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Evolutionary Informatics Lab website receives facelift

The Evolutionary Informatics Lab website has just undergone a major renovation, thanks mainly to our very own Atom and to Winston Ewert.

Evo Info Site

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34 Responses to Evolutionary Informatics Lab website receives facelift

  1. Well done.

  2. That is a very nice, friendly site.

    Well laid out with lots of info and very intuitive for a first-time visitor.

  3. Nice design ;-)

  4. The banner is especially gorgeous. :)

  5. Yup, the design is nice. But somehow an earlier comment of mine got lost…

    BTW: Could someone please have a look into the somewhat unusual use of the term mutation rate in your paper Efficient Per Query Information Extraction from a Hamming Oracle (mentioned by me earlier in this thread)?

  6. 6
    Sooner Emeritus

    Dr. Dembski,

    The errata page strikes me as an attempt to satisfy the letter of the law while neglecting the spirit of the law.

    If a published paper has errors, then why not correct the errors by adding footnotes to the digital copy disseminated online? If that is too much of a hassle, then why not add an errata page at the end of the paper?

    Evidently you insist on disseminating papers in precisely the format in which they were published. There is a separate webpage for each publication. If a paper has errors, why not note them on the webpage for that particular paper?

    Finally, there are more errors in “Conservation of Information in Search: Measuring the Cost of Success” than you have acknowledged. You and Prof. Marks have been alerted to four mistakes in mathematical calculation. As you know, they appear here in RationalWiki. I understand your reticence in citing that particular source. But we all find ourselves in binds at times.

    Incidentally, I believe that the RationalWiki author went there largely because it was hard to display mathematical expressions on his blog. If you write up mathematical errata in LaTeX, the question arises again as to why you would not add an errata page to the digital copy of the paper.

  7. Thanks to those who complemented the design.

    I’d like to highlight the fact that the lovely 3D DNA models were created by UD’s very own Apollos, the Blender wizard. He created it for an unrelated project, but I’ve found additional use for it on the EIL.

    SoonerE,
    As the designer of the site, I will take blame for any unusual layout decisions. There is a per paper errata coming, in addition to the site-wide errata page. As is mentioned on the site, this is just a first phase roll-out with additional fixes and upgrades being included as I find time for them.

    Atom

  8. DiEb,

    Sorry we haven’t addressed your comment, revamping the website has taken my focus lately.

    You are quite correct to point out the difference between the effective mutation rate and the parameter mutation rate. However, I think the parameter mutation rate is the one best used in this circumstance. We are interested in how an agent, such as Dawkins, might have constructed the algorithm. From that perspective we are interested in the numbers he put into the code not the measurement of the outcome of that process.

  9. Well, it doesn’t seem to be the usual definition (cf. Thomas Bäck: Evolutionary Algorithms in Theory and Practice, pp 198-232 – the first source of your paper). And you are not consistent with the previous paper: Conservation of Information in Search. The majority of agents seem to construct such algorithms with the effective mutation rate in mind.

  10. Sooner and DiEb,

    May I suggest you take a brief vacation from nitpicking at the EIL and direct your analytic skills to other concerns where your talents are needed more desperately (such as fraud in climate data). Unlike climate scientists, we are committed to truth and transparency. Also, unlike them, we do this work on our own time, without government funding.

    Your concerns will get addressed in due course.

  11. Dear Dr. Dembski,

    as you are committed to truth and transparency, I thought you would welcome my critique – I resent the characterization of nitpicking, though I mention minor errors, too…

    As I’m doing this in my own time, too, I’m able to choose the area of my concerns.

  12. 12
    Sooner Emeritus

    Atom,

    There is a per paper errata coming, in addition to the site-wide errata page. As is mentioned on the site, this is just a first phase roll-out with additional fixes and upgrades being included as I find time for them.

    Greater transparency, to borrow Dr. Dembski’s term, would be achieved by listing errata on the webpages for the papers in which they occur. It happens that this would also simplify the EIL web.

  13. Sooner E,

    While I’m sure you had good intentions with your idea that adding additional content to the individual publication pages would simplify the “EIL Web”, it does not simplify my life as a programmer. The relative ease of creating a new page (in HTML) rather than modifying a dynamic page heavily guided my decision in this first iteration.

    The errata will most likely be cross-linked in the future. As I said before, the site is a work in progress.

    Atom

  14. 14
    Sooner Emeritus

    Dr. Dembski,

    It happens that I do regard the errors in calculation as nits on a contortionist elephant:

    Conservation of information theorems indicate that any search algorithm performs, on average, as well as random search without replacement unless it takes advantage of problem-specific information about the search target or the search-space structure.

