Home » Evolution, Informatics, Intelligent Design » New Peer-Reviewed ID Paper — Deconstructing the Dawkins WEASEL

New Peer-Reviewed ID Paper — Deconstructing the Dawkins WEASEL

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 ]

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93 Responses to New Peer-Reviewed ID Paper — Deconstructing the Dawkins WEASEL

  1. From the paper:

    We consider searches that are asymptotically perfect, that is,
    will eventually succeed.

    Evolution does not do a search with the intent of finding any specific target at all and neither does the Dawkins Weasel algorithm.

    You could at any point, in a program based on the Weasel algorithm, replace the target string and the algorithm would home in on the new string.

    The analogy is like that of shooting at a static target, where you aim directly at the object, compared to shooting at a moving one, where you must lead it.

    We are searching for a target message of length L. In
    general, an (L+1)×(L+1) Markov matrix, P, has elements
    (P)k,? = pk,? (4)
    where pk,? is the probability of going to state k given we are
    in state ?.

    I’ve quoted this because some people on the ID side tend to state the probability of an event as the odds of getting from (state_0) to (state_2^target). Evolution should be mathematically expressed more like the above quote.

  2. In comparison, evolutionary search as modeled by Markov
    processes uses the Hamming oracle inefficiently.

    If you could come up with a mathematical analysis of a search algorithm that took into account a changing target, it would be a much better model of what evolution does.

    Evolution is the guy who walks through a hardware store and says, “this will work” as opposed to the engineer in a lab who says, “nothing else is acceptable.

    [The question of moveable targets is an interesting one, but moveable targets don't seem able to bear the weight that evolutionists want to place on them. Organisms, as they evolve and interact with their environment, may alter what counts as fit, but certain fundamental structures are presupposed by life, and these, it seems, constitute targets that are not moveable, such as the protein synthesis apparatus presupposed by all living forms. 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. Dawkins' METHINKS IT IS LIKE A WEASEL program, insofar as it is interesting at all, is interesting because it generates a meaningful (to us) string of characters and thus seems to be the conclusion of a search. Yes, the program can be adapted to converge on any other string of 28 characters, but for Dawkins to explain how a computer program that mimics Darwinian evolution could produce a purely random string is hardly interesting. It's that Dawkins' algorithm is successfully executing a search for a salient pattern that makes it interesting. Evolutionists might say that the mere reference to "search" suggests a teleology that is properly absent from evolution. ID theorists would say that that's begging the question, but even if evolution is presumed to be non-teleological, it still requires explanation why evolution is locating places in biological configuration space which in any other context we would regard as the outcome of a teleological process (i.e., search). Evolution, if you will, gives the appearance of "search," and that itself requires explanation. --WmAD]

  3. Congratulations!

  4. Wasn’t Atom involved in that research too?

  5. According to Wikipedia’s article on Dembski: “Computer scientist and number theorist Jeffrey Shallit states in an expert report that despite common claims in the popular and religious press, Dembski is not a scientist by any reasonable standard, has not published any experimental or empirical tests of his claims, submitted his claims to the scrutiny of his peers or published in a scientific journal.”

    I wonder when this will get corrected, now that Dembski keeps cranking out these papers with Robert Marks’s Evolutionary Informatics Lab. Any bets? I’d give it another five years.

  6. Maybe when he tries to buy a football team.

  7. Dr Dembski,

    From the bottom of p 292, left column:

    We first consider the case where there is a single child and then when K children are generated and the best fitness among the children is kept for the next parent.

    I’m pretty sure you mean “single parent” not “single child”, if you get a chance to correct the manuscript. It might also be nice at this point out that this is a standard ES( 1, lambda ) evolution strategy if your readers would like to pursue the literature on these algorithms. I think it would also be standard form to give a citation to Avida when you mention it.

    I’m glad to see that extracting information from an oracle has replaced smuggling in information. The fitness function is decoupled from the search algorithm, this is progress. Also nice to see the citation on antenna design.

    I’m beginning to sense the shape of the argument being built here, and in the previously mentioned Ewert 2009. Evolution can and does work, but inefficiently. ES, which like the real world only knows the previous generation, loses in efficiency of information extraction compared to a strategy that keeps knowledge of the entire history of queries.

    But I’m stll not seeing how to shift from “some algorithms are more efficient than others” to ID. If this is an ID paper, so is every paper in GECCO 2009. (Paging Jerry…)

  8. I’m pretty sure you mean “single parent” not “single child”

    No, the point there is that we are first considering the case of a single child and then extending to that the k children case.

    It might also be nice at this point out that this is a standard ES( 1, lambda ) evolution strategy if your readers would like to pursue the literature on these algorithms.

    If it would helpful, we’ll endeavor to include it in future. I’ve always found that particular syntax just odd and cryptic, but if it is a standard we should use it.

    I’m glad to see that extracting information from an oracle has replaced smuggling in information

    The fact that we are extracting information from an oracle means that we have an oracle which has a large amount of active information. Information is being put into the simulation by the use of this oracle. The smuggling has not been replaced, the smuggling is in the availability of an oracle.

    Evolution can and does work, but inefficiently.

    The point is that for any given oracle there is a variety of ways to extract the information from it. One of these ways is optimal. FOOHOA shows that there is a lot of information available from the oracle showing that it is very powerful. Search succeeds as a result of the oracle, the oracle is the source of information.

    We know where this oracle came from, humans designed it. Where does nature get a good oracle?

  9. Sincere congratulations to Ewert, Montañez, Dembski, and Marks. Having read it quickly, I’d say that this is the most interesting of the EIL papers for me.

    I was most interested in section V. I wish I had time to replicate those results and explore the characteristics of the winning functions. It seems that finding a function that achieves an optimal balance of performance and algorithmic simplicity could be a fruitful area of research.

    The paper also highlights a point of terminological confusion: Although active information is sometimes described as a measure of problem-specific information, this isn’t strictly correct. The relevant item of information in this paper is the knowledge that the oracle is a Hamming oracle, but the resulting active information depends very much on how that information is used. Section V shows that we can, for simple cases, find the maximum amount of active info achievable with this knowledge (given values for L and N), so we can uniquely quantify problem-specific information using the active info upper bound.

  10. I haven’t read the paper in detail yet. And it’s a little bit hard to figure out the number of queries needed on average for various combination of parameters from the three-dimensional pics of the Active information per query. I’d like to compare these numbers with mine for the algorithm mutating children with a fixed mutation rate for L=28 and N=27 and L=100 and N=2. An of course the numbers for K children each with a single mutation, again for L=28 and N=27!

    It’s good that the exchange of information from oracle to program is looked at now – that got muddled up earlier.

  11. Nakashima,

    Yeah, maybe this isn’t an ID supporting paper per se. But it is ID friendly and I can definitly see the scaffolding of an argument emerging from it. Perhaps an argument that Evolution is so inefficient that it cannot sustain positive mutations under the weight of all of the negative mutations. Maybe something like John Sanford’s “Genetic Entropy” argument.

  12. “so is every paper in GECCO 2009. (Paging Jerry…)”

    Having just looked in briefly before taking off for South America, I have to say yes. Every paper in genetics is an ID paper and all those geneticists are supporting the ID paradigm whether they know it or not . Let me know when you find one that is not.

    So is everybody here who is anti ID supporting ID, especially Nakashima. Why Nakashima? Because he tries harder than most and still turns up nothing.

    No one has been able to provide an alternative explanation yet. Not even Richard Dawkins or Jerry Coyne in their recent books.

