We’re not in Kansas Anymore

_{Clive Hayden

April 7, 2010

Education, Intelligent Design}

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I hesitate to bring attention to a blog, called Thoughts from Kansas, written by Josh Rosenau (a grad student completing a doctorate in the department of Ecology and Evolutionary Biology at the University of Kansas), because I don’t think it makes accurate arguments and doesn’t deserve to be promoted, even in a rebuttal. The blog amounts to inaccurate, prideful digs at ID and reminisces over a paper he wrote pertaining to what he perceives are the legal and social histories of Intelligent Design:

The paper’s title, “Leap of Faith: Intelligent Design after Dover” is a reference both to the chalky cliffs of the English Channel, to the town in which ID itself took a fall, and to the politically and economically suicidal effects of pushing creationism into public schools. Along the way, I was able to work in some other subtle digs at ID, including this summary of the recent history of the ID movement…

Way to work in subtle digs, it’s obvious he’s an unbiased academic who is only concerned with presenting the truth. Of course, ID has no basis in creationism, it is not concerned with any holy writ as a guide to its discipline. I’ve never read anything about “specified or irreducible complexity” in any sacred text nor encountered them in any religious observance.

William Dembski, once heralded on a book jacket as “the Isaac Newton of Information Theory,” has been reduced to rewriting and analyzing toy computer programs originally written for a TV series and popular books in the 1980s by biologist Richard Dawkins as trivial demonstrations of the power of selection. Dembski explained his poor record of publication in peer-reviewed scientific literature by saying, “I‘ve just gotten kind of blasé about submitting things to journals where you often wait two years to get things into print. And I find I can actually get the turnaround faster by writing a book and getting the ideas expressed there. My books sell well.” Alas, they don‘t convince mathematicians of his mathematical arguments…

Apparently Rosenau isn’t aware of the peer-reviewed IEEE publications from Drs. Dembski and Marks, Winston Ewert and George Montañez originating at their Evolutionary Informatics Lab:

Efficient Per Query Information Extraction from a Hamming Oracle “Winston Ewert, George Montañez, William A. Dembski, Robert J. Marks II”

Conservation of Information in Search: Measuring the Cost of Success “William A. Dembski and Robert J. Marks II”

Bernoulli’s Principle of Insufficient Reason and Conservation of Information in Computer Search “William A. Dembski and Robert J. Marks II”

Evolutionary Synthesis of Nand Logic: Dissecting a Digital Organism “Winston Ewert, William A. Dembski and Robert J. Marks II”

And Dr. Dawkins’ toy needed to be exposed as a farce, because a farce doesn’t illustrate anything except by deceit, and deceit is not an illustration. And alas, the Oxford mathematician John Lennox endorses Dr. Dembski’s mathematics. If you want to write a legal paper for the “lawyerly set”, at least get the story right. The rest of the paper is much of the same, a kind of disconnected cluster of arguments that reads like a brainstorm (concerned with quantity of arguments over quality), that could only persuade the uninformed.

