New Peer-Reviewed ID Paper — Deconstructing the Dawkins WEASEL

_{William Dembski

March 9, 2010

Evolution, Informatics, Intelligent Design}

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Winston Ewert, George Montañez, William A. Dembski, Robert J. Marks II, “Efficient Per Query Information Extraction from a Hamming Oracle,” Proceedings of the the 42nd Meeting of the Southeastern Symposium on System Theory, IEEE, University of Texas at Tyler, March 7-9, 2010, pp.290-297.

Abstract: Abstract—Computer search often uses an oracle to determine the value of a proposed problem solution. Information is extracted from the oracle using repeated queries. Crafting a search algorithm to most efficiently extract this information is the job of the programmer. In many instances this is done using the programmer’s experience and knowledge of the problem being solved. For the Hamming oracle, we have the ability to assess the performance of various search algorithms using the currency of query count. Of the search procedures considered, blind search performs the worst. We show that evolutionary algorithms, although better than blind search, are a relatively inefficient method of information extraction. An algorithm methodically establishing and tracking the frequency of occurrence of alphabet characters performs even better. We also show that a search for the search for an optimal tree search, as suggested by our previous work, becomes computationally intensive.

[ IEEE | pdf ]

Comments

Sooner Emeritus, Atom is right, you are coming across like a forum troll, not just on this thread, but it's been a general impression I've had of you. Tone down the rhetoric or you will be put into moderation for as long as I want you to be.Clive Hayden_{March 11, 2010
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We have empirical evidence that the mechanisms identified by modern evolutionary theory do, in fact, result in viable subsequent populations
Viable populations does not mean the search was successful in finding more complex rube-goldberg machines. Selection in the wild often selects for damaged genomes and less complex entitities. By way of analogy, consider the process of discovering short-length password versus long-length passwords. Real biological systems are akin to very long-length passwords. They possess complexity far above what is needed for mere survival. Natural selection as observed in the wild has a propensity to select for simpler solutions, if any solution at all (wingless beetles, blind cave fish, damaged bacteria in anti-biotic resistance, damaged cytoskeletons in pesticide resistant insects, sickle cell anemia in humans, etc. etc.). Selection in biological organisms has never been experimentally demonstrated to search with foresight toward solutions that are deeply integrated since, like a long password, all the components must be in place. It is NOT a proof to say that just because a function is implemented with fewer parts that somehow selection as a mechanism works to solve harder problems. This is like saying because one can solve a simple two letter irreducibly complex password, one can resolve a 30 letter irreducibly complex password! In fact it would seem, selection would actually work against discovery of deeply integrated complexity! In that sense, it is worse than blind search. This fact was not lost upon Michael Lynch who realized features of the genome could not evolve unless selection was removed. Those who say we evolved via mindless process don't grasp the fundamental issue posed by the problem of searching large spaces for certain solutions. Evolutionary algorithms don't solve passwords in computer security and neither do they solve the passwords of lock-and-key systems in biology. In both cases, the solution for password implementation comes from the foresight of a designer or some sort of surrogate oracle (such as the developmental programs which bring a human from embryo to adulthood).scordova_{March 11, 2010
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Sooner @ 55. You reject ontological naturalism but hold to methodological naturalism even in spite of its obvious lack of explanatory power re. information/language? Odd. Sooner @ 56. And what ways would those be, exactly? p.s. I note that you had probably the most typical reaction to my argument. You ignored it. Pretend like you are a scholar and I am the student. Enlighten me. No, really. I'll listen and change my mind if a better argument comes along.tgpeeler_{March 11, 2010
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Sooner E, I am referring to your posts on this thread. I have not read your other UD posts, but am referring to the consistent ad hominem in these. You wrote:
In any case, it’s not like I’ve pasted together an image of the DI pantheon and dubbed in farts.
So you can use other people's bad behavior as an excuse for your own rudeness?
For how many years, and in how many ways, have people tried to explain to Dembski what Dawkins was getting at in The Blind Watchmaker? If you believe that expressions of frustration are inappropriate at this point, then show me an instance in which Dembski has made a concession — not just on the Weasel program, but on any point.
This is old news. See http://evoinfo.org/WeaselWare.html. It reads:
Dr. Dawkins no longer possesses the original source code for his algorithm. Feeback and reflection have led the authors to conclude that an Evolutionary Search is the more likely interpretation for the type of search presented in TBW. Although Partitioned Search was the original interpretation, we have now expanded our analysis to include Evolutionary Strategies, thus covering all reasonable interpretations.
