Wagner’s Multidimensional Library of Babel (Piotr at UD)

I’ve wanted to start this discussion for several weeks, but wasn’t sure how to present Wagner’s argument. Fortunately Piotr has saved me the trouble with a post at UD.

Piotr February 24, 2015 at 1:35 pm
Gpuccio,

Do you mind if I begin with a simple illustrative example? Let’s consider all five-letter alphabetic strings (AAAAA, QWERT, HGROF, etc.). By convention, a string will be “functional” if it’s a meaningful English word (BREAD, WATER, GLASS, etc.). Functionality is therefore not a formal property of the string but something dictated by the environment. There are 26^5 = 11881376 (almost 12 million) possible five-letter strings. The number of five-letter words in English (excluding proper nouns and extremely rare, dialectal or archaic words) is about 6000, so the probability that any randomly generated string is functional is about 0.0005.

Any five-letter string S can produce 5×25 = 125 “mutants” differing from S by exactly one letter. If you represent the sequence space as a five-dimensional hypercube (26x26x26x26x26), a mutation can be defined as a translation along any of the five axes.

It would appear that the odds of finding a functional mutant for a given string should be about 125×0.0005 = 1/16 on the average. In fact, however, it depends where you start. If S is functional, the existence of at least one functional mutant is almost guaranteed (close to 90%). For most English words there are more than one functional mutants. For example, from SNARE wer get {SCARE, SHARE, SPARE, STARE, SNORE, SNAKE, SNARK…}. Though some functional sequences are isolated or form small clusters in the sequence space, most of them are members of one huge, quite densely interconnected network. You can get from one to another in just a few steps (often in more than one way), which is of course what Lewis Carroll’s “word ladder” puzzle is about:

FLOUR > FLOOR > FLOOD > BLOOD > BROOD > BROAD > BREAD

You can ponder the example for a moment; I’ll return to it later.

The Elephant in the Room

The whole thread is worth a look.

I might add that there is a rather crude GA at http://itatsi.com that does something not entirely unlike a word ladder.

352 thoughts on “Wagner’s Multidimensional Library of Babel (Piotr at UD)

  1. In his 1970 paper Natural selection and the concept of a protein space the late John Maynard Smith used the same word game as an example of the clustering in protein sequence space. His example was the four-letter-word ladder WORD -> WORE -> GORE -> GONE -> GENE.

  2. What gpuccio can’t seem to follow is that WORE ->->->GENE can be possible while WORE -> WENE is not.

    Gpuccio’s argument has always been that if there are no sequence similarities, there can be no descent.

  3. Joe Felsenstein,

    In his 1970 paper Natural selection and the concept of a protein space the late John Maynard Smith used the same word game as an example of the clustering in protein sequence space.His example was the four-letter-word ladderWORD -> WORE -> GORE -> GONE -> GENE.

    Wow, thanks! I didn’t know that. It just struck me as a nice analogy.

  4. Remember that even a near-hit is often still functional. Words can be read and understood even with spelling errors in them, so they don’t even have to be exact matches. If we allow understanding despite small amounts of spelling errors, all the more reason large amounts of “wordspace” can be bridged by mutations while still retaining functional words.

    Also, even with bad grammar sentences can still be read and understood, so they can also remain “functional” even if individual words might mutate fully into nonfunctionality, because the rest of the sentence “compensates” for the destroyed or misplaced word.

    Further still, there are many different concepts and ideas that can be relayed with sentences, just like there are many different organisms that live in totally different environments and through different means. So while one sentence initially is intended to convey some particular concept, mutate it enough and it stops communicating that concept effectively, but it might have taken on an entirely different but still comprehensible meaning.

    There is room for both deleterious, neutral and adaptive change at every level of written communication.

  5. Often forgotten in the analogising are the possibilities afforded by multi-residue mechanisms of mutation, and by redundancy eg from duplication. Insertions and deletions and consequent frame shifts, and recombinations, afford a vast increase in the dimensionality of the space, and redundancy allows an environmental context which is much more permissive than the network available to strings in a primordial alphabet soup.

    Eukaryotic meiotic recombination also affords the possibility of distributed processing, subdividing the ‘problem’ and evaluating at subgenome level with networking of surviving solutions to the multiple issues. (At which point the standard counter-bid is “heck your position can’t even account for recombination”).

  6. Allan Miller,

    The same happens in linguistics (e.g. a word may develop alternative phonetic realisations which are then grammaticalised as different lexemes; words can “contaminate” one another Humpty-Dumpty-style, like SMOKE x FOG > SMOG, or undergo composition followed by structural compression obscuring their origin, like Old English HLĀF-WEARD ‘bread-guardian’ > LORD). I use a grossly simplified model in the UD discussion only to illustrate my point: any amount of functionality can be reached even in a vast search space if functional structures are not randomly scattered but form a web, and if you start with something already functional.

  7. Folks like kariosfocus and gpuccio reject this because they are smart enough to realize that if the web analogy is true, ID is dead. Since biologists have assumed that new functionality was reachable, the only issue has been accumulating enough supporting data. This also explains why IDists Cling to Doug Axe.