    It takes more pages to disentangle your polymorphous misunderstanding of past work than are in “Conservation of Information in Search.”

    However, the fact that four nits of miscalculation inhabit a single section of an article by “the Isaac Newton of Information Theory” is of some interest. It is much easier to show people with a modicum of mathematical literacy that you’re not careful with your math than to explain to them a) the so-called “conservation of information” theorems and b) your misunderstanding of those theorems.

    So I say, more power to DiEb. It clearly takes him very little time to find errors that have eluded you, Prof. Marks, and your reviewers in the IEEE Systems, Man, and Cybernetics Society.

  15. 15

    DieB,

    Unless I’ve missed something. You are comparing two different scenarios. The two sources you cite are both dealing with bitstrings, binary strings. Here we are dealing with strings from a larger alphabet. Binary strings will have the effective and parameter mutations rates be the same thing.

    For a bitstring, the coder might do:

    for(int bit = 0; bit mut_rate) data ^= 1 << bit;

    In that case the effective mutation rate will be the same as the parameter mutation rate.

    In the case of a larget alphabet a coder will probably do:

    for(int letter = 0; letter mut_rate) string[letter] = random_letter();

    Its much more complicated to avoid replacing a letter with itself then it is to avoid replacing a bit with itself. In this case the effective mutation rate and the parameter mutation rate differ. Since our concern is with the parameters of the process, it makes sense (at least to me) to talk about the parameter mutation rate.

  16. 16

    Code got eaten by tag nastiness… Hopefully my point still makes sense.

  17. Sooner and DiEb,

    Since you are so concerned about errors, none of which impact the substance of the EIL’s papers (or have the IEEE referees been too lenient?), let me urge you to give us here in this thread a complete list of all of those that have not, in your view, been properly corrected or addressed. Please be very specific in terms of links, page numbers, and precise equations. Don’t just cite some other website.

    One of life’s little ironies is that in attributing error, one can in fact be committing an error. So perhaps your list of errors will be error free, in which case we will be grateful to you. But perhaps you are mainly blowing smoke.

    So, if you will, a complete listing of all the errors you’ve found …

  18. 18

    Dr. Dembski,

    I just rechecked DiEb’s corrections of your errors. He is right, and you are wrong.

    Prof. Marks has already maneuvered to get feedback by personal communication, evidently to avoid citation of sources he does not like. Thus I’m reluctant to give you a source other than RationalWiki to cite. If you agree first that you will cite the RationalWiki article, and not my comment on this blog, I will post a LaTeX enumeration of the four errors in calculation, along with a succinct explanation in plain language of how you’ve gone wrong.

  19. Dear Dr. Dembski,
    it’s Skitt’s law which states something like “any post correcting an error in another post will contain at least one error itself”. So, while I’m confident that my list is correct, there may be an error in it. But perhaps you could correct it, and we’ll converge to an ultimately error-free version of the paper?

    The format of UncommonDescent doesn’t allow for a display of mathematical expressions, so I put the list here.

  20. Sooner and Dieb,

    I know you think embarrassing Drs. Dembski and Marks somehow helps prop up your Neo-Darwinian worldview or whatever it is.

    But alas your unwittingly vociferous pedantry,like a wolf at wits end, is just morphing you into an annoyingly puerile yapdog.

    Hey, but if that’s what floats your boat…

    Eh, keep up er, the good work. And I mean that.

  21. Dear Dr. Dembski,

    essentially, it’s the same list I sent to you (info AT designinference.com) and Robert Marks (Robert_Marks AT baylor.edu) in an (unanswered) email on Oct 17, 2009. How time flies! Or as you put it Your concerns will get addressed in due course.

  22. sooner and dieb,

    And exactly why are evolutionists reduced to squabbling over the power of computer simulations to generate functional information of such a trivial level ? Is not it because we can find no examples of the material processes in the real world generating information?

