if the protein has the raw capability to perform a function, it is not at all clear that the protein would be recognized by other cellular machinery, properly transported to the necessary location, and successfully integrated into a cellular machine. We simply don’t know whether this would happen in particular cases. It might be just as likely that the protein would languish, be broken down, or even gum up an existing process. For example, if a cell somehow got a new gene to produce a dynein protein, on what basis would that protein help lead to a nascent cilium? Most proteins are significantly more complex than the intermediate operation instructions in Avida, and many additional proteins are needed, as well as a whole suite of integration and regulatory structures, in order to integrate the new protein into a working molecular machine. But in the Avida world, things are much simpler – conveniently so. Once an organism stumbles upon an intermediate operation, the integration takes place without any of the complexity or uncertainty extant in biotic reality. Rewards Along the Way I mentioned that “A large part of evolutionary critics’ argument from irreducible complexity is that there is unlikely to be a functional advantage for intermediate steps.” You have pointed out that: “. . . 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[y] deliberately make sure that the pathways to the rewarded functions require unrewarded steps.” Further: “The authors did not set out to demonstrate [a sequence of advantageous mutations that lead to a function], 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.” This is an interesting point and one worth exploring. I acknowledge that my choice of wording in referencing a “beneficial continuum” was poor. Yes, there were neutral and unrewarded steps along the way to EQU. So I should not have used the word “continuum,” as that might give the impression of an unbroken chain of always positive mutations, which, as you note, would be logically problematic. However, regardless of whether the chain occasionally broke (to maintain the metaphor) or the organisms were able to get back on track after veering off the trail (to mix metaphors), there was, nevertheless, a cumulative pathway, which was rewarded at regular intervals. Indeed, the authors note that: “. . . 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 would not preserve the simpler functions that provide foundations to build more complex features.” How much less often? “Indeed, none of these populations evolved EQU . . .” despite the fact that “these populations tested more genotypes, on average, than did those in the reward-all environment . . .” I don’t dispute, and I am confident Behe does not dispute, that if relatively simple mutations in a pre-existing organism can generate a meaningful survival advantage at key intervals along the path to a later function, that such might be within the reach of Darwinian mechanisms (depending upon population size, frequency of mutations, etc.). Behe’s point is that if intermediate steps do not confer a meaningful survival advantage, then such systems are not likely to evolve via Darwinian processes. That is precisely what these last 50 populations demonstrated. Again, the question is not so much whether every single possible step is handsomely rewarded (as in Weasel), or whether there are occasional neutral mutations or even side-steps and/or restarts (as in Avida). Rather, the question is whether there is a rich enough reward path from A to Z. The Avida paper demonstrates that without such a path, even a relatively basic “complex” function, like EQU, is not likely to evolve. In contrast, with enough rewards along the way, a cumulative pathway becomes possible. And that is precisely the question, isn’t it? In the real world of complex, functionally-specified, information-rich, integrated biological systems, does such an intermediate reward system actually exist? Avida, whatever its other merits, unfortunately cannot answer that question. Conclusion Avida is an interesting program that may have some utility in thinking through processes of mutation and selection. But it is clearly not (and I don’t believe the programmers have represented that it is) a faithful reproduction of any specific system in the real world, and its applicability to the real world is therefore suspect. In any event, whatever the authors’ or anyone else’s pretentions, Avida certainly has not refuted Behe’s contention that some sophisticated biological systems – requiring as they do, a suite of complex parts, coordinated construction, and precise integration – lie beyond the reach of Darwinian mechanisms.Eric Anderson_{October 15, 2011
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There you go again, Joseph: "there isn't any evidence...." Yes, there is, lots. You just don't accept that it is evidence. Most people do. The reason they do is that the model fits the evidence.Elizabeth Liddle_{October 14, 2011
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Joseph: your posts are evidence to support that claim :) Eugene: Darwinism doesn't have an "ideological base". It is no more atheistic than the theory of relativity or the theory of gravity. If it was taught in the USSR as an ideology then it was mistaught. It is not an ideology.Elizabeth Liddle_{October 14, 2011
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Neither palaeontology nor genetics help you. Ya see there isn't any evidence from genetics that demonstrates the transformations required are even possible- no way to test it. The theory of evolution relies on our ignorance and vast eons of time. And there isn't any confirmatory evidence for Darwinism- all we observe says darwinian mechanisms break things.Joseph_{October 14, 2011
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Well, yes, there is, Joseph. There's all of palaeontology and genetics. And yes, you can test it without assuming it. And there is no reason to "assume" that any theory is true until you get at least some confirmatory evidence. And while I tend to assume Darwinism is probably true, given all the confirmatory evidence, my reasoning has nothing to do with whether I'm a "materialist" or otherwise. I've been persuaded by Darwinism all my life. I've only been a "materialist" for a couple of years.Elizabeth Liddle_{October 14, 2011
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There isn't any evidence that living things diversed fromn a very simple common ancestor and there isn't any way to test the claim without first assuming it. And the only reason to assume darwinism or neo-darwinism is if you are a materialist...Joseph_{October 14, 2011
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Elizabeth,
You are profoundly misunderstanding the methodology of evolutionary biology.
Maybe I am. Maybe I'm not. Does it matter, if an uneducated child can be trained to draw the same conclusions in five minutes?ScottAndrews_{October 14, 2011
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Darwinism is not "a materialistic way of thinking". It's simply a theory of how living things could have diversified from a very simple common ancestor, as the evidence suggests they did. Scientific theories can sit quite comfortably with most ideologies, as long as that ideology is not anti-science. Unfortunately, many are. And I recall that Stalin didn't think much of Darwinism, promoting Lysenkoism instead, with appalling consequences for Soviet agriculture. When ideology trumps science, disaster too often results.Elizabeth Liddle_{October 14, 2011
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Elizabeth, BTW I did not mention Marxism. Communism was taught as a materialistic way of thinking, of which Marxism and Darwinism were only parts. Darwinism sat there quite comfortably.Eugene S_{October 14, 2011
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I agree, Scott, which is why I would call both GAs and Evolution undirected. As I said, it's perfectly possible to program a GA with a randomly selected fitness function, so the fitness function itself need not be "designed". In practice, of course, we use them for evolving solutions to problems we actually want to solve. So we design the fitness function - the "environment" in which our population will evolve, so that critters that at least partially solve our problem breed better. But we needn't. Or, we could choose a problem that the environment itself naturally "sets". For example, you could set up a GA to evolve a solution to water resistance - an optimal shape, perhaps. Yes, we would have "directed" the evolution of an optimally efficient shape in water, but it would be no different from the "natural" "direction" set by an aquatic environment to an evolving penguin, say. The environment, whether natural or artificial, simply sets the parameters within which the evolving population adapts. If one is directed, so is the other. If one is undirected, so is the other. GA fitness functions and natural environments are exactly equivalent.Elizabeth Liddle_{October 14, 2011
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I was not saying they were the same. I said they were similar. I think so because they share the same ideological base, i.e. atheism. "Theistic evolution" is a pathetic attempt to serve two masters. Children in the USSR were indoctrinated into both from a very young age in all years at school.Eugene S_{October 14, 2011
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Well Elizabeth I find it strange taht all evos can do is say IDists don't understand the theory of evolution but NEVER produce anything to support that claim.Joseph_{October 14, 2011
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