Home » Intelligent Design » A Search Algorithm, And A Prize

A Search Algorithm, And A Prize

There has been some discussion at UD about computational search algorithms, which is one of my specialties.

Just for fun, I’ve included some C source code here (as a .txt file), which is part of a research project. I’ll send a free set of my classical piano albums to the first person who runs the code and publishes the program output in the comments below, along with a correct guess as to what the ultimate purpose of the search algorithm is.

Please provide the following information: CPU clock speed and compiler used.

EIL members are not eligible.

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132 Responses to A Search Algorithm, And A Prize

  1. I know next to nothing, if anything at all, about C source code, but it’d be interesting to see your code come about via random variations and natural selection. Simply if only for the purpose of showing that it won’t come about via those methods. lol

    Good job though on the code, it looks fancy. lol

  2. factoring 523979429835916961

    nodes searched = 472, with 30 cutoffs.

    Time to factor: 1 milliseconds

    The hole is: 59699254
    prime factor #1 = 853043813, prime factor #2 = 614246797
    853043813 x 614246797 = 523979429835916961

    —————–

    My best guess is it prime-factors really big numbers really fast.

    I’ve no idea what “TheHole” is.

    CPU: Dual core 2.0 GHz AMD 64 X2
    MSVC++ 2008

  3. My best guess is it prime-factors really big numbers really fast.

    Correct. But the question is, Why would I want to do that? What would be the significance of factoring really big numbers really fast?

  4. Cryptography — key generation for comms or network security, or for testing key security?

  5. Compressing large streams of numbers?

  6. You’re generating RSA keys and TheHole is the coprime.

  7. 7

    factoring 523979429835916961

    nodes searched = 472, with 30 cutoffs.

    Time to factor: 0 milliseconds

    The hole is: 59699254
    prime factor #1 = 853043813, prime factor #2 = 614246797
    853043813 x 614246797 = 523979429835916961


    Intel Core2 Quad (2.4GHz)
    GNU C Compiler 4.3.2

    I don’t have any real guesses, I just wanted to try it. Could it have something to do with random number generation? Finding an effective modulus perhaps?

  8. 8

    You are trying to hack my credit card number that is supposedly secured by SSL encryption. :(

    I feel naked.

  9. tragic mishap: You are trying to hack my credit card number that is supposedly secured by SSL encryption.
    You guessed it! I’ll give tragic a prize.

    I’ll also give Apollos a prize for this: Cryptography, testing key security, RSA keys

    (Go here and you can find my e-mail info. Send me a mailing address and I’ll send you the albums.)

    For information on RSA encryption, factoring, and key security, go here.

    Here’s the relevance to ID: The security of RSA is based upon the difficulty of factoring large semiprimes (numbers that are the product of only two primes). A typical RSA key modulus is 1024 bits with two 512-bit prime factors. 2^512 is approximately 10^154, which is in the neighborhood of Dembski’s universal probability bound of 10^150. A blind search could never factor such a number. Factoring semiprimes of any significant size requires insight, planning, information, and intelligent design.

    If you discount comments, blank lines, and lines with only a curly brace, my entire factoring program is only about 115 lines of code. Here are some questions: How much time, and how much in the way of probabilistic resources would be required to evolve this program by random variation and natural selection, in a step-by-tiny-step fashion? Could this be done? What is the likelihood of improving it by randomly altering the code?

    Also note that the program is irreducibly complex, on many levels. Without the quicksort the binary search is useless. Without the binary search and the modulo divide operator the sieve won’t work. Without all of the above and much more, carefully orchestrated and properly timed, the tree search won’t work. All of the components must be in place simultaneously and functionally integrated.

    Of course, the program did evolve, but it did so by saltation and design. Each new version required the simultaneous altering of many components of the existing code, and the addition of new code. The implications concerning living systems should be obvious.

  10. On my drive out of DC yesterday, I passed the Puzzle Palace and the National Cryptographic Museum. Are your albums available to non-winners? iTunes?

  11. Are your albums available to non-winners?

    You can download them for free as MP3 files at my website, along with program notes.

    For those who are interested in cryptography, check out Simon Singh’s The Code Book. It’s a marvelously fascinating read. It was this book that got me interested in the field.

  12. GilDodgen “Of course, the program did evolve, but it did so by saltation and design. Each new version required the simultaneous altering of many components of the existing code, and the addition of new code. The implications concerning living systems should be obvious.”

    Can you expand on the implications please? It isn’t obvious to me!

  13. its been a while since I’ve looked at C code, and you didn’t have any pointers (*). I always like to throw a few of them in to keep anyone who was trying to update my code guessing…..

    you should move to C# or F#…you will be assimilated into the MICROSOFT EMPIRE…resistance is futile

  14. and yes my previous post was meant to start a programming language HOLY WAR…let the games begin…

  15. 15

    Hey Mr Jass, Gil may not be the brightest bulb when it comes to ID theory, but he is a polymath. He’s a great musician, adventurous hang glider and Harley biker. Don’t mess with him, Dude!

  16. Do we have a scot puppet?

  17. Apollos,

    On your machine the factorization should have taken a fraction of a thousandth of a second. Did you compile in debug or release mode?

  18. Gil, my bad. It was a debug build, the environment’s default configuration.

    Here’s the release output, which better matches your expectation…

    ———————
    factoring 523979429835916961

    nodes searched = 472, with 30 cutoffs.

    Time to factor: 0 milliseconds

    The hole is: 59699254
    prime factor #1 = 853043813, prime factor #2 = 614246797
    853043813 x 614246797 = 523979429835916961
    ———————

  19. Arthur Smith:

    “Hey Mr Jass, Gil may not be the brightest bulb when it comes to ID theory”

    May I dissent? I really think he is one of the brightest bulbs here!

    Very good post, Gil, and very good discussion. You #9 is exemplary.

  20. tsmith
    you should move to C# or F#

    My dear fellow, I did this at a very early age. My classical piano repertoire includes many works in both C# and F#, by many great composers, and in both major and minor keys.

  21. GSV:
    Can you expand on the implications please? It isn’t obvious to me!

    Check out DNA, mRNA, ribosomes, and protein synthesis. If the correspondence isn’t obvious, I can’t help you.

  22. Gil,

    Explain precisely how an extraterrestrial visitor, finding your source code etched in a stone on the summit of Mount Improbable, would assign high specified complexity to it.

    Better yet, give a mathematical definition of specified complexity that does not posit a pattern-recognizing entity that is itself of high specified complexity (the extraterrestrial visitor is an instance of Dembki’s semiotic agent).

    There is no way to infer that a text is a program, let alone a unique machine for which the text is a program. (For every text and every Turing-computable function, there is some universal Turing machine that, on input of the text as a program, computes the function.) And even if you are given a machine and a program, there is, under the Turing-Church thesis, and by Rice’s theorem, no algorithm to decide any nontrivial property of the function computed by the program.

    The upshot is that E.T. can say absolutely nothing about the purpose or function of your program. A string in the C language is no more revealing than a unary Turing machine description (e.g., a string of n dots indicating that a universal Turing machine should simulate the n-th machine in some recursive enumeration of Turing machines). Any analysis is limited to the text itself. (“Gee, Oolon, look at all them dots lined up in a row. What would do that?”)

    There are several fundamental reasons you are marveling over your program. First, you believe that you are a marvel. Second, you believe that the things you do are marvels in and of themselves. Third, you believe that anything as marvelous as you would marvel at what you do.

    Your program has neither intrinsic meaning nor intrinsic purpose. Only by telling us a great deal in a shared language about what you do with the program can you make it into something marvelous.

    Chimpanzees in the wild break twigs from trees, and then strip away the leaves. They push the stripped twigs into termite mounds, and pull them out slowly to catch termites to eat. For a fact, E.T. will not know that your program is a tool until he sees you use it. Beyond that, it is possible that E.T. will be only slightly more impressed with your program than with a stripped twig.

  23. Sal Gal — Explain precisely how an extraterrestrial visitor, finding your source code etched in a stone on the summit of Mount Improbable, would assign high specified complexity to it.

    The design is pretty evident. There is a pattern (brackets appearing at intervals, repeating symbols etc.) showing specificity, and the probability of them appearing by chance are exceedingly low.

    Granted, it may not be so easy to determine that it was a computer program.

  24. Check out DNA, mRNA, ribosomes, and protein synthesis. If the correspondence isn’t obvious, I can’t help you.

    The correspondence is not at all obvious. I can only guess that you cling to the outdated metaphor of the genetic program. “When the only tool you have is a hammer, every problem looks like a nail.”

    Hacking is not going to establish anything in ID. If you want to model certain biological processes as computation, you had best learn the fundamental results in the theory of computation.

  25. 25

    Tribune7

    The design is pretty evident. There is a pattern (brackets appearing at intervals, repeating symbols etc.) showing specificity, and the probability of them appearing by chance are exceedingly low.

    The same is true of stone polygons on the tundra (or Mars).

  26. The same is true of stone polygons on the tundra (or Mars).

    And would the probability of those stone polygons appearing on tundra be akin to that of Gil’s program being etched in stone?

  27. Sal Gal,

    All I can do is marvel at your sophistry.

  28. tribune7 (23):

    The program makes a pretty picture. What of it? The probability of looking around and seeing a pretty picture is high.

    Something funny about the ID obsession with the Weasel program is the oblivion to the context in which Hamlet says, “Methinks it is like a weasel.” On most days, in most places, you can look into the sky and match many patterns.

  29. All I can do is marvel at your sophistry.

    Why not exhibit the grace to ask for clarification of what you do not understand?

  30. Sal Gal –On most days, in most places, you can look into the sky and match many patterns.

    And how specific would they be? Is that a bunny or a giraffe?

    And regardless none of them would have a complexity anywhere near as high as Gil’s program.

  31. “Explain precisely how an extraterrestrial visitor, finding your source code etched in a stone on the summit of Mount Improbable, would assign high specified complexity to it.”

    They will probably use a similar, highly accurate and much more sophisticated type of design detection method, similar to ID’s.

    Explain how we would not assign CSI if we found a type of code unknown to us and unknown to what known natural phenomena can generate. If a code has known origins then design becomes obvious. If it doesn’t then we apply the method. Its a useful tool, one which resident Darwinians apparently still have a difficult time understanding.

  32. 32

    Has anyone ever noticed that Sal sounds just like Ray?

  33. Sal and all:

    I don’t know if an ET would recognize Gil’s program as a program ig he found it etched in stone. Maybe yes, maybe not. That’s not the point. The point is the “we” can recognize it as a program, because we have enough information about the context.

    And, in the biological world, the context is that we have programs running under our eyes. Why shouldn’t an ET recognize that an enzyme is performing its function? Or that the flagellum proteins are deviced to provide motion? In the same way, if an ET could observe Gil’s program running on a computer, and the outputs of his program in use in the right context, do you really think that they could not infer design?

    So, I do not just “marvel at your sophistry”. You know I admire it. But still sophistry it is.

  34. Sal Gal:

    Why not exhibit the grace to ask for clarification of what you do not understand?

    Sorry Sal, but trying to explain computational number theory to you would be as futile as trying to explain calculus to someone who can’t add fractions.

  35. 35

    tribune7 [30],

    Sal Gal –On most days, in most places, you can look into the sky and match many patterns.

    And how specific would they be? Is that a bunny or a giraffe?

    And regardless none of them would have a complexity anywhere near as high as Gil’s program.

    Sal Gal’s point, I believe, is that Hamlet and Polonius are engaging in a bit of design detection. They are imaginatively supplying designs that are not there — like, Sal Gal suggests, IDers in general.

    See the text here and search for “weasel.”

  36. Gal and Kellogg,

    Pardon my French, but you guys are just pissing in the wind.

    Send me some code. I’ve sent you mine.

    We’ll compare notes.

  37. 37

    Gil,

    “pissing” followed by “Send me some code. I’ve sent you mine”?

    Really? Are we dropping trou here? Or do such double entendres arrive naturally?

    No need to compare code. I’m pretty sure yours is shorter.

  38. What is trou? I’m not familiar with this word.

  39. 39

    trousers.

  40. Gil:

    Sorry Sal, but trying to explain computational number theory to you would be as futile as trying to explain calculus to someone who can’t add fractions.

    Go easy on him, Gil. We can’t all be computer/math experts and Evo Info Lab associates.

  41. LOL, David. I don’t know if a little gal like me can compete with the big boys.

    ROTFLOL, R0b. “Sal Gal” is the nickname of my favorite niece.

    You’re funny too, Upright BiPed. I sound just like the guy who invoked Rice’s theorem in arguing that the CSI of the function of a program is incomputable. Google, and ye shall find. Unlike the IDists here, I actually work with Dembski’s latest definition, not an amorphous feeling of “what CSI means to me.”

  42. Sal:

    “Unlike the IDists here, I actually work with Dembski’s latest definition, not an amorphous feeling of “what CSI means to me.”

    I think you know even too well that many of us actually work with a very clear and detailed definition of FSCI which, while being a little different from Dembski’s latest, is perfectly appliable to biology, and is as distant as possible from “an amorphous feeling of “what CSI means to me.””

  43. Gil:

    “Check out DNA, mRNA, ribosomes, and protein synthesis. If the correspondence isn’t obvious, I can’t help you.”

    I would like to point out this isn’t a very good way to get your message across, RTFM without even pointing out a manual is annoying.

    Here are your original questions about your program:

    “How much time, and how much in the way of probabilistic resources would be required to evolve this program by random variation and natural selection, in a step-by-tiny-step fashion? Could this be done? What is the likelihood of improving it by randomly altering the code?”

    Taking them one at a time:

    I have no idea do you? How could you calculate this? How does one measure ‘probabilistic resources’ for this program? What does evolve mean for non replicating streams of 1s and 0s? What is the means of evolution for this program? Does the environment, effectively the OS in the computer, change also?

    Artificially yes of course it easy to write some code that changes, say, one character at a time and then tries to compile the code, any compilation errors result in non fit code. Anytime the code does compile we have a fit program for some measure of fitness, by checking the output we could measure if it was fitter.

    Given an infinite amount of time and a measure of fitness after each random alteration that discards the less fit and keeps the most fit the likelihood is 1 you will get an improved program.

  44. gpuccio:

    “I think you know even too well that many of us actually work with a very clear and detailed definition of FSCI”

    There is a beach I saw on a recent BBC program called Coast called Chesil Beach. This is an 18 mile arc of steep shingle and at the western end (Bridgeport) there is fine shingle and as you travel east the shingles get larger until you reach Portland where we have stones that are fist sized.

    What is the FSCI of this beach? As I see it this beach has a high FCSI which is odd as this beach was not formed by an intelligent agent.

    Can you help me here?

  45. 45

    gpuccio:

    I think you know even too well that many of us actually work with a very clear and detailed definition of FSCI…

    It would be a kindness, sir, if you would provide that definition for those of us who need to be reminded.

  46. David –Sal Gal’s point, I believe, is that Hamlet and Polonius are engaging in a bit of design detection. They are imaginatively supplying designs that are not there — like, Sal Gal suggests, IDers in general.

    Sincere thanks for the lesson in Shakespeare but the analogy compares an ephemeral opinion to the concrete. You can’t falsify what one sees in the clouds. We can falsify descriptions of protein sequences and DNA, and we can falsify claims that only things of known design have the same traits as those of protein sequences and DNA.

  47. 47

    Gpuccio

    Yes please. I too have been asking what is FCSI. Is it a measrable quantity? What units? etc?

    An example or two to help us join up the dots would be helpful. For instance, can youmeasure how much FCSI there is in a molecule of the 9 amino acid polypeptide, oxytocin?