Everybody makes mistakes and you can't hold a grudge against Dr. Dembski when he's publicly acknowledged the issue on his site. As for your "pre-computation era" challenge, it may be the case that the term originated with computation algorithms. Does that mean that evolutionary problems cannot be modeled as search problems? If that is the case, you should contact Lenski, Adami, Schneider, et al, since their evolutionary models explicitly try to find targets (EQU in the Avida case and a 16-binding site phenotype in the ev case) and work as search problems. I'm still not seeing the main thrust of your argument. What exactly are you saying, specifically, about the work presented in the paper? Please lay it out simply, because at this point I just hear frustration on your part and not much to discuss in the way of specific paper contents. Anyway, Winston is a good, extremely bright guy so any ill will you have against him is misdirected. I'm sure he'll interact with you if you want to discuss technical points about his research. But I'm also pretty sure he'll stay away from people who come across like forum trolls. AtomAtom_{March 11, 2010
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tgpeeler @53,
OK, so far so good, but can we just declare “minds,” for one, out of bounds, as an a priori premise that is not subject to further analysis? After all, it is logically possible that minds actually exist apart from brains. So maybe they do. How to tell?
Why do you need to have "minds" excluded? I, as an Evo, have no problem with the term mind and brain being used in different contexts as they are not equivalent terms. As a computer analogy, the brain is the CPU, RAM and ROM, while the "mind" is what happens when the brain starts executing the scheduled processes. If you halt the CPU, the "mind" ceases to exist as no code is being executed. All the instructions and data are still there but since it isn't running, you'll see no output and no communications. The mind is explainable naturally, so if you're going to take a naturalistic point of view, you have to take it all. "I think, therefore I am", basically says that. The brain executes, and the mind results.Toronto_{March 11, 2010
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P.S.--I've got other ways of knowing about matters of ultimate concern.Sooner Emeritus_{March 11, 2010
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tgpeeler, Methodological, not philosophical, naturalism here. I hold that science leads only to instrumental knowledge.Sooner Emeritus_{March 11, 2010
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Atom,
Your posts resemble rants more than they do reasoned invitations to dialogue. You should have someone vet your posts for tone.
Have you read my posts in other threads? In any case, it's not like I've pasted together an image of the DI pantheon and dubbed in farts. Dembski's trumpeting that he has deconstructed the Weasel program when he has not so much as comprehended it as a model, rather than an engineered solution to a problem, is deeply annoying. Invitation to dialog? For how many years, and in how many ways, have people tried to explain to Dembski what Dawkins was getting at in The Blind Watchmaker? If you believe that expressions of frustration are inappropriate at this point, then show me an instance in which Dembski has made a concession -- not just on the Weasel program, but on any point. (He almost conceded that the explanatory filter was defunct, but then decided that it had to remain "the best thing since sliced bread.") As Barr recently pointed out in First Things, Dembski's constant "I'm right, and you're all wrong" does not pass for discourse with scientists. A bit of context in what Dembski wrote:
The denial that evolution constitutes a search thus seems strange and indeed insupportable. Do a search on the phrase "evolutionary search," and you'll find many, many hits.
