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.

http://www.uncommondescent.com/darwinism/the-elephant-in-the-room/#comment-550345

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. phoodoo,

    Where is the magic variation that will make them better? We still haven’t found it in all the years of looking at dog breeds?

    Better than what? At what?

  2. Richardthughes,

    They’ve had 20 years! Seems fair to declare it impossible … ! The only successful evolutionary experiment will be one which sees the lab staff trapped behind benches by their hideous mutant creations.

  3. Creodont said:

    Evolutionary processes/events DO account for the existence of the Pekingese and Basset Hound, and you cannot produce any evidence to show that humans or any other so-called ‘intelligent designer’ designed-created the mutations or anything else within the ancestors of Pekingese Dogs and Basset Hounds that resulted in the existence of Pekingese Dogs and Basset Hounds.

    I didn’t say humans or intelligence designed the mutations; I said that without selective breeding and artificial population maintenance, those breeds of dogs would not exist. Selective breeding and artificial population maintenance are necessary, but not sufficient, causes for their existence and are not Darwinian in nature. So, Darwinian evolutionary forces cannot account for their existence, even if a Darwinian cause (random mutation) is also required in the generation of such breeds.

    For the Gazillionth time, no one is denying that humans manipulate or ‘design’ some things. Some of those things are labeled, by humans, as ‘artificial’.

    And some are labeled “natural”. Some are labeled “intelligently designed”. Some are labeled “chance outcomes”. Some are labeled “Results of natural law.” Humans can indeed make such distinctions or else such labels would not exist.

    Allan Miller said:

    Incremental change can generate an apparently IC system in the absence of barriers.

    That’s a fairly vague assertion that may or may not have any realistic connection to actual biological situations. The assertion in question is that in terms of biological evolution, chance variations (not just “incremental”) and natural selection are sufficient to explain what we find. You apparently provide an interesting answer:

    Pure NS and vertical inheritance were deemed insufficient to account for the data. But they put the work in. They didn’t demand that the keepers of the prior MS prove sufficiency, they demonstrated insufficiency.

    Obviously one of the problems (as you illustrate) is that Darwinists don’t attempt to show the sufficiency of their proposed mechanisms and don’t demand such sufficiency be demonstrated. They simply have faith that Darwinistic processess are sufficient.

    I wonder if that would work in any other science? What if a doctor didn’t have to demonstrate that a diagnosis was sufficient to account for the symptoms? What if an astrophysicist didn’t have to demonstrate that an explanation was sufficient to account for the orbital characteristics of planet or moon? What if an engineer didn’t have to demonstrate the sufficiency of his designs to meet earthquake codes in California?

    The onus is on you.

    Once again, the onus is on both sides that make a positive assertion, whether or not it is the unscientific habit of Darwinists to simply assume their mechanisms sufficient to the task.

    You are making the positive claim that it is IC, which requires more than merely noting that the parts presently interdepend. And you need to say why your explanation is a better fit to the data.

    No, it is a fact that some such phenomena are irreducibly complex, which only means that without even one of its parts, it cannot serve the function it serves with that part. Of course IC mechanisms can be generated incrementally; that doesn’t mean they can be generated by Darwinian processes.

    However, it’s not just IC features/systems Darwinists must show their processes sufficient in accounting for.

  4. Supposing we could measure mutation rates and per generation and use those to calculate how much genomic variation over time that would create?*

    *I don’t know if this has been done / results but the premise is simple, if you travel 3 miles an hour we can extrapolate you can travel 3000 miles in a 1000 hours…

  5. RichardHughes said:

    Supposing we could measure mutation rates and per generation and use those to calculate how much genomic variation over time that would create?*

    Simple variation isn’t enough. Generating new building-block shapes in enough quantity and in proximity (both in time and space) with enough other building-block shapes is only the bare beginning of what is required to generate a highly complex, functional mechanism.

    *I don’t know if this has been done / results but the premise is simple, if you travel 3 miles an hour we can extrapolate you can travel 3000 miles in a 1000 hours…

    You are assuming your conclusion via contrived analogy here; that the observed Darwinian process of “taking a step” is sufficient to ultimately account for the step-by-step arrival at any known destination (any known biological feature). The moon is 225,000 miles away; can you walk to the moon?

    You can get closer to it by walking up a high mountain (given it is overhead at the time), but you cannot take any number of walking steps and get to the moon.