  48. 48

    tribune7:

    We can falsify descriptions of protein sequences and DNA, and we can falsify claims that only things of known design have the same traits as those of protein sequences and DNA.

    Do it!

  49. GSV, Adel DiBagno, Arthur Smith:

    Sorry to be late in answering.

    About FSCI.

    Just a summary, to begin (the subject has been debated many times, but I am ready to discuss any details you like). I will give a very restrictive and explicit definition, which can be applied to biology.

    We define FSCI any information which has the following characteristics:

    1) It is a digital sequence (IOW, it can be read as a sequence of digital values, like the sequence of the results of the tossing of a coin, or the sequence of nucleotides in DNA).

    2) It is functionally specified. IOW, the sequence, in the appropriate context which can read and use it, can convey the information necessary to realize a well recognizable function. For instance, a sequence of 0s and 1s (as can be read in the tossing of a coin, or any other system which can be read as a sequence of bits) is functionally specified if, say, it corresponds to some important mathemathical object, like pi, or to a sequence of bits which, when inputted in a specific computer, behaves as a functional software. Please note that the function must be explicitly definable, and the context is essential to define it.

    3) It is complex (unlikely), in the Dembski sense of the word. IOW, the probability of attaining that sequence randomly, in the system where the sequence is found, must be extremely low, lower than a threshold which can be conventionally defined in various ways, in different systems. The important point is that the threshold must be low enough to make the random hypothesis really unacceptable from an empirical point of view.

    The probability is meant as the probability of the functional set (all possible sequences which retain the defined function). If we can assume an uniform distribution, the probability is simply the ration between the number of functional sequences and the total search space.

    In order to keep the length of my posts acceptable, I would stop here for the moment. I want to remark that the above definition is relative to a very specific subset of the more general concept of CSI. CSI is a concept referring to “any” information which can be in “any” way specified. In my definition, I have given many additional restraints (the information has to be digital and not analogic, the specification must be of the functional type), because those restraints allow us to go with very simple, objective and quantitative definitions, and they apply perfectly to the object of our discussion (biological information). So, in the biological field, nothing important is lost by those restraints, and much is gained in clarity and objectivity.

    I will be happy of any comment or discussion on these points,, and then I would go on discussing the application of the above concepts to the quantification of FSCI in functional proteins.

  50. Oops! I am afraid I forgot one of the points which make the definition complete, and which has been well established by Dembski in his EF. I add it here:

    4) There must be no known procedure based on laws of necessity which can output that specific sequence in that system. IOW, the observed sequence cannot be explained by any known mechanism based on necessity.

  51. 51

    gpuccio,

    Thank you for your responses.

    No rush. Good work requires time.

    Now, would you be so kind as to respond to Arthur’s request:

    For instance, can youmeasure how much FCSI there is in a molecule of the 9 amino acid polypeptide, oxytocin?

    And if I wouldn’t be presuming too much, I would like to know how does ID deduce function given only a specific sequence?

  52. Arthur Smith:

    “An example or two to help us join up the dots would be helpful. For instance, can youmeasure how much FCSI there is in a molecule of the 9 amino acid polypeptide, oxytocin?”

    Well, while I wait for comments on the theoretical part, I would like to answer that just to jump to a practical application. I cannot answer your question with absolute precision (I would need to do extensive research to do that), so I will give an answer based on some assumptions, which can be true or not, but which can certainly be verified.

    1) We have to define explicitly a function for oxytocin, and to provide a measurement of that function and a threshold based on that measurement in order to define if the function is present or not in a specific system. Let’s assume, for instance, that we define as function the ability to determine a certain level of uterine contraction in a certain percentage of patients, at a certain dose.

    2) We have to know how many sequences bear that function according to our definition of it. To make calculation easier, I will give here another simple restraint: we will consider only sequences of the same length as oxytocin.

    3) The functional complexity of oxytocin will be the ratio of that number of sequences to the total number of sequences of that length. We assume here an uniform distribution of the random generation of aminoacid sequences in a biochemical system. That would require further discussion, but for the moment I will go on.

    So, if we assume that the only sequence of 9 aminoacids which retains the function as defined above is the molecule of oxytocin (which may be true or not), then the probability of oxytocin will be:

    20^-9, which is about 2^-27

    If we express FSCI as

    -log(probability)

    then the FSCI will be about 27 bits. (I apologize for my goofy mathematics, I hope the concept is clear enough).

  53. Adel DiBagno:

    As you can see, I did my homework before reading you request :-)

    You ask:

    “And if I wouldn’t be presuming too much, I would like to know how does ID deduce function given only a specific sequence?”

    I don’t know if I understand you question correctly. ID does not deduce function. We “observe” function in existing sequences. For instance, if we have the sequence of a protein in a genome, and we know from empirical observation that that sequence codes for a specific protein, and that that protein has a specific function, which we can observe in a specific living cell, then we say that the gene is a functional sequence.

    We have to give an explicit definition of the function and a threshold for it only in order to be able to quantify the FSCI, because we have to define quantitatively the functional subset. Obviously, our measurement will depend on our definitions, but given a certain definition, the measurement is explicit (although not necessarily easy).

  54. gpuccio,

    So, as I suspected, intelligent design is in the eye of the intelligent designer. Dembski has the sense at least to try to define specification in terms of restricted agents.

    Since the semiotic agents that formulate patterns to eliminate chance are finite rational agents embodied in a finite dimensional spacetime manifold (i.e., our universe), there are at most countably many of them, and these in turn can formulate at most finitely many patterns. Accordingly, the totality of patterns that S’s cognitive apparatus is able to distinguish is finite; and for all such rational agents embodied in the finite dimensional spacetime manifold that is our universe (whether it is bounded or unbounded), we can represent the totality of patterns available to such S’s as a sequence of patterns T1, T2, T3, … This sequence, as well as the totality of such agents, is at most countably infinite. Moreover, within the known physical universe, which is of finite duration, resolution, and diameter, both the number of agents and number of patterns are finite.

    I believe there is paradox, even in Dembski’s approach, because he gets compact descriptions from agents (each has a cognitive apparatus and is rational, though he eschews mention of intelligence) which must be of high CSI. He does, however, try to define the effect of a higher type of intelligence in terms of a lower type. It seems that you feel no compunction about predicating the existence of intelligent design from the get-go, and then setting intelligent designers loose to recognize intelligent design. You have only circularity and begging of the question — no definition.

  55. Sal:

    we have been here before. I can only answer you as I have always answered.

    1) It’s not me who am setting intelligent designers loose to recognize intelligent design. Intelligent designers, in the form of humans, have been there for a long time before I was born, and have always recognized intelligent design. Intelligent designers are an empirical fact, and not a philosophical abstraction. That’s, probably, why you don’t like them.

    But I suspect that you are an intelligent designer too, though in disguise as an intelligent deviser of abstract speculations.

    2) I have no circularity. And I do have a definition. My definition is empirical, and can be applied to empirical facts. You know, that’s what we do in science. I know you have not a high opinion of science, and we have many times shared common reservations about the extreme and blind faith in science which has polluted our culture, but as you probably know I retain a great respect for good science, and good science is what we are trying to do here. If you are not interested in that, I have not much to add.

    3) The definition is a definition. It is not circular. I have been accused of circularity many times about my definitions, but as soon as we go into details about where that circularity would be, no one has ever been able to show it. So please, as I have great respect for your intelligence, do try.

    The definition is not circular because it starts from empirical concepts, each one as explicitly defined as possible, and it defines a specific form of observable information. I suspect that you think that my definition has metaphysical implication, or that in itself it should be evidence of intelligent design. That is not true. My definition of FSCI is exactly what I have said it to be: a definition, and operational tool. It serves to be used in a more general argument, which I have not yet made on this thread. That more general argument is the basis for the design inference. And, if and when we arrive at it, you will see that it is not circular, too.

    So, to sum up: my definition is only a definition, a tool to recognize what complies with the definition and what doesn’t. The only critic you can do is to show that, as an empirical tool, it does not work: for instance, that there are empirical objects, of the form requested by the definition, which cannot be categorized according to the definition itself. If you can do that, please be my guest. And if you are still convinced that there is circularity in the definition, please show where it is. We are here to discuss.

  56. GP;

    I add that sometimes, function is structural or linguistic, though the algorithmic or data structure forms are the easiest to understand.

    In the linguistic case, as has already been repeatedly raised, say 143 or more ASCII characters in contextually responsive, more or less correct English would be a reasonable threshold for FSCI.

    A good structural case — and note, life for biology is “defined” in light of known major cases and family resemblance thereto [so much for the "that's woolly" and refusing to look at descriptive statements tied to key cases as yardsticks objections . . . -- would be a digital form of the specification for say a functioning stone arrowhead.

    This case brings out the observation side: arrowheads must be shaft-able, must not overbalance the arrow, and must nor derange flight [e.g. by being excessively asymmetrical or planing in the air]. On hitting say a deer they must be capable of crippling wounds.

    An arrowhead is not usually designed digitally, but the information is digitisable. And, the odds of a natural stone meeting the above criteria is utterly so remote as to be practically impossible, though logically possible. many shapes are possible of course, but hey will all fit into an island or at least an archipelago of function, even flu- flus for birds. [Birds being fragile you use a blunt ended arrow, often with a puff at he trailing end not normal fletching.]

    The island or archipelago of function is tiny in the sea of possible configs that are produced by natural forces of chance + necessity. but, archaeologists, professional or amateur, routinely identify arrowheads from natural stones of similar size.

    And, if we find an arrowhead on Mars, we will instantly recognise it form its functionally specific complex information linked to the achievement of an intelligent purpose.

    GEM of TKI

  57. PS: Chesil beach is great for kotching smooth hounds mon [just like the Palisadoes tombolo . . . see if you can spot where that is . . . which also has some shingling, can be great for jacks and the odd snook or two], but is a manifestation of beach dynamics [chance + necessity working on particulates or bigger fragments in a watery, wavy medium near land], not of FSCI. FSCI is about FUNCTIONING information, and shingle rocks are not driving algorithms, or expressing information in languages or functioning as a purposeful structure that requires precise and otherwise improbable specification of the elements and their relationships.

  58. gpuccio I appreciate the reply. A few questions for you:

    1) It is a digital sequence (IOW, it can be read as a sequence of digital values, like the sequence of the results of the tossing of a coin, or the sequence of nucleotides in DNA).

    Can you tell me what information can’t be encoded in bits as a digital sequence?

    2) It is functionally specified. IOW, the sequence, in the appropriate context which can read and use it, can convey the information necessary to realize a well recognizable function. For instance, a sequence of 0s and 1s (as can be read in the tossing of a coin, or any other system which can be read as a sequence of bits) is functionally specified if, say, it corresponds to some important mathemathical object, like pi, or to a sequence of bits which, when inputted in a specific computer, behaves as a functional software. Please note that the function must be explicitly definable, and the context is essential to define it.

    Who or what defines what is ‘important’? How would we know if something is important unless we know everything about it? For example is the fact that DNA is made up of 4 ‘characters’ important or merely an accident of design?

    3) It is complex (unlikely), in the Dembski sense of the word. IOW, the probability of attaining that sequence randomly, in the system where the sequence is found, must be extremely low, lower than a threshold which can be conventionally defined in various ways, in different systems. The important point is that the threshold must be low enough to make the random hypothesis really unacceptable from an empirical point of view.
    The probability is meant as the probability of the functional set (all possible sequences which retain the defined function). If we can assume an uniform distribution, the probability is simply the ration between the number of functional sequences and the total search space. .

    Can you calculate this for Chesil Beach? An 18 mile stretch of stones sorted by size.

    In order to keep the length of my posts acceptable, I would stop here for the moment. I want to remark that the above definition is relative to a very specific subset of the more general concept of CSI. CSI is a concept referring to “any” information which can be in “any” way specified. In my definition, I have given many additional restraints (the information has to be digital and not analogic, the specification must be of the functional type), because those restraints allow us to go with very simple, objective and quantitative definitions, and they apply perfectly to the object of our discussion (biological information). So, in the biological field, nothing important is lost by those restraints, and much is gained in clarity and objectivity.

    Can you give me an example of information that isn’t specified? Often it is a good idea to define something that doesn’t meet the criteria to understand the criteria better.

    4) There must be no known procedure based on laws of necessity which can output that specific sequence in that system. IOW, the observed sequence cannot be explained by any known mechanism based on necessity.

    What about unknown procedures? Before electricity was discovered lightening was the Gods doing battle!

  59. PS: Chesil beach is great for kotching smooth hounds mon [just like the Palisadoes tombolo . . . see if you can spot where that is . . . which also has some shingling, can be great for jacks and the odd snook or two], but is a manifestation of beach dynamics [chance + necessity working on particulates or bigger fragments in a watery, wavy medium near land], not of FSCI. FSCI is about FUNCTIONING information, and shingle rocks are not driving algorithms, or expressing information in languages or functioning as a purposeful structure that requires precise and otherwise improbable specification of the elements and their relationships.

    Can you show your working here please?

    One could argue that life is merely chemical dynamics to counter this assertion of yours, the only way to show this is wrong is to calculate the relevant FCSI.

  60. kairosfocus:

    I obviously agree with you on the points you raise. I have made it clear that I was giving specific restraints in my definition so that the discussion could be simple and explicit. I prefer to discuss digital information because analogic information poses different problems, and in the end we are interested here especially to genomic information, which is digital.

    Linguistic information is certainly a form of functional specification (the function is to convey a meaning in a specific language). But, again, genomic information, at least at the level of protein coding, which is the best known, is not linguistic, but conveys purely functional data (the primary structure of the protein). There is probably a linguistic aspect in the genetic code, but for the moment I am not dealing with it here.

    So, as you know, I always keep in mind the biologic model, because it is simple, clear and absolutely relevant to ID. But again, the definition I gave above is in no way universal, and is absolutely targeted to the biological-genomic context.

  61. 61

    gpuccio on the FSCI of oxytocin:

    …the FSCI will be about 27 bits.

    That lies well within the Universal Probability Bound of 500 bits.

    Does it therefore follow that oxytocin is not designed?

  62. 62

    gpuccio:

    ID does not deduce function. We “observe” function in existing sequences. For instance, if we have the sequence of a protein in a genome, and we know from empirical observation that that sequence codes for a specific protein, and that that protein has a specific function, which we can observe in a specific living cell, then we say that the gene is a functional sequence.

    Please forgive the ignorance that prompted my question. I was, and still am, struggling to understand what the concept of FSCI brings to science.

    I think a source of my confusion is not having a clear idea of the distinctions between FSCI and CSI.

    Would you be so kind as to delineate the differences? And explain the contribution of each to scientific progress?

  63. 63

    And I wonder whether the FSCI calculation for oxytocin yields a different value from the CSI calculation. If not, why not? If so, why so?

    That might help.

  64. Adel:

    First, I appreciarte that you are clearly a serious person, so I will take time to help.

    Go back to Orgel et al, 1973 on. [Cf the UD WACs and glossary.]

    that is, complex specification distinguishes biomolecules from crystals [high order] and random tars [random, non-functional sequences]. The specification in the original cases is of course both informational and in the context that these molecules do the work of life in the cell.

    CSI is actually a GENERALISATION from FSCI, i.e it asks about other kinds of specification and the underlying issue of specification in general. That is how we come to Trevors and Abel on three kinds of sequence complexity. It will help you to read this paper. And look very carefully at the 3-d illustrative graph:

    (i) orderly sequences are highly algorithmically compressible and show little complexity or algorithmic functionality: e.g. . . . DDDDDDDDD . . .