I know you're a very bright person (or two). Can you not tell merely by the challenge I've posed where the notion of "evolutionary search" originated? I offered Winston the opportunity to exhibit some integrity, namely by acknowledging that to make something of the frequency of usage of "evolutionary search" is to beg the question of whether nature is engineered. As a scholar, I would love to learn of pre-1970 biologists saying that evolution constitutes a search. To my knowledge, not even Sewall Wright, with his emphasis on fitness landscapes, suggested such a thing. There is occasional analysis of whether a biological system is optimal by some criterion invoked by the scientist, but without suggestion that the objective of optimizing the criterion inhered in nature. The earliest references to evolutionary search I have found are in connection with computing. Fogel, Owens, and Walsh, for instance, refer to evolutionary search when they use the technique of evolutionary programming to solve search problems. In short, "evolutionary search" is engineering shorthand for application of evolutionary computation to solution of search problems. As best I can tell, the pioneers of evolutionary computation did not get the notion of evolutionary search from biologists, but instead drew an analogy between fitness functions in biological models and objective functions in engineering applications. To return to the notion of an invitation to dialog, what usually happens when I post something like this is that it does not bring an overt response, but rather a shift in rhetoric with no acknowledgment of the cause.Sooner Emeritus_{March 11, 2010
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Sooner @ 50 "I sincerely care about students, and I hope that Winston will consider carefully whether he has put the cart in front of the horse (i.e., the conclusions ahead of the research)." That's fantastic! I must presume that you will find my last post to be completely congenial because you hold doing research before coming to conclusions in such high regard. Since naturalism, by definition, (Cambridge Dictionary of Philosophy) is a presumption rather than an argued theory. page 563.tgpeeler_{March 11, 2010
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Sooner, etal Warning, amateur philosopher at play... It seems to me that much of this discussion misses the point. If I understand the overall context of the "debate" out here and elsewhere, which is intelligent design (mind) vs the current incarnation of a naturalist explanation for life and everything else (physics plus time plus genetics) i.e. neo-Darwinian evolution, then I think there is a much simpler approach to resolving this argument. It may be useful to temporarily set aside the back and forth regarding the extraction of information, the odds of information being randomly generated, and so forth and look at the problem from a strictly logical, in so far as I am capable of that, point of view. If naturalism means that "the spatio-temporal world, or nature, is all there is" and that "nature is causally closed" (there is more to it but these are two fundamental intellectual commitments that the naturalist must make, else he is not a naturalist), then we see that the only explanatory tool that the naturalist has is the laws of physics. For if the material world (plus abstracta like math and laws) is all that exists and that world is causally closed, then only the laws of physics can have explanatory power. "Spooky" immaterial things like minds or souls and God do not exist and therefore do not have explanatory power. How could they if they aren't real? OK, so far so good, but can we just declare "minds," for one, out of bounds, as an a priori premise that is not subject to further analysis? After all, it is logically possible that minds actually exist apart from brains. So maybe they do. How to tell? If we reject the obvious evidence of our very existence as self-aware, thinking, feeling, choosing, beings that innately understand that the concept of right and wrong is real, there is still another way to come at this. Let me pretend for a moment to be a naturalist. I say that minds do not have causal power in nature for two reasons. First, because they don't exist. Second, because even if they did I have no idea how an immaterial mind could possibly interact with the material world. (But oddly enough, I have no problem with the immaterial laws of physics having causal power in a material world.) So when presented with any effect in the world I have to explain it in terms of the laws of physics, or admit that I do not have the resources to do so, or I can also merely deny the existence of the effect in question. (A favorite tactic - "apparent" design, the "illusion" of purpose, and so on.) When someone asks me to explain the existence of design, or purpose, or the moral law in terms of the laws of physics the problem becomes clear. I don't have to explain those things in terms of physics. After all, how could I since these (alleged) things are immaterial and physics tells me about how quarks and leptons (material things) act. I respond that I cannot explain this mythical abstract entity because I don't need to. Well, ok. But still there seems to be something "like" design that exists else why would people in the evolutionary camp say that the evidence for design is almost overwhelming, or that biologists constantly have to remind themselves that what they see is not actually designed but only apparently designed? In any case, in this instance, to deny design creates no obvious logical contradiction for me, the naturalist. So now we are in the awkward position of weighing evidence. Who has the stronger evidence for design, or for no design? Aside from the problem of how I could, as a naturalist, know about fake design apart from the existence of actual design, I can always, in the end, just deny the existence of design. But here's where things get interesting to me. Leaving aside the implications for biology for the moment, let's see if naturalism as an ontological and methodological project can account for the phenomenon of human information. The ontological part is easy. You (the naturalist) cannot deny the existence of information (a real, I claim, abstract entity) because you are using information to deny the existence of information. It’s as if I deny my own existence. To do that I must exist in the first place. So the gambit of denying the existence of this immaterial thing, information, is unavailable to the ontological naturalist. So how about the methodological naturalist? Surely if I can explain this information in terms of the laws of physics I can at least consign it to the realm of the abstracta I already acknowledge like mathematics and the laws of physics. In any case, if my explanation in terms of physics is true then I don’t need “mind” or “design” to explain anything. Oddly enough, one of the first objections I get to what I am about to say is “well what is information anyway?” I refer to M-W online: "the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something (as nucleotides in DNA or binary digits in a computer program) that produce specific effects: a signal or character (as in a communication system or computer) representing data: something (as a message, experimental data, or a picture) which justifies change in a construct (as a plan or theory) that