Comments

Mr Ewert, No. The hamming distance measures the distance from my position to a target. As Dawkins himself pointed out that is emphatically not what is going on in nature. Relative reproductive success is way different then measuring how close I am to a target. Great, I think we all agree that a paper criticising Weasel on the basis of its Hamming fitness function has focused on the least relevant part of Dawkins' trivial example of cumulative selection. The success of *-ES algorithms or FOOHOA is not based on any “specialness” to the algorithms. The success must be credited to the abilities of that oracle. I have to disagree. ES and other EA would still work better than random generate and test even in the presence of very noisy fitness functions. The specialness of these algorithms is their simplicity and how they model aspects of biological reality, not the particular fitness function of a specific problem.Nakashima_{April 12, 2010
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A usually, I'm not glad with the way the word information is used, and I don't think that the definition of active information is very helpful, as it only looks at the size of an underlying set Ω but not on the functions - which are generally in the focus of the NFLT.: We have seen that the char. functions of one certain element and the Hamming distances to a certain element both form classes of functions of size |Ω| Have a look at a third set of functions of size |Ω| which I will call eben's spoilers: Enumerate the N^L elements of Ω and define the function set of functions es(ω,φ) by es(ω,ω) = 0, es(ω,φ) = #ω if ω ≠ φ So, es(ω,...) tells you either: you found the value or you didn't find the value, but it is... . A "search" on this set of functions can be completed in one step - I suppose that's the optimal set of functions when you make a search. Obviously, this set of functions isn't c.u.p. (a minimal c.u.p. set of functions including the es(ω,...) would have (N^L)^2 elements - not that many in comparison with all functions on Ω taking values 0..N^L)DiEb_{April 12, 2010
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Mr. Ewert, are you under the impression that your "Hamming Oracle" paper published in the IEEE symposium proceedings was peer-reviewed? If so, please explain how the peer review process for symposium proceedings differs from the peer review process in mainstream scientific journals. Thank you.PaulBurnett_{April 11, 2010
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Nakashima-san, Take the next step. Is a Hamming distance oracle an apt model for the biological process of relative reproductive success?
Assuming not, then neither is Dawkins Weasel, worse, Dawkins WEASEL is maketed as how a blind watchmaker would work. The idea is to show how much info the oracle needs to make it perform better than blind search. Without that info, it is blind, and so will WEASEL be blind, and so will Darwinian selection in the wild. That means without an informed source to form the fitness function in the wild, Darwiniain evolution in the wild will not resolve structures that are likened to login/password pairs, and there are many such systems in biology like that. Consider that an un-informed hamming oracle will not solve the passwords to any given computer system. Similar problems emerge in biological systems where the fitness function must somehow have resources and foresight to resolve a password like structure.scordova_{April 11, 2010
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Is a Hamming distance oracle an apt model for the biological process of relative reproductive success? No. The hamming distance measures the distance from my position to a target. As Dawkins himself pointed out that is emphatically not what is going on in nature. Relative reproductive success is way different then measuring how close I am to a target. The problem is generally posed as: find the minimum of an unknown function f, knowing that f belong to a class of functions F. Yes, but by restricting F to some subset of all possible fitness functions I have gained some prior knowledge about the fitness functions I will actually have to optimize. That way I can gain performance in the functions I am interested in by reducing performance in the functions that I will never have to optimize. But doing so requires that I somehow know how the set is restricted. Picking F as a random subset of all possible fitness functions will probably produce a non c.u.p. set. So I can almost certainly find a better then random algorithm on that set. The problem is that knowing that F is a random subset does not help produce a smart algorithm. I need to know what is in F. In order to construct a better search algorithm, I need to know.WinstonEwert_{April 11, 2010
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Winston, Mustela Nivalis was a sock puppet that I have banned twice before, so this makes a third time.Clive Hayden_{April 11, 2010
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cumulative selection does work far better than blind search.
Not if the fitness functions are blind to the target. :-) Thus the "blindwatchmaker" hypothesis is not aided by WEASEL or any similar simulation. It's is therefore an illegitimate and misleading simulation clouding scientific understanding. The IEEE papers are helping set the record straight.scordova_{April 11, 2010
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Mr Ewert, The success must be credited to the abilities of that oracle. Take the next step. Is a Hamming distance oracle an apt model for the biological process of relative reproductive success?Nakashima_{April 11, 2010
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Suppose that I am given a fitness function from an unknown source and am asked to perform a search on it. The problem is generally posed as: find the minimum of an unknown function f, knowing that f belong to a class of functions F. Under the usual assumptions - i.e., everything is finite - there are more possible classes of functions F which are not c.u.p., than those which are c.u.p - so, generally it does make sense to look for an algorithm which works better than random search.DiEb_{April 11, 2010
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The NFLT are formulated for sets of functions which are closed under permutation. The set of characteristic functions of single elements on the set Ω is such a c.u.p. set - so, you can't outperform random search if the only values you get from your oracle are found and not found. The set of the functions of Hamming Distances to the elements of Ω is of the same size as the previous set, but it isn't c.u.p. So, the NFLT doesn't apply.DiEb_{April 11, 2010