  13. at II C: Results: Figure 2(B) shows the active information per query for the ratchet strategy given different alphabet sizes and message lengths. Increasing the message length does not appear to significantly change the efficiency of active information extraction. However, increasing the alphabet size has a rather noticeable effect.

    One should thinks so : As I calculated earlier – when discussing Conservation of Information in Search – Measuring the Cost of Success – the expected number of queries for the One Child Ratchet Algorithm (a more common name would be ES(1+1)) with exactly one mutation per child is

    E(Q) = (N-1) * H_(1-βL)* L

    so that the average information per query is

    I = log(N)/(N-1) * 1/H_(1-βL)

    (β: rate of correct letters to start with
    H_k: k-th harmonic number)

    The effect of log(N)/(N-1) is noticeable, the effect of of 1/H_(1-βL) less so.

  14. Collin:

    But it is ID friendly and I can definitly see the scaffolding of an argument emerging from it. Perhaps an argument that Evolution is so inefficient that it cannot sustain positive mutations under the weight of all of the negative mutations.

    If so, then that’s an interesting twist, given Marks & Dembski’s previous statements. In Life’s Conservation Law, they said that information comes only from intelligence. Since Darwinian evolutionary processes have active information, they must be designed. Are they now saying that evolutionary processes are designed, but not designed well enough to hit the target in the allotted time?

  15. WinstonEwert,
    Thanks for that bit of clarification, as I am lost as to exactly what has been accomplished in the paper. If you could would you clear up a few points for me?

    From all evidence I have been exposed to, the principle of Genetic Entropy holds for all beneficial biological adaptations, that is that the “beneficial adaptation” always comes at a loss of information that was already present in the genome ,,, I am guessing that to correctly model what we actually see in life, the information available for a search after a successful “beneficial” adaptation should be decreased within/from the oracle??? Am I correct to think this? Or am I off base?

    also of note; Behe has clearly clarified in “The Edge” that all known successful evolutionary searches for a beneficial adaptation are severely restricted to a couple of coordinated point mutations,,, Is this what you find in your model as well? Or am I off base again?

  16. bornagain77,

    the “beneficial adaptation” always comes at a loss of information that was already present in the genome

    That is probably true, although I wouldn’t state it quite so universally. There is difference though. In biology there is no easy way to improve something. It is very difficult to come up with a cluster of mutations to implement a new and useful feature. On the other hand, breaking something in a useful way is much easier. Weasel only has to change one letter to be correct. As a result, WEASEL is not really bound by that restriction.

    Is this what you find in your model as well? Or am I off base again?
    Weasel does not get a large benefit from multiple mutations since it can proceed one mutation at a time. The Avida simulation does have multiple muations however. Avida has a much higher mutations rate then biology with a much smaller genome. The result is that it can accumulate larger mutation sizes then a realistic biologic case.

  17. Mr. Ewert,

    First of all, congratulations on this paper, as well as the Avida paper.

    Where does nature get a good oracle?

    How did you determine that the oracle is good? What is nature’s search space and target?

    One point that may bear noting: Talk of oracles and problem-specific knowledge may give some people the mistaken impression that active information necessarily comes from an intelligent source. But we can pick any deterministic natural process, declare that the outcome is the target, and we have boatloads of easy active information. Non-randomness implies causality, not necessarily sentience.

  18. Toronto:

    If you could come up with a mathematical analysis of a search algorithm that took into account a changing target, it would be a much better model of what evolution does.

    The moving target search is doesn’t help the Darwinian argument.

    What this would imply is once evolution finds a solution, then next day it is invalid because what worked yesterday, won’t today.

    This is like finding a password and then immediately it becomes useless for the next go around.

    And even granting this is the way evolution works, it is no way to accumulate complexity, but it rather guarantees only the simplest solutions will be found since the wealth of prior evolutionary search discoveries become invalidated by the moving target.

    The solution you propose doesn’t help the Darwinian case.

  19. Let me elaborate a little on my last comment.

    Darwinian evolution presumes that complexity is added piece by piece, that once a solution is found selection will continue to favor it and then favor subsequent improvements.

    But a moving target implies selection will no longer favor a solution once it is found. What works today, is rejected tomorrow.

    For example, the idea that a piece of what will be eventually part of a bacterial flagellum will be discovered and preserved will fail in a moving target search. The reason the piece was accepted today would not be grounds for it to be accepted in the future, in fact, it would be selected against since the newly favored target would cause rejection of the previously selected target, and hence the pre-cursor is disposed of like an expired password.

  20. I started to have a closer look at the paper (section I, II, III A, III B, III C).

  21. scordova @19,

    But a moving target implies selection will no longer favor a solution once it is found. What works today, is rejected tomorrow.

    Selection “implies” the target,meaning that the target is not explicitly defined by some other process.

    Selection allows a mutation to survive as a match to a different target, and this is what is wrong with modeling evolution as a single target search algorithm.

    A proper model of evolution as a search algorithm would be multiple varying targets with varying population sizes, coupled with feedback.

    In real life, a predator’s food supply is inversely proportional to his success in getting it, and that is reflected in the oscillating population sizes of predators and their prey.

    Both predator and prey actively modify each other’s selection criteria in an arms race. Longer legs in the prey might help it outrun it’s predator but would also allow it to walk further into a pond to hunt for it’s own food.

    Here we have two areas a mutation would be selected for even though the original mutation/selection was due to only one of them.

    None of this type of feedback is in the search algorithm, yet it will impact on selection.

    While eventually they may, currently, Dembski-Marks don’t go far enough in their work to say it pertains to evolution.

  22. Evolution, if you will, gives the appearance of “search,” and that itself requires explanation. –WmAD]

    Thank you for your reply.

    I agree 100% that it gives the “appearance” of a search.

    If we’re going to model evolution as a search algorithm though, we really need to get closer to what it really is which is a search for multiple dynamic targets, coupled to multiple feedback mechanisms, with a varying population size.

    Now something like that would give both sides a model they could work with.

  23. How did you determine that the oracle is good?

    The oracle is good because it is possible to extract a large amount of active information from it.

    What is nature’s search space and target?

    The search space is the space of all biological forms. The simplest way of looking at the target is to view it as a moving target always targeting something better then the current point. However, appealing to a moving target is really not going a help a search process.

    At any rate, if you are going to take that position it means that most if not all computer simulations of evolution are invalid.

    But we can pick any deterministic natural process, declare that the outcome is the target, and we have boatloads of easy active information.

    In doing so, you’ve create a target and search algorithm pair which match exactly. The search algorithm essentially knows what the target is. You don’t the equivalent of taking a negative. You already knew the outcome of the process, you’ve just transformed that into a target.

    That is a neat trick you can pull but its not going to help evolution find a way to let the deer escape from the lion. The whole point of a search process is that you don’t know what the target is. Hopefully, you’ll be able to recognize what you are looking for when you see it.

  24. 24

    WinstonEwert at 8,

    Where does nature get a good oracle?

    If we use the model of an oracle-led search (keeping in mind that it is a model) then the oracle is nature. That is, the determinant of fitness is the laws of physics and chemistry, the environment, and even the rest of the organism’s population.

    What we observe is that the mechanisms identified by modern evolutionary theory are capable of communicating the results from that “oracle” such that they are represented in subsequent populations.

    These mechanisms don’t have to be optimal, just good enough.

  25. @20 Mustela Nivalis

    I think you are missing the point. Stating the Oracle is nature is about as empty a statement as can be made.