    (ii) random sequences are very incompressible algorithmically [you have to repeat them to get them correctly, e.g. the lottery winner combi], but are highly complex [take up a lot of bits to say them], and have low algorithmic functionality: e.g. . . . yhr6edbktyd . . .

    (iii) Functional sequences a re a bit less complex [languages have in them some redundancy], and are a bit less resistant to compression than random sequences [sometimes you can shorten the program] but are high on algorithmic function: . . . START, aa1, aa2, aa3, . . . ., aa100, STOP, express, fold, and presto you have Cytosine C, say for a frog. [I know I am leaving off important bits and pieces of the story]

    Now, too, we have bits as a unit of info capacity. We know that beyond 500 – 1,000 bits, the whole observed universe acting as a search engine is not going to be able to search at random or equiv enough of the configs to make it plausible that chance-based searches are able to get the high degree of contingency implicated.

    For oxytocin etc, you will need to ask wha tis the info capacity, and so fart we work on GP’s numbers, giving 27 bits of functional storage capacity — a short string length. So, we look at hat in context and say this part is too short for us to say on functional specification + complexity alone, IT is specifically designed.

    However, it works in a context 9funcitonality is like that: parts come together and work together to give a whole that functions], and that context has so many other units of high complexity and specificity, that we can see the whole is designed. It is likely that oxytocin is simply a small cog in the overall system.

    As to metrics of CSI, FSC etc, the point is that length has different units, which may for practical pur5poses say the same thing. Since FSC and FSCI are subsets of CSI, metrics to these will be metrics of CSI. The general metric proposed by Dr Dembski in 2005 is applicable, though a bit cumbersome. Durston et al have done a metric on FSC that looks at populations of functional proteins etc, and then uses the h metric of info theory to deduce a number of functional bits. beyond a reasonable threshold, we may infer that the search space is beyond reach of chance processes on the gamut of our observed cosmos.

    At a much simpler level, we folks here at UD have simply observed that we often use functional bits in our digital age. For instance the screen you are reading probably has 24-bit or more pixel colour depth [8 bits each R, g, B], and is probably far beyond 800 x 600 pixels [480 k pixels]; which together give a working bit capacity on tehorder of 111 mbits. Similarly, a DVD has 4.5 or so gigabytes.

    Now, just 1,000 bits opens up a config space of 2^1,000 or, over ten times the SQUARE# of the number of quantum states of our observed cosmos over its working life. |the observed cosmos working as a search engine could not sample enough of the space to make us confident that random searches could reasonably get to the shores of the islands of relevant function. But of course designers like us routinely generate that many functional bits and more.

    So, we have used a simple — non info theorist’s –rule of thumb for hte rest of us. if you see at least 500 – 1,000 bits,a nd you observe a specific function, and you see that his is not credibly a forced outcome, then the best conclusion is that this is functionally specific information of sufficient complexity that you can comfortably infer that the object manifesting it is designed.

    (The threshold is actually very — GP would for good reason say excessively — stringent. The number of C-atoms and other requisites of complex cell type life in our cosmos is a lot smaller than the number of atoms of H and He, and the habitable zones in which searching for e.g. first life could happen are a much smaller sector of the relevant spiral and barred spiral galaxies. Ellipticals are out, irregulars are worse out, and you have to be in a just right zone to have the heavy elements with enough “peace” to have long term environmental stability sufficient for life etc. 75% of atoms are H, and most of the rest is He. And the heavier stuff is not evenly distributed by any means. As to criteria for getting to life like ours on a planet suitable to support hat, the odds get longer and longer as we go along. And that is before you get to first life, which on reasonable amalyses will require 600 k bit6s or so of DNA style information, apart from the info stored in the structure of the cell — DNA is more a database than a computer.]

    Trust that helps.

    GEM of TKI

  65. Adel,

    Read a biology book. FSCI is the same thing as the central dogma or transcription and translation. It was one of the key insights by Francis Crick just after discovering the double helix. It led to the decoding of the DNA and amino acids. It is just making the analogy that this similar process happens elsewhere in language and computer programming. It was this analogy that led Crick to his hunch that what would be seen in genome was the same as was done in cryptography and language.

    Now when you see FSCI, think Central Dogma or language or computer programming. It is that easy.

  66. Adel DiBagno:

    kairosfocus has already answered some of your questions. Anyway, I will add my answer too (which is not essentially different), hoping that it may help. Let’s go point by point:

    “That lies well within the Universal Probability Bound of 500 bits.”

    That’s true. In my definition, you may notice that I have not given a threshold. I think the threshold should be chosen according to the context. While Dembski’s UPB is certainly appropriate for an universal approach to the problem of design detection, in the biological context I strongly believe that we could reasonably assume a more practical threshold: I propose something like 170 bits (a probability of about 10^-50). That should be more than enough for empirical purposes.
    Anyway, even with that threshold, oxytocin has a definitely lower complexity.

    “Does it therefore follow that oxytocin is not designed?”

    No, it just means that design is not objectively detectable with enough certainty by the EF. It could be, in other words, a false negative. The EF is extremely permissive of false negatives, with the aim of practically eliminating false positives. And it should be very clear that very simple things “can” be designed, but that in that case design cannot be reliably detected by the EF.

    “I was, and still am, struggling to understand what the concept of FSCI brings to science.”

    The concept of FSCI is fundamental if we want to make a quantitative assessment of the probabilistic credibility of darwinian mechanisms. In that sense, it is absolutely necessary for an evaluation of both darwinian evolution theory and ID theory. Which is, I believe, what we are discussing here.

    “I think a source of my confusion is not having a clear idea of the distinctions between FSCI and CSI. Would you be so kind as to delineate the differences? ”

    Let’s say:

    CSI (generic definition): any kind of information complex enough and which can be specified in one of many possible ways (to be specified), like compressibility, pre-specification or functional specification.

    FSCI: any kind of information complex enough and which is functionally specified. For my purposes, I limit the present discussion to digital FSCI. FSCI is a subset of CSI. Digital FSCI is a subset of FSCI.

    “And explain the contribution of each to scientific progress?”

    The biggest contribution of the concept of FSCI to progress is/will be to allow falsification of the darwinian theory. It’s no small deal.

    “And I wonder whether the FSCI calculation for oxytocin yields a different value from the CSI calculation. If not, why not? If so, why so?”

    If we make the calculation according to the method I have shown, there is no difference, because what we measure is the complexity, not the specification, in the sense that the specification is 0 or 1 (no specification = no FSCI, specification: FSCI is measured as its complexity). In theory, we could attribute a coefficient for function, but in general I think it is simpler to consider specification as a binary value.

    In cases of CSI where the specification is not functional, an explicit method must be given in each case to decide if specification is present or not. In the case of biological function, the method I have given in this post is perfectly appropriate.

  67. GSV (#58):

    “Can you tell me what information can’t be encoded in bits as a digital sequence?”

    Any information can probably be encoded as a digital sequence. What I meant is that the information we observe must “already” be encoded as a digital sequence. You certainly understand that it isn’t the same thing.

    “Who or what defines what is ‘important’? How would we know if something is important unless we know everything about it? For example is the fact that DNA is made up of 4 ‘characters’ important or merely an accident of design?”

    I did not mean to open a controversy about “importance”. I made the example of pi, which is an important mathemathical object, because anyone who knows mathemathics could agree on that. A random number is a mathemathical object, but it has no known function. The point is that a function must be clearly recognizable, as in the case of pi. I agree that some apparently random number could be a special mathemathical object with a function which we still don’t know, but that’s not a problem. In that case, we have a false negative, and we cannot detect design. But if we find the binary sequence of pi, and it is complex enough (let’s say the first 1000 figures), than we can detect design.

    “For example is the fact that DNA is made up of 4 ‘characters’ important or merely an accident of design?”

    I have not discussed the genetic code as a designed code, because that would require a different approach. For the moment, I would stick to digital sequences, like protein genes.

    “Can you calculate this for Chesil Beach? An 18 mile stretch of stones sorted by size.”

    I don’t think Chesil Beach is a digital sequence bearing functional information.

    “Can you give me an example of information that isn’t specified? Often it is a good idea to define something that doesn’t meet the criteria to understand the criteria better.”

    That’s easy: any random sequence of nucleotides which does not code for a functional protein. You will object: it could have some other functional specification. But again, we are interested only to specifications we can recognize. False negatives are accepted as part of the game.

    “What about unknown procedures? Before electricity was discovered lightening was the Gods doing battle!”

    Again, we are interested only in procedures we know. New procedures will certainly be evaluated when they are known. We are making science, not religion. Weare not looking for absolute truth. we are just looking for best expèlanations.

    Moreover, a procedure of necessity could not be known in details, but still be conceivable in principle. But when no procedure of necessity can be conceived even in principle, then I am afrais that the vague notion that “maybe some day we could see things differently” is really of no interest to the scientific debate.

  68. Adel,

    The concept for CSI is more vague than FCSI or FSCI because it tries to do a lot more. It is very general concept and an attempt to conclude intelligence in the widest range of phenomena possible. As such, this general measure seems a little vague to most because it apparently can only be expressed in some complicated mathematically formulas. I am on record that for evolution this concept should be abandoned because it is not needed for the much simpler subset which is FCSI or FSCI.

    While the mathematics for CSI can be daunting, FCSI is quite simple and is a subset of CSI that does not need a mathematical description to understand. It is

    Information – DNA sequences are an example

    Complex – not compressible but use your own intuitive understanding of complexity and it will work

    Specifies – the information specifies something else or designates something else. For DNA it is a protein or a RNA polymer.

    Function – the thing specified is also complex and has a function. In the case of proteins, these are very functional and work together with many other proteins in a systematic way to perform very complicated processes. For example, how does a protein get made and then get to the exact spot in the cell or organism to be functional. It is a process of several proteins working together with the appropriate code implanted in the genome in the DNA. It is a process that boggles the mind in preciseness but all of it is encoded in the genome as if the genome knew ahead just what was expected.

    There is a measure called FSC or functional sequence complexity that assesses the complexity of the sequence and essentially its rareness. This part of it is a little complicated but in general the main concept is very simple.

  69. gpuccio, jerry, kairosfocus,

    Thank you all for your helpful comments. I am a slow thinker, so please don’t think I have ignored you if you don’t see responses from me quickly.

    But there is one thing that gpuccio said that is simple enough for me to appreciate, because it so candidly asserts the goal of the Intelligent Design project and the part that FSCI plays in it:

    The biggest contribution of the concept of FSCI to progress is/will be to allow falsification of the darwinian theory. It’s no small deal.

    My difficulty with that goal is its negativity. From my limited readings in the history of science, mainly Thomas Kuhn, it appears that theories are overcome by the encroachment of new theories that explain the data better. Providing a better explanation would be considered a positive, not a negative contribution to science, I think. Since scientific explanations involve causal chains (and since the source [cause] of design in Intelligent Design theory has been ruled out as an object of study), what new purchase on nature does Intelligent Design theory provide to the scientist?

    Sorry to keep asking questions, but I would also like to know about any other contributions of FSCI to scientific progress.

  70. Adel:

    “My difficulty with that goal is its negativity. From my limited readings in the history of science, mainly Thomas Kuhn, it appears that theories are overcome by the encroachment of new theories that explain the data better.”

    the design theory does explain the data better. Falsification of the current (wrong) theory is only a part of it. The positive part of ID includes scientific perspectives about the nature of consciousness and intelligence, the complete or incomplete determinism of observed nature, the relationship between computation and creativity, the nature of life, and so on. All of these are very positive problems. ID, like any other scientific theory, starts from the observation of data: designed objects, the process of design, the nature of designers. It is just a first, important attempt at approaching scientifically facts we have always had under our eyes, and whose appropriate intepretation has been prevented by scientific prejudice and materialistic ideology, through the instrumentality of wrong theories like darwinian evolution and strong AI. ID is not the only approach which is contributing to change that scenario of scientific thought, but its role is certainly fundamental.

    “Since scientific explanations involve causal chains (and since the source [cause] of design in Intelligent Design theory has been ruled out as an object of study), what new purchase on nature does Intelligent Design theory provide to the scientist?”

    The source of design is not ruled out as an object of study. That is a common misunderstanding. ID is at present mainly a theory about design detection, and therefore can tell us nothing (or very little) about the nature of the designer, his methods and modalities of implementation of design, his purposes and so on. But that does not mean that all those aspects are not open to scientific inquiry. In an ID scenario, all those aspects can and will be investigated scientifically, but that will require new approaches and methods, and certainly new data. Naturally, nobody can now how far the current or future scientific methods can bring us on that way. We have to try to know that. But ID is the necessary premise to do that.

    “what new purchase on nature does Intelligent Design theory provide to the scientist?”

    ID is a new scenario, and one which is infinitely richer than the existing ones. In the current scenarios, reality is interpreted as a completely blind and objective dominion, and all subjective realities (consciousness, purpose, design, intelligence, feeling) are just ignored or interpreted as byproducts of strange and undefined mechanisms. In ID, consciousness, intelligence and purpose are empirically observed and investigated for what they are, an essential and common part of reality, detectable both as designers (humans) and designed objects, and a whole field of reality, biological reality, is shown to share the same characteristics as designed objects. That’s a completely new perspective (for contemporary science, at least). And one which will change all the future of science. It is a true scientific revolution, in the sense of Kuhn, and one of an extremely universal nature.

  71. gpuccio #67
    I did not mean to open a controversy about “importance”. I made the example of pi, which is an important mathemathical object, because anyone who knows mathemathics could agree on that. A random number is a mathemathical object, but it has no known function. The point is that a function must be clearly recognizable, as in the case of pi. I agree that some apparently random number could be a special mathemathical object with a function which we still don’t know, but that’s not a problem. In that case, we have a false negative, and we cannot detect design. But if we find the binary sequence of pi, and it is complex enough (let’s say the first 1000 figures), than we can detect design.

    I see your point but I don’t think this is very useful without a mathematical reasoning behind the importance. Pi is important because it is the ratio of a circle’s circumference to the radius. We have a reason it is important.
    What is the measure of ‘importanceness’ for non mathematical objects?

    I don’t think Chesil Beach is a digital sequence bearing functional information.

    Why not? If I encoded the beach such that a stone’s size and location were represented by a byte of information we’d notice that this string had a pattern, that is a stone’s location was related to the size. Why isn’t this functional information? This is the output of a sorting process no different to a computer’s sort algorithm. Compare it to a ‘normal’ beach if you’d like.
    I think this is the heart of what I don’t understand about the concept. Do the waves have a high FCSI then not the beach?

    That’s easy: any random sequence of nucleotides which does not code for a functional protein. You will object: it could have some other functional specification. But again, we are interested only to specifications we can recognize. False negatives are accepted as part of the game.

    OK I see that. But what about false positives?
    Here is what you said originally:

    4) There must be no known procedure based on laws of necessity which can output that specific sequence in that system. IOW, the observed sequence cannot be explained by any known mechanism based on necessity.

    This will lead to false positives not false negatives. How do you filter those out?

  72. Adel said,

    “Providing a better explanation would be considered a positive, not a negative contribution to science, I think.”

    What FSCI does is show that the proposed explanations for the creation on new complex capabilities are deficient and one should look elsewhere. It does not necessarily point directly at an intelligence but that current explanations fail because there are hurdles they cannot get over. So look for another explanation.

    And in the wings is an explanation that can explain how to get over the hurdles. As obnoxious as this explanation is to many people, it is always there and the more alternatives that go down in flames the more likely it will be offered as a possibility. Never is it a certainty because there is always the possibility that another explanation will arise and it could be the actual one. But all the current explanations are deficient which is why they are having all these conferences and debate within evolutionary biology.

