Ubiquitin: a challenge for evolutionary theory?

Glancing at Uncommon Descent (I still do as Denyse O’Leary often reports on interesting science articles, as here*, and the odd comment thread can still provide entertainment), I see an OP authored by gpuccio (an Italian medical doctor) entitled The Ubiquitin System: Functional Complexity and Semiosis joined together, telling the story of the ubiquitin protein and its central role in eukaryote biochemistry in some considerable detail. The subtext is that ubiquitin’s role is so widespread and diverse and conserved across all (so far known) eukaryotes, that it defies an evolutionary explanation. This appears to be yet another god-of-the-gaps argument. Who can explain ubiquitin? Take that, evolutionists! I’m not familiar with the ubiquitin system and thank gpuccio for his article (though I did note some similarities to the Wikipedia entry.

In the discussion that follows, gpuccio and others note the lack of response from ID skeptics. Gpuccio remarks:

OK, our interlocutors, as usual, are nowhere to be seen, but at least I have some true friends!

and later:

And contributions from the other side? OK, let’s me count them… Zero?

Well, I can think of a few reasons why the comment thread lacks representatives from “the other side” (presumably those who are in general agreement with mainstream evolutionary biology). 

  1. In a sense, there’s little in gpuccio’s opening post to argue over. It’s a description of a biochemical system first elucidated in the late seventies and into the early eighties. The pioneering work was done by Aaron Ciechanover, Avram Hershko, Irwin Rose (later to win the Nobel prize for chemistry, credited with “the discovery of ubiquitin-mediated protein degradation”, all mainstream scientists.
  2. Gpuccio hints at the complexity of the system and the “semiotic” aspects. It seems like another god-of-the-gaps argument. Wow, look at the complexity! How could this possibly have evolved! Therefore ID!  What might get the attention of science is some theory or hypothesis that could be an alternative, testable explanation for the ubiquitin system. That is not to be found in gpuccio’s OP or subsequent comments.
  3. Uncommon Descent has an unenviable history on treatment of ID skeptics and their comments. Those who are still able to comment at UD risk the hard work involved in preparing a substantive comment being wasted as comments may never appear or are subsequently deleted and accounts arbitrarily closed.

I’m sure others can add to the list. So I’d like to suggest to gpuccio that he should bring his ideas here if he would like them challenged. If he likes, he can repost his article as an OP here. I guarantee that he (and any other UD regulars who’d like to join in) will be able to  participate here without fear of material being deleted or comment privileges being arbitrarily suspended.

Come on, gpuccio. What have you got to lose?

906 Replies to “Ubiquitin: a challenge for evolutionary theory?”

  1. Kantian Naturalist Kantian Naturalist
    Ignored
    says:

    Have anyone associated with the ID movement shown any interest in the psychology of how human beings design things? And what is it about the word “design” which so significant here? Is designing the same as tinkering? Inventing? Manipulating? Creating? Is design synonymous with intelligence or a specific use of intelligence?

    It always has seemed to me that the ID movement relies on a simplistic and I think deeply flawed picture of what human beings do when they create or design something. It’s a picture in which the person first conceptualizes what it is that he or she is going to make, and then brings it about that something in the world resembles the imagined design. But that’s how how we actually create and design. Design involves nuanced attention to the properties of the material you’re working with, which in turn requires a great deal of background knowledge acquired through experimentation, instruction, and trial-and-error. You have to know how much elasticity, rigidity, sheer resistance, etc you’re going to get from woods, metals, stones and rocks, bone, papers, textiles, plastics . . . all of which is a result of socio-cultural practices that go back tens and even hundreds of thousands of years.

    There’s also the rather interesting question, “do organisms even appear to be designed?” The ID folks almost always assume that the answer to this question is agreed to be “yes”, with the evolutionists then trying to dismiss the obvious. Well, organisms certainly don’t look designed to me! I simply don’t have the intuition that molecular biochemical reactions look anything like machines or languages — whichever might be the favored metaphor de jure of ID folks.