    What in nature provides feedback about an intermediate state i.e. one that does not provide an immediate benefit. Natural selection cannot give feedback about an intermediate state since there is no survival benefit at this point.

    Therefore it is essentially a blind search. Since the search space in so massive mutation and natural selection by themselves simply don’t have the time/resources/opportunities to find beneficial states without an Oracle helping or essentially reducing the search space.

    This is what Weasel and Avida do. So where does nature get the Oracle?

  26. Off Topic: Now this is cool:

    Leading Intelligent Design Advocate Challenges Former President of American Association for the Advancement of Science (AAAS) to Debate:

    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.

    http://www.evolutionnews.org/2.....n_adv.html

  27. 27

    I said, “Where does nature get a good oracle”.

    Certainly we can treat nature as something of an oracle. But its not a good oracle. The NFLT tells us that across the space of all possible oracles all search algorithms have equally bad results. We have no reason to suppose that an evolutionary strategy will be able to use a nature-based oracle in an effective manner.

  28. Cable @23,

    What in nature provides feedback about an intermediate state i.e. one that does not provide an immediate benefit.

    From our point of view, i.e., of life, nature is not a series of quantum states.

    Our fitness in our environment is not measured every hour, season, anniversary, or at any fixed interval.

    While a mathematical model has a frequency of testing for fitness, it is not applicable to real-time life.

    Any mutation that does not negatively impact an organism’s fitness will survive just like any other neutral characteristic.

    If we use the model of an oracle-led search (keeping in mind that it is a model) then the oracle is nature.

    Please keep in mind as was mentioned by Mustela Nivalis, we are dealing with a model and we should treat it as such.

  29. @William Dembski
    Amusing thought: the remarkably good performance of the FOO Hamming oracle algorithms for the Hamming oracle results in a much worse performance of this algorithm for other oracles – an obvious conclusion of the New Free Lunch theorem.

    @Winston Ewert: using the standard notation helps. But at least be consistent – your variance of ES(1+1) is introduced as the Rachtet Strategy in this paper, and was called Optimization by mutation with elitism in Conservation of Information.

  30. scordova at 18 & 19

    The same argument works against an Intelligent Designer. If an ID creates a set of DNA that works in one environment and that environment changes so much the DNA doesn’t work anymore, the ID will have to either design some updated DNA or watch his creation die.

  31. Mr Ewert,

    If the model is that the oracle is a channel through which information is returned in response to queries, then I would say that it is inaccurate to say that nature is its own oracle. Rather, differential survival is the oracle.

    Differential survival is a noisy channel. There is no guarantee that it is a “good oracle”. But nature doesn’t have a choice of oracles.

  32. 32

    Cable at 25,

    I think you are missing the point. Stating the Oracle is nature is about as empty a statement as can be made.

    Any emptiness is a limitation of the model, not of the observed ability of the mechanisms identified by modern evolutionary theory to modify subsequent populations in response to feedback from the environment.

    What in nature provides feedback about an intermediate state i.e. one that does not provide an immediate benefit. Natural selection cannot give feedback about an intermediate state since there is no survival benefit at this point.

    True, as far as it goes. However, neutral and even mildly deleterious mutations can persist and spread through a population.

    Therefore it is essentially a blind search.

    This is incorrect and does not follow from your premises.

    Since the search space in so massive mutation and natural selection by themselves simply don’t have the time/resources/opportunities to find beneficial states without an Oracle helping or essentially reducing the search space.

    The mechanisms identified by modern evolutionary theory do not search the whole space of possible viable organisms. They can be modeled (and again, it’s important to realize that this is just a model) as searching the immediate neighborhood of known-viable organisms. Empirical evidence shows that this is a useful strategy.

  33. 33

    WinstonEwert at 27,

    I said, “Where does nature get a good oracle”.

    Certainly we can treat nature as something of an oracle. But its not a good oracle. The NFLT tells us that across the space of all possible oracles all search algorithms have equally bad results.

    Actually, the No Free Lunch theorems tell us that a particular algorithm will perform no better than blind search on average across all possible search spaces. That’s completely immaterial to this discussion, however.

    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.” There is no “search for a search,” the fitness landscape, while dynamic, is a given.

    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 (in the form of differential reproductive success) from the environment. This isn’t a surprise — if those mechanisms weren’t useful in this particular search space, we would see different, more useful mechanisms instead (or we wouldn’t be here to discuss it in the first place).

    We have no reason to suppose that an evolutionary strategy will be able to use a nature-based oracle in an effective manner.

    Of course we do. It’s called empirical evidence. We can see these mechanisms working.

  34. 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.

  35. 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 hits

  36. 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.

  37. “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?

  38. 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.

  39. 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.

  40. 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.

  41. “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.

  42. 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.

  43. 43

    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.

  44. 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.

  45. 45

    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.

  46. 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.

  47. 47

    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.

  48. Sooner Emeritus,

    http://citeseerx.ist.psu.edu/v......1.48.3041
    http://www.opticsinfobase.org/.....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.

    Atom

  49. 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.

  50. Correction: it looks like you wanted citations before 1969 (upper date.) Did Dr. Dembski say the phrase predated that date?

  51. 51

    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.

  52. 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.

    Atom

  53. 53

    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).

  54. 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.

  55. 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.

  56. 56

    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.

  57. 57

    tgpeeler,

    Methodological, not philosophical, naturalism here. I hold that science leads only to instrumental knowledge.

  58. 58

    P.S.–I’ve got other ways of knowing about matters of ultimate concern.

  59. 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.

  60. 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.

    Atom

  61. 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.

  62. 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).

  63. 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.

  64. 64

    WinstonEwert at 53,

    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.

    You’re just repeating yourself, not explaining your reasoning. At 42 you responded to my argument that “There is no ’search for a search,’ the fitness landscape, while dynamic, is a given.” with
    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.

    This does not follow. I’m not sure it’s even coherent. “Irrelevant” to what, specifically?

    The fact remains that the No Free Lunch theorems are not applicable to discussions of biological evolution because the fitness landscape is a given. There is no search for a search. Just because a particular strategy isn’t better than blind search on average over all search spaces does not mean that the strategy cannot perform better, even significantly better, than blind search on the particular fitness landscape we find in the real world.

    “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.

    The mechanisms identified by modern evolutionary theory explain the observed fossil record as well as empirical evidence from genetics and many other disciplines. All of those different sets of observations lead to the same set of conclusions. There is no circularity.

    If your model says that what we observe in the real world can’t happen, the problem is more likely with your model than with the real world.

  65. As a scholar, I would love to learn of pre-1970 biologists saying that evolution constitutes a search.

    If evolutionary biologists failed to realize the importance of the problem defined by the question of searches, then that only reinforces how incompetent and clueless the evolutionary community was/is to opine that they’ve solved the problem of the evolution of complexity and design.

    If what you hint at is true, then it is high time evolutionary biology be subject to more scientific scrutiny and rigor from outside the field of evolutionary biology. As the premeire organization for the science of information, the IEEE’s involvement in this question is thoroughly appropriate.

    The evolutionary community should have been far more welcoming of objective criticisms from the engineering community.

  66. Mustela Nivalis:

    The mechanisms identified by modern evolutionary theory explain the observed fossil record as well as empirical evidence from genetics and many other disciplines. All of those different sets of observations lead to the same set of conclusions. There is no circularity.

    Similarity of form does not necessarily imply common ancestry.

    We don’t even know if prokaryotes and eukaryotes share a common ancestor. Woese said we might have to drop the hypothesis of common ancestry of the first prokaryotes and eukaryotes. The similarities need explanation by other mechanisms.