    So we cannot say they do not recognize the problem, only that they arbitrarily ignore one solution and then tell the public and students that everything is hunky dory.

  73. GSV:

    I am not so interested to deepen the discussion about “important” mathematical objects, because I don’t see the relevance to biology. Anyway, my idea is: if a digital string encodes anything which a mathematician would recognize as a mathematical object which has a special function in mathemathics (like pi, or e) or in physics (like a very precise measure of some physical constant), then I would say that such a string is functionally specified because it encodes for something which is extremely useful in a specific context. I will accept the judgement of mathematicians about the objective relevance of the object encoded.

    “What is the measure of ‘importanceness’ for non mathematical objects?”

    The measure is the existence of a function. A series of letters which encodes a well recognizable meaning in english is functional. A computer code is functional. A protein gene is functional. And so on.

    “Why not? If I encoded the beach such that a stone’s size and location were represented by a byte of information we’d notice that this string had a pattern, that is a stone’s location was related to the size. Why isn’t this functional information?”

    Well, first of all I don’t know Chesil Beach, and maybe that’s why I miss the relevance of your example. Anyway, I think that you again make confusion between a digital string of information, and an object which can be digitized. IOW, if we observed a string of DNA whose sequence of bits corresponded to the topography of Chesil Beach, that would be digital functional information, and the function would be to describe an existing object, Chesil Beach. But the Beach in itself is not a digital string, and has not a function, at least as far as I know.

    “I think this is the heart of what I don’t understand about the concept. Do the waves have a high FCSI then not the beach?”

    Why should the waves have a high FSCI?

    “This will lead to false positives not false negatives. How do you filter those out?”

    You are right. The EF is designed to avoid false positives in the sense of a random origin of the observed string. If there were a necessity explanation, that would be a false positive. But the point is:

    1) Appealing to a vague and completely unknown necessity explanation, not even vaguely conceivable, is more a philosophical stance than a real argument. Such an argument could be advanced against any form of scientific knowledge: “we could some day find a better explanation, so your explanation is not good”. That’s nonsense. A necessity explanation is of any value only if it exists, is known abd can be verified or falsified. Otherwise, it’s just myth.

    2) There are important theoretical reasons why no necessity explanation is appropriate top explain the kind of information we see in biological digital strings. For that, see for example the fundamental paper by Abel and Trevors.

  74. jerry:

    While the mathematics for CSI can be daunting, FCSI is quite simple and is a subset of CSI that does not need a mathematical description to understand.

    You said in an earlier thread that “In FCSI the information under analysis is doing the specifying”, but “In CSI the information is what is specified (the opposite of FCSI)”. My questions are:

    1) Why does the S stand for “specified” rather than “specifying” in FCSI/FSCI?
    2) How can FCSI be a subset of CSI if one is specified and the other specifies?
    3) Do other ID proponents agree with the distinction you make, namely that one is specified and the other specifies?

  75. gpuccio:

    Any information can probably be encoded as a digital sequence. What I meant is that the information we observe must “already” be encoded as a digital sequence.

    Actually, we observe physical phenomena and model them as digital information or digital sequences. If by “digital” you mean discrete (and I can’t think of what else you would mean), QM says that everything in the universe is digital.

    The measure is the existence of a function. A series of letters which encodes a well recognizable meaning in english is functional. A computer code is functional. A protein gene is functional. And so on.

    One problem I have is that “function” seems no less subjective than “specification”.

    For instance, jerry says that DNA sequences that are used to identify a criminal are not function because:

    The connection is mediated by an intelligent person and does not automatically specify something else as DNA does with a protein. The connection would disappear with out the intelligent intermediary who is the one actually making the connection.

    The rule that function cannot be mediated by an intelligent person seems ad hoc. That same rule would indicate that Venter’s watermarks and English messages are not functional.

  76. 76

    jerry [65]

    Read a biology book.

    You are irritating. Grow up. Learn to address people with respect and courtesy, as gpuccio does. You are not DaveScot, and if that’s whom you’re emulating, you are embarrasing yourself and the cause of ID.

    FSCI is the same thing as the central dogma or transcription and translation.

    If it’s the same thing, what does it add? Why give it a different name? What is the point?

    It was one of the key insights by Francis Crick just after discovering the double helix.

    Crick and Watson proposed the double helical structure of DNA in 1953. In what year did Crick coin the term Central Dogma? What experimental work did Crick do to establish the Central Dogma? When did Crick employ the term FSCI?

    It led to the decoding of the DNA and amino acids. It is just making the analogy that this similar process happens elsewhere in language and computer programming.

    To what does ‘it’ refer?

    Now when you see FSCI, think Central Dogma or language or computer programming. It is that easy.

    Easy, but what does FSCI add to the Central Dogma or language or computer programming? Or to biological science?

    The concept for CSI is more vague than FCSI or FSCI because it tries to do a lot more. It is very general concept and an attempt to conclude intelligence in the widest range of phenomena possible.

    Very helpful. You make me wonder why there is a need to “conclude” [sic] intelligence in the widest range of phenomena possible? Looks like an agenda has motivated devolopment of the concept of CSI. So much for scientific objectivity.

    I am sadly disappointed.

  77. 77

    Not “devoloping,” developing.

    When I’m not so irritated, I spell better.

  78. R0b:

    “QM says that everything in the universe is digital.”

    I would suggest that we stay tuned to the model to which my definition is targeted: protein coding genes. A sequence of nucleotides is digital because it is based on an alphabet of 4 letters and words of 3 letters. It is a digital string of information. The physical structure of DNA, the configuration of all other atoms, does not matter here: it is just the sequence of the nucleotides which carries the information. Moreover, the information is symbolic, in the sense that it codes for another molecule, the protein, and it is the protein which has the function.

    So, to be more precise, here we have a double layer of function: a symbolic, linguistic function in the DNA (its sequence carries information to build another molecule); and a biochemical function in the final protein. In a sense, even the protein carries a symbolic information, because the primary structure is related to the final function in a very indirect way. But the symbolic nature of the information is more evident in the DNA.

    Now, I am not saying that the symbolic nature of the information is necessary to have FSCI. A protein has FSCI as its DNA gene, because the sequence of aminoacids is a digital sequence based on a 20 letters alphabet, and the sequence, and only the sequence, determines the final function. But if we consider the DNA as the carrier of the information, and the protein as the carrier of the function (as is appropriate), the symbolic and digital nature of biological information is even more evident.

    So, I don’t understand you worries about the ultimate digital nature of reality (which I can agree on). From that point of view, we could never distinguish between digital and analogic information, which would be a very unpractical position. I can’t understand why concepts which are very simple and self-evident everywhere else must become a problem as soon as we speak of ID.

    “One problem I have is that “function” seems no less subjective than “specification”.”

    You have strange problems. Let’s go again to the model we are interested in, functional proteins. Functional proteins are functional because they accomplish some specific task in their natural environment. Enzymes are highly powerful to catalyze biochemical reactions which otherwise would never take place. That’s not something we deduce, that’s something we observe. Indeed, for proteins, the first thing we know is their function, and then we try to understand how they can accomplish it in terms of tertiary structure, and so on. We don’t have to discuss about which is the function: for most proteins, we know it. And we know, dramatically, that if the protein changes, the function is often lost. That’s what monogenic diseases are about.

    So, why do you say that the function is “subjective”? It is not, in no way. Obviously, we have to describe it subjectively with words, and there may be different ways of doing that. Many proteins have multiple functions. And we can measure a function, and that again requires some subjective adaptation. But the function itself is absolutely objective, as well know those who have lost it.

    I don’t want to answer for jerry, but I don’t see any significant difference between “functionally specified” and “functionally specifying”, in the following sense: the first means that the sequence is specified because it has a function; the second means that the sequence is specifying a function. It’s only a matter of words. For DNA, we can well say that it is specified because it has the function of conveying the right sequence to the translation system, and it is specifying because it specifies that sequence. Both things are true, and, as you can see, they ultimately express the same concept, in different ways.

    Finally, I would agree with jerry about the difference between DNA as a functional sequence, and DNA as something which can be recognized as unique for forensic applications. They are two different things. Any complex sequence is unique and can be recognized, but that does not mean that it is functional. If various objects are marked with 100 figures numbers, and that allows us to identify them, the single numbers are complex but not functional, while the whole system of marking and identification is certainly complex and functional. Again, these should be very simple concepts.

  79. gpuccio:

    I would suggest that we stay tuned to the model to which my definition is targeted: protein coding genes.

    Sure, we can restrict the scope of FSCI/FCSI/FSC to protein coding genes, as Durston, Chiu, Abel, and Trevors seem to do. But consider the argument by which designed is inferred from FSCI:

    On massive evidence, such cases [FSCI] are reliably the product of intelligent design, once we independently know the causal story. So, we are entitled to (provisionally of course; as per usual with scientific work) induce that FSCI is a reliable, empirically observable sign of design.

    The basis of that induction makes no sense unless FSCI is well-defined in a general context. If we can’t look around and determine whether the things we observe are FSCI or not, this “massive evidence” doesn’t exist. (And until actual studies are done, there is nothing scientific about this evidence.)

    So, I don’t understand you worries about the ultimate digital nature of reality (which I can agree on). From that point of view, we could never distinguish between digital and analogic information, which would be a very unpractical position.

    Any physical system (except ultimately elemental quanta) can be modeled as digital or analog. So the digital/analog distinction is conceptual, not empirical.

    So, why do you say that the function is “subjective”?

    Why do you claim that it isn’t? If you had an objective operational definition for the term, then we could be confident that people could independently apply that definition and come to the same conclusion as to whether something is functional or not. But you have offered no such definition.

    In the context of genes, functional seems to mean coding. Except in the case of Venter’s watermarks, which jerry’s logic says are non-functional, but Durston and kairosfocus say are functional.

    In the context of sequences of symbols, functional seems to mean “meaningful in some language”. That would seem to apply to both natural and computer languages. But some computing systems will accept any sequence as meaningful.

    Both things are true, and, as you can see, they ultimately express the same concept, in different ways.

    And yet jerry regards them as distinct, even opposite.

    If various objects are marked with 100 figures numbers, and that allows us to identify them, the single numbers are complex but not functional,

    That is exactly what Venter’s watermarks do. Durston and kairosfocus see them as functional, but you seem to disagree.

    Again, these should be very simple concepts.

    There’s no question that it’s a superficially simple concept. The question is whether it’s well enough defined to be the subject of scientific hypotheses and claims. Sometimes simple concepts even turn out, on closer scrutiny, to be nonsensical, as in the concept of a “complete and consistent number theoretical system”.

  80. tragic mishap: You are trying to hack my credit card number that is supposedly secured by SSL encryption.
    Gil: You guessed it! I’ll give tragic a prize.

    My reply to tragic was tongue-in-cheek. I have no nefarious intentions, and I’m not trying hack anyone’s credit card number. Computational number theory and computing power have advanced to the point where what was once thought to be impossible, is possible. This is a contemporary manifestation of the history of cryptography. Every new algorithm in cryptography throughout history was initially declared to be insoluble, but they were all eventually cracked.

    See below for a very recent example:

    http://www.tgdaily.com/content/view/40765/108/

  81. R0b,

    The use of DNA as it used in forensics is certainly useful, but it is not FSCI in this sense. It is like a finger print or eye scan or some other identifying characteristic of anything. It identifies the whole to which it is a part. I do not know what sections of the DNA are used for identification but it does not necessarily have to be the same DNA that is used in specifying something else such as a protein or a RNA strand. Maybe someone here who is familiar with the process can tell us what is used for identification.

    Now if you want to go off and argue that this DNA specifies the person, then I guess you can. But that is just saying that certain parts can identify the whole. A lot of other things can also do that but when it specifies a process of building a polymer with very sophisticated capabilities that it becomes FSCI.

    I fail to understand all the fuss paid to this simple but powerful concept. The only reason I can see is people feel somehow they must be impeach the usefulness of this and this is a fruitless task because all biology recognizes the relationships that are here. It is only on this site that there seems to be a compulsion to impugn it or nitpick every small thing about it. It must be because it represents a real threat to one’s arguments.

  82. jerry

    I do not know what sections of the DNA are used for identification but it does not necessarily have to be the same DNA that is used in specifying something else such as a protein or a RNA strand. Maybe someone here who is familiar with the process can tell us what is used for identification.

    Biologists refer to it as junk DNA.

  83. R0b:

    “The basis of that induction makes no sense unless FSCI is well-defined in a general context.”

    But FSCI is well defined in a general context, even in the restricted form I have given. That restricted form is perfectly enough to justify the claim that:

    “On massive evidence, such cases [FSCI] are reliably the product of intelligent design, once we independently know the causal story.”

    Indeed, just language and computer programming would be enough for that, and they are clear examples of FSCI, and of digital FSCI. Take the case of a computer code written in C. for instance. It is perfectly equivalent, conceptually, to a DNA code. It is symbolic and digital, it has to go through a translation system (the compiler) to convey its information to the final thing (the program itself), and the final thing is functional (it can do specific things in the right context).

    So, the ability of humans to generate easily and abundantly language and computer programs is certainly “massive evidence”. Those things are always the product of the intelligent design of humans, as far as we can observe. The fact that humans can generate CSI in other forms, like analogic CSI (Mount Rushmore, paintings, arrow heads, and so on) is just another form of the same process, but requires a different and more general approach to be formalized satisfactorily. That’s what Dembski is trying to do.

    But again, by restricting the discussion to digital FSCI for the purpose of discussing the origin of biological information, nothing is lost, not the specificity of the concept, and not the massive evidence (may be the evidence would be a little bit more massive if we included other kinds of CSI, but we are not looking for perfection). And, on the contrary, much is gained in terms of objectivity, formal completeness and simplicity. But, perhaps, that’s exactly what somebody does not like.

    “If we can’t look around and determine whether the things we observe are FSCI or not, this “massive evidence” doesn’t exist.”

    But we can do that. My definition is very clear, and I have answered all your questions about what is FSCI or not. We just need digital strings of information (already coded into digital form), complexity above a conventional level, and a recognizable function conveyed by that information (more on that later). If all of these characteristics are present, you have FSCI. If even one is missing, you have not. If the function is not recognizable, then you have not FSCI (but it could be a false negative, in case a function is present but we don’t recognize it). Similarly, we can have false negatives in the case of function present, but complexity too low. All that is essentially the EF, with a restricted definition of specification. And it works fine.

    “(And until actual studies are done, there is nothing scientific about this evidence.)”

    I don’t understand to which studies you are referring. Do you want me to publish a series of short programs in C, to demonstrate that they are digital, functional and complex, and that I am the author? Or shall we send the posts in this thread to Nature as an example of FSCI? Ah, but I am afraid we would not pass peer review! :-)

    “Any physical system (except ultimately elemental quanta) can be modeled as digital or analog. So the digital/analog distinction is conceptual, not empirical.”

    Again, I don’t follow you. Can’t you understand the difference between a vynil record and a CD? Well, that’s enough. I am restricting my definition to CDs. And not because vinyl records are not information, but because they are in a different form. Talking of the information on CDs, I can easily count the bits, verify the changes caused even by a single bit modification, and so on. So what is so difficult in restricting the definition, for convenience, only to that form of information?

    “Why do you claim that it isn’t? If you had an objective operational definition for the term, then we could be confident that people could independently apply that definition and come to the same conclusion as to whether something is functional or not. But you have offered no such definition.”