    The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.
    http://www.mdpi.com/1422-0067/10/1/247/pdf
    http://mdpi.com/1422-0067/10/1/247/ag

    Now please be reasonable sooner and dieb, you guys are here on this site arguing the absurd position that purely material processes “within the evolutionary program that was designed by a intelligent programmer” are solely responsible for generating this paltry sentence ’ “METHINKSITISLIKEAWEASEL”. And do you care to tell me exactly why evolutionary algorithms are not writing the computer programs themselves since:

    “Human DNA is like a computer program but far, far more advanced than any software we’ve ever created.”
    Bill Gates, The Road Ahead, 1996, p. 188

    Why is this? If evolution is such a powerhouse that it can easily generate the massive amounts of complex functional information we witness in all the life around us, with, as far as we can tell from the fossil record, scarcely any experimentation into radically novel structures from a base structure, why is it that Bill Gates does not have millions of random number generators and selection software set up to generate “more highly evolved” forms of software? Don’t you guys find this even a little bit suspicious? Why should you be so stubborn as to deny what is obvious? Really, is your worldview, that you ultimately came from a mudpuddle that important to you, that you are reduced to arguing for the absurd? What in the world is the payoff for you to do as such?

    further notes:

    A review of The Edge of Evolution: The Search for the Limits of Darwinism
    The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155). http://creation.com/review-mic.....-evolution

    Richard Dawkins’ The Greatest Show on Earth Shies Away from Intelligent Design but Unwittingly Vindicates Michael Behe – Oct. 2009
    Excerpt: The rarity of chloroquine resistance is not in question. In fact, Behe’s statistic that it occurs only once in every 10^20 cases was derived from public health statistical data, published by an authority in the Journal of Clinical Investigation. The extreme rareness of chloroquine resistance is not a negotiable data point; it is an observed fact.
    http://www.evolutionnews.org/2.....est_s.html

    An Atheist Interviews Michael Behe About “The Edge Of Evolution” – video
    http://www.in.com/videos/watch.....34623.html

    The NCSE, Judge Jones, and Bluffs About the Origin of New Functional Genetic Information – Casey Luskin – March 2010
    http://www.discovery.org/a/14251

    It should be noted that evolutionists like to play head games with Claude Shannon’s broad definition of information since “non-functional” information bits may be considered information in his broad definition, yet when looked at carefully, Shannon’s work actually fully supports Intelligent Design as is illustrated in the following video and article:

    DNA and The Genetic Code Pt 3 – Perry Marshall – video
    http://www.youtube.com/watch?v=FtMQUFOwEFo

  23. Sooner,

    Robert Marks is the corresponding author on the papers in question. It is appropriate for him to be the contact person for DiEb and anyone else about them. That said, I’m not sure where you’re getting the impression that Prof. Marks has made any concessions to DiEb. Is DiEb himself suggesting to you that major retractions are on the way? I meet with Prof. Marks weekly and the impression I get from him is that you all are not to be taken very seriously.

    By the way, what exactly are your qualifications? Bob Marks is world-class in the field of computational intelligence (which includes evolutionary computing). Do you care to dispute this? How do your publications stack up with his?

    It seems to me that you confuse two types of errors. There are what you regard as misconceptions on our part about evolution. From our vantage, you are the ones with the problem of misconceiving. Then there are the straight-up mathematical/arithmetic errors (like an exponent being too large or too small). The latter errors are easily correctible and in no way undermine the conclusions we draw.

    I’ve opened this forum for you to lay out both types of errors. You prefer simply to cite a long messy response that takes our paper without permission in full and then intersperses comments.

    Having raised the charge of error, you now seem unwilling here to enumerate them. Another insulting post from you here in which you blow smoke and avoid specifics, and who knows, you may need to find another forum…

    Oh, was that a threat?

  24. Dear Dr. Dembski,
    does it make sense to comment while my previous two comments are still held in moderation? Well, I’ll try:
    1. I have not conferred with Sooner Emeritus. However, Rob Marks told me that he preferred an email conversation over entries on blogs and wikis. Nevertheless, I carry on commenting on UD – and rationalwiki
    2. I don’t know whether there are concessions made to me, or whether there are major retractions on the way. Sadly, Rob Marks never addressed the content of my concerns to me directly. But if you are talking about The Search for a Search, I can only hope that the Horizontal No Free Lunch Theorem – if it still exists – and its proof will look considerably different in the upcoming publication from the one in the draft.
    3. Here, I’m talking only about a couple of minor mathematical errors in Conservation of Information in Search, errors which could have been correct much earlier.
    4. Generally, I have no problems with the conclusions you draw within your papers. Mostly, I can’t follow the statements about your papers as made in the podcast with C. Luskin (something like: driving a nail in the coffin of Darwinian evolution – I don’t know whether I understood that absolutely correctly), and in the announcements here at UD (deconstructing Dawkins’s weasel)…
    5. A concise list of these minor errors is just one click away.

  25. I do not understand the complaint by Sooner Emeritus. He says he has corrected four mistakes and has noted them on his website. But when I went to the link I found only one item marked as an “error.” I do not know enough math to understand it. Since the page is a Wiki much like Wikipedia, it has a “history” and a “talk” page attached. I tried to find the list and found it has been mistakenly put on the talk page. He claims the errors are here.