represents physical or mental experience or another construct” So we get from this that information is “something” (an attribute, here) that is encoded into an arrangement of something physical that produces effects in the world. In other words, something immaterial. BTW, this is recognized in the anti-ID world too, that information is immaterial. See Crick, Meyr, Dawkins, Yockey, Küppers, and a host of others. Well, how to explain this information, this “thing” that is encoded into some physical substrate, in terms of physics (and time)? Well, one cannot and here’s why. The key is in the “encoding.” How is information “encoded” into a material substrate? It turns out that a language is the only thing that allows for the encoding of information. So what is a language? I refer again to M-W online: “a formal system of signs and symbols (as FORTRAN or a calculus in logic) including rules for the formation and transformation of admissible expressions.” In any conceivable context, this part of the definition of a language is true. A language is a system of symbols and rules for the arrangement of those symbols so as to encode information. So just by following the chain, so to speak, I now realize that what I have to explain, in terms of physical laws, if I want to maintain my naturalist position, is the existence of language, i.e. symbols and rules. Well the game is up as you can surely see. There is no part of physics that has a thing to say about symbols (the representation of one thing for another) or the rules for arranging those symbols to encode information. What part of physics bears on why “cat” means a certain kind of mammal and why “act” means to do something, something done, or a segment of a play, for instance? No part of physics does that. Not being a physicist I had to see if I was missing something so I talked to a professional (Ph.D., full professor, student of Richard Feynman at Cal Tech, etc… in other words someone who knows) the other day and asked him: what does general relativity or quantum physics or the Standard Model or string theory or super-string theory have to say about symbols and rules? Well the answer is nothing. One doesn’t need to be a physicist to see that. None of these things bear on symbol sets and their rules since that’s not what physics is about. Physics is about quarks and leptons and forces, stuff like that. And it will never be about anything else. By definition. So naturalism fails. I cannot deny information without using information and I cannot ever, ever explain information by means of physics no matter how much time I have (it’s a logical impossibility). So I am, as we used to say, out of Schlitz. Not only is naturalism false, it isn’t even possible for it to be true. Not ever. Now I have taken this to the next logical (I think) step and made the argument, here and elsewhere, that if the explanation of life demands the explanation of information, and it does, then any naturalistic account of life fails, not just the current version, neo-Darwinian evolutionary theory. Needless to say this generates heated response. Because what I am saying is that not only is the current naturalistic story of life not true, it is impossible for it to be true. And not just this story (NDE) but any future version of this story. And who am I to make such a bold claim? Good question. I may be stupid, arrogant, not a scientist, not an expert, have no (scientific) credentials, etc… but it seems that none of these objections, which I have faced often enough, (and they may all be true, certainly the last three are and I’m sure from time to time the first two are) are germane to the question at hand or my argument of it. I will be interested in any response.tgpeeler_{March 11, 2010
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Could you please explain your reasoning behind this claim? If you want to model biological evolution as a search, then you must use the known laws of physics and chemistry and the observed environment of the organisms under consideration as the “search space." If the properties that make evolutionary search algorithms work are particular to the world of physics and chemistry, the success of all evolutionary simulations is irrelevant. . We have empirical evidence that these mechanisms open up new niches to those subsequent populations (see the peer-reviewed literature on nylonase, Lenski’s citrate consuming e. coli, and antibody resistence, to name just three). Those are neat, but very small compared to the large complexity of biological creatures. We have empirical evidence in both the fossil record and the comparison of modern genomes that these mechanisms operate successfully over deep time. That reasoning only works if we know that the biological change recorded in the fossil records is the result of an evolutionary search mechanism. Darwinian theory is proposed as an explanation for what we find in the fossil record. It is circular to argue from the fossil record that the mechanism must work. The question is whether the mechanism can explain the record. Try searching with Google Books, setting the upper bound of the date range to 1969 The earliest result from Google Scholar is 1964. (There are others listed even earlier, but I don't think the dates like 1753 are accurate). Google Books gives many results given an upper bound of 1969, 5 pages in fact. The earliest of the examples it turns up is in 1906. Whatever you think is the origin of the phrase I'd have to suggest that it did not originate in 1969 as you claim. This is an embarrassment for you, because it indicates that you have not even slight familiarity with the literature on the algorithms you criticize. Why? because I find the syntax odd and cryptic? I am familiar with the syntax, I just think its a bad choice. In my opinion it looks like Perl syntax. (my apologies to any Perl fans). If I'm not familiar with the algorithms, demonstrate where I'm wrong and I freely admit it. Don't get all blustery about how I dislike that syntax. You’re also going to have to get around to reading for yourself at least the more heavily cited papers in the NFL literature You have no idea what I've read. The remainder of the FOOHOA is best explained by example You are complaining that I used examples to explain the algorithm? For my part I'd rather put it in a more precise pseudocode. However, most of the readers would probably not prefer that method. An example was simply the best way of explaining the aspect of the algorithm I was discussing at that point time. The appropriateness of describing the algorithm that way does depend on the situation. If the paper's purpose were to present FOOHOA, it would have included a much more precise statement of how it worked. In the case of this paper, the intent is to show that there is a lot of information available from the oracle. Now, don't get me wrong. If I've confused something I want to know before I make any more of a fool of myself then I already have. Thus far, you have done nothing to demonstrate inaccuracies in the paper (apart from the mistake in the references).WinstonEwert_{March 11, 2010
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Sooner Emeritus wrote
I’m "accusing" Winston of being bright enough to see that his mentors adduce "arguments" to their preconceptions, rather than proceed explicitly from a mathematical model of search to proof of conclusions.