    I don’t think it is difficult to give definitions of function, but still that would bring about infinite discussions with you and others, and do you know why? Because you just have to deny what is obvious. So, let’s put it this way:

    I can define function in an universal way only as something which can be recognized as purposeful by an intelligent agent. Is that definition subjective? No. It is based on intelligent agents, but you know, intelligent agents exist, and are a very important part of reality. The problem is only there, and again it is merely ideological. If you deny the existence of realities like intelligence, consciousness and purpose, then the discussion will never go on. ID is based on the empirical recognition that such realities do exist, and that they are empirically observable and describable.

    Strangely, it seems that biologists have not your difficulties in understanding what the function of a protein is. You can find those functions listed in any public protein database. Maybe you should warn them that they are not making true science, and that they have been corrupted by those devious ID people. Why do they insist that proteins serve for a purpose?

    Or just take a program which does not work and input it to your “computing systems will accept any sequence as meaningful” and use it. But please, could we be associates in commercializing that computer system? I believe we could solve some of our personal problems… :-)

    So, an object or a system are functional when they serve for a recognizable purpose, and purposes only originate in conscious beings. Conscious intelligent beings easily recognize purpose. Even if there can be controversy in some cases, we can well restrict our definition to cases where purpose is easily recognized by all, or at least by the majority.

    Machines are functional. Computer programs are functional. Language is functional. Proteins are functional. If a machine which did something stops working, you know it has to be fixed, If a protein is crucially changed, it becomes non functional, and disease ensues. What is subjective in all that?

    “In the context of genes, functional seems to mean coding.”

    No, in that context functional means coding for a functional protein (I am still restricting the discussion to protein coding genes, which are the usual object of darwinian evolution). It is important that we refer to the function of the protein, because that’s the basis of the phenotype.

    “Except in the case of Venter’s watermarks, which jerry’s logic says are non-functional, but Durston and kairosfocus say are functional.”

    First of all, jerry is entitled to his opinions, and sometimes our opinions differ. My view is clear enough: if the function is to mark something uniquely, then the whole system which accomplishes that can be recognized as functional, but not necessarily the part which is used as a mark. So, Venter and his laboratories and his watermarks are certainly a functional system. I don’t know what his mark is, but if it is just a random sequence, it is not functional in itself. If, on the other hand Veneter uses an objectively recognizable sequence, like the first 500 figures of pi, or the phrase “Hey, I am Venter, how are you? You are certainly aware that I did this, because you are just reading my signature. Best regards” then I would say that he is using a functional string in the context of a bigger functional system. Is that clear enough?

    “In the context of sequences of symbols, functional seems to mean “meaningful in some language”. That would seem to apply to both natural and computer languages. But some computing systems will accept any sequence as meaningful.”

    Again, the fact that a computer system accepts some string does not mean anything. A computer just does what you order. The problem is, what meaning can be conveyed to a conscious intelligent being by that string? Or, if we speak of a non linguistic string, what function can be accomplished by that information? What can it do? Is what it does recognizable as a purpose?

    “And yet jerry regards them as distinct, even opposite.”

    And so? I don’t accept Dembski as an authority, I may well not accept jerry as an authority (my apologies to Dembski and jerry, I am just making an important point). Do we really need authorities to discuss? Does ID really need to be based on the authority of somebody, to be true?

    “That is exactly what Venter’s watermarks do. Durston and kairosfocus see them as functional, but you seem to disagree.”

    See my discussion above.

    “There’s no question that it’s a superficially simple concept. The question is whether it’s well enough defined to be the subject of scientific hypotheses and claims.”

    I do believe it is.

    “Sometimes simple concepts even turn out, on closer scrutiny, to be nonsensical, as in the concept of a “complete and consistent number theoretical system”.

    Sometimes it happens. That just means that in all other times simple concepts just work. Obviously, you have to judge case by case. Generalizations will not bring us anywhere. I have tried to give you very detailed reasons why I believe that “these” simple concepts do work.

  84. GP, Jerry et al:

    Excellent points. Quite productive discussion!

    A few remarks:

    1 –> Analogue vs Digital. Yes, the Q-world picture is digital, but that does not obviate the value of the analogue approach. Indeed, for a great many things, before we can use them we have to get back from digital to analogue. On the other hand, it is true that any analogue info can be reduced to digital form, and such can be reduced to appropriately formatted and organised strings of bits. (but if you have ever used and anlaogue computer, you will see that it can work with differential eqns easily that would tax teh most sophisticated mathematicians to analyse on calculus principles. Just so, no one knows how to integrate e^-[x^2], apart from numerically, i.e by going to a digital filter approach.]

    2 –> FUNCTION, whaz dat? Ans, look at concrete examples and build up your concepts from describing what you see on a family resemblance basis, then try to pin down fine borderlines. You will see that the common features are parts that fit together in wholes, and that the wholes do a job. The parts that contribute to the job are functional, those that do not are non-functional. e.g. Letters –> Words –> sentences –> communication (linguistic). e.g. 2 letters –> reserved and internally defined words –> C format lines of code –> C format programs; thence Source code –> compiler –> Object [assembler thence machine] code –> memory storage –> execution –> machine implements program. Eg 3 G/C/A/T monomers –> DNA chains –> unzip, RNA –> ribosomes, enzymes etc –> aa strings –> fold and agglomerate –> proteins –> Cell works –> life. e.g. 4 resistors, transistors, capacitors, IC’s, transducers, Cu traces on circuit board etc –> electronic circuits –> apply power and inputs –> a radio that can be tuned to listen to your fav FM station. Observe the common pattern here,and the diverse contexts. Also, that function once complex requires very specific elements put together in very specific ways, under very specific circumstances to get out the result. Such clusters are maximally improbable on undirected contingency, but are routine, observed products of intelligence.

    3 –> But anything direction can do chance can do too! Sure, lucky noise, given enough gamut and a randomiser to drive it can in principle do just about anything. But, on the scope of large configuration spaces — what “complexity” is about — we are looking at such long odds of getting there by chance that EMPIRICALLY chance is not a likely cause of the outcomes. [And that is exactly what the Weasel program so used by Mr Dawkins ducks.]

    4 –> Well, what about unknown mechanical forces, aka unknown necessity? mechanical forces of course do not produce high contingency; that’s how we recognise them. What this question is really raising, then, is the question of whether the laws of our cosmos are set up to make the production of life not a contingency but a sure thing. To do that, requires a lot of fine tuning, starting form setting up a universe in which life facilitating terrestrial planets on which C-based, aqueous medium cell based lifeforms are possible. It turns out that that is so complex and finely tuned a balance, that it raises the question posed by — you guessed it — Sir Fred Hoyle: did someone monkey with the physics to make life possible? And it goes one better, it demands positive programing of the universe to make life inevitable. On our massive experience, what is responsible for programs? (In short, this has not got rid of the issue, but has pushed it up a level.)

    5 –> Well, don’t the laws of nature make chem evo and life evo inevitable? First, thermodynamics implies that simpler, more energetically favourable chemicals will uterly dominate any pre-biotic environment so we do not even get to the full set of required monomers for life, much less to the complex organisation of same that we find as an irreducibly complex system in life. Second, DNA is not constrained to load for proteins by the laws of chemistry, no more so than the chemistry of paper and ink forces what is written to appear. And, on the relevant statistics and probabilites, the laws of thermodynamics are just about the strongest laws we have. Information and organisation will not on the gamut of our universe or any other one with similar laws, spontaneously form life. But, we know that design can easily form complex functional entities, even those based on the nanotechnology of information-rich polymers.

    _______________

    That much is pretty clear. just, it is not welcome to the friendly local magisterium; one of whom just tried to “out” me in the obvious hpe that he would thereby do me harm. All he has manged to do is to expose his utter irresponsibility and want of basic civility.

    There is a name for such uncivil behaviour; retaliation against whistleblowers.

    I think there are some laws about that.

    GEM of TKI

  85. 85

    I would just like to quickly thank all of those involved (kairo, gpuccio, etc.) for taking the time to discuss these concepts (FSCI, CSI, function). I would also like to second the notion that this has been a rather productive discussion.

    Though I’ve been “lurking” here for only the past several months, it seems more is accomplished in a topic such as this than in others (for example, Darwin’s racism). I don’t mean to say that I don’t enjoy posts concerning evolution/Darwin and some of these other extraneous topics, I just believe a topic like this is conducive to a more candid and intellectual climate. In short, I look forward to more posts of this nature.

    To avoid derailing discussion any longer, I would just like to once more say thanks!

  86. 86

    gpuccio,

    I admire your patient willingness to answer all questions put to you. And I regret that I have to disagree with some of your answers. But I do disagree and I must so inform you.

    When I started to comment on this thread, I thought that the concepts of FSCI and CSI might lead to new insights into biology. I thought that the mathematical tools developed by Dr Dembski would enable us to distinguish biologically meaningful sequences from nonsense sequences.

    Now, gpuccio and the others commenters here have claimed that FSCI depends on the findings of working scientists to identify function. It is thus a parasitic notion (parasitic in a descriptive, not pejorative sense). Only after experimental data have shown that a sequence is functional, can an FSCI expert make a guess that it might be beyond the bounds of naturalistic causation. So, FSCI appears to be useless in any scientific sense.

    gpuccio [70]

    Adel:

    “My difficulty with that goal is its negativity. From my limited readings in the history of science, mainly Thomas Kuhn, it appears that theories are overcome by the encroachment of new theories that explain the data better.”

    the design theory does explain the data better.

    This assertion needs supporting evidence. It currently stands only as an opinion.

    Falsification of the current (wrong) theory is only a part of it. The positive part of ID includes scientific perspectives about the nature of consciousness and intelligence, the complete or incomplete determinism of observed nature, the relationship between computation and creativity, the nature of life, and so on. All of these are very positive problems. ID, like any other scientific theory, starts from the observation of data: designed objects, the process of design, the nature of designers. It is just a first, important attempt at approaching scientifically facts we have always had under our eyes, and whose appropriate intepretation has been prevented by scientific prejudice and materialistic ideology, through the instrumentality of wrong theories like darwinian evolution and strong AI. ID is not the only approach which is contributing to change that scenario of scientific thought, but its role is certainly fundamental.

    Opinions. No examples or evidence were provided above.

    “Since scientific explanations involve causal chains (and since the source [cause] of design in Intelligent Design theory has been ruled out as an object of study), what new purchase on nature does Intelligent Design theory provide to the scientist?”

    The source of design is not ruled out as an object of study. That is a common misunderstanding. ID is at present mainly a theory about design detection, and therefore can tell us nothing (or very little) about the nature of the designer, his methods and modalities of implementation of design, his purposes and so on. But that does not mean that all those aspects are not open to scientific inquiry. In an ID scenario, all those aspects can and will be investigated scientifically, but that will require new approaches and methods, and certainly new data. Naturally, nobody can now how far the current or future scientific methods can bring us on that way. We have to try to know that. But ID is the necessary premise to do that.

    That the source of design is not ruled out by design theorists is evidently an extremely common misunderstanding in these precincts. How will it be investigated? Is it natural or supernatural? Is it possible to choose, so one can proceed to evaluate the claim?

    “what new purchase on nature does Intelligent Design theory provide to the scientist?”

    ID is a new scenario, and one which is infinitely richer than the existing ones. In the current scenarios, reality is interpreted as a completely blind and objective dominion, and all subjective realities (consciousness, purpose, design, intelligence, feeling) are just ignored or interpreted as byproducts of strange and undefined mechanisms. In ID, consciousness, intelligence and purpose are empirically observed and investigated for what they are, an essential and common part of reality, detectable both as designers (humans) and designed objects, and a whole field of reality, biological reality, is shown to share the same characteristics as designed objects.

    Neuroscientists will be surprised to learn that they ignore and misinterpret consciousness, purpose, design, intelligence, feeling, and all the other mental activities that humans and our nonhuman biological brethren experience.

    That’s a completely new perspective (for contemporary science, at least). And one which will change all the future of science. It is a true scientific revolution, in the sense of Kuhn, and one of an extremely universal nature.

    On the contrary, design theories are as old or older than recorded history. So far, the score for naturalistic science as an explanation of nature is high. The score for design theories is zero.

  87. Adel:

    I appreciate your input, and obviously respect your positions. Let me just add some comments, in the hope that they may useful to a reciprocal understanding.

    “It is thus a parasitic notion (parasitic in a descriptive, not pejorative sense). Only after experimental data have shown that a sequence is functional, can an FSCI expert make a guess that it might be beyond the bounds of naturalistic causation. So, FSCI appears to be useless in any scientific sense.”

    I don’t understand what you mean. Proteins we find in biological beings are practically always functional. The problem is not to determine their function (although sometimes that requires time), but rather to understand the relationship of function to dtructure, and especially how that function arose. Both darwinian theory and ID are about the “origin” of biological information.

    If you read the Durston et al. paper about protein families and the special method they give to measure functional bits in them, you will see that such an approach, based essentially on the concept of FSCI, can open vast insight regarding the relationship between proteins and the quantity of information necessary to implement a function. The real proble, today, is to measure the target space, the functional space: how many different sequences can implement a function, and what is the topographical structure of those islands of functionality in the general search space?

    Those are crucial problems for any theory of origins, and while protein engineering is giving us new insights about them, they are still largely unsolved. The concept of FSCI, and practical methods to measure it, like that proposed by Durston, can greatly help to investigate those new territories, while the conventional and universallyb accepted view of random search and NS, without any quantitative assessment of the model, is really a science stopper.

    “This assertion needs supporting evidence. It currently stands only as an opinion.”

    A design scenario allows us to reason in very natural terms about objects which do appear designed. It allows us to detect the connections, to investigate the general plans, and to learn about the strategies of the designer, without having to forcibly “explain” all those things in term of an innatural theory which does not work and cannot work. Indeed, most reasonings in biology and medicine are teleologic, even if they are disguised as non teleologic just to comply with the accepted dogma.

    The simple truth is that design “can” explain what we observe in bilogy, and darwinian theory cannot. That is not only an opinion. The whole ID theory is behind that, and we have only scratched the surface of it in our discussions on this thread. For instance, I have just given an operating definition of FSCI, but we have in no way deakt with how it brings to the design inference. And we have in no way treated in detail the reasons why darwinian evolution cannot work. So, when you say that “it’s only an opinion”, you seem to forget that we haven’t yet discussed the motivations behind that opinion. To begin with, you asked for a definition of FSCI, and I have given it. Please, make further questions, and you will receive answers. Nothing has to be accepted as simple opinion.

    “Opinions. No examples or evidence were provided above.”

    I have given only a brief summary of vast scenarios. I have dedicated hours and hours to the discussion of those themes here, form ID proper to strong AI, form the definition of consciousness to the problem of free will, and I am ready to repeat it all, if you are interested. But I cannot give you everything in one short post. But I have suggested some important points, especially the concept that consciousness and its properties are empirical data, and that unless and until we have a satisfying explanation of them in terms of other types of data (material objects) we have no right to either ignore them or consider them as a byproduct of those objects.

    “That the source of design is not ruled out by design theorists is evidently an extremely common misunderstanding in these precincts. How will it be investigated? Is it natural or supernatural? Is it possible to choose, so one can proceed to evaluate the claim?”

    The source of design can be investigated exactly like any other thing which we do not understand, but whole effects we can observe. Take the mysterious “dark energy”, for instance. We know nothing about it. We don’t even know if such a thing really exists. And yet, it is at present the main object of investigation of many physicists and astrphysicists. Why? Because we observe effects which we cannot explain otherwise.

    The same is true of the effects of biological design: we cannot explain them otherwise. that’s why the source of design must be investigated, even of at present we know nothing about it.

    You seem to share the common prejudice that we in ID expect form our theory only a confirmation of the existence of God. That is not true. Personally, I need no confirmation of the existence of God from science. I am rather sure of that, and ID will not add anything to that.