    But I yet do not understand. Two of the four “errors” look like the same text to me.

  26. sooner, looked over your corrections,
    From the impression I get from the extremely confident comments on the page, it seems you guys have all the kinks worked out for evolutionary algorithms. As well, I surmise you guys, from your overly confident manner, have now clearly elucidated how to get massive amounts of functional information from nothing but purely material evolutionary processes within a simple computer program that can be easily designed by a single competent software engineer (atom are you listening?). I will admit I was skeptical at first at such a astonishing breakthough as you were claiming in foundational mathematics (indeed I feared for your sanity at such grandiose ravings as to have solved such a monster problem of generating novel complex functional information from purely material processes), but who can argue with such solid proof as you have now presented on such a impeccable source of rationalwiki (I’ll skip over seeing an actual demonstration for the generation of massive amounts of functional information since I know you would not neglect such a important thing as actually proving what you claim can happen actually can happen). Seeing as all you have left to do is dot some i’s and cross some t’s, I will make my rounds to the various ID websites and tell them to shut their doors as it is all but over now. I will also notify Bill Gates so he can set up your ingenious solution to his massive problem of designing better computer programs and fire his thousands of software engineers. You don’t mind if I put you in for a Nobel while I’m at it do you?,,, Or maybe, on second thought, I better just sit back and listen to this song:

    Fantasy – Earth, Wind & Fire
    http://www.youtube.com/watch?v=mjxdmsXzwmQ

  27. 27

    DieB,

    Thanks for the corrections, and thank you for putting them in an easily accessible format.

    1. I think you are correct, although for consistency it might make more sense to flip the fraction.
    2. Again you are correct, we have lost the negative.
    3. I don’t see your point. Numerical evaluation gives me the same results before and after that step (adjusting for the missing negative you pointed out.)
    4. This appears to be a consequence of three.

    Again, thanks for the errors. I’ll make sure it is put up on the site with proper references once we have that section ready on the site (which will be when me and Atom finish writing it)

  28. 28

    DieB,

    I think I see your problem with (3) now. The actual problem is introduced in the previous equation, not the one you show.

  29. Excellent job, as usual, Atom.

  30. Dieb:

    But if you are talking about The Search for a Search, I can only hope that the Horizontal No Free Lunch Theorem – if it still exists – and its proof will look considerably different in the upcoming publication from the one in the draft.

    If the EIL hasn’t realized that the Horizontal NFL is fundamentally nonsensical, hopefully they will do so before the paper is published. Far from nitpicking, this error is significant, and it illustrates a few cautionary points:

    1) Peer review is only as reliable as the reviewers. (Recall that the Search for a Search paper was accepted for publishing.)

    2) As several critics have pointed out, Dembski’s concepts, both old and new, are more clear when stated in terms of probability than in terms of information. It’s too easy to be misled by connotations of terms like active information, which apparently led the EIL to come up with their mistaken concept of active entropy. When restated in terms of probability, some of the EILs statements turn out to be trivial, or even tautological, and we see that the EIL’s NFL-based ideas are inapplicable to empirical questions like ID vs. MET.

  31. 31
    Sooner Emeritus

    Winston Ewert,

    DiEb left out of the synopsis the error in line 7. Here is the plain-language gloss I promised:

    DiEb identifies in his article an expression in which active information is negative, when it should be positive. He also shows that D&M have a negative number of queries for a perfect search. When D&M divide the endogenous information by that number of queries to get the average active information per query, they preserve the sign error, and also lose track of a factor of 2. The factor-of-2 error propagates to their next expression, but they evidently detected the sign error with a sanity check, and eliminated it.

    I was not counting the numerical error that DiEb identifies. There are a total of five errors.

  32. 32
    Sooner Emeritus

    P.S.–The “lost” factor of 2 is a missing factor of 1/2 following the division.

  33. Dear Dr. Dembski,

    I meet with Prof. Marks weekly and the impression I get from him is that you all are not to be taken very seriously.

    Does this mean that the paper A Search for a Search will appear as drafted? And who is you all?

  34. Judging from the fact that – after a year of contributing to this site – I’m still hold in moderation, I have to assume that I’m classified as Potential Trouble. That’s unfortunate, but I can’t see what I can change about it, as I’m an ID-critic.

    However, I would see it as a courtesy if the moderation process could be accelerated a little bit: In a discussion, it’s a little bit annoying if a comment doesn’t appear for over fifteen hours…

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