    Until you demonstrate that the destination is achievable via darwinian steps, you are only assuming it is. If Darwinists are going to claim Darwinism is sufficient, the onus is on them to demonstrate it.

  6. William J. Murray:
    RichardHughes said:

    Supposing we could measure mutation rates and per generation and use those to calculate how much genomic variation over time that would create?*

    Simple variation isn’t enough.Generating new building-block shapes in enough quantity and in proximity (both in time and space) with enough other building-block shapes is only the bare beginning of what is required to generate a highly complex, functional mechanism.

    *I don’t know if this has been done / results but the premise is simple, if you travel 3 miles an hour we can extrapolate you can travel 3000 miles in a 1000 hours…

    You are assuming your conclusion via contrived analogy here; that the observed Darwinian process of “taking a step” is sufficient to ultimately account for the step-by-step arrival at any known destination (any known biological feature).The moon is 225,000 miles away; can you walk to the moon?

    You can get closer to it by walking up a high mountain (given it is overhead at the time), but you cannot take any number of walking steps and get to the moon.

    Until you demonstrate that the destination is achievable via darwinian steps, you are only assuming it is. If Darwinists are going to claim Darwinism is sufficient, the onus is on them to demonstrate it.

    And you’ve let the cat out of the bag William. The only thing that would be acceptable under those criteria is a step by step narrative, and trust me there are a lot of steps. But lets return to sufficient mechanisms:

    In the example you give, can you supply a similar level of description for design? If not, why do you hold that as a hurdle?

    We know unguided creative forces exited during time periods in question*. We do not know if any design forces existed in the same period. Therefore NDE wins the sufficient mechanisms argument before ID even starts.

    *You are welcome to attack this premise. I wouldn’t want to deny the world of such comedy.

  7. Above comment borked. My bit:

    And you’ve let the cat out of the bag William. The only thing that would be acceptable under those criteria is a step by step narrative, and trust me there are a lot of steps. But lets return to sufficient mechanisms:

    In the example you give, can you supply a similar level of description for design? If not, why do you hold that as a hurdle?

    We know unguided creative forces exited during time periods in question*. We do not know if any design forces existed in the same period. Therefore NDE wins the sufficient mechanisms argument before ID even starts.

    *You are welcome to attack this premise. I wouldn’t want to deny the world of such comedy.

  8. RichardHughes said

    And you’ve let the cat out of the bag William. The only thing that would be acceptable under those criteria is a step by step narrative, and trust me there are a lot of steps.

    Acceptable to whom? A step-by-step narrative isn’t the only thing that would be acceptable to me or to many others; however, the problem is that Darwinists make no falsifiable case that Darwinistic mechanisms are capable of generating such features even in principle. As you have admitted, the do not even require their theory be shown sufficient in the first place. It’s all taken on faith.

    In the example you give, can you supply a similar level of description for design? If not, why do you hold that as a hurdle?

    The “level of description” you refer to is your in your own mind. I only ask that Darwinists who claim sufficiency back that claim up – not with a step by step accounting – of course that is absurd. But rather that the show that the path to the destination is in principle something that can be plausibly achieved by walking in the first place.

    We know unguided creative forces exited during time periods in question*. We do not know if any design forces existed in the same period. Therefore NDE wins the sufficient mechanisms argument before ID even starts.

    Mere presence doesn’t qualify an explanation as sufficient. You might as well claim gravity is proven a sufficient cause of the generation of biological features back then because it was **present**.

    Seeing as you’ve presented no evidence that Darwinism can be shown to be sufficient, I’ll assume you agree that it’s sufficiency is really nothing more than a matter of ideological faith.

  9. I’ve had a go tidying up your comment, Rich. Let me know if OK and if you want me to delete the duplicate.

    The “quote in reply” button does not reproduce quoted text and the final “close blockquote” sometimes lurks out of sight as a trap for the unwary. 🙂

  10. William J. Murray: Seeing as you’ve presented no evidence that Darwinism can be shown to be sufficient, I’ll assume you agree that it’s sufficiency is really nothing more than a matter of ideological faith.

    Indeed, for Darwinian evolution to explain the whole sequence of events from the origin of life to the current green or dead leaf on the tip of every branch, there has to be an unbroken chain of survival and reproduction for Darwinian evolution to explain what we see.