  8. Have any creationists/IDists responded to this line of research, or to The Arrival of the Fittest?

  9. Axe limits his spaces unrealistically, tending towards non-evolutionary mechanisms of change. Serially disabling residues only on the protein surface, for example, is not available to evolution – replication/mutation/recombination/transcription/translation: none of these processes have any idea where the protein surface is. Once you allow interior amendment, again you have access to a much more subtle and connectable space, since the interior change affects what can happen at the surface.

    As to generating a protein chimera and demonstrating inactivity … this would be convincing if this was the only chimera available, ever. Still, it takes a certain kind of dedication to spend lab hours in search of negative results.

  10. Allan Miller: Still, it takes a certain kind of dedication to spend lab hours in search of negative results.

    Negative results pay his bills.

    As for the ID response to Wagner, there’s this:

    http://www.evolutionnews.org/2014/11/arrival_of_the091261.html

    To make the hunt easier for evolution, Wagner imagines a fantasy land with treasures all over the place, right near each other: “Wagner finds that he does not have to travel very far along these mutational pathways before he encounters new neighbourhoods, where the networks produce different products,” Pagel explains sympathetically while personifying evolution. “For instance, a network that can consume glucose might lie near one that can consume other fuels, such as acetate.” Yes, and if a squid had wings, it could fly like an albatross. After all, they are neighbors.

    These simplistic propositions would wither before Dembski’s No Free Lunch and Meyer’s Signature in the Cell, but since Nature is unfriendly to challenges to natural selection, Pagel’s endorsement echoes around the world. The unreflective now know how the squid took wing and began to fly.

    That seems to be their response.

    And gpuccio is unimpressed..

  11. Piotr Gasiorowski:
    Allan Miller,

    The same happens in linguistics (e.g. a word may develop alternative phonetic realisations which are then grammaticalised as different lexemes; words can “contaminate” one another Humpty-Dumpty-style, like SMOKE x FOG> SMOG, or undergo composition followed by structural compression obscuring their origin, like Old English HLĀF-WEARD ‘bread-guardian’ > LORD). I use a grossly simplified model in the UD discussion only to illustrate my point: any amount of functionality can be reached even in a vast search space if functional structures are not randomly scattered but form a web, and if you start with something already functional.

    http://en.wikipedia.org/wiki/Portmanteau

  12. petrushka(quoting ENV): To make the hunt easier for evolution, Wagner imagines a fantasy land with treasures all over the place, right near each other: “Wagner finds that he does not have to travel very far along these mutational pathways before he encounters new neighbourhoods, where the networks produce different products,” Pagel explains sympathetically while personifying evolution.

    I’ll note that O’Leary seems to find a fantasy land with treasure all over the place. Whenever she wants to criticize science, there is always something available for her to sneer at.

  13. There needs to be some biological equivalent of Clarke’s law:

    Any version of ID that is consistent with all the evidence is indistinguishable from evolution.

  14. Just a post to note that the debates are still raging at UD. Barry seems to have selected four or five evilutionists to remain alive. Fortunately, they are good.

  15. This, however, has to do more with the structural limitations of the English lexicon and the distribution of possible word lengths than with the nature of the search. The word-ladder thought-experiment wasn’t supposed to be an exact analogy of evolutionary “searches” (for one thing, “functional” DNA sequences are of neither fixed nor limited length; for another, there are many possible types of mutations beside single point substitutions). I just wanted to highlight one point: if functionality obeys some external constraints (here, the “Englishness” of words), functional structures are not randomly dispersed in the sequence space. They tend to cluster together and to form an interconnected web, rather than a rugged landscape with towering lonely peaks. That’s also part of Andreas Wagner’s message.

    The Elephant in the Room

    Might I point out that gpuccio is willfully obtuse when it comes to evolutionary algorithms. They don’t work,and he’s not ever going to admit they do.

    Plus, he exhibits a raging case of metaphor reification. This is common to most IDists. First you make an analogy between biology or chemistry. Then you point out the limits of the analogous system, be it computer programs or GAs or whatever. then you argue that the same limitations apply to chemistry.

    So if mutation breaks a computer program, then mutation can’t help but break genomes.

    If word ladders can’t reach all English words, then evolution could not have reached all current sequences. For gpuccio, this applies to orphan protein coding sequences.

    He will never change his mind on this.

  16. I am particularly amused by the ID argument that language evolution is the result of design.

  17. Yes, get them talking about linear strings, and then all linear strings are supposed to have the same properties regarding the packing and connectedness of their sequence spaces, and the effect of string length and residue variation on those parameters. Which is clearly bogus.

  18. petrushka:
    I am particularly amused by the ID argument that language evolution is the result of design.

    Don’t they wish.

    The mindless (or actually, in a way mindful, but unreasonable) retention of obsolete spellings (think of the French “h,” and the mess English is with regard to spelling), irregular verbs, and strange etymological connections are what show language not to be designed, with intelligence working to conserve the illogical, and in other cases to rationalize the irrational.

    If the very lack of overall design in language evolution can be christened “Design,” then the even greater lack evidence of intelligent intervention in biology can be pretended to also be “Design.” Works better than finding genuine evidence for design in life.