What exactly, in specifics, is your accusation? That Drs. Dembski and Marks have certain biases in their research (as all people do)? Do you have some work to show that their proofs are in error (where mathematical) or that their experiments were performed poorly or reported incorrectly? Again, I hear seething from you but not much substance.
I’m "accusing" Winston of having a good enough education in computer science to know better than to write, "The remainder of the FOOHOA is best explained by example." (I seem to recall that partitioned search, falsely attributed to Dawkins, was "best explained" similarly in an article by Dembski and Marks.)
So Winston's FOOHOA should have been fleshed out more clearly for the sake of those who couldn't follow the high level discussion? Perhaps. But space constraints on submitted papers cause trade-offs in level of detail versus depth of explanation.
It’s one thing to see Dembski and Marks make mud in the literature
Again, vitriol. They're active in producing peer-reviewed research and presenting it to their peers. Ad hominem like that has no place in civil conversation.
...and another altogether to see a student vest faith in them before doing his own review of the literature.
How are you so sure that Winston has not done his own research, including reading relevant primary literature? Have you asked him? Perhaps you're one of his professors and can tell us first hand? (Or perhaps you know nothing of the sort.)
I sincerely care about students, and I hope that Winston will consider carefully whether he has put the cart in front of the horse (i.e., the conclusions ahead of the research).
As you can read in the paper, much experimental research work was done in arriving at the conclusions. Your criticism has no weight.
In his role as a computer scientist, Winston is doing theoretical computer science — poorly.
Again, ad hominem without giving a specific example of where Winston does anything "poorly." Which parts of his experiments do you find inaccurate or poorly performed? Your posts resemble rants more than they do reasoned invitations to dialogue. You should have someone vet your posts for tone. AtomAtom_{March 11, 2010
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Atom, I'm "accusing" Winston of being bright enough to see that his mentors adduce "arguments" to their preconceptions, rather than proceed explicitly from a mathematical model of search to proof of conclusions. I'm "accusing" Winston of having a good enough education in computer science to know better than to write, "The remainder of the FOOHOA is best explained by example." (I seem to recall that partitioned search, falsely attributed to Dawkins, was "best explained" similarly in an article by Dembski and Marks.) It's one thing to see Dembski and Marks make mud in the literature, and another altogether to see a student vest faith in them before doing his own review of the literature. I sincerely care about students, and I hope that Winston will consider carefully whether he has put the cart in front of the horse (i.e., the conclusions ahead of the research). In his role as a computer scientist, Winston is doing theoretical computer science -- poorly. If he has not already taken a graduate course in the theory of computation, he should do so as soon as possible, and should seek to make his own work like that of his proper role models.Sooner Emeritus_{March 11, 2010
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Correction: it looks like you wanted citations before 1969 (upper date.) Did Dr. Dembski say the phrase predated that date?Atom_{March 11, 2010
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Mustela @ 43 "All machines of which I am aware operate within the bounds of known physics. Do you have an example of one that does not?" No one will. What I can point to however, is virtually any machine on the planet and we will see that the laws of physics, in and of themselves, are unable to account for the creative and specific arrangements of different elements/components that are assembled to accomplish a certain purpose. Or so it seems to me. It seems so obvious but I'm not a "professional" so maybe it's just me.tgpeeler_{March 11, 2010
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Sooner Emeritus, http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.48.3041 http://www.opticsinfobase.org/ol/abstract.cfm?uri=ol-25-14-1025 http://portal.acm.org/citation.cfm?id=500436 From the first page of a google search on "evolutionary search" What is it exactly you're accusing Winston Ewert of not understanding? Your post is somewhat obscure (while quite vitriolic in tone.) Winston is a bright guy, I'd be careful about questioning his understanding without evidence. AtomAtom_{March 11, 2010
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Winston Ewert, One of your coauthors, William A. Dembski, says,
Do a search on the phrase "evolutionary search," and you'll find many, many hits.