  2. colewd
    Ignored
    says:

    John Harshman,

    It’s whether ubituitin could evolve, and you should remember that those are different questions.

    How do you determine if something “could evolve”?

  3. colewd
    Ignored
    says:

    Alan Fox,

    Yes, indeed. Except that it’s not a scientific argument. It claims a false dichotomy; no current scientific explanation for an evolutionary pathway, then that pathway must, by default, have a “design” explanation. And that “design” explanation has no content. There’s no mechanism. There’s no candidate. There’s just wishful thinking.

    If IC is not a scientific argument, what type of argument is it?

    The argument is a counter argument to Darwin’s proposed mechanism of random mutation and natural selection. Is Darwin’s argument scientific? If so, why is the counter argument not?

    The design argument is an argument based on inference to the best explanation. Darwin argued using the same criteria.

  4. colewd
    Ignored
    says:

    Kantian Naturalist,

    It always has seemed to me that the ID movement relies on a simplistic and I think deeply flawed picture of what human beings do when they create or design something. It’s a picture in which the person first conceptualizes what it is that he or she is going to make, and then brings it about that something in the world resembles the imagined design. But that’s how how we actually create and design. Design involves nuanced attention to the properties of the material you’re working with, which in turn requires a great deal of background knowledge acquired through experimentation, instruction, and trial-and-error. You have to know how much elasticity, rigidity, sheer resistance, etc you’re going to get from woods, metals, stones and rocks, bone, papers, textiles, plastics . . . all of which is a result of socio-cultural practices that go back tens and even hundreds of thousands of years.

    Would it change your argument if the proposed design was a video game?

  5. Kantian Naturalist Kantian Naturalist
    Ignored
    says:

    colewd: The argument is a counter argument to Darwin’s proposed mechanism of random mutation and natural selection. Is Darwin’s argument scientific? If so, why is the counter argument not?

    Because evolutionary theory has (a) proposed a variety of mechanisms whereby evolution has occurred and (b) discovered empirical confirmation for those mechanisms. ID has done neither. It’s a strictly negative argument. It doesn’t offer anything positive in its place. There are no proposed mechanisms whereby intelligent design takes place, and no suggestions on how to test for it.

    The design argument is an argument based on inference to the best explanation. Darwin argued using the same criteria.

    This indicates a serious misunderstanding.

    Evolutionary theory does involve an inference to the best explanation. But it also tests that inference by asking, “what should we expect to discover if the posit were correct, and what measurements can we perform to see if those expectations match what is empirically available to us?”

    By contrast, design theory does neither of those things. It makes the inference to the best explanation — and then stops.

    Design theory would be a scientific theory only if coming up with an interesting hypothesis were all that there is to science. But that’s just not true. Hypotheses have to be tested against how the world actually is, and design theory doesn’t do that.

    (It was the complete inability of everyone at Uncommon Descent to grasp this elementary point which led to my leaving that forum. I can only afford to waste so much time in these discussions.)

  6. Kantian Naturalist Kantian Naturalist
    Ignored
    says:

    colewd: Would it change your argument if the proposed design was a video game?

    It would prompt a slight revision. But even in that case you have to know different computing languages allow you to do in them, and even if you’re starting from scratch with a new computing language, you’re still limited by the physical constraints of processor speed and memory size.

  7. GlenDavidson
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    says:

    colewd: If IC is not a scientific argument, what type of argument is it?

    The argument is a counter argument to Darwin’s proposed mechanism of random mutation and natural selection. Is Darwin’s argument scientific? If so, why is the counter argument not?

    You have to make the case for IC being a counter argument to Darwin’s mechanism, not just declare it to be so. I know you believe the BSers of ID while disbelieving the truth-tellers of science, but that does not turn the BS that they say into truth, whatever you think.

    You just make baseless claim after baseless claim. Of course you don’t know science, but your ignorance does nothing to justify your adoption of pseudoscientific nonsense as your standard of truth. It’s very much the case that IC would be expected from evolution, especially over billions of years, while you have no evidence of an intelligent agent that could produce anything of the sort during the vast bulk of earth’s existence.