    Glen Davidson

  19. I’ve long known about word ladders but beyond basic knowledge of their existence I’ve never given them so much as a second thought. Curiosity made me Google them and I discovered some beautiful images that can only be described as landscapes.

    The Longest Word Ladder Puzzle Ever

    TSZ is great.

    Chrome does not like Google to not be capitalized!

  20. It’s quite symbolic that Lewis Carroll’s original solution “evolving” APE into MAN:

    APE > ARE > ERE > ERR > EAR > MAR > MAN,

    has been replaced by a shorter alternative path:

    APE > APT > OPT > OAT > MAT > MAN

    (discovered, by the way, many years ago independently by several Martin Gardner fans, see the chapter on the games and puzzles of Lewis Carroll in “Mathematical Diversions”).

  21. And of course if you allow a path to visit the next dimension:

    APE -> CAPE -> CAP -> MAP -> MAN

    or

    APE -> CAPE -> CANE -> CAN -> MAN

    Mind you, Joe doesn’t believe proteins can extend, so that path is unavailable to biological strings 😉

  22. Allan Miller,

    APE > ATE > MATE > MAT > MAN
    APE > ARE > MARE > MAR > MAN
    APE > ARE > MARE > MANE > MAN
    APE > NAPE > NAP > MAP > MAN
    APE > RAPE > RAP > RAN > MAN
    APE > ALE > MALE > MANE > MAN
    APE > GAPE > GAP > MAP > MAN
    etc., etc., etc.

    Gorblimey, higher dimensions make evolution too easy!

  23. Petrushka said:

    Any version of ID that is consistent with all the evidence is indistinguishable from evolution.

    And, any version of Darwinism that is consistent with all the evidence is also indistinguishable from “evolution”, if we’re defining “evolution” as a sum of pertinent evidence without metaphysical interpretations.

    Competing theories can both be consistent with the evidence yet posit different kinds of causes. ID theory and Darwinism are certainly consistent with evolutionary evidence; the question is which one better accounts for that evidence.

  24. William J. Murray: ID theory and Darwinism are certainly consistent with evolutionary evidence; the question is which one better accounts for that evidence.

    But, William…

    There is no ID theory. Nobody – Nobody! – has formulated a testable ID theory, yet.

  25. William J. Murray:
    Petrushka said:

    And, any version of Darwinism that is consistent with all the evidence is also indistinguishable from “evolution”, if we’re defining “evolution” as a sum of pertinent evidence without metaphysical interpretations.

    Competing theories can both be consistent with the evidence yet posit different kinds of causes. ID theory and Darwinism are certainly consistent with evolutionary evidence; the question is which one better accounts for that evidence.

    I wrote this on AtBC recently:

    The problem isn’t just that evidence for design isn’t found, evidence contrary to design is rife in life.

    There are the vestigial organs, like our coccyx (minor function, clearly not best-served by fused tail vertebrae) and teeth in juvenile platypuses, to mammalian spermatogenesis which can’t occur at typical mammalian body temperatures–while in birds it can happen at rather high body temperatures. Birds have a “pecten” that, along with other factors, helps to provide them very good eyesight, while we’re stuck with less good eyes, yet mammals have the three ear bones that transfer signals into liquid well and other vertebrates don’t get those.

    Why not? It’s evolution, we’re all stuck with our inheritances (barring HGT, barely a factor, if at all, for most vertebrates), with apparently no intelligence figuring things out and doing a bit of genetic engineering, or whatever. Maybe the designer chooses not to do so? OK, but then where’s the design?

    Evolutionary evidence exists as evidence that evolution occurs quite apart from being anti-design evidence. However, evolutionary evidence is also evidence against design, because any reasonable expectation for design is that design should transcend the limits imposed by mere evolutionary mechanisms.

    Glen Davidson

  26. There is, of course, one little noted argument against biological design,

    No one can do it. No one can demonstrate, even hypothetically, how it might be done.

    The much derided concept of emergence figures in. Not a mystical version of emergence, but simply the observation that we can’t predict the properties of new coding sequences, and even if we could predict the chemical properties, we cannot predict the effect on phenotype or on reproductive success.

    We can copy genes, but we cannot make them de novo. Not without mimicking evolution.

  27. petrushka:
    There is, of course, one little noted argument against biological design,

    No one can do it. No one can demonstrate, even hypothetically, how it might be done.

    The much derided concept of emergence figures in.Not a mystical version of emergence, but simply the observation that we can’t predict the properties of new coding sequences, and even if we could predict the chemical properties, we cannot predict the effect on phenotype or on reproductive success. …

    Unless, of course, one’s hypothesized “designer” is the Big-O god, Omniscient.

    The more the IDers bang on about how “design” is necessary to reach isolated islands of gene function, and the more fervently they believe that unguided evolution cannot possibly do anything “significant” “complex” “specified” (or whatever their alphabet soup of the week is) then the more they unwittingly reveal that their choice is the Supernatural Big-O entity which can just know. Know without having to rely on experimentation, without risking failure, without consuming the computational resources of the whole universe …

    And of course, if you’re Big Daddy-O, you don’t have to demonstrate how biological design can be done. You just know what needs to be done, and you do it. Let there be light. Done and dusted. What would be the point of trying to explain methods and materials to mortal humans, anyways?