    Evolutionary theories don’t explain the fossil record, actually the fossil record accords better with the notion of sudden independent emergence than gradual evolutionary sequence!

  67. 67

    scordova at 66,

    Evolutionary theories don’t explain the fossil record, actually the fossil record accords better with the notion of sudden independent emergence than gradual evolutionary sequence!

    My interest in this thread is to discuss the applicability of the paper referenced above to biological evolution. If you’re just going to continue to make baseless assertions that ignore the past 150 years of scientific progress, then this will be my last response to you.

  68. My interest in this thread is to discuss the applicability of the paper referenced above to biological evolution. If you’re just going to continue to make baseless assertions that ignore the past 150 years of scientific progress, then this will be my last response to you.

    150 years of ideas that don’t even account for the problems that are the focus of the problems such as those in this paper.

    I hardly call the circular reasonings of 150 years of evolutionary theories (which you repeat over and over) as scientific progress, but rather evidence of illogical and uncritical thinking. Hardly the stuff of real science.

    this will be my last response to you

    That’s fine, but I’m free to respond and highlight when you resort to circularly reasoned talking points and appeal to the literature put together by a community of evoltuionary biologists unqualified to speak on the evolution of information in machine archtictures such as biological systems.

    You’ve appealed to circularly reasoned, unqualified opinions form the evolutionary community (such as you did with the fossil record), and I merely pointed out they fail as objections to the paper publised in the IEEE since the objections you put forward mis-state the real situation, namely, evolutionary theories are on shaky ground via many lines of empirical evidence.

    To criticize the paper succefully, you’ll need direct empirical observation of selection in the wild in real time that resolves complex structures. Since no such data exists, you appeal to the large body of speculations (such as evolutionary theories) developed over 150 years, rather than direct empirical observations.

    Speculations are fine, but call them what they are, speculations, not scientific facts.

  69. Mustela @ 64 “The mechanisms identified by modern evolutionary theory explain the observed fossil record as well as empirical evidence from genetics and many other disciplines. All of those different sets of observations lead to the same set of conclusions. There is no circularity.”

    I’m aware of only two mechanisms in modern evolutionary theory and they are the laws of physics and genetic mutations. Are there others? Oh yes, natural selection. Aptly described by Dawkins in this way “All appearances to the contrary, the only watchmaker in nature is the blind forces of physics, albeit deployed in a very special way.”

    In other words, natural selection is code for “physics that looks like design.” As opposed to what, the ‘regular’ physics? I am ready and willing to read an account of how physics accounts for the genetic code and the biological information contained in that code.

  70. Clive,

    Please don’t ban Sooner before he responds to my screed on naturalism. :-)

  71. Toronto @ 59

    “Why do you need to have “minds” excluded?”

    I do not. Indeed I argue for Mind/mind as the source of all information. It’s the naturalist who insists upon denying ontological status to ‘mind.’ I am merely pointing out the insanity of that position.

    “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.”

    Hmmm. Computer analogies don’t really do much for me in this realm as they always leave unmentioned the intelligence contained in the CPU. As an EVO, how do you explain the intelligence in the CPU?

    “The mind is explainable naturally, so if you’re going to take a naturalistic point of view, you have to take it all.”

    What do you mean that the mind is explainable naturally? And I am decidedly NOT taking a naturalistic point of view. Do I have a massive failure to communicate here?

  72. scordova @ 65 “The evolutionary community should have been far more welcoming of objective criticisms from the engineering community.”

    And what? Admit defeat? Abject and ignominious defeat? Total and unconditional defeat?

    The word “engineer” connotes design every bit as much as the word “design” does! Of course they will ignore the engineers. I recognize that this is not news to you. :-)

  73. LOL tgpeeler @ 71,

    Cool Hand Luke “Failure To Communicate.”
    http://www.youtube.com/watch?v=l_aVuS7cOIQ

    I wish someone would communicate to me exactly how “mind” is explained naturally when the double slit experiment has shown that the “quantum information wave” will not collapse to its “uncertain” 3-D material-particle state until a conscious observer is present. Exactly how does a 3-D material entity give rise to the consciousness upon which the 3-D material entity is dependent on for its own existence.

    Dr. Quantum – Double Slit Experiment & Entanglement
    http://www.metacafe.com/watch/.....anglement/

  74. LOL tgpeeler @ 71,

    Cool Hand Luke “Failure To Communicate.”
    http://www.youtube.com/watch?v=l_aVuS7cOIQ

    I wish someone would communicate to me exactly how “mind” is explained naturally when the double slit experiment has shown that the “quantum information wave” will not collapse to its “uncertain” 3-D material-particle state until a conscious observer is present. Exactly how does a 3-D material entity give rise to the consciousness upon which the 3-D material entity is dependent on for its own existence? Can a son be his father’s father?

    Dr. Quantum – Double Slit Experiment & Entanglement
    http://www.metacafe.com/watch/.....anglement/

  75. 75

    Atom,

    First, thank you for letting me know that Dembski and Marks have a basis for saying that they have partially satisfied their obligation under the IEEE Code of Ethics to correct their errors. I think they’d be on better ground if “the authors” were explicitly identified on the WeaselWare web page, and on better ground yet if the footnote were added to the TSMC-A paper disseminated by the EIL. There are also obvious mathematical errors that have been identified at RationalWiki, and I recommend that Dembski and Marks toe the ethical line by placing corrections in other footnotes, with citation of the source.

    —————

    The idea of making a search tree the canonical representation of an infinite class of deterministic search algorithms that “do the same thing” is due to me. I in fact shared that way of looking at search algorithms with one of the authors of the latest paper a couple years ago. It’s not a deep insight, but it makes concrete a number of aspects of “no free lunch” that are otherwise abstract and difficult to understand. And the “search for a search” is greatly simplified by searching over trees instead of algorithms.

    In my opinion, my contribution of information — considerably more than that regarding search trees — has led to confusion of basic matters I thought were straightened out a number of years ago. You keep asking me for specific criticism, but you should understand why I’m reticent to supply more information.

    The matter of Winston Ewert truly does put me in a bind. I have been struggling to reorganize and condense a critique of the work of Dembski and Marks, and I decided last night that it might help me if I explained to you and Winston at least their misinterpretation of the so-called conservation of information theorems. I’m on short leash now, so I’ll have to keep the benefit of the writing to myself.

    I’ll contribute instead a link to prior work Ewert et al. should know about:

    A Study of Some Implications of the No Free Lunch Theorem (2008)

    Andrea Valsecchi and Leonardo Vanneschi

    Abstract

    We introduce the concept of “minimal” search algorithm for a set of functions to optimize. We investigate the structure of closed under permutation (c.u.p.) sets and we calculate the performance of an algorithm applied to them. We prove that each set of functions based on the distance to a given optimal solution, among which trap functions, onemax or the recently introduced onemix functions, and the NK-landscapes are not c.u.p. and thus the thesis of the sharpened No Free Lunch Theorem does not hold for them. Thus, it makes sense to look for a specific algorithm for those sets. Finally, we propose a method to build a “good” (although not necessarily minimal) search algorithm for a specific given set of problems. The algorithms produced with this technique show better average performance than a genetic algorithm executed on the same set of problems, which was expected given that those algorithms are problem-specific. Nevertheless, in general they cannot be applied for real-life problems, given their high computational complexity that we have been able to estimate

  76. 76

    tgpeeler at 69,

    Mustela @ 64 “The mechanisms identified by modern evolutionary theory explain the observed fossil record as well as empirical evidence from genetics and many other disciplines. All of those different sets of observations lead to the same set of conclusions. There is no circularity.”