It's distressing to think that a graduate student might emulate his "scholarship." Try searching with Google Books, setting the upper bound of the date range to 1969, to find the actual origin of the phrase. (I've done quite a bit of additional work to uncover evidence that the concept predates the phrase, and have found none.) You can demonstrate your scholarly integrity by reporting to everyone here what you find. I'm calling on you because I've never seen Dembski admit to error. You write,
I’ve always found that particular [ES(1, lambda)] syntax just odd and cryptic, but if it is a standard we should use it.
This is an embarrassment for you, because it indicates that you have not even slight familiarity with the literature on the algorithms you criticize. More particularly, you are not familiar with reference [1] of a paper of which you are the lead author. By the way, you've misspelled the name of the author of [1]. The "a" in "Back" should have two dots above. (When the umlaut-a is unavailable, as here, the correct spelling is "Baeck.") You're also going to have to get around to reading for yourself at least the more heavily cited papers in the NFL literature. You've attempted to repeat here and in another thread the misunderstandings of Dembski and Marks, and have not done terribly well at even that. You, as a graduate student in computer science, should know more about analysis of algorithms than Dembski and Marks do. You should insist on stating a model of probabilistic computation, and on writing out algorithms in terms of that model. Many of the errors of Dembski and Marks are attributable to the fact that their "clear writing" about algorithms is in fact not mathematically explicit.Sooner Emeritus_{March 11, 2010
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scordova @35,
If selection picks whatever target it wants, then the meaning of “target” is meaningless. A random walk would just as well work since it is looking essentially for nothing!!!
We are in 100% agreement. Since it is not "looking" for anything in particular, anything workable stops the "search". Here's an Evo analogy of evolution: A mechanic walking through a wrecking yard looking for something he can use for the car he's building. Here's an ID analogy of evolution: An engineer walking through a wrecking yard searching for a 57 Chevy 265/265 camshaft and distributor. Notice the difference, both in procedure and the odds of success. You are trying to refute your definition of evolution, not ours, with your search models.Toronto_{March 11, 2010
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WinstonEwert at 42, "There is no 'search for a search,' the fitness landscape, while dynamic, is a given." Nothing theoretically prevents the fitness landscape in nature from being well-matched with an evolutionary search strategy. However, some points are in order. 1. If you are going to take that stance all computer simulations of evolution are irrelevant. Could you please explain your reasoning behind this claim? 2. The well-matchedness itself demands an explanation. I've had a similar conversation with the always interesting CJYman here. It might be possible to construct a cosmological ID argument based on the No Free Lunch theorems, but within the domain of biological evolution, there is no search for a search. "Of course we do. It’s called empirical evidence. We can see these mechanisms working." Is the fitness function in nature well matched with a genetic algorithm? It is matched well enough or else we wouldn't observe these mechanisms in the first place. You claim that we have empirical evidence that this is the case. Certainly, we have seem some neat adaptations. However, what we have actually observed is tiny compared to what needs to be explained. We have in no way come close to demonstrating that the natural fitness function is well suited to genetic algorithms. We have empirical evidence that the mechanisms identified by modern evolutionary theory do, in fact, result in viable subsequent populations. We have empirical evidence that these mechanisms open up new niches to those subsequent populations (see the peer-reviewed literature on nylonase, Lenski's citrate consuming e. coli, and antibody resistence, to name just three). We have empirical evidence in both the fossil record and the comparison of modern genomes that these mechanisms operate successfully over deep time. While not by any means exhaustive, the evidence strongly supports modern evolutionary theory.Mustela Nivalis_{March 11, 2010
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All machines of which I am aware operate within the bounds of known physics. Do you have an example of one that does not?