    God’s will be done. Orchids and hummingbirds. Even loa loa filariasis. And malaria and sickle-cell anemia.

    No wonder the IDers try as hard as they can not to mention God in the context of responsibility for “biological design”. They’re not all idiots, after all.

  28. Alan Fox said:

    There is no ID theory. Nobody – Nobody! – has formulated a testable ID theory, yet.

    Of course they have. There are many versions of the ID theory already in use that are tested every day via various kinds of research and investigation. Forensics and cryptography are a couple. SETI is another.

    In biology, the fact that many scientists and others have attempted to disprove via science the theoretical claims of ID proponents, such as the irreducible complexity of some particular biological item, demonstrates the falsifiable nature of those theoretical claims.

    Even the FSCI or “remote islands of function” claims have been at least attempted to be disproven, demonstrating that such claims are accepted as (de facto) falsifiable by those doing that work.

    Of course, I don’t expect you to be able to admit this, even to yourself.

    GlenDavidson said:

    The problem isn’t just that evidence for design isn’t found, evidence contrary to design is rife in life.

    “Bad design” is not a sound argument against design, nor is it evidence of any significant sort against design.

  29. hotshoe said:

    The more the IDers bang on about how “design” is necessary to reach isolated islands of gene function, and the more fervently they believe that unguided evolution cannot possibly do anything “significant” “complex” “specified” (or whatever their alphabet soup of the week is) then the more they unwittingly reveal that their choice is the Supernatural Big-O entity which can just know.

    Until unguided evolution can be shown capable of developing such functions there’s no reason to assume, much less believe, that it did so.

  30. “Bad design” is not a sound argument against design, nor is it evidence of any significant sort against design.

    I didn’t say “bad design,” I said “design” that doesn’t transcend evolutionary limitations. Even a tinker’s kludges regularly do that.

    Misrepresenting the issue over and over again doesn’t constitute an argument. It merely demonstrates how devoid of thought ID is.

    Glen Davidson

  31. William J. Murray,

    Of course they have. There are many versions of the ID theory already in use that are tested every day via various kinds of research and investigation. Forensics and cryptography are a couple. SETI is another.

    Let the equivocation commence.

  32. GlenDavidson said:

    I said “design” that doesn’t transcend evolutionary limitations.

    Perhaps you mean that evidence for design would have to be beyond what Darwinism could deliver. Evolution can be a product of chance and natural laws/natural selection, or a product of design, or a product of both categories. Saying that design evidence should transcend evolutionary evidence is bad logic.

    That is exactly what the ID argument states; that at least some of the evolutionary evidence indicates insertions of information beyond the reach of Darwinian mechanisms. ID doesn’t challenge evolution, it only challenges that Darwinian mechanisms are categorically sufficient. ID is certainly consistent with the evolutionary evidence; it certainly doesn’t need to “transcend” it. It only has to be a better explanation than Darwinian forces.

  33. Allan Miller said:

    Let the equivocation commence.

    That you think those are equivocations demonstrates you do not understand the ID argument.

  34. William J. Murray:
    GlenDavidson said:

    Perhaps you mean that evidence for design would have to be beyond what Darwinism could deliver.

    Perhaps I use terms correctly, rather than as pseudoscientists do.

    Evolution can be a product of chance and natural laws/natural selection, or a product of design, or a product of both categories.

    Weather can be a product of chance and natural laws/natural selection, or a product of design, or a product of both categories.

    So what? We have good evidence of “natural” causes, no evidence of “design,” for weather. Likewise for evolution, for which deniers fail to provide any evidence any “design” intervening. Which was my point, and you only dither over not using your misleading rhetoric rather than dealing with the issues raised.

    Saying that design evidence should transcend evolutionary evidence is bad logic.

    Except that people know very well what I mean by it, and even UD not infrequently uses “evolution” in just such a manner. I don’t have any reason to comport to the unscientific demands typical of the fraud of ID.

    That is exactly what the ID argument states; that at least some of the evolutionary evidence indicates insertions of information beyond the reach of Darwinian mechanisms.

    Yes, then why don’t life-forms really show that (I don’t care about statistical bafflegab), show real honest evidence of design? Why does life that rarely if ever undergoes HGT remain derivative like inheritance predicts, rather than “designs” being portable like real designers effect? Answer the question if you’re genuinely interested in the issue, don’t just state the same dreadful nonsense that never persuades people who care about epistemologic standards.

    ID doesn’t challenge evolution, it only challenges that Darwinian mechanisms are categorically sufficient. ID is certainly consistent with the evolutionary evidence; it certainly doesn’t need to “transcend” it. It only has to be a better explanation than Darwinian forces.

    No, it has to show evidence of design, when all we have (barring HGT) is evidence of vertical inheritance. That was my point, which you’ve avoided in order to merely repeat standard ID tripe.

    Glen Davidson

  35. William J. Murray:
    In biology, the fact that many scientists and others have attempted to disprove via science the theoretical claims of ID proponents, such as the irreducible complexity of some particular biological item, demonstrates the falsifiable nature of those theoretical claims.

    Even the FSCI or “remote islands of function” claims have been at least attempted to be disproven, demonstrating that such claims areaccepted as (de facto) falsifiable by those doing that work.