    I’m aware of only two mechanisms in modern evolutionary theory and they are the laws of physics and genetic mutations. Are there others? Oh yes, natural selection.

    The laws of physics are at a different level of abstraction and so may not be convenient to use in the analysis. At one appropriate level, I would include mutation, genetic drift, and selection in the list of evolutionary mechanisms. At a more detailed level, I’d include Allen MacNeill’s list of sources of variation.

    I am ready and willing to read an account of how physics accounts for the genetic code and the biological information contained in that code.

    I’d suggest starting with a good organic chemistry text and working your way up to graduate level biochemistry to get the basics. There are a lot of directions to go from there depending on your interests.

  77. 77

    [off-topic] tgpeeler,

    This happens to be a thread regarding a paper in a field about which I know a great deal. Why this “I’m calling you out, dude” bit about naturalism? Itchy trigger finger?

    From scientific method to methodological naturalism: the evolution of an idea

    In response to the appearance of Scientific Creationism and its growing popularity in conservative Protestant circles in the 1960s, Paul de Vries proposed a way of thinking about the scientific enterprise that he named “methodological naturalism.” As a professor of philosophy at Wheaton College, de Vries found himself at the intellectual center of American evangelicalism and sought to offer his students an alternative to Scientific Creationism on the one hand and “evolutionistic scientism” on the other, both of which de Vries thought distorted science and manipulated faith. (1)

    As a methodological naturalist, I must object to the notion that science is a means of arriving at knowledge of all things. If I did not, I would be an ontological naturalist. So telling me that naturalism does not permit explanation of this, that, or the other thing you want explained is vacuous.

    Bang. You’re not dead. But I’m outta here.

  78. 78

    You’re just repeating yourself, not explaining your reasoning

    Sorry, allow me to try explaining myself more clearly and carefully.

    We have this model of evolution as a search process. All search processes are clearly restricted by the NFLT and similar results. Your claim is that we escape this implications because we do not care about the average performance of a evolutionary search across all search problems just the one in nature. There is one very complex, dynamic fitness landscape provided in nature. This is, as you say, a given. So, under this idea nature works well with an evolutionary search even though on average a randomnly selected landscape would not. Essentially, we have a good landscape.

    Two questions arise as a result of this. Is it true? Why is it true?

    First, the question, Is it true? Does the natural fitness landscape really work well with the evolutionary search process?

    Here is where I was saying that the computer simulations are irrelevant. They tell me nothing about whether or not nature has a fitness landscape suitable for genetic algorithms. However, upon further reflection I suppose that it is possible that some property X of a fitness landscape exists. If we can show that property X applies both to nature and some computer simulations those simulations could help demonstrate that property X gives rise to fitness landscape where evolutionary search performs well.

    As for the fossil record, evolution has clearly been very successful. The question is why? One possible explanation is that it has had a fitness landscape which works well with a Darwinian search process. The particular issue under consideration here is whether or not the fitness landscape really looks like that. We can only use the success of evolution to prove that point if we assume or can show that this is the only possible explanation.

    As for the second question, Why is it true? If we assume, for the sake of argument, that the fitness landscape is well suited for evolutionary search, we then must ask why? If the fitness landscape were chosen randomly from a uniform distribution of all fitness landscapes then NFLT says we should expect no algorithm to do better then random sampling. Clearly, we are doing better then random sampling. Are we just lucky? Is there some particular property in the way that the fitness landscape is generated that makes it produce more useable landscapes? These are the questions that need asking.

  79. 79

    I’ll contribute instead a link to prior work Ewert et al. should know about:

    I don’t have access to it right now, but I’ll read it when I get a chance.

  80. Sooner Emeritus,
    From your handle I believe you are a teacher. Let me express my personal dismay that someone as close minded, as you have demonstrated yourself to be, has any hand in teaching our young children.

    You expressed: “I’m “accusing” Winston of being bright enough to see that his mentors adduce “arguments” to their preconceptions”

    And then you went on to attack his mentors, which I shall not reopen that wound:

    Yet to turn this around, are you bright enough to see where your own personal preconceptions adduce your arguments?:

    For example, You readily admitted that you follow methodological naturalism, so let’s unpack the preconception that you readily admit to:

    “There are more things in heaven and earth, Horatio, Than are dreamt of in your philosophy.”
    William Shakespeare – Hamlet

    The artificial imposition of the materialistic philosophy onto the scientific method has blinded many scientists to the inference of God as a rational explanation in these questions of origins. In fact, the scientific method, by itself, makes absolutely no predictions as to what the best explanation will be prior to investigation in these question of origins. In the beginning of a investigation all answers are equally valid to the scientific method. Yet scientists have grown accustomed through the years to the artificial imposition of the materialistic philosophy onto the scientific method. That is to say by limiting the answers one may conclude to only materialistic ones, the scientific method has been very effective at solving many puzzles very quickly. This imposition of the materialistic philosophy onto the scientific method has indeed led to many breakthroughs of technology which would not have been possible had the phenomena been presumed to be solely the work of a miracle. This imposition of materialism onto the scientific method is usually called methodological naturalism, methodological materialism, or scientific materialism etc… Yet today, due to the impressive success of methodological naturalism in our everyday lives, many scientists are unable to separate this artificial imposition of the materialistic philosophy from the scientific method in this completely different question of origins.

    A Question for Barbara Forrest
    http://darwins-god.blogspot.co.....rrest.html

    In fact, I’ve heard someone say, “Science is materialism.” Yet science clearly is not materialism. Materialism is a philosophy which makes the dogmatic assertion that only blind material processes generated everything around us, including ourselves. Materialism is thus in direct opposition to Theism which holds that God purposely created us in His image. Furthermore science, or more particularly the scientific method, in reality, only cares to relentlessly pursue the truth and could care less if the answer is a materialistic one or not. This is especially true in these questions of origins, since we are indeed questioning the materialistic philosophy itself. i.e. We are asking the scientific method to answer this very specific question, “Did God create us or did blind material processes create us?” When we realize this is the actual question we are seeking an answer to within the scientific method, then of course it is readily apparent we cannot impose strict materialistic answers onto the scientific method prior to investigation.
    In fact when looking at the evidence in this light we find out many interesting things which scientists, who have been blinded by the philosophy of materialism, miss. This is because the materialistic and Theistic philosophy make, and have made, several natural contradictory predictions about what evidence we will find. These predictions, and the evidence we have found, can be tested against one another within the scientific method.