    But I do expect from ID and science a better understanding of observable reality, and of the designed aspects which I perceive in it. You ask: “Is it natural or supernatural?” The only reasonable answer is that I don’t know, If I knew, I would not need to investigate. I don’t even understand what “natural” and “supernatural” mean. I am always uncomfortable with those words, as I am uncomfortable whenever the scientific discussion about ID is mixed to religious problems. I don’t like that. I don’t like that at all.

    “Is it possible to choose, so one can proceed to evaluate the claim?”

    Anyone can choose as he likes, and investigate whatever claim he likes. That is one of the few rules of science.

    “Neuroscientists will be surprised to learn that they ignore and misinterpret consciousness, purpose, design, intelligence, feeling, and all the other mental activities that humans and our nonhuman biological brethren experience.”

    Neuroscientists will be surprised of many things, believe me. I am speaking, obviously, of materialist neuroscientists, but they are the vast majority. I don’t know if they ignore consciousness (some certainly do, however bizarre that may seem), but they certainly misinterpret it. And I, as a human, and in the name of our nonhuman biological brethren who cannot take part in this blog, do rebel against that. My experience, and the experience of all my brethren, cannot be denied in the name of ideology. Hofstadter and the likes of him can go on affirming that my consciousness is just a loop in a software, and famous neurologists can well write in popular magazines that the origin of consciousness from the material brain is absolutely proved, but I know better.

    “On the contrary, design theories are as old or older than recorded history. So far, the score for naturalistic science as an explanation of nature is high. The score for design theories is zero.”

    I know very well how old they are. that’s why I added “for contemporary science, at least”. Indeed, universal non teleologic thought is only a recent anomaly in the history of human culture, and it will not last.

    And the score for naturalistic science as an explanation of material non living nature is high, while that score as an explanation of biological information and of conscious beings is absolutely zero. That’s where design theories score very well.

  88. 88

    I appreciate your input, and obviously respect your positions. Let me just add some comments, in the hope that they may useful to a reciprocal understanding.

    I thank you for all of your good efforts to increase my understanding, and I think you can tell that you have succeeded. But I doubt that my poor efforts have accomplished anything.

    You have shown me that ID may promise much, but so far has delivered no new causal explanations to our understanding of nature. You insist that the contrary is the case, but you (and the ID movement) have offered only hopes and promises, while mainly expending your collective energies disparaging scientific naturalism.

    I doubt that anyone could find a way to raise any doubts in your mind that your hostility to science as currently practiced is misplaced. (Parenthetically, I have been stunned by the intensity of that hostility.)

    I’ll be watching for the causal explanations that you promise will be generated from ID theory. As long as they are lacking, I will take the liberty of pointing out their absence.

    Best wishes for now,

    Adel

  89. Adel,

    OK, that’s fine for me, I will not insist any more. Just a personal clarification, if you allow.

    I have certainly no hostility to science as currently practiced in general. Indeed, I have great admiration for good science, wherever it is practiced, and I know that a lot of good science is being practiced in all fields, including biology. I am sorry if I have given you the impression that I am against naturalistic science. Indeed, I currently practice naturalistic science in my field, which is medicine.

    But it is true that there is something in the current scientific environment for which I have, if not hostility, certainly great distaste: it’s the dogmatic materialistic prejudice, as it is expressed in the two great scientistic philosophies which dominate our culture: darwinian evolution and strong AI. Both, IMO, have nothing to do with good science, and are rather general (and bad) philosophies of reality. Both have contributed almost nothing to a real understanding of nature, and have on the contrary imposed to our times a lot of false and unsupported notions and an almost universal cognitive arrogance which is the true contrary of what science should be. For those two theories, I have no sympathy at all. All that, obviously, is my personal view, and I don’t expect you to agree.

    But again, I love science. Indeed, I have always expressed here my firm conviction that the affirmation of ID will come, is coming, thanks to the growing understanding of biology which is daily provided by the work of those who seriously operate to find new data. The fact that those data are currently intepreted according to the official theory of darwninian evolution is not really important: data are data, and in the long term they will support the best theory.

    Please excuse the intensity of my expressions, which comes from a deep sense of commitment to what I believe to be scientific truth. Best wishes for you too.

  90. gpuccio,

    The essence is that you’re asking us to accept that empirical observations compel us to accept an empirically unobservable cause. You would prefer to excise your “definition” of FSCI from this context, but I will not agree to that.

    You claim to be committed to empiricism. But intelligence is a classic example of a hypothetical construct. Your belief, based purely on introspection, that your invisible intelligence causes you to create designs out of nothing has precisely the same epistemological status as the belief of some people that their invisible love causes them to emit certain sorts of behavior. Many people have claimed that an invisible love, much like that they experience inwardly, permeates the universe, just as you claim that an invisible intelligence, much like that you experience inwardly, permeates the universe.

    What we experience inwardly is of enormous value to us as human beings, but it will never be, in and of itself, empirical in character. When people give similar verbal reports of non-empirical observation, the reports themselves are empirical data, but not the reported observations. You have appealed illogically to the wisdom of the ages and the vox populi regarding the existence of the process of intelligent design. They do nothing to confer empirical status on introspective experience of intelligence in action.

    Introspection was a key component of the work of Wilhelm Wundt, at the advent of experimental psychology. But it was soon abandoned by experimental psychologists, not out of philosophical commitment to materialism, but because experimental results based on the reports of subjects asked to introspect proved difficult to replicate. I should point out also that we know from anthropological studies that there are huge cultural differences in what people say about their inward sense of self. It is hardly a given that an organism we consider to exhibit “intelligence” explains its actions in similar terms.

    Dembski attempts to gain physical status for intelligence by a) eliminating for some entity (e.g., the flagellum) explanations framed strictly in terms of empirically observable phenomena and b) arguing then that what introspection leads us to believe is the cause of our designs is the best cause to assign to designs of unknown origin. As I indicated above, he attempts to avoid circularity and paradox by defining CSI in terms of semiotic agents, and not unrestricted intelligent agents.

    You, in contrast, beg the question of — engage in circular argument regarding — the physical existence of intelligence in presenting FSCI as a marker of the action of empirically unobservable intelligence on empirically observable matter. You say, in essence, that we know we are intelligent designers, and that if we can locate empirical phenomena with properties like those of our artifacts (i.e., with high FSCI), then we are justified in saying that they were caused by intelligence.

    You are not the empiricist you make yourself out to be. Show me intelligence. That failing, show me even that there might be something non-diffuse you refer to with the term. I contend that you cannot make even “design-generating intelligence” clear-cut. Exceedingly few people are good both at designing software systems and at designing fugues. You might think that people who do well at designing mathematical proofs usually would do well at designing software, but it is often not the case. (Remember the vanished Matlab program of Dembski and Marks?) It is abundantly clear that there is a wide range of cognitive processes generating phenomena we casually refer to as “designed.” The entity you would appeal to in explaining biological phenomena is nebulous even in human psychology.

    The fact that a term seems clear in meaning in ordinary discourse does not imply that it has much scientific utility. There was a time when earth, air, fire, and water seemed like good elements. Only when people worked at framing explanations in terms of those elements did it become apparent that they were scientifically useless. The ethologists and psychologists who study phenomena that fall under the rubric of “intelligence” do not use the term to explain — not without restrictive operational definition, anyway.

  91. jerry:

    Now if you want to go off and argue that this DNA specifies the person, then I guess you can. But that is just saying that certain parts can identify the whole. A lot of other things can also do that but when it specifies a process of building a polymer with very sophisticated capabilities that it becomes FSCI.

    Of course a lot of other things can do that, and that’s my point. Please show me where in the definition of FSCI it says that the information in question must specify a “a process of building a polymer with very sophisticated capabilities” in order to be FSCI.

    If FSCI is well-defined, why can’t ID proponents agree on whether watermarks are FSCI?

  92. “If FSCI is well-defined, why can’t ID proponents agree on whether watermarks are FSCI?”

    What point are you making? That the definition could be written a little more tight or that the concept is not useful, or that you thing the concept is too general. Your MO seems to be how I can find a glitch is something. Does the watermark or DNA pattern define the individual as the DNA code defines the polymer? No of course not.

    So why don’t you take a crack at the best definition of FSCI and we can discuss it.

  93. gpuccio:

    But FSCI is well defined in a general context, even in the restricted form I have given.

    Not sure what that means. Can you point me to the general context definition that you’re referring to?

    “On massive evidence, such cases [FSCI] are reliably the product of intelligent design, once we independently know the causal story.”

    Indeed, just language and computer programming would be enough for that, and they are clear examples of FSCI, and of digital FSCI.

    No, to show that FSCI is a reliable indicator of design, you can’t just offer a few examples of designed FSCI. You also have to show that FSCI is consistently absent from non-designed things.

    And, on the contrary, much is gained in terms of objectivity, formal completeness and simplicity. But, perhaps, that’s exactly what somebody does not like.

    I don’t know who you’re talking about, but demonstrable objectivity and formality are exactly what ID critics have been calling for from the ID community. The objectivity of ID measures could be demonstrated by showing that people independently come up with the same results when using those measures, but nobody on the ID side has tried to demonstrate that.

    “If we can’t look around and determine whether the things we observe are FSCI or not, this “massive evidence” doesn’t exist.”

    But we can do that.

    Great! Where’s the data published?

    I don’t understand to which studies you are referring. Do you want me to publish a series of short programs in C, to demonstrate that they are digital, functional and complex, and that I am the author?

    That’s a great idea. To do so, you would have to flesh out what it means to be functional and what it means to be complex. Durston et al have tackled the latter, and their definition of complexity turns out to be based on probability. (Is yours also?) This is problematic for the same reason that Dembski’s measures are — namely that it requires calculating probabilities under a MET hypothesis.

    Durston et al, from what I can see, never define “function”. Although the examples in their paper all deal with biological function, Durston’s discussions on this site make it clear that his measure isn’t restricted to biology. So it appears that we can choose any characteristic of the object in question and call it a function.

    For instance, I could say that the function of the 104.27-pound rock in my yard is to exert 104.27 pounds of force on the ground. I could argue that the odds of the rock having this exact weight are pretty slim, thus complexity. I could even fulfill your digital requirement by noting that the rock is composed of discrete atoms.

    You could, of course, come up with some reasons to reject my claim that this rock has FSCI, and we could debate till the cows come home. And that is exactly the problem with the current state of the FSCI concept.

    “Any physical system (except ultimately elemental quanta) can be modeled as digital or analog. So the digital/analog distinction is conceptual, not empirical.”

    Again, I don’t follow you. Can’t you understand the difference between a vynil record and a CD?

    Certainly. The signal from a CD player’s optical transducer is run through an ADC, processed by digital componentry, and then run through a DAC. The signal from a record player’s transducer is processed by analog componentry.

    You and kairosfocus (who is, if I recall correctly, the inventor of the FSCI concept) need to get on the same page. Kairosfocus argues that, “Mona Lisa etc are digitisable, so the use of a digital reference is without loss of generality. (For that matter, the structure of a workable stone arrowhead is digitisable.)”

    I know what you mean when you say digital, but differentiating digital from analog empirically, as opposed to conceptually, is a fuzzy concept.

    But you seem to be saying that the digital requirement is your own restriction for the sake of discussion, and not part of the FSCI definition proper, so I’ll stop making a mountain out of a molehill.

    - continued -

  94. I don’t think it is difficult to give definitions of function, but still that would bring about infinite discussions with you and others, and do you know why? Because you just have to deny what is obvious.

    Actually, I think it’s the lack of solid definitions that brings about infinite discussions. See the example of the 104.27-pound rock in my previous post.

    Obviousness is in the eye of the beholder. The history of science is replete with struggles against notions that are obvious to a lot a people, but wrong.

    I can define function in an universal way only as something which can be recognized as purposeful by an intelligent agent. Is that definition subjective? No.

    Maybe “purposeful” means something different to you than it does to me. To me, it means intentional, but that would render an FSCI-based design inference nothing but question-begging.

    And I would say that such recognition most certainly is subjective. Intelligent agents have all kinds of different ideas with regards to what phenomena are purposeful.

    Strangely, it seems that biologists have not your difficulties in understanding what the function of a protein is.

    I have no problem understanding what the functions of proteins are. What I don’t understand is what your objective distinction between function and non-function is.

    Or just take a program which does not work and input it to your “computing systems will accept any sequence as meaningful” and use it. But please, could we be associates in commercializing that computer system?

    Gladly — such systems are trivial to make. That doesn’t mean that every program is useful.

    So, an object or a system are functional when they serve for a recognizable purpose, and purposes only originate in conscious beings.

    So, to infer design via FSCI, you must determine that the object has function. To determine that it has function, you must show that it serves a conscious being’s purpose. Doesn’t that smack of circularity?

    No, in that context functional means coding for a functional protein (I am still restricting the discussion to protein coding genes, which are the usual object of darwinian evolution).

    Is that your opinion of what functional means, or is that part of an established definition? If so, can you tell me where it’s published?

    First of all, jerry is entitled to his opinions, and sometimes our opinions differ. My view is clear enough:

    How can FSCI be defined objectively and still be a matter of opinion?

    The problem is, what meaning can be conveyed to a conscious intelligent being by that string?

    Are coding genes nonfunctional before they’re decoded by intelligent humans?

    And so? I don’t accept Dembski as an authority, I may well not accept jerry as an authority (my apologies to Dembski and jerry, I am just making an important point). Do we really need authorities to discuss? Does ID really need to be based on the authority of somebody, to be true?

    Certainly not. But it’s hard to see FSCI as an objective concept when its handful of promoters don’t agree on what constitutes FSCI.

  95. 95

    R0b,

    “You also have to show that FSCI is consistently absent from non-designed things.”

    You asked for context. Can you name a non-designed object that carries data (in a digital and conventional code, no less) that is used to create function in a separate object.

  96. jerry:

    So why don’t you take a crack at the best definition of FSCI and we can discuss it.

    I don’t know what the best definition of FSCI is. It’s your (kairosfocus, jerry, gpuccio) concept, not mine.

  97. Upright BiPed:

    Can you name a non-designed object that carries data (in a digital and conventional code, no less) that is used to create function in a separate object.

    If the definition of FSCI is “carries data (in a digital and conventional code, no less) that is used to create function in a separate object”, then I can certainly come up with non-designed examples. Your response will be that the object isn’t really digital, or that it isn’t encoded in a real code, or that the characteristic that I posit as function doesn’t count as function. See the rock example in [93].

    In answer to jerry, yes, my point is that the definition needs to be tightened. ID claims constitute nothing less than a scientific revolution, and such revolutions require rigor.

  98. Upright Biped asks: “You asked for context. Can you name a non-designed object that carries data (in a digital and conventional code, no less) that is used to create function in a separate object.”

    My brain.

  99. 99

    R0b, if you’ve skimmed any of my comments, you’ll not be surprised if I don’t like to play words game while there is an elephant in the room. I think what is good for the goose is also good for the gander. Popper would be proud.

    A code is data (meaning) sent from one entity, through a channel, to another entity to be interpreted as meaning. In the case of DNA, the data is digital (AGTC) and provides the information necessary to create function in protiens and processes within the organism.

    You have some non-designed examples of that?

  100. 100

    iconofld, you’re assuming your conclusions.

  101. Upright Biped: iconofld, you’re assuming your conclusions.

    Not at all. My brain’s unique, and there’s no evidence that it was designed, and no known candidate for the designer. My brain also contains some brand new information that no other brains contain, as does yours. No-one designed that information.

    Does my brain contain new and unique FSCI, or not, in your opinion?