That misconstures what I wrote, I specifically said "transcend" and I also said, machines don't "violate" physical law. One can operate within the laws of physics and chemistry, but also transcend them. A computer operates within the laws of physics and chemistry, but its salient features are independent of physical law. Chemist and mentor to two Nobel Laureates, Michael Polanyi published dicussions about machine independence from physical law.
The massive amount of documentation of empirical observations in the peer-reviewed literature refutes your assertion.
Massive amounts of literature by unqualified evolutionary biologists like Richard Dawkins. Darwinian storytelling isn't science, the IEEE is much better qualified to adjudicate matters of design and complexity, not Richard Dawkins and his little weasel.
My point, to which you did not respond, was that the real world of known physics and chemistry, as well as the existing environment, must be used as the “oracle” if the model is to be extended to biological evolution.
This is ironic. It's not like evolutionary biology use physics and chemistry to build models of natural selection. Ernst Mayr himself said story telling is more appropriate for evolutionary biology, not experiments! Information processing systems must by nature be transcendent to the physics and chemistry upon which the information resides. Transcend does not mean violoate. The same software and information can reside on multiple kinds of physical mediums, that is because information transcends (not violates) physics and chemistry. Transcend means that it has qualities independent of physical and chemical law. Software is decoupled from physical hardware because it is presumed to have a transcendance from physical and chemical law. Biological systems are not defined with recourse to purely chemical and physical constructs, but rather forms and organization. You can't use Schrodinger's equation or various other laws of physics and chemistry to decide if an object is "living". That is because living systems transcend (not violate) physical law. Incorporating laws of physics and chmistry into the question of the evolution of integrated information is largely a side-show. Computer languages and information are assumed to have a certain transcendance from physical medium. That's why most books on Computer Languages don't delve into the physics of computers. Software is conceptually decoupled from hardware. And the irony is that anyone would use that as criticism against the IEEE paper, especially since evolutioanry biology is notoriously averse to incorporating physics and chemisty in defending evolution, but rather resorts to story telling.scordova_{March 11, 2010
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scordova at 34, "If you want to model biological evolution as a search, then you must use the known laws of physics and chemistry" The known laws of physics don’t find solutions to integrated complexity. You cut my statement in half, leaving the impression that I was saying something entirely different. Please be more careful with your quoting. My point, to which you did not respond, was that the real world of known physics and chemistry, as well as the existing environment, must be used as the "oracle" if the model is to be extended to biological evolution. Integrated complexity (as in machine) by definition must transcend (not violate) laws of physics and chemistry. All machines of which I am aware operate within the bounds of known physics. Do you have an example of one that does not? "It turns out that, in the search space of our real world, the mechanisms identified by modern evolutionary theory work sufficiently well to allow populations to change in response to feedback" No they do not The massive amount of documentation of empirical observations in the peer-reviewed literature refutes your assertion. that is merely an assertion by unqualified evolutionary biologists on the question of information. No, it is what we observe in the real world. The IEEE is the proper forum for disucssin the evolution of complexity, not evolutionary biology. The paper under discussion does not apply its arguments to any observed biological artifact or process.Mustela Nivalis_{March 11, 2010
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Rather, differential survival is the oracle. Right, that is a more accurate way of stating it. There is no “search for a search,” the fitness landscape, while dynamic, is a given. Nothing theoretically prevents the fitness landscape in nature from being well-matched with an evolutionary search strategy. However, some points are in order. 1. If you are going to take that stance all computer simulations of evolution are irrelevant. 2. The well-matchedness itself demands an explanation. The point of the regress of search for the search is that we cannot improve our results by looking for a good search algorithm because that will be even harder then just doing the search in the first place. Of course we do. It’s called empirical evidence. We can see these mechanisms working. Is the fitness function in nature well matched with a genetic algorithm? You claim that we have empirical evidence that this is the case. Certainly, we have seem some neat adaptations. However, what we have actually observed is tiny compared to what needs to be explained. We have in no way come close to demonstrating that the natural fitness function is well suited to genetic algorithms. “We also show that a search for the search for an optimal tree search, as suggested by our previous work, becomes computationally intensive.” For small cases, we can actually consider all possible search strategies and determine which one on average succeeds in the fewest query. This tells us the maximum amount of active information per query that we can extract from the oracle. Essentially, it establishes how powerful the oracle is.WinstonEwert_{March 11, 2010
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"What works today, is rejected tomorrow."