    For a quick overview here are a few:

    1.Materialism predicted an eternal universe, Theism predicted a created universe. – Big Bang points to a creation event. -

    2. Materialism predicted time had an infinite past, Theism predicted time had a creation – Time was created in the Big Bang. -

    3. Materialism predicted space has always existed, Theism predicted space had a creation (Psalm 89:12) – Space was created in the Big Bang. -

    4. Materialism predicted at the base of physical reality would be a solid indestructible material particle which rigidly obeyed the rules of time and space, Theism predicted the basis of this reality was created by a infinitely powerful and transcendent Being who is not limited by time and space – Quantum mechanics reveals a wave/particle duality for the basis of our reality which blatantly defies our concepts of time and space. -

    5. Materialism predicted the rate at which time passed was constant everywhere in the universe, Theism predicted God is eternal and is outside of time – Special Relativity has shown that time, as we understand it, is relative and comes to a complete stop at the speed of light. (Psalm 90:4)-

    6. Materialism predicted the universe did not have life in mind and life was ultimately an accident of time and chance. Theism predicted this universe was purposely created by God with man in mind – Every transcendent universal constant scientists can measure is exquisitely fine-tuned for carbon-based life to exist in this universe. -

    7. Materialism predicted complex life in this universe should be fairly common. Theism predicted the earth is extremely unique in this universe – Statistical analysis of the hundreds of required parameters which enable complex life to be possible on earth gives strong indication the earth is extremely unique in this universe. -

    8. Materialism predicted much of the DNA code was junk. Theism predicted we are fearfully and wonderfully made – ENCODE research into the DNA has revealed a “biological jungle deeper, denser, and more difficult to penetrate than anyone imagined.”. -

    9. Materialism predicted a extremely beneficial and flexible mutation rate for DNA which was ultimately responsible for all the diversity and complexity of life we see on earth. Theism predicted only God created life on earth – The mutation rate to DNA is overwhelmingly detrimental. Detrimental to such a point that it is seriously questioned whether there are any truly beneficial mutations whatsoever. (M. Behe; JC Sanford) -

    10. Materialism predicted a very simple first life form which accidentally came from “a warm little pond”. Theism predicted God created life – The simplest life ever found on Earth is far more complex than any machine man has made through concerted effort. (Michael Denton PhD) -

    11. Materialism predicted it took a very long time for life to develop on earth. Theism predicted life to appear abruptly on earth after water appeared on earth (Genesis 1:10-11) – We find evidence for complex photo-synthetic life in the oldest sedimentary rocks ever found on earth -

    12. Materialism predicted the gradual unfolding of life to be self-evident in the fossil record. Theism predicted complex and diverse life to appear abruptly in the seas in God’s fifth day of creation. – The Cambrian Explosion shows a sudden appearance of many different and completely unique fossils within a very short “geologic resolution time” in the Cambrian seas. -

    13. Materialism predicted there should be numerous transitional fossils found in the fossil record, Theism predicted sudden appearance and rapid diversity within different kinds found in the fossil record – Fossils are consistently characterized by sudden appearance of a group/kind in the fossil record, then rapid diversity within the group/kind, and then long term stability and even deterioration of variety within the overall group/kind, and within the specific species of the kind, over long periods of time. Of the few dozen or so fossils claimed as transitional, not one is uncontested as a true example of transition between major animal forms out of millions of collected fossils. -

    14. Materialism predicted animal speciation should happen on a somewhat constant basis on earth. Theism predicted man was the last species created on earth – Man himself is the last generally accepted major fossil form to have suddenly appeared in the fossil record. -

    As you can see when we remove the artificial imposition of the materialistic philosophy, from the scientific method, and look carefully at the predictions of both the materialistic philosophy and the Theistic philosophy, side by side, we find the scientific method is very good at pointing us in the direction of Theism as the true explanation. -

    So Sooner Emeritus, I know my words will probably have little effect on correcting you on your “beam in the eye” blatant hypocrisy you have chosen to criticize the speck in your brother Dembski’s eye with, but at least I hope my words will bring the point home that you are not nearly on as firm a footing as you think you are.

    Romans 1:20
    For since the creation of the world God’s invisible qualities—his eternal power and divine nature—have been clearly seen, being understood from what has been made, so that men are without excuse.

    Materialism – The Hijacking Of Science By Methodological Naturalism – Dr. Thomas Kindell – video
    http://www.metacafe.com/watch/.....aturalism/

  81. Mr. Ewert @ 23:

    The search space is the space of all biological forms. The simplest way of looking at the target is to view it as a moving target always targeting something better then the current point.

    We can certainly model nature this way. We should note that this model, as it stands, makes no predictions. Had we, for instance, defined the search space to be smaller, we might observe nature stepping outside of it, and we would know that our model was inaccurate. But we know by definition that biological forms will always fall within the space of all biological forms. And there is no empirical observation that could falsify any choice of target.

    Which raises a question: How do we know that our assessments of active information and the goodness of oracles are correct if we can’t test the models on which those assessments are based?

    That fundamental problem aside, your choice of target is interesting. Given biological form X, which is known to replicate imperfectly, how improbable is it that a slightly better (which I assume means more likely to replicate) form will arise?

    That is a neat trick you can pull but its not going to help evolution find a way to let the deer escape from the lion.

    True, but it does help someone who’s looking for active information in nature. In fact, it renders the task trivial.

  82. scordova:

    Evolutionary algorithms don’t solve passwords in computer security and neither do they solve the passwords of lock-and-key systems in biology.

    Nor do designers. If no information is available (as the word “password” implies), designers are no better than evolutionary algorithms at finding a target. And if information is available, intelligence is not necessarily required to obtain or utilize it. Information transfer may consist of nothing more than a causal relationship.

  83. Sooner @ 77

    I’ll be gone for a week with no access to a computer. I’ll read the article you linked when I get a chance. I assumed that as a scholar you would be interested in engaging my argument. Particularly since it opposes your world view. I like to mix it up. If you have a better argument then so be it. But I don’t know what it is or how you defeat mine. Anyway, I’m out of here too. Regards…

    p.s. meanwhile I suggest you reread bornagain77 @ 80 until you get it. I will be.

  84. Mr. Ewert:

    If the fitness landscape were chosen randomly from a uniform distribution of all fitness landscapes then NFLT says we should expect no algorithm to do better then random sampling. Clearly, we are doing better then random sampling. Are we just lucky? Is there some particular property in the way that the fitness landscape is generated that makes it produce more useable landscapes? These are the questions that need asking.

    What you’re asking is why the fitness landscape looks like figure 1 instead of figure 2 in this paper. In other words, why does nature have a paucity of algorithmic information? That question is beyond the reach of both science and math, even though the EIL seems to think that they have the answer. But would an information-rich universe require an explanation any less than our information-poor universe?

    It’s ironic that low algorithmic information entails high active information, especially since Meyer characterizes CSI as having high algorithmic information (the opposite of Dembski’s definition of CSI).

    One final note: I can’t conceive of any state of affairs that couldn’t be modeled as having positive active information. So when the EIL asks for an explanation for active information, they’re asking why there is something instead of nothing, as Haggstrom pointed out awhile back.

  85. 85

    WinstonEwert at 78,

    We have this model of evolution as a search process. All search processes are clearly restricted by the NFLT and similar results.

    Let’s be very clear. The No Free Lunch theorems only apply to the performance of a particular strategy averaged over all possible search spaces. Those theorems do not “restrict” “all search processes.”

    There is one very complex, dynamic fitness landscape provided in nature. This is, as you say, a given. So, under this idea nature works well with an evolutionary search even though on average a randomnly selected landscape would not. Essentially, we have a good landscape.

    It seems that we are in agreement that the physical world represents one particular search space in your model. That’s good progress. I would phrase your statement about “nature works well” differently. It isn’t that nature works in some sense with an evolutionary search; the core observation is that the mechanisms identified by modern evolutionary theory are sufficiently effective at allowing the fitness of subsequent populations to reflect the environment in which they find themselves that those populations frequently are viable and produce viable child populations.

    It is possible to model those mechanisms as a strategy for searching the viability space close to the current population. The model is not the reality, though. It isn’t meaningful to talk about a “good landscape”, reality is what it is.

    Two questions arise as a result of this. Is it true? Why is it true?

    First, the question, Is it true? Does the natural fitness landscape really work well with the evolutionary search process?