    Surely, it’s a stretch for the mind to think that could be the case. Yet, if you take the trouble to focus in and examine what evidence there is, it all seems to confirm that pattern and nobody has managed to conceive of an alternative explanation. “Intelligent Design” theorists have as yet to come up with any sort of plausible scientific hypothesis. Michael Behe, in my view the best ID has in the form of a scientifically credentialed theorist, has so far only developed his “irreducible complexity” argument, that evolution is true as far as it goes, but insufficient. His alternative explanation has not gone further than “Poof”.

  11. William:

    “A step-by-step narrative isn’t the only thing that would be acceptable to me or to many others; however, the problem is that Darwinists make no falsifiable case that Darwinistic mechanisms are capable of generating such features even in principle”

    Tell me what that looks like, what data you’d find acceptable.

    And then show me how ID is superior in this regard.

  12. William,

    Here’s your chance to quote the other William:

    As for your example, I’m not going to take the bait. You’re asking me to play a game: “Provide as much detail in terms of possible causal mechanisms for your ID position as I do for my Darwinian position.” ID is not a mechanistic theory, and it’s not ID’s task to match your pathetic level of detail in telling mechanistic stories.

    I love the Williams. 🙂

  13. Hey Keith’s!
    I got Jerry Coyne to sign you a copy of WEIT. I know you live that stuff. Will swap for beer.

  14. William J. Murray: But rather that the show that the path to the destination is in principle something that can be plausibly achieved by walking in the first place.

    Does Lenski’s demonstration count as a “destination”?

    There we see a wide array of genetic changes, some evolutionary adaptations.

    What would be an acceptable demonstration that unguided evolution can create novelty? What is the minimum you would accept?

    however, the problem is that Darwinists make no falsifiable case that Darwinistic mechanisms are capable of generating such features even in principle.

    I make the prediction that E.coli can evolve to grow on some alternate grown mediums if exposed for sufficient time. That would appear to be something significant, no?

    Is that change, requiring genetic changes plus some evolutionary adaptations a “feature” that would count under your metric?

    The researchers also found that all Cit+ clones sequenced had in their genomes a duplication mutation of 2933 base pairs that involved the gene for the citrate transporter protein used in anaerobic growth on citrate, citT. The duplication is tandem, resulting in two copies that are head-to-tail with respect to each other. This duplication immediately conferred the Cit+ trait by creating a new regulatory module in which the normally silent citT gene is placed under the control of a promoter for an adjacent gene called rnk. The new promoter activates expression of the citrate transporter when oxygen is present, and thereby enabling aerobic growth on citrate

    Does any of that “count” as a “destination” William? Is that change sufficient to count? If not, what would be an acceptable demonstration?

  15. phoodoo,

    Better than hip dysplasia, cystinuria, von Willebrand’s disease, epilepsy, elbow dysplasia, gastric torsion, patellar luxation…..

    So intelligent design is a poor substitute for the real thing, you are saying …

  16. William J. Murray,

    Me: Incremental change can generate an apparently IC system in the absence of barriers.

    WJM: That’s a fairly vague assertion that may or may not have any realistic connection to actual biological situations.

    In response to the vague waffle that comes from Creationists, it’ll do. If Part B can be added to Part A, and they both co-evolve, they can become inextricably linked. Since this is a perfectly plausible scenario, YOU have to deal with it, and say why it does not apply in Your Specific System X. The flagellum, let us say. Why is that IC, in the can’t-evolve sense? What is the definitively IC thing about it? It’s not enough to say that parts cannot now be removed. I cannot remove your heart or your blood, and they both co-depend. That does not make the circulation system IC.

    Obviously one of the problems (as you illustrate) is that Darwinists don’t attempt to show the sufficiency of their proposed mechanisms and don’t demand such sufficiency be demonstrated. They simply have faith that Darwinistic processess are sufficient.

    I wonder if that would work in any other science?

    What, like ID you mean? Humans design fridges, evolution can’t do anything, therefore [handwave] Design? You could try it. Oh, I see you have.

    No, it is a fact that some such phenomena are irreducibly complex, which only means that without even one of its parts, it cannot serve the function it serves with that part. Of course IC mechanisms can be generated incrementally; that doesn’t mean they can be generated by Darwinian processes.