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Mustela Nivalis, Our posts were hitting a variety of issues in each go, do you mind if I try to focus on one at time? Firstly, we should make sure that we have the same understanding of the No Free Lunch theorems. The actual theorems state that for any given performance criteria the distribution of values from that criteria are independent of the search algorithm when averaged over all possible fitness functions. The same is not true if we restrict or otherwise bias the set of possible fitness functions. For example, if we restrict the set of fitness functions to be only those functions that look like hamming distances to the target, we can clearly produce a much better algorithm as both WEASEL and FOOHOA demonstrate. Suppose that I am given a fitness function from an unknown source and am asked to perform a search on it. What are the implications of the NFLT? I can make no assumptions about the kind of function I am looking at. Under such a circumstance, the best I can hope for is to get the average performance. However, as NFLT shows this is independent of the algorithm chosen, so it doesn't matter what algorithm I choose. (It should be noted that in real life I may well be able to assume that certain types of problems are more common then others and use this bias to my advantage. But in that case I have some sort of information about the problem. I am assuming here that I have no such information) Do our understands align?WinstonEwert_{April 11, 2010
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Our intent was not to make arguments about the relative efficiency of hamming string extraction algorithms. The intent is to show how powerful the hamming oracle is. The different algorithms have different levels of success in extracting that information, but the oracle is shown to be very powerful. FOOHOA is very good at extracting the information from the oracle thus demonstrating how much information is available. The success of *-ES algorithms or FOOHOA is not based on any "specialness" to the algorithms. The success must be credited to the abilities of that oracle.WinstonEwert_{April 11, 2010
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WinstonEwert at 24, "the weasel algorithm knows, cumulative selection does work far better than blind search." But why? It's nice to see you back on the blog, Winston. What I was trying to determine in my conversation with scordova is why he was claiming that Marks and Dembski had made some sort of "case" against Dawkins' algorithm. Dawkins never claimed that it was more than a toy demonstration of cumulative selection, so there is no case to be made. That being said, your question is interesting on a couple of levels. Rather than repeat our previous conversation at: https://uncommondescent.com/evolution/new-peer-reviewed-id-paper-deconstructing-the-dawkins-weasel/ I suggest we continue from my comment 85 there. Make sense?Mustela Nivalis_{April 11, 2010
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Mr Ewert, But why? There are several key differences - the comparison of entities against each other as well as against the oracle, and the preference based on that comparison. These points make the weasel algorithm an apt model (in these aspects, at least) for nature. This is the only reason to be interested in it, not because of its efficiency. Criticising Weasel on the grounds of its efficiency entirely misses the point of its aptness. Nature is not efficient. A more efficient algorithm, can easily be a less apt model.Nakashima_{April 10, 2010
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the weasel algorithm knows, cumulative selection does work far better than blind search. But why?WinstonEwert_{April 10, 2010
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scordova at 22, "What is it that you think the Marks and Dembski paper shows?" That Dawkins Weasel wasn’t a blind watchmaker, but an intelligently guided watchmaker. The selection in Dawkins Weasel was anything but blind, but on the contrary, intelligently designed. Dawkins never claimed otherwise, so this is not a particularly interesting conclusion. Dawkins describes the purpose and limitations of his toy program just a page or two after describing the algorithm: Although the monkey/Shakespeare model is useful for explaining the distinction between single-step selection and cumulative selection, it is misleading in important ways. One of these is that, in each generation of selective 'breeding', the mutant 'progeny' phrases were judged according to the criterion of resemblance to a distant ideal target, the phrase METHINKS IT IS LIKE A WEASEL. Life isn't like that. Evolution has no long-term goal. There is no long-distance target, no final perfection to serve as a criterion for selection, although human vanity cherishes the absurd notion that our species is the final goal of evolution. In real life, the criterion for selection is always short-term, either simple survival or, more generally, reproductive success. If, after the aeons, what looks like progress towards some distant goal seems, with hindsight, to have been achieved, this is always an incidental consequence of many generations of short-term selection. The 'watchmaker' that is cumulative natural selection is blind to the future and has no long-term goal. As anyone who has implemented, or even simply played with an implementation of, the weasel algorithm knows, cumulative selection does work far better than blind search. That's the only pedagogical point of Dawkins' much abused toy program and it is not contradicted by the Marks and Dembski paper.Mustela Nivalis_{April 10, 2010
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What is it that you think the Marks and Dembski paper shows?
That Dawkins Weasel wasn't a blind watchmaker, but an intelligently guided watchmaker. The selection in Dawkins Weasel was anything but blind, but on the contrary, intelligently designed.scordova_{April 10, 2010
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The "Hamming Oracle" article by Ewert, Dembski, et al, was not published in a "peer-reviewed IEEE publication" - it was published in a collection of papers presented at an IEEE electrical engineering symposium, which had nothing whatsoever to do with biology. "Papers presented at the (symposium) appear in a Proceedings Volume..." - http://www.ssst-usa.org/ The term "intelligent design" does not appear in the article.PaulBurnett_{April 9, 2010
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Sal, I would like to contribute, but the moderation policy is quite tiresome: my last comment on this thread is now kept in moderation for more than two hours, while a comment at another thread is still waiting for approval after ten hours.DiEb_{April 9, 2010
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scordova at 20, It would seem then that the result is Dembski and Marks paper were not so much wrong, but understated their case. Had they dealt with the real weasel, they would have had an even stronger case against Dawkins. What case? Implementing the weasel algorithm defined in The Blind Watchmaker is a trivial programming exercise and all correct implementations show that the algorithm finds the target phrase. What is it that you think the Marks and Dembski paper shows?Mustela Nivalis_{April 9, 2010