    The landscape is a given. It doesn’t “work” with anything. The evolutionary mechanisms we observe in the real world can, as it turns out, be modeled to a certain extent as a search strategy. That model strategy is, unsurprisingly, better than blind search when applied to the search space modeled on the real world.

    The reason it is unsurprising is that we wouldn’t observe these mechanisms if they didn’t work in the real world. We’d either observe different mechanisms or we wouldn’t be here to observe anything.

    Here is where I was saying that the computer simulations are irrelevant. They tell me nothing about whether or not nature has a fitness landscape suitable for genetic algorithms.

    That’s not actually the case. If the fitness function in the model is based on the real world and the search strategy is modeled on evolutionary mechanisms, it would be surprising if the simulations didn’t produce useful results (e.g. finding the target in your model).

    However, upon further reflection I suppose that it is possible that some property X of a fitness landscape exists. If we can show that property X applies both to nature and some computer simulations those simulations could help demonstrate that property X gives rise to fitness landscape where evolutionary search performs well.

    Close. It’s not that the property gives rise to fitness landscapes, it’s that a strategy modeled on observed evolutionary mechanisms performs better than blind search on search spaces modeled on the real world.

    As for the fossil record, evolution has clearly been very successful. The question is why? One possible explanation is that it has had a fitness landscape which works well with a Darwinian search process.

    Again, we have to be careful not to confuse the model with what is being modeled. Just because it is possible to model some aspects of evolutionary mechanisms as a search strategy does not mean that they are a search strategy. The map is not the territory.

    The particular issue under consideration here is whether or not the fitness landscape really looks like that.

    That’s not an issue at all. We observe certain mechanisms that result in differential reproductive success. We observe that those mechanisms operate in the real world. That can give us data to formulate a model of a fitness landscape, but whether we can model it or not, eppur si muove.

    We can only use the success of evolution to prove that point if we assume or can show that this is the only possible explanation.

    I’m sorry, but I have no idea what you mean by this statement.

    As for the second question, Why is it true? If we assume, for the sake of argument, that the fitness landscape is well suited for evolutionary search,

    Again, this is backwards. The real world is what it is. If the mechanisms identified by modern evolutionary theory were not capable of operating in the real world, we wouldn’t observe them. We do observe them. If your model says we shouldn’t, it is your model that is lacking.

    we then must ask why? If the fitness landscape were chosen randomly from a uniform distribution of all fitness landscapes then NFLT says we should expect no algorithm to do better then random sampling.

    That is not what the No Free Lunch theorems say. Regardless of the fitness landscape, some strategies will perform better than blind search and others will perform worse. What the NFL theorems say is that no strategy will perform better than blind search over all possible fitness landscapes.

    Clearly, we are doing better then random sampling.

    Yes, and the NFL theorems don’t provide a reason to be surprised at this. Once again, there is just one real world to which we have access. If the mechanisms we observe didn’t work in that world, we wouldn’t observe them in the first place.

    Are we just lucky? Is there some particular property in the way that the fitness landscape is generated that makes it produce more useable landscapes? These are the questions that need asking.

    Like I said above, you might be able to make a cosmological ID argument from those questions, but if you want to support the idea of ID in biological evolution, the NFL theorems aren’t going to help you.

  86. 86

    Mustela,

    If the mechanisms identified by modern evolutionary theory were not capable of operating in the real world, we wouldn’t observe them. We do observe them. If your model says we shouldn’t, it is your model that is lacking.

    We most certianly do not observe them, that is precisely why evolutionary algorithms like Avida were conceived, because of the lack of observation in real time. Your argument strikes me as saying that simulation either way, for or against evolutionary algorithms, has no purchase on reality, but this would cut both ways, and render Avida et al useless and non-explanatory too.

  87. 87

    Clive Hayden at 86,

    We most certianly do not observe them

    Are you seriously asserting that we do not observe random mutation, genetic drift, and differential reproductive success in populations of real biological organisms?

  88. I’ve a problem with your mutation rates: what you describe as mutation rate μ isn’t what is observed when looking at the outcome of your algorithm – the effective mutation rate is just μ * (N-1)/N…

    You got the effective mutation rate right in your earlier paper Conservation of Information in Search – Measuring the Cost of Success ? where you looked at a bit string: here, you toggled a bit with rate μ, sensibly forbidding that a bit changes into itself.

    I think that this is the usual procedure.

  89. Are you seriously asserting that we do not observe random mutation, genetic drift, and differential reproductive success in populations of real biological organisms?

    Let’s ground this discussion in reality, shall we? You know he’s not saying that. We’re all fully aware of the real-life simplistic examples involving low information content. No one is every denying those and it gets quite tiring to see people like you refer to them constantly as if they end all discussion.

    We know that Natural Selection is the causal component of Darwinism. We can look at GAs, or evolutionary searches, and see that fitness functions do work when properly balanced (aka nature providing the oracle in the context of this paper).

    The problem is that Darwinists presume this balancing act and thus that natural selection is capable of operating uniformly. As in, for ALL targets in a search space there exists environmental factors capable of creating diversifying or directional selection to the extent that features become fixated within a population. I have no problem with the assertion that this works for SOME cases, just not ALL.

    The reason I think this is an issue is since selection usually relies on environmental factors (I say usually since there is artificial selection like with dogs). While some factors are generalized, some factors must be very specific in order for the funneling effect to work. What if, like with these peacock feathers, the factors are very rare or don’t even exist? That means that in order for Darwinism to work not only does Functional Complexity have to emerge it must be paired with a rare event that offers selective pressure.

    Now ID proponents don’t dispute the notion of stabilizing selection. They dispute the notion that there’s a kind of selection other than stabilizing selection that can operate successfully to the point of macro-evolution. This does not mean that selection in general does not happen per se (think finch beaks, blind cavefish, malaria, ice fish, etc.) but Berlinski would probably say it’s not special enough that should not warrant a separate categorization. Or at least that directional selection is exceedingly rare and can only operate under limited conditions/environments and thus for a very short amount of time (or at least it better be short lived…directional selection tends to decimate a population as was seen with the finches). Personally I’m fine with people making these categorical distinctions since they’ve only been shown to be capable of trivial changes.

    Now as I’ve pointed out before the major issue is that natural selection is essentially a funnel, and it must be balanced in order to function as an oracle that can produce results. For an example, a while back I had an experiment with a GA that performed word searches. Going from memory here, so short version is that there were multiple versions of the fitness function: a) pseudo-random search b) a function that attempted to emulate Darwinism c) a function that incorporated some active information about the target d) explicit directed front-loading. The target was less than 200 informational bits but only C and D were capable of finding it. The most difficult target at 360 informational bits required D.

    The point is that selection must be constrained and balanced long enough that the trait becomes fixated. The problem with the finch example is that once the environment changes back to normal the finch population also reverts back to being a mixed population based upon continuous variation. As in, the changes purportedly funneled by directional selection don’t stick (they are not fixated). Some Darwinists like to say that in order for such changes to fixate that the environment must be permanently altered as well. Well…in the finches case it’s apparent by their dwindling numbers that this might likely cause extinction of that population within that environment. Even if they did survive and the trait did fixate within the population it’s unknown whether the finches would permanently lose the ability to produce beaks of different sizes if the environment changed once again far off into the future.

    A Darwinist put it this way: “sufficient conditions for long-term improvement [and fixation, I might add] to be likely are quite complicated.” Tell me about it… Here’s an example with flying squirrels, which have numerous balanced morphological changes in order to properly glide.