    What? This is just Mk 1 robo-denial. “Of course everything that Darwinists say can happen can happen. Doesn’t mean it happened.”. Parts can be added serially, by duplication and mutation. When there is selection upon the pairing, they can co-evolve to become mutually essential for the combined function. You need to understand that principle in order to rule it out in a specific situation.

  17. William J. Murray,

    Darwinists don’t attempt to show the sufficiency of their proposed mechanisms and don’t demand such sufficiency be demonstrated.

    So how come they came up with any refinements at all to the theory? Drift, LGT, the merger of genetics? You are just blowing smoke. A great deal of work has been done on the sufficiency of the theory and its necessary extension. It cannot be summed up in a sound-bite. Start with those authors I mentioned (like you will!).

  18. Here’s the sequence:

    1) Everyone thought everything was separately created.
    2) Darwin demonstrated a mechanism by which the environment could ‘select’ those variants that did best in it. He was a bit hazy on the source of the variation, but recognised the conclusion that it would lead to common descent.
    3) Doubters: “Is that sufficient?” Supporters: “Yes, as far as we can tell”
    4) Mendelian heredity and evolutionary theory were merged.
    5) Doubters: “Is that sufficient?” Supporters: “Yes, as far as we can tell”
    6) The discovery of Drift, LGT, the detailed mechanisms of inheritance and the genetic code, the rise of molecular phylogenetics confirming the genetic relatedness of all living things.
    7) Doubters: “Is it sufficient?” Supporters: “Yes, as far as we can tell”
    Doubters: “You said that last time” “Yes, but there were new disoveries”.

    See what’s going on? It’s not a continual back-to-the-drawing-board reboot, it is ongoing confirmation in detail, that long-term change occurs through generational change. 1) is clearly not supported. So Creationists have been trying to find employment for God as a tinkerer. Pick a system, challenge the Darwinists to prove the sufficiency of known mechanisms to account for it. And of course any evidence provided can simply be denied. It’s easy. No point getting your hands grubby opening a textbook. Yet, the sufficiency of Design is never doubted for a second, no evidence required. Design can move individual molecules, design can, without them reacting until all is just so. Some go so far as to call the Design Inference ‘mandated’ by the supposed failure of a particular Darwinian explanation in detail. It’s pure double-standard bullshine.

  19. phoodoo:
    Richardthughes,
    At being a car.

    What are the qualifications for being a car? 4 tyres, a steering wheel, an engine and a seat for the driver? Looks like the Yugo qualifies. One car might be better at driving fast, or have superior handling properties, that doesn’t mean it’s better “at being a car”. The property of car does not come in degrees.

  20. phoodoo:
    Allan Miller,

    Better than hip dysplasia,cystinuria, von Willebrand’s disease, epilepsy, elbow dysplasia, gastric torsion, patellar luxation…..

    In the mean time dogs have learned to rely on vision to a higher extend, be much better at interpreting human desires through gauging their bodylanguage and are used in everything from herding sheep to finding explosives.

    You seem to think the evolution of dogs has been somehow “downhill”. Dogs are an extremely successful species, the fact that they are dependent on humans for their survival is irrelevant. Adaptation doesn’t mean getting better at everything, it means adapting to a specific circumstance. Wolves adapted to humans and became many different breeds of dogs. Dogs aren’t worse than wolves at anything but “being wolves”. But they’re better at being dogs.

    Evolution is a tradeoff, there is no perfect organism that does “the best” everywhere. Whales can’t walk around on land any more. Omg loss of function, degeneration, it’s still “just an animal”. That is about as stupid as your “it’s still just a bacterium” retort.

  21. William J. Murray,

    WJM said:

    “I didn’t say humans or intelligence designed the mutations…”

    Way to miss my points.

    “And some are labeled “natural”. Some are labeled “intelligently designed”. Some are labeled “chance outcomes”. Some are labeled “Results of natural law.” Humans can indeed make such distinctions or else such labels would not exist.”

    Way to miss my points.

    ETA: Oh, and lose the ‘Darwinian’, ‘Darwinistic’, ‘Darwinism’ crap.

  22. I was looking at a word ladder solver web page and noticed that the solutions never seem to have backwards steps. To invoke one of KF’s favorite constructions, they have “virtual latching”.