    Of course, I don’t expect you to be able to admit this, even to yourself.

    Nice try. IDists make plenty of claims – irreducible complexity, islands of function – etc. These claims can be demonstrated to be factually incorrect. But, WJM, none of these claims are entailed by any “ID theory”, so ID remains unfalsifable, just like Last Thursdayism. Or your delightfully arrogant version of solipsism. Yawn.

    “Bad design” is not a sound argument against design, nor is it evidence of any significant sort against design.

    True, as written. But “Bad design” is an argument against certain specific designers. Such as omnipotent ones. And the retreat to an “ineffable, inscrutable” omnipotent designer which typically follows is, how should I put it, awkward for your “falsifiable” argument…

  36. DNA_Jock said:

    Nice try. IDists make plenty of claims – irreducible complexity, islands of function – etc. These claims can be demonstrated to be factually incorrect. But, WJM, none of these claims are entailed by any “ID theory”, so ID remains unfalsifable, just like Last Thursdayism.

    Of course, in general ID cannot be falsified because we know it is a fact – humans, at least, utilize ID to generate artifacts. We know there are some artifacts that require ID as part of the explanation. In the scientific sense, to falsify a particular ID claim is to simply show there is a better explanation for that specific claim that doesn’t require the involvement of intelligent design, or to show the claim false via evidence. So, of course specific ID claims can be falsified – many scientists have published many works doing exactly that.

    Specific ID claims contain specific falsifiable entailments, such as the claim that the bacterial flagellum is irreducibly complex, or such as the claim that the building of novel, moderate-size proteins requires goal-specific information.

    The ideological mantra that ID “has no entailments” or “cannot be falsified” would be the equal of a claim that Darwinism “has no entailments” or “cannot be falsified”. Darwinisn and ID are classes of theories and claims, not specific, testable claims in themselves.

  37. GlenDavidson said:

    Perhaps I use terms correctly, rather than as pseudoscientists do.

    Terms must be used in context and in a way that doesn’t muddy up the debate. Since ID has no quarrel with any aspect of evolution besides the ideological assumption of the sufficiency of chance and natural selection as causal categories, and since there appears to be no evidence that chance and natural selection are sufficient, ID’s argument is with Darwinism (the assumption that RM & NS are sufficient) and not “evolution”, per se.

    Your use of the term “evolution” assumes that evidence for evolution is evidence for Darwinism and against ID, when that simply is not the case.

    So what? We have good evidence of “natural” causes, no evidence of “design,” for weather. Likewise for evolution, for which deniers fail to provide any evidence any “design” intervening.

    The argument is not about the weather. As far as I know, no ID theorists have made any specific claims about the weather. As far as there being evolutionary evidence for design (whether or not it “intervenes”), of course there is – first, there is the prima facie evidence virtually all biologists agree to, that living things look as if they are designed. Other evidence for design is the code and translation systems utilized; the existence of irreducibly complex systems; the existence of highly organized, complex physical systems that perform exacting, detailed functions; etc. In fact, Darwin’s theory was intended to account for the appearance of design in biology, and he even used ID evolution (breeding) as an example.

    Except that people know very well what I mean by it

    Then when you said:

    …design should transcend the limits imposed by mere evolutionary mechanisms.

    … you must be implying that you can tell us what the limits are to “mere evolutionary mechanisms”, so that you would know when a biological artifiact had qualities that exceeded the capacity of evolutionary (Darwinian) mechanisms to produce. Otherwise, your statement simply makes the ideological assumption that all the evidence we currently have can be generated by Darwinian mechanisms.

    Can you tell me some of the limitations of Darwinian evolution, meaning, what we can and cannot expect RM & NS to produce in a given time-frame, with a given set of resources?

    Yes, then why don’t life-forms really show that (I don’t care about statistical bafflegab), show real honest evidence of design?

    I’m not sure how much more “real” and “honest” evidence of design can get than having highly organized and complex code and translation systems, or 3D printing mechanisms that utilize a unique medium that they themselves are made of and found nowhere else. The real and honest evidence of design runs rampant through all living things, which is why honest biologists admit this overwhelming appearance of design and why virtually all evolutionary papers utilize design terminology in their descriptions.

    Why does life that rarely if ever undergoes HGT remain derivative like inheritance predicts, rather than “designs” being portable like real designers effect? Answer the question if you’re genuinely interested in the issue, don’t just state the same dreadful nonsense that never persuades people who care about epistemologic standards.

    If you insist on being focused on where evidence of design is in your opinion slim or contra-indicative, or how it doesn’t appear in some cases in a manner you would find indicative of design, then you’re not interested in an honest debate. It would be like finding evidence of artifacts on another planet and you pointing to a landscape some distance away with no such features and saying “why does this area appear to be non-designed?” or pointing at one of the artifacts in question and asking “Why isn’t it just all straight lines and right angles? Why does this one side appear to be just a natural pattern of rocks?”

    No, it has to show evidence of design, when all we have (barring HGT) is evidence of vertical inheritance. That was my point, which you’ve avoided in order to merely repeat standard ID tripe.