    You really ought to go back to square one and get a good education in science. Unfortunately, you neither want one nor see any need to do so when you can parrot appalling nonsense from IDists

  8. colewd
    Ignored
    says:

    Kantian Naturalist,

    Because evolutionary theory has (a) proposed a variety of mechanisms whereby evolution has occurred and (b) discovered empirical confirmation for those mechanisms. ID has done neither. It’s a strictly negative argument. It doesn’t offer anything positive in its place. There are no proposed mechanisms whereby intelligent design takes place, and no suggestions on how to test for it.

    Thanks for the response. My argument was actually comparing irreducibly complexity as a counter argument to random mutation and natural selection. Can I substitute ID for IC or does this change your argument?

  9. colewd
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    says:

    GlenDavidson,

    You have to make the case for IC being a counter argument to Darwin’s mechanism, not just declare it to be so.

    So you are claiming that IC is not a counter argument to RMNS? I think you can disagree with the argument but on what basis do you claim that it is not an argument at all?

    Darwin made that case that evolution required small changes over time.

    “If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find no such case.”

    Well, Darwin here created a situation where his opponent needed to prove a negative. In all fairness Darwin had very little knowledge of the cell. Behe made a cleaver challenge by showing a difficult situation for Darwin’s theory which was a 30 protein complex called the bacterial flagellum. Since all the parts were needed for the flagellum to function a massive amount of random genetic change is required to create this motor in order to get the advantage of mobility. Forming this motor with Darwin’s mechanism is indeed highly improbable.

  10. Entropy Entropy
    Ignored
    says:

    gpuccio:
    Of course, you could at least acknowledge that the concept of God has absolutely no role in my scientific reasonings about biological ID

    Actually, no. In order to “infer” intelligent design gpuccio is supposedly thinking about human designs as the “examples.” Apparently no problem, right? Except that these very designers are made of the very things gpuccio is trying to blame on design. They’re biological. Given that, gpuccio cannot actually use human design as examples to infer design in nature. Otherwise, the natural question to ask would be: ok, since designers are composed of the things you claim to be designed, then how does your proposed designer function without those very things that make up designers? This kind of questioning would quickly reveal the truth: the design “inference” is all about “God.” It’s not scientifically sound, it’s not philosophically sound. It’s religion trying very hard to hide behind poor philosophy and poor science.

    When I’m told that nothing in nature can produce this kind of “information” (or whatever other anthropomorphized “feature”) my immediate answer is: of course it does! I see it all the time all around me!

    Normally, the creationist, ahem, the IDer, guessing what I meant, asks me to show so in things other than life forms.

    OK then, let’s forget about life forms: where do you see such a thing yourself?

    The IDer thinks it’s a check mate! Human design! Muahahahahahaha!

    But humans are life forms. You said “other than life.” Why should I ignore all of life except humans? If I’m going to include humans to infer design of the very things that make a human, then I should be able to use life itself as examples of naturally produced “function,” and “complexity” and “specified information,” and whatever else I like. After all, if you can break your own rules, so can I, right?

    Etc.

  11. Entropy Entropy
    Ignored
    says:

    colewd:
    If IC is not a scientific argument, what type of argument is it?

    A god-of-the-gaps argument.

    colewd:
    The argument is a counter argument to Darwin’s proposed mechanism of random mutation and natural selection.

    That’s not Darwin’s proposed mechanism. That’s neo-Darwinism. Either way, IC is not a counter argument to that mechanism. There’s no mechanism being proposed. Actually, IDiots insist that they don’t want to talk about “the designer,” and therefore are refusing to even try and talk about a mechanism. A mechanism would include the tools used by the designer, where she took the energy from, how did she managed to introduce more designs each time across millions of years, as life developed in the planet (by all appearances evolutionarily, which would be one more mystery to explain), how she was able to design the life of our planet without leaving a trace of her presence, even after repeated introduction of designs from time to time. Whether she did it all alone, of if she had/needed a little help from her friends, Etc. That’d lead to many more questions, but, of course, because they know that this is a problem, IDiots try and excuse themselves behind that claim that the “design inference” is not about the designer. Really? Why the hell not?! That would be the very first problem to solve! Otherwise there’s no design to infer!

    colewd:
    Is Darwin’s argument scientific?