    Is it possible to construct a word ladder that requires one of the steps to be less adapted than a previous step? That once you have at least one letter that matches its place in the target word, to have a subsequent step with fewer matches?

  23. Virtual latching allows compensating mutations. A match can be lost if the count of matches does not decline. ARMY to ARMS satisfies my request, but my heart of hearts wants one that starts with no matches.

  24. http://www.uncommondescent.com/evolution/evolution-needs-a-library-of-platonic-forms/

    UD got around to having a discussion.

    Gpuccio notes that there are isolated islands in the dictionary that cannot be connected by word ladder.

    Thank you, gp for confirming that you can’t make negative arguments about the territory from the map, or by reifying a metaphor.

    ETA:

    Wagner uses word ladder in an attempt to communicate a concept. Those who have a vested interest in not understanding the concept will concentrate on the limits of the metaphor, without stopping to test the original object.

    Wagner’s argument can be summarized as:

    1 Word ladder works for protein coding sequences.
    2. Coding sequences can be thought of a Platonic forms. Perhaps in the same sense that atoms and electrons are classifiable as discrete types. Assuming the “reader” is constant, the sequences have an objective meaning.
    3. There are an astronomical number of equivalent coding sequences, and they can be connected like word ladders.
    4. Coding sequences can be connected by single substitutions to sequences having different meanings. Making possible the process of duplication followed by mutation to new function.
    5. Borrowing a phrase from Wallace, sequences can diverge indefinitely from the original type.

  25. To extend the metaphor, how may of those isolated words have synonyms (perform the same function) that are not isolated? 😉

  26. keiths: I’ve read Wagner’s book, and it’s bad news for ID, cover to cover.

    Yes, but gpuccio simply denies that it’s true. After all, ATP coding sequences are conserved, so there is no connecting web.

    That was simple.

    I’m not exaggerating. His argument is that conserved sequences prove that functional sequences are isolated.

  27. Piotr: (are you still here?)

    I’m looking at the UD thread and disagreeing with your assessment of Wagner’s style.

    The problem with his style is that his metaphors are expansive rather than careful. He is trying to reach a friendly audience rather than to convert a hostile audience.

    Since I don’t think hostile audiences ever convert, I think it’s good to have explanations that open the mind and trigger new ways of thinking about complicated things like multidimensional connectedness.

    Screw the gpuccios. They have the intellectual ability to understand biology, but have chosen, for theological reasons, to quote mine and cherry pick ideas and concepts.

  28. Would anyone like to join the discussion at UD? I’ve read several papers by Wagner and his collaborators, but not Arrival of the Fittest yet (I know it only via snippets and reviews). Comments from someone who’s actually read it would be valuable.

  29. I was banned, so I have to comment here. Keiths and I have read the book.

    Gpuccio is making a testable claim, but unless every evolutionary biologist is wrong, gpuccio is wrong.

    It is simply dishonest to take a few conserved sequences, which represent a fraction of coding DNA, and argue that all, or most, DNA cannot change.

    Wagner does discuss this. Keiths can correct me on this if I’m wrong, but I’m pretty sure that highly conserved sequences are regarded as ancient and mostly concerned with critical functions, like ATP.

  30. petrushka,

    Well, that’s the definition of “highly conserved”. And despite the regrettable tendency to overuse the term — Larry Moran had a post about that a few weeks ago — most proteins are anything but highly conserved.

  31. Piotr Gasiorowski:
    petrushka,
    Well, that’s the definition of “highly conserved”. And despite the regrettable tendency to overuse the term — Larry Moran had a post about that a few weeks ago — most proteins are anything but highly conserved.

    Which is why it is dishonest to portray the exceptional as the dominant mode. Gpuccio knows enough biochemistry to avoid this.

    ETA:

    I agree with Keiths. Wagner’s book is death to ID. The only way it isn’t death to ID is if it’s factually wrong. Which is why gp has to assert it’s factually wrong.

  32. petrushka,

    I’m here. I have enjoyed reading Wagner’s papers, but I honestly think his pop-science style is overburdened with (partly obscure) metaphors. I understand what he means despite rather than with the help of such devices. Let me emphasise that he says very important things. And, to quote one of Feynman’s bon mots, ‘Hell, if I could explain it to the average person, it wouldn’t have been worth the Nobel prize.’

  33. Why not just say

    Dim ATP ()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()() as byte

    and be done with it?

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