  102. Upright BiPed:

    A code is data (meaning) sent from one entity, through a channel, to another entity to be interpreted as meaning.

    I think that until you put some restrictions on what constitutes “code” and “meaning”, any causal effect fits your description.

    I don’t blame you for thinking that I’m playing word games. I mean, it’s all so simple, right? But good definitions are prerequisite to the ultimate discussion on whether the FSCI-based inductive design inference has legs. I think there are problems lurking in that logic, and which problems need to be resolved depends on how exactly FSCI is defined.

  103. 103

    iconofld,

    I see instead that you not only like to play word games, as conventionalist go, you’re lousy at it.

  104. 104

    R0b

    CODE: “A code is data (meaning) sent from one entity, through a channel, to another entity to be interpreted as meaning.”

    MEANING: “provides the information necessary to create function in proteins and processes within the organism.”

    Since “any causal effects fits my definition” please provide one that was not designed.

  105. Wow! You get distracted one moment, and here you find a lot of work to do!

    R0b, I start with you (Sal, just wait a moment…) :-)

    “Not sure what that means. Can you point me to the general context definition that you’re referring to?”

    As I have said, the same exact definition I gave for FSCI applies not only to biological information, but to widespread human artifacts like linguistic outputs and computer programs. Isn’t that a general enough context for our reasoning?

    “No, to show that FSCI is a reliable indicator of design, you can’t just offer a few examples of designed FSCI. You also have to show that FSCI is consistently absent from non-designed things.”

    And it is! Can you show any non designed thing which exhibits FSCI, according to my definition? And please, don’t come with the notion that we could always find one oin a remote future… The empirical evidence that FSCI is not present in non designed things is overwhelming.

    “The objectivity of ID measures could be demonstrated by showing that people independently come up with the same results when using those measures, but nobody on the ID side has tried to demonstrate that.”

    Why do you say that? If you apply the context I have given, the measures will always be the same, except for when assumptions or approximations have to be made (which is perfectly natural in empirical science). The fact that others may fix the context differently does not mean anything. Measures are relative to a context, and can be done in different ways. I insist that my definition is objective and formally correct, and nobody has really shown why it would not be. All your objections, or Sal Gal’s, have nothing to do with the substance of the definition.

    “Great! Where’s the data published?”

    Great! the appeal to authority again! My compliments… As far as I can say, each time someone here has asked whether some appropriate object (avccording to my definition) exhibited FSCI or not, I have always answered in detail. Please show me a digital sequence for which we cannot say if it exhibits FSCI (and again, don’t appeal to the possible false negatives, which are absolutely expected). The fact is: millions of human artifacts and of biological code do exhibit FSCI, and no known non designed object does. Do you agree on that or not? And if not, please give examples.

    “To do so, you would have to flesh out what it means to be functional and what it means to be complex. Durston et al have tackled the latter, and their definition of complexity turns out to be based on probability. (Is yours also?)”

    Yes.

    “And that is exactly the problem with the current state of the FSCI concept.”

    Absolutely not! Your examples are not correct. A stone is not a digital sequence conveying information. Its dicrete atoms cannot be read as digits conveying functional information. Is it so difficult to understand that in DNA each nucleotide is one of four letters of an alphabete, and that a sequence of aminoacids is written in that way, by means of ordered codons of three letters, and that sucj a sequence ios read for the DNA, via mRNA, by a sophisticated translation mechanisms, which knows exactly which aminoacid to choose according to the codon it reads, and that the resulting protein does things which nothing in the universe could spontaneously do? How can you seriously compare that to the random position of atoms in a stone?

    Again, and I hope for the last time: my definition requires a readable sequence of numbers, and that series of number must convey sone very specific, functional information, of the type we find in machines, in computer programs and proteins: the ability to accomplish a task which would be impossible without that specific information, and which has a well recognizble utility and purpose, so that without it a specific and desired result cannot be obtained. Now, if you and Sal Gal want to show how many strange concepts I have used in the last phrase (purpose, desired result), please be my guests, but I cannot follow you further on that line of reasoning. For me, all that is obvious and clear, and I agree with you on one thing, we could debate till the cows come home, but the reason for that is, for me, certanly different than for you.

    “But you seem to be saying that the digital requirement is your own restriction for the sake of discussion, and not part of the FSCI definition proper, so I’ll stop making a mountain out of a molehill.”

    Thank you. It’s beautiful to be understood, sometimes.

    And yes, I usually agree with kairosfocus, but we can also have different views on some detail. We do not plan positions in advance, and our affinity is completely spontaneous. As a rule, when I discuss I don’t like to be tied to the positions of others, be it my best friend or my worst enemy. I just speak for myself, a bad habit I cannot get rid of.

    - continued -

  106. Upright BiPed“iconofld,

    I see instead that you not only like to play word games, as conventionalist go, you’re lousy at it.”

    I’m not playing word games. My question was serious. Does my brain contain new and unique FSCI or not, in your opinion?

    I haven’t been playing word games elsewhere when I’ve asked people whether they think functional proviruses are designed, and whether they contain FSCI, or not.

    I won’t ask questions that I wouldn’t be prepared to answer myself if they were asked of me.

  107. R0b:

    “See the example of the 104.27-pound rock in my previous post.”

    See my answer in my previous post.

    “Obviousness is in the eye of the beholder. The history of science is replete with struggles against notions that are obvious to a lot a people, but wrong.”

    And it is obviously (sic) infinitely more repleted with things which areobvious to almost all because they are true. To show that something obviously obvious is wrong is certainly possible, but it usually requires, rather than brute force, valid and detailed arguments, which frankly I can’t see in your reasoning.

    “To me, it means intentional,”

    Not exactly. I would rather say: fulfilling a task which appears related to some intention. The function is objectively observable, while the conclusion that it is the product of a conscious intention is the result of our design inference. So, in the blood clotting cascade, it is observable that each step is connected to the following one, and that the useful result is the final one (blood coagulation), but we have to decide if such a functional relation is really the product of design (conscious purpose) as it seems, or iof it can be explained as some random or necessity output.

    “but that would render an FSCI-based design inference nothing but question-begging”

    No, as I have explained. The function in FSCI is observable. How can you deny that the function in blood coagulation is observable? One thing is to observe a functional mechan ism, and another thing to asceratin how it came into being. Again, it’s complexity which allows us to stay away from possible apparently functional structures whcih are simple enough to originate by chance.

    “And I would say that such recognition most certainly is subjective. Intelligent agents have all kinds of different ideas with regards to what phenomena are purposeful.”

    I know of no biologist or medical doctor who doubts that the phenomenon of blood coagulation is purposeful and that it serves the function to avoid the certain death of every individual for even a minor wound. Again, hemophiliacs know that very well. Would you argue with them that coagulation function is a subjective concept?

    “What I don’t understand is what your objective distinction between function and non-function is.”

    Coagulation factors are functional if they can bring to normal coagulation. Hemoglobin is functional if it can bind oxygen according to a very specific pattern. Transcription factors are functional if they can bind to DNA in very specific ways. If any of those proteins changes, even a little, so that it cannot do those things any more, that is non function. What is difficult to understand in that?

    “Gladly — such systems are trivial to make. That doesn’t mean that every program is useful.”

    But the point was exactly that: to maje the program which does not work work. Ah, but you have used the word “useful”! Be careful…

    “So, to infer design via FSCI, you must determine that the object has function.”

    I must determine that the object has observable function, IOW that it does something which appears to have a purpose.

    “To determine that it has function, you must show that it serves a conscious being’s purpose.”

    No, you are wrong. We observe the function, but we are not sure if it is a real function (the product of a conscious purpose) or an apparent function (the product of chance and/or necessity which has assumed a pseudofunctional structure). That’s where complexity, and the design inference, are necessary.

    “Doesn’t that smack of circularity?”

    No. Your wrong interpretation is circular, not my true argument.

    “Is that your opinion of what functional means, or is that part of an established definition?”

    It’s my opinion of what functional means for a protein coding gene. I am very confident that most people in the world who know what a protein coding gene is would agree with me.

    “If so, can you tell me where it’s published?”

    Oh, again! Must I tell you where it’s published that a protein coding gene is functional if it codes for its correct protein? Or where it’s published that a car is functional if it moves? Or a radio if it receives radio programs and translates them into sounds? Shall I go on?

    “How can FSCI be defined objectively and still be a matter of opinion?”

    I don’t want to spoil your ideals, but have you ever heard that people entertain different opinions even about the most objective issues? (and no, I was not thinking of darwinian evolution… ) :-)

    “Are coding genes nonfunctional before they’re decoded by intelligent humans?”

    I don’t think I understand the question. Coding genes are functional if they carry functional information (the right sequence for a functional protein), and non functional otherwise. Intelligent humans certainly need to decode them to verify that.

    “Certainly not. But it’s hard to see FSCI as an objective concept when its handful of promoters don’t agree on what constitutes FSCI.”

    Your concept of objectivity seems too connected to the vote of the majority for my taste. I am definitely a minority guy.

  108. iconofid:

    You ask:

    “Does my brain contain new and unique FSCI or not, in your opinion?”

    I can’t speak for others, but my answer is definitely yes.

  109. 109

    iconofld,

    “Does my brain contain new and unique FSCI or not, in your opinion?”

    Your brain is not the issue. The idea that your very own thoughts creating unique pathways in your brain is not the issue either.

    The questions you raise end in the same spot every time. Could your brain exist, with all of your very own uniqueness, without the biological processes that made up its existence in the first place?

    With or without your uniquness, the brain systems themselves remain unaccounted for.

    At one point in the history of this planet there were no brains, or anything else made of living tissue. Now there is.

    You are a materialist, I presume. Can you please specify what are the material properties of hydrogen, oxygen, nitrogen, iron, ect., that would cause those chemicals to become organized into coordinated structures that record their existence?

  110. gpuccio says: “iconofid:

    You ask:

    “Does my brain contain new and unique FSCI or not, in your opinion?”

    I can’t speak for others, but my answer is definitely yes.”

    I agree. I’d see this as evidence of the natural emergence of new FSCI.

  111. 111
    George L Farquhar

    gpuccio

    No, you are wrong. We observe the function, but we are not sure if it is a real function (the product of a conscious purpose) or an apparent function (the product of chance and/or necessity which has assumed a pseudofunctional structure). That’s where complexity, and the design inference, are necessary.

    Can you give me an example of this process?

  112. 112
    George L Farquhar

    Upright Biped

    You are a materialist, I presume.Can you please specify what are the material properties of hydrogen, oxygen, nitrogen, iron, ect., that would cause those chemicals to become organized into coordinated structures that record their existence?

    Can you specify the non-material properties that would cause them to do so?

  113. 113

    “I’d see this as evidence of the natural emergence of new FSCI.”

    …and all it took was for some helium, carbon, nitrogen to form and record their existence so your brain could someday exist.

    Were did that come from?

    (shrugs)

  114. 114

    helium…I’m killing myself.

  115. iconofid:

    “I’d see this as evidence of the natural emergence of new FSCI.”

    Not me. But I could not discuss that kind of issues, even hypothetically, without going into deeply metaphysical subjects about highly mysterious questions, such as: how does the unique identity of each of us arise?

    And I try never to use the word “natural”: it means nothing. My position is more or less that everything is natural, or everything is supernatural, as you prefer.

    So, while I bow to the unique treasure of your human identity, I keep my polite reservations about its possible emergence as a product of mere randomness and/or necessity.

  116. Upright BiPed “The questions you raise end in the same spot every time. Could your brain exist, with all of your very own uniqueness, without the biological processes that made up its existence in the first place?”

    No, certainly not.

    “At one point in the history of this planet there were no brains, or anything else made of living tissue. Now there is.”

    Quite right.

    “You are a materialist, I presume. Can you please specify what are the material properties of hydrogen, oxygen, nitrogen, iron, ect., that would cause those chemicals to become organized into coordinated structures that record their existence?”

    By a materialist, presumably you mean someone who looks for natural causes for natural phenomena? If so, yes, but it’s no grand philosophy, just that I know of no evidence for such a thing as the “non-natural”.

    You’re not asking me the physics of what causes chemical reactions, presumably. You’ll agree that chemicals react, and that that creates new chemical formations. There’s no law of chemistry or physics that I know of that prevents chemicals forming into formations that self replicate, so I see no difference between that chemical phenomenon and any other that we see around us.

    The “property” you’re asking for is presumably, then, the ability to react in many different ways in many different environments.

  117. 117

    Upright BiPed,

    Your question “Where did that come from?” would seem just a mirror image of the infinite loop argument ID opponents have been warned not to make. If I can’t make it about the designer, I don’t think you should be able to make it about new FSCI/FCSI.

  118. Sal:

    I have read your last post with great interest. Your arguments are deep and consistent, but they just demonstrate that our fundamental views of reality are very different. So, while admiring as usual your intelligence and creativity, I have to reject them as a whole.

    But obviously, I don’t want to engage with you here in a confrontation of general world views. I would like only to briefly address the main points of divergence, just for your satisfaction, and then stay happy that we think differently.

    I “am” committed to empiricism. But my empiricism does include subjective experience. None of your arguments against that is convincing for me.

    The fact that you seem to forget is that “all” experience is subjective. The experience of the senses and of so called objective data is no exception. The experience of reason is no exception.

    In no way I can give priority of knowledge to a part of our experience (sensory experience of external objects, inductive reasoning, logic) against all the rest. The intuition of consciousness and of its qualities and activities has absolute priority in our experience, and so it should have in our wisdom (including science).

    Science, philosophy, art, psychology, religion, are all different facets of the same search for truth. Each gives its contribution, and all are connected.

    You reservations about the non objective nature of subjective experience bears no sense for me. I could just have the same reservations about the non objective nature of objective experience. To me, there is nothing more certain and more real than the existence of my “I”, not even the existence of matter. The fact that inner experiences can be described in different ways does not make them in any way less real and objective: everything in the universe can be described in different ways, and words are in themselves elusive symbols.

    I am not arguing for subjectivism; on the contrary, I am arguing for the absolute objectivity of all that exists, and for the noble attempt which is the privilege of human cognition (not only of human reason) to search for some sense in such a contradictory context.

    Indeed, intelligence is in a way a secondary matter: consciousness is the primitive issue, and intelligence is one of its activities. Consciousness does not only perceive and cognize: it has needs, enjoys and suffers, loves and desires, imagines and creates, and as a result of all that it wills, and it wills freely. Consciousness creates and destroys, and has nothing to do with the imaginary determinism which misguided reason projects on everything, or with the empty constructions of some human philosophy which forgets its true purposes and the impellent needs of the perceiving I.

    Consciousness is not a loop of objective calculations, not an explosion of bits, or a display of parallel arithmetics. Purpose is not a category of reason, but a very intense experience of the soul.

    So, excuse me for this (very subjective) expression, but I cannot follow you on those territories. My personal cognitive world is probably different, and in my world those poor arguments about consciousness, intelligence and purpose remain simple and valid.

  119. gpuccio, well stated in #105 and #107.

    I would just like to add a couple things.

    ?Definition of a code: Given a source with probability space [Omega, A, p(A)] and a receiver with probability space [Omega, B, p(B)], then a unique mapping of the letters of alphabet A onto letters of alphabet B is called a code. Here p(A) is the probability vector of the elements of alphabet A and p (B) is the probability vector of the elements of alphabet B. (Perlwitz, Burks and Waterman, 1988). According to this definition, which is very simple, DNA is a code, whereas the atomic configuration in a stone is not a code.

    Function can be seen in a couple different ways and both are useful to ID.