    Yes.

    colewd:
    If so, why is the counter argument not?

    Because Darwin’s proposals did not rely on poor philosophy.

  12. GlenDavidson
    Ignored
    says:

    colewd: GlenDavidson,

    You have to make the case for IC being a counter argument to Darwin’s mechanism, not just declare it to be so.

    So you are claiming that IC is not a counter argument to RMNS?

    You could try reading what I wrote, and realize that you need to make a case for what you’re claiming, rather than trying to pretend that I wrote something else.

    I think you can disagree with the argument but on what basis do you claim that it is not an argument at all?

    I didn’t say it wasn’t an argument at all, I said you need to make a (good) case for it. Despite that, of course I did point out that evolution is expected to produce IC non-magically, so again, why don’t you read what is written?

    Darwin made that case that evolution required small changes over time.

    “If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find no such case.”

    And? What does this have to do with anything? We’re not beholden to Darwin, by the way, and there is some contention about whether it’s always been so slight, especially in very early life.

    Well, Darwin here created a situation where his opponent needed to prove a negative.

    He was discussing gradual change. Clearly there are much better possibilities for falsification, but he was saying that he didn’t see any great leaps in life. Well, what of that?

    One certainly would think that life that was designed would be filled with aspects that couldn’t evolve gradually, indeed, or even at all, given the fact that evolution is poor at transferring complex genetic information across lineages, while design would be expected to do so. But then we don’t see the transfer of designs in life like we do in actual design, do we? Since he was arguing against Paley, because a number of biologists believed it, well, it’s not a bad argument. Nothing to do with IC, though, since IC could easily enough arise via gradual changes.

    In all fairness Darwin had very little knowledge of the cell. Behe made a cleaver challenge by showing a difficult situation for Darwin’s theory which was a 30 protein complex called the bacterial flagellum. Since all the parts were needed for the flagellum to function a massive amount of random genetic change is required to create this motor in order to get the advantage of mobility. Forming this motor with Darwin’s mechanism is indeed highly improbable.

    Yes, old fatuous crap from Behe, which wasn’t even original with him. And he didn’t bother to show how it was designed, or any candidate for a designer who could do it. And since you just glom onto anything that claims to support your pet ideas, you trundle this garbage out repeatedly, never once making a case for design, nor seeming to recognize the importance of doing so.

    Glen Davidson

  13. John Harshman John Harshman
    Ignored
    says:

    colewd:
    John Harshman,

    How do you determine if something “could evolve”?

    More importantly, how do you determine if something “couldn’t evolve”?

  14. Adapa
    Ignored
    says:

    colewd:
    Forming this motor with Darwin’s mechanism is indeed highly improbable.

    How improbable? Show us the calculations and justify any assumptions you make. Otherwise you’re just spouting off one more tired and completely unsupported IDiot talking point.

  15. colewd
    Ignored
    says:

    Entropy,

    Actually, Idiots insist that they don’t want to talk about “the designer,”

    The identification of the designer is interesting but not the design argument. You are correct that mutation was not part of Darwin’s theory. I think random variation is the change mechanism along with natural selection. He specifically describes morphological variation. This is specifically what the IC argument challenges. Can random variation and natural selection build a structure made of several matching parts, where all the parts are necessary for a specific advantage to be reached.

    On the macro level I introduced powered flight as an advantage that required irreducible complexity. The problem however really surfaces at the cellular level and molecular machines is what Behe chose to surface the problem with Darwin’s claim.