I don't think that this is a good pro-ID argument because the same is true for anything designed: If changes of the environment are accepted old earth ID proponents have to either assume further intervention of the designer or front-loading of a surplus of information to deal with environmental challenges. Alternatively, one may take a younger earth or rather cosmos (see your own blog's name) position which rejects any changes apart from genetic degeneration. However, I am not sure if a young earth position is really compatible with ID as usually propagated at UD.osteonectin_{March 11, 2010
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As a brainstorm, here is something to consider. Informed oracles are analogous to the foresight of an engineer or intelligent designer when designing interlocking components of a system. In biological systems there are many lock-and-key, login/passoword-type systems and formal protocols, some very complex and some resembling rube-goldberg machines. A randomly mutating protein would not be expected to have better insight than an oracle with foresight (be it a intelligent designer or surrogate like the developmental programs which form an embryo into a human). Hence, Dawkins blindwatchmaker will not work as well as an informed oracle with foresight. Real watchmakers aren't blind, and they also have foresight and insight. The question is will Darwinism work to create systems that need foresight of the interlocking parts. The question of oracle efficiency is very relevant to the quesiton of required foresight. If the blindwatchmaker has no foresight, then it is doubtful it will resolve the problems of biological complexity where there are many systems analogous to login/password systems. But designer with pre-meditation could have sufficient oracle knowledge to create the protocols, the login/password pairs, the lock-and-key systems (like protein-protein binding sites). The knowledge is there because designer knows ahead of time how both sides of a lock-and-key system are to be designed. Blind watchmakers will be hard pressed to make anything but trivial lock-and-key mechanisms, not to mention, any mechanism whatsoever in the first place. Computer languages are not created via blindwatchmakers because computer languages require oracle like insight in their creation. Life is rich with computer languages. The IEEE has published many articles on the computer languages in living systems, and will continue to.scordova_{March 11, 2010
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I like the approach that the authors are taking in their critique of evolutionary theory. In the past, critics of evolution have found a good criticism (like complexity of the eye) and then proclaimed the death of Darwinism. It was a big step and was refutable. So scientists got psychologically innoculated against "Darwinism is Disproven!" headlines. But what these authors are doing is systematically building a case against evolution without making large inferrential leaps. If they show why evolution fails, without telling why evolution fails, scientists will come to the conclusion on their own. This is how mainstream science is usually done anyway; by incremental steps.Collin_{March 11, 2010
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Toronto @28
Any mutation that does not negatively impact an organism’s fitness will survive just like any other neutral characteristic.
Thats the problem though. The scenario you describe in the equivalent of a blind search. There is just not enough time or resources for random mutation and natural selection to work in the scenario you describe. The Weazel and Avida programs were written precisely because of this. And they introduce an Oracle. But you seem to agree nature does not have one. It therefore follows that there must be something more than random mutation and natural selection.Cable_{March 11, 2010
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"We also show that a search for the search for an optimal tree search, as suggested by our previous work, becomes computationally intensive." Can someone explain to me what this means?Collin_{March 11, 2010
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If you want to model biological evolution as a search, then you must use the known laws of physics and chemistry
The known laws of physics don't find solutions to integrated complexity. Integrated complexity (as in machine) by definition must transcend (not violate) laws of physics and chemistry.
It turns out that, in the search space of our real world, the mechanisms identified by modern evolutionary theory work sufficiently well to allow populations to change in response to feedback
No they do not, that is merely an assertion by unqualified evolutionary biologists on the question of information. The IEEE is the proper forum for disucssin the evolution of complexity, not evolutionary biology.scordova_{March 11, 2010
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Selection “implies” the target,meaning that the target is not explicitly defined by some other process.
What determines if it is a target toward development of integrated complexity or one away from integrated complexity? If selection picks whatever target it wants, then the meaning of "target" is meaningless. A random walk would just as well work since it is looking essentially for nothing!!! By that twited definition of target, selection always hits its target because it really wasn't looking for one in the first place. Whatever place differential reproductive success hits is by your definition a "hit". This is a meaningless tautology: 1. what is a target? whatever selection hits 2. what does selection hit? the target it hitsscordova_{March 11, 2010
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The Discovery Institute has invited Dr. Francisco Ayala to debate the thesis of the book Signature in the Cell: DNA and the Evidence for Intelligent Design with the book’s author, Dr. Stephen Meyer.
I guess Ayala will now have to actually read the book, which he obviously had not done based on his review.uoflcard_{March 11, 2010
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