    Whether or not evolution occurred entirely via vertical inheritance is irrelevant to ID theory. Selective breeding can be entirely vertical; however, selective breeding is an ID process. You can’t get a population of Pekingese and Chihuahuas without evolutionary ID.

    In any event, we do have evidence of an apparent massive insertion of unprecedented functional information (body plans) in a relatively short span of time: it’s called the Cambrian Explosion.

  38. William J. Murray:
    GlenDavidson said:

    Terms must be used in context and in a way that doesn’t muddy up the debate.

    You mean so that you can muddy up the debate–as if there’s any real question what the scientific theory of evolution is.

    Why should we credit voodoo evolution?

    and since there appears to be no evidence that chance and natural selection are sufficient, ID’s argument is with Darwinism (the assumption that RM & NS are sufficient) and not “evolution”, per se.

    Oh, so you ignore the evidence that there’s no design affecting evolution. That was the point, and all of this blather merely smothers up that crucial matter.

    Your use ofthe term “evolution” assumes that evidence for evolution is evidence for Darwinism and against ID, when that simply is not the case.

    What’s this “Darwinism,” your bogus term for evolutionary theory? How bizarre that you complain to me about using terms right, while you bring in “Darwinism” as if that were the proper term for evolutionary theory (in the US). We know how that term is not only regularly misused at UD to pretend some a priori commitment to Charles, but, worse, to pretend that non-Darwinian mechanisms are somehow a problem for current evolutionary theory.

    If you want us to see evolutionary evidence as favoring any other idea, you’re going to need an idea, not the bunch of apologetic junk involving evolution, cosmology, and neuroscience that the pseudoscience of ID encompasses. ID doesn’t explain evolution, or really anything.

    The argument is not about the weather. As far as I know, no ID theorists have made any specific claims about the weather.

    Oh, the fraud of ID doesn’t question weather, so I needn’t worry about magic involving weather? How does that fit into epistemology?

    As far as there being evolutionary evidence for design (whether or not it “intervenes”), of course there is – first, there is the prima facie evidence virtually all biologists agree to, that living things look as if they are designed.

    What a crock. You don’t know that at all, and I wouldn’t even care if it’s true, since it’s just a matter of prejudice, not of evidence that really supports any “appearance of design” in life. But I do care that you make such a nonsense claim–or can you actually back that up (like I have to ask)?

    Other evidence for design is the code and translation systems utilized; the existence of irreducibly complex systems;the existence of highly organized, complex physical systems that perform exacting, detailed functions; etc.

    How does that become evidence for design? Explain the extremely derivative nature of life using design. That is entailed by evolution, not by ID. Although I can’t think of anything today’s fraud of ID really does entail (since it disavows meaningful design claims that are refuted by the evidence), no matter the shouting about complexity, etc.

    In fact, Darwin’s theory was intended to account for the appearance of design in biology,

    You never really back up your claims, do you?

    More properly, Darwin’s theory was intended to account for the appearance of evolution in biology.

    and he even used ID evolution (breeding) as an example.

    No, as an analogy. Don’t you get anything right?

    … you must be implying that you can tell us what the limits are to “mere evolutionary mechanisms”, so that you would know when a biological artifiact had qualities that exceeded the capacity of evolutionary (Darwinian) mechanisms to produce.

    What a ridiculous fantasy. We know of some of the limits of evolution (sans ID BS), such as its essentially derivative nature. Which I mentioned, and which you, instead of actually dealing with, ignore and move on to invent bizarre ideas about what I “must be implying.” I’m not writing about the idiocies of ID with its pretensions to know what evolution (sans ID BS) can’t do, I’m writing about what is known, the highly derivative nature of non-magical evolution. That you ignore the well-known reasons why the honest version of ID is contraindicated only suggests that you can’t deal properly with facts that tell for evolution and against design.

    Otherwise, your statement simply makes the ideological assumption that all the evidence we currently have can be generated by Darwinian mechanisms.

    Mere nonsense. I wrote that we have evidence for “natural” mechanisms for evolution and none for design. That’s what’s important, not your goalpost moving.

    Can you tell me some of the limitations of Darwinian evolution, meaning, what we can and cannot expect RM & NS to produce in a given time-frame, with a given set of resources?

    Can you deal properly with what I wrote, with what clearly is entailed by evolutionary theory and not by any honest ID inferences?

    I didn’t claim to care about the purported gaps that IDiocy wants to fill with its God.

    I’m not sure how much more “real” and “honest” evidence of design can get than having highly organized and complex code and translation systems, or 3D printing mechanisms that utilize a unique medium that they themselves are made of and found nowhere else.

    How about some portability of “design”? Oh right, you’re ignoring the actual evidence, to insist that the unevidenced prejudice that the evolving DNA with its translation system is evidence of ID. It isn’t (not without something far more indicative of design, anyway), you haven’t provided any such evidence, and you’re again ignoring the evidence against ID that the extremely derivative nature of non-poof evolution that is entailed by its mechanisms that was actually provided.

    I gave evidence against what an honest ID would entail, you just spout fraudulent ID nonsense, as if I’m supposed to accept its “truth.”

    The real and honest evidence of design runs rampant through all living things, which is why honest biologists admit this overwhelming appearance of design

    Do they? Evidence, please. Which I know is not forthcoming. Evidence isn’t your friend.

    and why virtually all evolutionary papers utilize design terminology in their descriptions.