    Dawkins speculated that falling from trees provided the environmental funnel. As in, death by falling acted as the oracle. How many squirrels died jumping out of trees before some of them found out that they were lucky enough to have mutant extra skin along with modifications to the spine and ligaments in order to allow them to glide? How many squirrels have to fall to their deaths for such a change to become fixated in the population? Do we have any data at all on deaths caused by falls or is it all speculation? The automatic tendon locking mechanisms of such creatures should keep most of the corpses of natural deaths up in the trees I would imagine. What environment would provide this selective pressure? Unfortunately for such speculations, ordinary squirrels have been observed to fall from great heights with little or no injury. So are we now forced to hypothesize a limited set of environments which may include trees that would regularly cause death by falling?

    The reason I ask all this is because evolutionary biology claims to have all this predictive power, so answering these questions should be easy. If this particular hypothesis (death by falling providing the environmental pressure; or the causal factor in nature that is the oracle) does not match reality what scenario is plausible? After all, there needs to some sort of plausible scenario since these traits are shared in divergent species and are supposed to be the result of convergent evolution.

    The fairly recent article HOW TO MAKE A FLYING SQUIRREL: GLAUCOMYS ANATOMY IN PHYLOGENETIC PERSPECTIVE (2007) makes the suggestion that since leaping distance scales with size that a smaller species would benefit more from gliding. So perhaps the selective pressure would be a smaller species competing with a larger species? Unfortunately, no data is provided for this hypothesis so we cannot evaluate whether this would provide enough selective pressure. It might be another peahen story-telling session… (if you don’t know what I’m referring to search UD regarding sexual selection)

    They also briefly mention that evolving from a ground-based ancestor would be unlikely, presumably because of the low positive selective pressure for gliding. But again, we’re back to the problem of needing regular directional selection in order to fixate these changes in the population. Also, in order for these changes to be beneficial in the first place they have to be balanced (look up that squirrel article to see just how balanced). And if they’re not balanced they’re unlikely to provide much benefit (it’s neutral) and thus will be lost.

    Having said all that, in general I don’t see an issue with unguided Darwinian mechanisms being capable of making these particular changes considering their “relative” simplicity and apparent modularity (then again, it may be front-loading) which “I” think “might” allow for a stepwise pathway. I just think it disconcerting that the focus of that recent article–which should represent the latest findings on this subject–seemed to be on making comparisons between samples. Neo-Darwinian mechanisms as the source of evolution were generally assumed to function, without any evidence of this being the case. The problems related to natural selection were never addressed. This is ironic since the article is entitled “HOW To Make a Flying Squirrel”.

    Now Darwinists almost always start with the assumption of simplicity giving rise to higher complexity (I say almost since there are plenty of examples of systems being broken yet providing a survival benefit in a particular environment). Some ID proponents present this alternate scenario: What if ALL of the original squirrels could glide? After all, it’s far easier to suffer a deleterious mutation, and the survival benefit from this particular feature is negligible in most circumstances. The same could be said of the bat, where some species have echolocation and others do not. What if the original bat had echolocation and then over time some divergent lines lost it? Now before anyone accuses me of being a YEC, which I’m not, while this scenario is compatible with YEC/OEC there could be ID-compatible front-loading hypotheses where the change program self-terminates at the final form and then deleterious mutations eventually occur. Of course, that would be specific to only one of the variants of front-loading hypotheses where the final form is completely preloaded instead of just a morphological matrix of viable components.

  90. We’re all fully aware of the real-life simplistic examples involving low information content. No one is every denying those and it gets quite tiring to see people like you refer to them constantly as if they end all discussion.

    The reason for that is simple. There are always ID proponents that claim that NO information can be created by evolution. See for example bornagain77:

    basically falsification boils down to no demonstration of any information generation from material processes whatsoever, (a fact which you will vehemently attack but alas you cannot produce any empirical evidence to the contrary)

    In fact, I went through just that very painful process of producing examples where information is actually produced… but alas, bornagain77 abandoned that discussion, rather than admitting that he was wrong. Because of those cases, you have to start by showing that ANY information can be created. Once that is established, you can move on.

    By the way, the supposed ‘second law of information’ states that information can only be created by an intelligence. How is that squared with your post?

  91. Part of the reason I rarely participate on UD now is because I feel like I’m merely repeating myself most of the time. And the Darwinists are repeating the same mistakes…sometimes from the same people.

    An old discussion from 2008 covers most of the tangential issues that this current discussion has missed so far:

    http://www.uncommondescent.com.....iterature/

    Besides the flying squirrel example here’s another example relevant to this new paper:

    “The indirect pathway is presumed to be composed of small changes since that is what is required by MET in order to reach long-range targets. And each step is considered independently in reference to the EF.

    For a specific example, the Explanatory Filter can take multiple types of inputs (which also makes it susceptible to GIGO and thus falsification). Two are (a) the encoded digital object and (b) hypothetical indirect pathways that lead to said objects. My name “Patrick” is 56 informational bits as an object. My name can be generated via an indirect pathway in a GA. An indirect pathway in a word-generating GA is likely composed of steps ranging from 8 to 24 informational bits.

    Let’s say you take this same GA and have it tackle a word like “Pseudopseudohypoparathyroidism” which is 30 letters and 240 informational bits. It can be broken down into functional components like “pseudo” (48 informational bits) and “hypo” (32 informational bits). Start with “thyroid” (56 informational bits). For this example I’m not going to check if these are actual words, but add “ism”, then “para”, and then “hypo”. “hypoparathyroidism” is a functional intermediate in the pathway. The next step is “pseudohypoparathyroidism”, which adds 48 informational bits. Then one more duplication of “pseudo” for the target.

    That may be doable for this GA but what about “Pneumonoultramicroscopicsilicovolcanoconiosis” (360 informational bits) or, better yet since it’s more relevant Dembski’s work (UPB), the word “Lopado­temakhoselakhogaleo kranioleipsanodrimhypo­trimmato silphiokarabomelitokatakekhymeno kikhlepi­kossyphophattoperisteralektryonopto kephalliokigklo­peleiolagiosiraiobaphtraganopterýgn” (1464 informational bits [which may have been corrupted in the database]). I’m not going to even try and look for functional intermediates.”

    To make it clear why this old example is relevant today, an oracle would be required for this english-based evolutionary search to function. The oracle in this case would be the function that recognizes valid parts of an English word.

    This oracle, which allows for simpler words to be reached, could be likened to the oracles which function in nature which also allow for simple targets to be reached. In my example a different category of oracle is required to reach the English word that’s 1464 informational bits. What kind of oracle is required for nature to do similar?

    At this point ID proponents would refer to ID-compatible hypotheses. Darwinists, apparently based upon this thread, are reduced to flinging insults and sniping at minor issues.

  92. hrun0815,

    1. I don’t know what discussion you’re referring to since I rarely visit UD nowadays. It’s possible you were talking past each other, with you referring to a basic definition of information (which can include noise) and bornagain77 was referring to CSI or FCSI. In that case imprecision in the usage of terminology would underly that discussion. I don’t know. But if bornagain77 was claiming that no type or category of information can be derived from “evolution” then he’d be mistaken.

    2. “By the way, the supposed ’second law of information’ states that information can only be created by an intelligence. How is that squared with your post?”

    Speaking of imprecise terminology…you’re referring to the “Law of Conservation of Information” which also refers directly to specified complexity (CSI) and not just “information” in a base sense. My first post in this thread was long. Can you specifically point out how it conflicts?

  93. Also, the LCI is was discussed here:

    http://www.uncommondescent.com.....formation/

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