    1. Function can simply be referred to as the transfer of energy to perform work as a by-product of organized units (where that organization is not defined by mere regularity nor by the physical laws of the material used).

    Here are some quotes by George Gaylord Simpson and then Michael Polonyi referring to these concepts:

    ““In the face of the universal tendency for order to be lost, the complex organization of the living organism can be maintained only if work – involving the expenditure of energy – is performed to conserve the order. The organism is constantly adjusting, repairing, replacing, and this requires energy. But the preservation of the complex, improbable organization of the living creature needs more than energy for the work. It calls for information or instructions on how the energy should be expended to maintain the improbable organization. The idea of information necessary for the maintenance and, as we shall see, creation of living systems is of great utility in approaching the biological problems of reproduction.”

    George Gaylord Simpson and William S. Beck, Life: An Introduction to Biology, 2nd ed. (London: Routledge and Kegan, 1965), 145

    “A shaping of boundaries may be said to go beyond a mere fixing of boundaries and establishes a ‘controlling principle.’ It achieves control of the boundaries by imprinting a significant pattern on the boundaries of the system. Or, to use information language, we may say that it puts the system under the control of a non-physical-chemical principle by a profoundly informative intervention.”

    –Michael Polanyi, “Life Transcending Physics and Chemistry,” Chemical & Engineering News (21 August 1967): 64.

    2. Function can also be seen in the mathematical sense as a *specific input* providing *one output*.

    3. Both of the above definitions of information provide all that is needed on order to refer to function.

    Of course, function by itself will not help us arrive at an inference to previous intelligence.

    How about coded information that provides function? Well, this brings us to functional specificity, since we are discussing an event which can be formulated as an independent pattern: event (function) –formulated as its–> pattern (code).

    Although, no one has yet provided evidence of functional codes forming absent previous intelligence, the ID hypothesis doesn’t stop here. We need Functionally Specified Complexity.

    …and of course, we all know that complexity is measured by measuring the probability of finding all specified patterns of same length as said specified pattern against all probabilistic resources (number of trials in space and time) available.

    … and thus we have FSCI.

    As an aside it is interesting to note, as Hubert Yockey has in “Origin of life on earth and Shannon’s theory of communication,” Computers and Chemistry 24 (2000) 105–123, that “The transmission of genetic messages from the DNA to the protein tape as conceived in molecular biology” follows the same system/pattern as “The transmission of information from source to destination as conceived in electrical engineering.”

    …interesting since that type of pattern is the result of intelligent engineering.

    Is there any reason we would expect un-intelligent processes to create such a system? Is there any reason to rule out intelligence as a creation of such a system? Evidence either way?

  120. 120

    Iconofld,

    “By a materialist, presumably you mean someone who looks for natural causes for natural phenomena?”

    I would say that is partially correct, but doesn’t fully express materialism in the dress it wears today. I think IDist in general all look for material causes. I have never read a work by a design proponent that said “and then a supernatural force…” I don’t think such material exist, but it wouldn’t interest me to read it if it did. The distinction I make is someone who arbitrarily removes from knowledge one of the three observable causes in nature – about the things he cannot answer, and realistic, can barely fathom. I don’t think those who swear to empiricism, or those who know the most about the issue, should claim to have any more command over what they know than what they know. I think the history of mankind, even the recent history of mankind, supports that idea without question. This includes science, politics, law, and religion in equal measure. What I dislike most are persons who agree with that statement in one breath, then subvert it the next. There is little doubt it is the most common mistake man makes, and material science makes it with metronomic regularity.

    I agree with you that “non-natural” is sometimes as useless as “natural”, the question is what is. The evidence for ID is purely empirical and every reasonable person can acknowledge that. Philosophical questions of what design might mean are what they have always been.

    The reason I asked the question I did, is to set out that the material elements of the universe offer no explanation to the questions that men and women ask.

    Your answer, “The “property” you’re asking for is presumably, then, the ability to react in many different ways in many different environments” is therefore insufficient, nor do I believe you intended it to be comprehensive.

    We know why water boils off the sidewalk on a cold day, we know what happens to iron molecules that mix in different environments, and why undissolved proteins adhere to the surface tension of oxygen and hydrogen. We haven’t even the faintest clue why chemical elements would organize themselves into layers of highly-coordinated organizations operating off information and recording their existence in digital code. Any answers to the question of “why” are idle. I also find it interesting that if one could somehow start with the nose on their face and travel back through time, and through every chemical reaction that lead to its existence, he would have to stop at the information that distinguishes living tissue from inanimate material – and could go no further. That is where the material trail ends.

    So what we have are professional mathematicians arguing over trivialities blown up to be earth shattering differences, public campaigns devoted to ridiculing all those that don’t drink the Kool-Aid, research papers that say one thing yet describe another, and legal maneuvers sent in from the back room – and all the while, we haven’t a material clue.

    The only thing we know capable of what we see in molecular life is an act of volitional agency. Selection for fitness at the nucleic level. Period.

    Perhaps we could at least agree that (S)cience would be more intellectually honest if it returned to healthier sense of humility on such issues.

  121. CJYman:

    Thank you for your very beautiful post, wich gives unexpected and very rigorous support to my poor intuitive concepts, confirming that what is obvious is sometimes obvious for a reason.

    Your efforts to find an objective definition for function are really remarkable and, as far as I can judge, very satisfying. I humbly suggest, however, that the concept of recognizable apparent purpose by intelligent observers is not without merit, and can be an useful complement to more “objective” definitions.

    And finally, I am always in awe at quotations from Polanyi: thank you also for that.

  122. 122

    CJY, thank you as well for the more rigorous definitions.

    The definition you’ve given regarding function is engineering based – which makes all the more sense (and clarity).

  123. gpuccio:
    “the concept of recognizable apparent purpose by intelligent observers is not without merit, and can be an useful complement to more “objective” definitions.”

    I agree completely; the main reason why I posted what I did is more so because I am amazed that some people just don’t seem to get it yet. I am surprised that we still have to go over these basic fundamentals with some people who claim to have enough knowledge of ID that they can critique it. And of course, I do think that the subjective aspect can only really come into play in the scientific arena once a more objective definition is given. But, of course, there still is room for the subjective complement as you put it. We are subjective beings after all and everything we do has a subjective element in it — we wouldn’t know about the objective if we had no subjective experience (but that is another topic for a more philosophical discussion).

    … and I too am amazed at the insights of Michael Polonyi.

  124. GP & CJY:

    Good work.

    If one denies our own intelligence we have no grounds for intelligent discussion.

    And if you are forcesd to reject the blatant fact that we form concepts out of experiences then seek to define to identify borders, then you don’t understand how we learn or how definitions work.

    Tell me folks: how can you tell that a definition is failing?

    ANS: it does not accurately agree with examples and /or does not properly exclude counter-examples. So, examples — empirics — MUST come first, and serve to give flesh to definitions.

    So, now take the text in this post assuming it is beyond 143 ASCII characters:

    1 –> Can you see that this has given us a quantity of functional information, based on stringing characters, words and the underlying ideas they express together in accord with certain rules for them working together?

    2 –> That this 1,000 bit limit in the 143 7-bit characters constraint has given us a reasonable threshold of complexity for which we have excellent grounds to see that the observed universe acting as search engine could not reasonably come near to, per chance + necessity search resource exhaustion?

    3 –> Do we not see that intelligences — of which we are undeniably [on pain of absurdity] examples of — routinely produce such?

    4 –> Worse, for the code that makes this post work as a post? [Do we not see that we can measure it in working -- functional bits? That it exists in a context of irreducibly complex entities that must all work together in ways that are do co adapted that chance is maximally unlikely for this to work?]

    5 –> Do we not see that DNA is similarly digital, algorithmically functional complex code, of measurable bit capacity . . . starting not at 1 k bit but 600++ k bits?

    6 –> that is is a part of a similarly irreducibly complex nanotech, algorithmic, code based information processing entity in the heart of the cell? [Using codes that we have partly decoded too.]

    7 –> That this is known to be reprogrammable [both by viruses and Venter et al as well as recombinant DNA technology!], i.e we have a nanotech, self-replicating COMPUTER in the heart of the cell?

    8 –> that we know a source for computers, and we have excellent reason to see that chance + necessity on the gamut of our cosmos cannot reasonably be seen as capable of spontaneous generation of that irreducibly complex entity?

    9 –> That such things are plainly — beyond REASONABLE doubt — the product of not only highly intelligent but highly sophisticated design, operating on a level that is way beyond our own current capacity?

    but, nah, that cannot be . . . it just may point in directions the friendly local magisterium does not want us to go:

    It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door. {Lewontin, NY Review of Books, 1997. Since made dogmatically “official” by the C21 magisterium — NAS, NSTA, NCSE, judge Jones, the new atheists, et al . . .]

    It’s high time to overthrow that magisterium and its chains of mental slavery!

    GEM of TKI

  125. CJYman @ 119,

    I just downloaded and read the Perlwitz, Burks, and Waterman paper “Pattern Analysis of the Genetic Code” (1988). I can’t find in it the definitions you’ve given for a code. They begin with a statement that the mapping from RNA triplets to amino acids and STOP is a code. tRNA is the physical instaniation of this code.
    By your definition, DNA is not a code. It might be ‘language A’ in the mapping to mRNA, and that very simple mapping is a code. I think that by your definition, the mapping of A to A would be a code just a bit simpler than the DNA to mRNA code, and that kind of code is used in rocks all the time for crystal growth.

  126. Pendulum:

    I am not a mathemathician, but I don’t understand your objection. Here is the definition given:

    “Definition of a code: Given a source with probability space [Omega, A, p(A)] and a receiver with probability space [Omega, B, p(B)], then a unique mapping of the letters of alphabet A onto letters of alphabet B is called a code. Here p(A) is the probability vector of the elements of alphabet A and p (B) is the probability vector of the elements of alphabet B.”

    It is very clear that DNA maps onto mRNA and, Through that, onto proteins. The two processes are different. Mapping ot mRNA is a mapping where each nucleotide in DNA maps to the complementary nucleotide in mRNA. That’s certainly a mapping, but one whose only function is to “export” the information in DNA to the translation system. The single letters are not the same (the alphabet is complementary in mRNA), but the information is exactly the same.

    But the true mapping takes place in the translation system. Here, the units of A which map onto B are not the single nucleotides, but the codons. Each of the 64 codons maps unequivocally to one aminoacid, or to a stop signal. That’s, IMO, is a code according to the above definition. PERLWITZ, BURKS, AND WATERMAN seem to agree, given that in their paper they write:

    “The genetic code is examined in a new and systematic fashion: we consider the code as mapping of one finite set (the 64 codons) to another (the 20 amino acids).”

    You can object that in reality it’s the mRNA which physically maps onto the protein. That’s true, but the information in mRNA is the same as the information in the gene (except for post-transcriptional modifications, which have an important role, but for simplicity we won’t discuss them here).

    So, I can’t understand your argument, and least of all the reference to crystals. What maps to what, in crystals?

  127. Hi gpuccio,

    What I objected to in CJYman’s post was that it seemed from his formatting that he was attributing all the Omega, probability vector stuff in the quoted definition to Perlwitz, et al. But the PBW paper doesn’t say that. If that is a quote, it is a quote of someone else.

    I quite agree that for purposes of discussing the DNA-mRNA code, we can leave out discussions of introns etc. The point is that a mapping exists, and it is very simple.

    Crystal growth is just the very very simple map of a language onto itself. In cryptography, a substitution cipher is a mapping of the letters of a language onto themselves. The Ceasar cipher, or ROT13 are examples.

    A mapping from the language {Na, Cl} to the language {Na, Cl} for example, can grow salt crystals. A previous post wanted to dismiss the atomic structure of rocks out of hand. I was trying to point out some rocks, those that contain crystals, at least, do have an atomic structure dictated by a code.

  128. Mappings, alphabets, and codes exist platonically, so physical systems technically cannot be a codes, although codes may be involved in how we model such systems.

    Any system with law-like behavior can be modeled using a mapping from cause to effect. Consider the rock in my yard — there is a mapping between the number of atoms in the rock and the force felt by the ground underneath. And considering how many different options there are with regards to the number of atoms in a rock, the alphabet is enormous.

    Stepping back a little, the objective seems to be to define FSCI such that it’s a property of some biological systems and some man-made artifacts, and nothing else. I think that the current status of the definition doesn’t accomplish that, but it could do so with some more fleshing out.

    The argument would then presumably be:
    1) All FSCI of known provenance is designed.
    2) By induction, we conclude that all FSCI is designed.
    3) Some biological structures have FSCI.
    4) Therefore, those biological structures are designed.

    But that logic doesn’t stand on its own. Consider another application of this logic:

    1) All FSCI of known provenance is designed by humans.
    2) By induction, we conclude that all FSCI is designed by humans.
    3) Some biological structures have FSCI.
    4) Therefore, those biological structures are designed by humans.

    This conclusion is clearly wrong.

    The fact that biology and artifacts have the common property of FSCI may be best explained by the ID hypothesis, or it may be better explained by a different hypothesis. I think it depends very much on how the definition of FSCI is fleshed out.

  129. Pendulum:

    OK, I accept the point about crystals in good faith. Anyway, crystals obviously don’t qualify as FSCI because thay lack complexity and can be explained through necessity, as discussed many times. That is true of all forms of “self-organizing” structures, a la Prigogyne.

    And let’s remember that in proteins it’s not just the existence of the code which qualifies as FSCI (although it is in itself a rather stunning fact), but rather the information which is conveyed by the code: the thousands and thousands of different functional proteins, each of them in average of hundreds of aminoacids.

  130. I think we can agree on many points in the terns of your last post. I would only add the following:

    1) The design inference is not a logical demonstration, not a syllogism, and not a deductive argument. It is an empirical inference to the best explanation available, and as such all that we need is a rationale for the inference, logical explanatory consistency and sufficiency, and the lack of any better explanation (indeed, IMO, of any other explanation).

    2) It is true that your syllogism in the second form is not true. But I have argued many times that the positive element in ID consists in our personal experience (subjective and objective) of the design process in humans, an experience which directly connects the design process to consciousness and intelligence and purpose, and not necessarily to just being humans. In that sense, any conscious intelligent being (if such will be shown to exists beyond humans) can qualify as a designer. Aliens are a good example of that reasoning (as even Dawkins has admitted). But obviously, non material entities could also qualify, for those who believe they exist.

    The fact is, it is being conscious and intelligently conscious, being able of representation, logical reasoning, inference, purpose, and so on, which apparently allows humans to be designers.

    So, the ID inference is a quite reasonable explanation of biological realities, which share with other designed things all the characteristics of the products of design. Humans could qualify as designers, but there are obvious reasons to believe that they were not around when those things started to happen. So, other conscious intelligent beings could qualify as designers of biological realities. The existence itself of biological information is a good prompt to ask ourselves if such designers exist, and what they could be.

    As we have said many times, the design inference in itself does not tell us much, if anything, about the nature of the designer and about the modalities of design implementation, but as I have debated many times, those points are certainly open to scientific inquiry.

    In the meantime, the design inference for biological information remains a reasonable and sound theory. The lack of any other credible non design theory can only give it further weight.

  131. I’ve said before that to me, intelligence has to do with behavioral complexity, and also the degree of perceptual discrimination and acuity. So that if you have a program that does almost the same thing regardless of input (for example possibly because the program can only “see” the first n-bits of any input, then it is relatavely unintelligent. Or if you have a program that sees a much larger percentage of its input and furthermore the output it generates is highly variable, not trivially deducible from the input via any simple program for example, than that program is more intelligent.

    [also off-topic]

  132. (the above post was in the wrong thread.)

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