    Wow, people utilize familiar English in their papers. There’s plenty of that outside of evolutionary papers as well, so that non-biologic chemistry is not infrequently written up in teleologic terms.

    If you insist on being focused on where evidence of design is in your opinion slim or contra-indicative, or how it doesn’t appear in some cases in a manner you would find indicative of design, then you’re not interested in an honest debate.

    I gave evidence against design, so quit misrepresenting what I did. As my main point, I didn’t say that it doesn’t appear, but that there is ample evidence against it. You give me no proper evidence for ID, ignore the evidence against what an honest ID would entail, or at least expect, and misrepresent what I actually did, while asserting a lack of honest engagement on my part. Powerful lamp in your projector.

    It would be like finding evidence of artifacts on another planet and you pointing to a landscape some distance away with no such features and saying “why does this area appear to be non-designed?” or pointing at one of the artifacts in question and asking “Why isn’t it just all straight lines and right angles?Why does this one side appear to be just a natural pattern of rocks?”

    What an inept and inapt analogy. A landscape isn’t an integrated whole, and I wasn’t claiming merely that there isn’t evidence for design somewhere. Plus, you haven’t discovered any artifacts.

    It’s a complete flop, except that it provides more chance for you to ignore the evidence against inherent design claims.

    Whether or not evolution occurred entirely via vertical inheritance is irrelevant to ID theory.

    More nonsense. Design has never been so limited–unless it’s within ag breeding with its limits of inheritance.

    Selective breeding can be entirely vertical; however, selective breeding is an ID process.You can’t get a population of Pekingese and Chihuahuas without evolutionary ID.

    Well, it isn’t a normal “ID process,” but, more importantly, such vertical transmission is clearly due to natural limits that humans haven’t been able to transcend until recently (and still not too powerfully). Is the Designer supposed to be as limited as humans were prior to genetic engineering?

    If not, it’s clearly another appalling disanalogy.

    In any event, we do have evidence of an apparent massive insertion of unprecedented functional information (body plans) in a relatively short span of time: it’s called the Cambrian Explosion.

    Evidence please. Oh right, we’re supposed to just accept the claims of ID, while you ignore the fact that this “massive insertion” of information happens to be as derived as evolution (by observed causes) entails. IOW, there’s more of that evidence against ID from the Cambrian radiation, while you make the bald claim that it’s the miracle or “design” that ID claims occurred.

    Glen Davidson

  39. William J. Murray: In any event, we do have evidence of an apparent massive insertion of unprecedented functional information (body plans) in a relatively short span of time: it’s called the Cambrian Explosion.

    This “relatively short span of time” – could you tell me how long it was, more or less? Do you even know?

    Is it also the case that given a longer span of time evolution, unaided by Intelligent Design, could also have achieved what design achieved in the “explosion”?

    Or are these “body plans” unachievable except via ID?

    I await your non-answers with relish.

  40. William J. Murray: That you think those are equivocations demonstrates you do not understand the ID argument.

    When you stop making arguments and provide some experimental evidence then *perhaps* ID will get somewhere. Until then it’s just you, Joe, BA77 and KF at UD all talking to each other. Get’s boring huh, which is why I guess you are here. At least here your ideas get talked about, as opposed to ignored at UD. How’s that thread you started going?

  41. Me: Let the equivocation commence.

    WJM: That you think those are equivocations demonstrates you do not understand the ID argument.

    That you pretend that they are not equivocations demonstrates that you are happy to perpetuate a fraud. Deductive reasoning, plus some involvement of conscious entities, do not an ‘ID theory’ make. You might as well include auditing while you are at it.

    Here is your own ‘side’s statement:

    “The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection. ”

    Forensics does not hold that certain features of a crime are best explained by an intelligent cause. Cryptography does not hold that certain features of messages are best explained by an intelligent cause. SETI does not hold that certain features of incoming radio frequencies are best explained by an intelligent cause. These fields owe nothing to the work ‘ID scientists’, and there is no import of techniques from them into the ID field, such as it is. To claim them for ‘ID’ is decidedly dubious.

  42. William J. Murray:
    Of course, in general ID cannot be falsified because we know it is a fact – humans, at least, utilize ID to generate artifacts. We know there are some artifacts that require ID as part of the explanation.

    You are equivocating “ID”, conflating known examples of artefacts with “features of the universe” of unknown origin.
    As predicted.

    In the scientific sense, to falsify a particular ID claim is to simply show there is a better explanation for that specific claim that doesn’t require the involvement of intelligent design, or to show the claim false via evidence.So, of course specific ID claims can be falsified – many scientists have published many works doing exactly that.

    Specific ID claims contain specific falsifiable entailments, such as the claim that the bacterial flagellum is irreducibly complex, or such as the claim that the building of novel, moderate-size proteins requires goal-specific information.

    Precisely. But, thanks to the deliberate vagueness of the “certain features of the universe”, no individual ID claim is entailed by the ID theory.

    The ideological mantra that ID “has no entailments” or “cannot be falsified” would be the equal of a claim that Darwinism “has no entailments” or “cannot be falsified”.Darwinisn and ID are classes of theories and claims, not specific, testable claims in themselves.