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Now, you have lost me completely. What do you think is the case against Dawkins? Perhaps you should re-read the paper in question - it can be easily found at the EIL.DiEb_{April 9, 2010
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So, I’ll state for you and the record: partitioned searches will find targets better on average than the real Weasel
It would seem then that the result is Dembski and Marks paper were not so much wrong, but understated their case. Had they dealt with the real weasel, they would have had an even stronger case against Dawkins. They were thus too conservative in their critique.scordova_{April 9, 2010
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Thanks DieB.scordova_{April 9, 2010
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And now to elaborate: the partitioned search as described in the paper provided an quite uncommon fitness function, which not only gave the number of correct letters (L - HammingDistance), but the position of the correct letters. Dembski et al. then gave a stochastic algorithm for which I calculated the expected number of queries to be E[Q]≈N*H(L), (N: size of the alphabet, L: length of the word, H(k): k-th Harmonic number). In the same paper, they showed that there is a deterministic algorithm which uses N queries at most (it's rather the Hangman game). So, I'll state for you and the record: partitioned searches will find targets better on average than the real Weasel. or, to be more correct: there will always be a deterministic algorithm which finds the target with a lesser number of queries than the Weasel algorithm does on average.DiEb_{April 8, 2010
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fbeckwith:
Perhaps I am mistaken, but is it not the case that Richard Dawkins has never published in a peer-reviewed philosophy or theology journal even though his entire book, The God Delusion, is a treatise on theology?
Professor Beckwith, Have you read The God Delusion? It's not a treatise on theology, but a critique of theistic belief.
And if that is the case, then why isn’t that book treated with deeper suspicion and ridicule by those who claim that in principle, and not a consequence of ideology, they maintain the sanctity of peer-reviewed publications?
I'm not aware of anyone who claims that every non-peer-reviewed publication must automatically be treated with ridicule and suspicion. The criticism of Dembski (and other ID proponents) is not that they publish non-peer-reviewed books or articles; it's that despite claiming that ID is science, they have an extremely poor publication record in the peer-reviewed literature.
Also, why is peer-review good? Is it because it contributes to greater accuracy and a closer proximity to the truth? That seems correct.
Yes.
But such goods only make sense when we think of human beings has the sorts of beings that a proper end to which they ought to strive. But the notion of “proper ends” depends on the idea of final causes that these folks reject.
Not at all. If scientists want to approach the truth, then peer review is a good idea. If scientists wanted to avoid the truth, then peer review would be a bad idea. As it happens, they seek the truth, and so peer review is considered a good thing.pelagius_{April 8, 2010
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yes.DiEb_{April 8, 2010
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Dieb, Does the parititioned search perform better in finding the target than the real (Dawkins) weasel. Surely you can answer with a simple yes. A simple answer to help those less familiar with the subject. :-) Thanks in advance.scordova_{April 8, 2010
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Perhaps I am mistaken, but is it not the case that Richard Dawkins has never published in a peer-reviewed philosophy or theology journal even though his entire book, The God Delusion, is a treatise on theology? And if that is the case, then why isn't that book treated with deeper suspicion and ridicule by those who claim that in principle, and not a consequence of ideology, they maintain the sanctity of peer-reviewed publications? Also, why is peer-review good? Is it because it contributes to greater accuracy and a closer proximity to the truth? That seems correct. But such goods only make sense when we think of human beings has the sorts of beings that a proper end to which they ought to strive. But the notion of "proper ends" depends on the idea of final causes that these folks reject. In that case, what could be the grounds for suggesting that Bill Dembski has not fulfilled his proper ends? If it is that the entire scientific infrastructure is a social construction, then the enterprise is a useful fiction--like the rules of Monopoly or Stratego--and thus carries no normative weight. So, Mr. Rosenau, here's your assignment: come up with an intellectually persuasive way to defend your normative judgments based exclusively on efficient and material causes. Good luck.fbeckwith_{April 8, 2010
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Not necessarily because if the partitioned search performs better than Dawkins real weasel then a critique that demonstrates the insufficiency of the partitioned search will by implication demonstrate the insufficiency of Dawkins Weasel.
I don't follow this logic. And my argument is that the given rationale for the paper to be pro-ID doesn't hold any longer. Of course, there may be other arguments how this paper is still pro-ID, I just haven't heard those yet.DiEb_{April 8, 2010
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The partitioned search as described in the paper Conservation of Information in Search does need quite a different fitness function (or oracle, if this pleases you more) from the weasel, and all the algorithms described in the later papers. The real weasel doesn't find targets well - in terms of the number of queries necessary: Dembski et al. have shown in their last paper that there are deterministic algorithms which are way more efficient. In fact, if we understand the oracle/fitness function thoroughly, we may be able to construct even an optimal algorithm: that's what the Search for a Search is about, I think. The advantages of the weasel are the typical advantages of evolutionary algorithms: 1. it is easy to program 2. it is easy to understand 3. it gets results even when we don't understand the fitness functions completely (think TSP) As I said earlier: it isn't about being the theoretically fittest, it's about being the fittest present - the story of the two hunters, the bear, and the pair of running shoes springs to my mind...DiEb_{April 8, 2010
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