    I am not sure what you mean by the phrase “would be the equal of” here. The two statements “ID has no entailments” and “‘Darwinism’ has on entailments” are equal in the sense that both are falsifiable claims. One is true and the other is false.
    I invite you to make ID history by producing a testable claim that is entailed by ID theory which states:

    The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

  43. That you pretend that they are not equivocations demonstrates that you are happy to perpetuate a fraud. Deductive reasoning, plus some involvement of conscious entities, do not an ‘ID theory’ make.

    They are not equivocations or fraudulent references to ID; they are examples of a general ID theory (that some things cannot be adequately explained without reference to a purposeful intelligence) being used to make specific claims of the involvement of ID. Again, that you consider such examples fraudulent demonstrates your confusion about what ID really is.

    Forensics does not hold that certain features of a crime are best explained by an intelligent cause.

    Forensics must hold that certain features of a theoretical crime scene are best explained by an intelligent cause or else it cannot reach a conclusion that any crime has occurred at all.

    Cryptography does not hold that certain features of messages are best explained by an intelligent cause.

    Of course it does, otherwise there would be reason to suspect there was a purposeful secret code embedded in the messages.

    SETI does not hold that certain features of incoming radio frequencies are best explained by an intelligent cause.

    It holds that certain potential features of incoming signals would be best explained by intelligent causes, otherwise their search would be futile.

    If one cannot admit these things, as I said, honest debate about ID is simply not possible.

  44. DNA_jock said:

    You are equivocating “ID”, conflating known examples of artefacts with “features of the universe” of unknown origin.

    It’s not a conflation; such artifacts are “features of the universe” that are known to have been generated by ID, and are recognized to not be explicable without reference to ID. General ID theory doesn’t focus solely on items of “unknown origin”, obviously, since all ID advocates make use of examples of ID which are known to have been produced by ID agents. That you consider what are presented as bona fide examples of ID to be “equivocations” demonstrates that you either do not understand ID theory or are only interested in dismissing the idea.

    But, thanks to the deliberate vagueness of the “certain features of the universe”, no individual ID claim is entailed by the ID theory.

    Nor does it need to be. We know ID exists; it is a fact. The only relevant question is if specific claims of ID causation can be supported/falsified, and they can be.

    I am not sure what you mean by the phrase “would be the equal of” here. The two statements “ID has no entailments” and “‘Darwinism’ has [no] entailments” are equal in the sense that both are falsifiable claims. One is true and the other is false.

    “Darwinism” refers to the random mutation and natural selection causal categories. We know both exist and are facts; nothing can falsify them as explanatory categories; the only question is if specific claims of their sufficiency as explanations in particular cases, such as in the case of the bacterial flagellum, hold up to investigation.

  45. GlenDavidson said:

    What’s this “Darwinism,” your bogus term for evolutionary theory? How bizarre that you complain to me about using terms right, while you bring in “Darwinism” as if that were the proper term for evolutionary theory (in the US).

    “Darwinism” refers to the position that random mutation and natural selection are sufficient, as causal categories, to explain all evolutionary evidence. For example, Darwinism is insufficient in explaining the evolution of Chihuahuas and Pekingese; ID is required (as a causal category) in the explanation (selective breeding).

    Because such breeds exist, and because humans have directly modified the genes of living organisms, we know for certain that Darwinism is an insufficient explanation for ALL evolution; the only question is how much of evolution requires ID beyond what humans are known to have been responsible for.

  46. William J. Murray:
    Forensics must hold that certain features of a theoretical crime scene are best explained by an intelligent cause or else it cannot reach a conclusion that any crime has occurred at all.

    Can you show in a book about forensics where they talk about “an intelligent cause”? Of course you cannot. Much less is there any forensics book saying something about ID theory contributing to forensics. Forensics owes absolutely nothing to ID. Your attempted parallel proves nothing. The fact that you are still not grasping this shows how disingenuine you are.

    Of course it does, otherwise there would be reason to suspect there was a purposeful secret code embedded in the messages.

    Where does cryptography talk about “purposeful code” and “an intelligent cause”? And where do they talk about how ID theory contributed to cryptography? They don’t.

    It holds that certain potential features of incoming signals would be best explained by intelligent causes, otherwise their search would be futile.

    And where do SETI researchers talk about “an intelligent cause” and ID theory’s contribution to their research? Different from ID theorists, SETI researchers have a pretty good clue about what they are looking for: Corporeal intelligent beings who are able to produce and convey messages roughly the same way as humans do. These suppositions are empirically falsifiable, which cannot be said about ID theory.

    If one cannot admit these things, as I said, honest debate about ID is simply not possible.

    The debate becomes honest the moment you become honest. You are the only obstacle here.

  47. William J. Murray: The only relevant question is if specific claims of ID causation can be supported/falsified, and they can be.

    I can’t see how you can say that and this on the very same page:

    William J. Murray: In any event, we do have evidence of an apparent massive insertion of unprecedented functional information (body plans) in a relatively short span of time: it’s called the Cambrian Explosion.

    and expect anyone to take you seriously.

    Please support/falsify that claim or withdraw it.

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