  16. John Harshman John Harshman
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    says:

    colewd: On the macro level I introduced powered flight as an advantage that required irreducible complexity. The problem however really surfaces at the cellular level and molecular machines is what Behe choose to surface the problem with Darwin’s claim.

    It’s a failure of imagination. You can’t imagine that a complex adaptation could be built in any other way than by the serial addition of invariant parts (in which only the end product is functional) or by simultaneous poofing of all parts. There are many other possible pathways that would leave each intermediate step favored by selection. Some of them have been explained to you, and you have been shown the fossil or phylogenetic evidence of their past existence. That really should have settled the matter.

  17. GlenDavidson
    Ignored
    says:

    IDiots try and excuse themselves behind that claim that the “design inference” is not about the designer. Really? Why the hell not?! That would be the very first problem to solve! Otherwise there’s no design to infer!

    One might begin to solve the problem by finding designed stuff, like Lowell’s canals on Mars. Of course you have to know (or at least assume in order to be able to find evidence for it) something about the designer, like that it thinks rationally and acts for purposes, but that seems reasonable for anything that we’d think counts as a “designer.”

    To be sure, there needs to be at least some evidence that a designer could exist, like the time and resources to evolve, unless you have evidence of minds that didn’t need to evolve. That’s a serious problem for IDists. Of course the lack of foresight, purpose, and rational “transcendence” of evolution’s limitations are rather more serious problems, since really good evidence for design would be good evidence for an intelligence existing at the time it was made.

    Glen Davidson

  18. GlenDavidson
    Ignored
    says:

    colewd: On the macro level I introduced powered flight as an advantage that required irreducible complexity.

    Which would prove nothing on its own at all. The mere fact that IDiots parrot that line proves nothing. You also stated:

    You have a fundamental problem with your whole analysis, a flying animal requires precise engineering, not the co-option of parts designed for something else.

    The latter being what is actually found.

    I showed you the evidence that powered flight is excessively complex, due to evolutionary co-option that a good human designer wouldn’t retain. At the least, the human would simply start with fewer bones, not start with many and fuse them together. Your dismissal of that evidence with a projection of your bias onto others was hardly a worthy response.

    Glen Davidson

  19. colewd
    Ignored
    says:

    GlenDavidson,

    I showed you the evidence that powered flight is excessively complex, due to evolutionary co-option that a good human designer wouldn’t retain.

    Can you give an example of a group of human designed flying objects that can group replicate and obtain energy on their own?

    What evidence do you have other then fossil similarity and speculation that bird bones are fused bones?

  20. colewd
    Ignored
    says:

    John Harshman,

    It’s a failure of imagination. You can’t imagine that a complex adaptation could be built in any other way than by the serial addition of invariant parts (in which only the end product is functional) or by simultaneous poofing of all parts.

    Can you give an example of a complex and efficient machine built with unmatched parts outside of biology?

  21. GlenDavidson
    Ignored
    says:

    colewd:
    GlenDavidson,

    Can you give an example of a group of human designed flying objects that can group replicate and obtain energy on their own?

    Why no, human objects didn’t evolve. What relevance does this have to your lack of evidence for your many claims meant to deny reality?

    What evidence do you have other then fossil similarity and speculation that bird bones are fused bones?

    What evidence do you have other than similarity that American languages evolved from a common ancestor?

    And I showed you evidence that the bird “bones” (future bone, cartilage at the time) fuse. Your extreme bias and denial do not turn that into “speculation” as you falsely call it.

    Glen Davidson

  22. colewd
    Ignored
    says:

    GlenDavidson,

    And I showed you evidence that the bird bones fused. Your extreme bias and denial do not turn that into “speculation” as you falsely call it.

    No, you showed me speculation that bird bones fused. The speculation was based on the assumption that evolution is true. No one in there right mind would believe that 9 bones fused into 4 without an a-priori commitment to a speculative inference.

    You believe this fusion occurred based on your extreme bias and denial that the grand claims of evolution are wild speculation.

  23. Alan Fox Alan Fox
    Ignored
    says:

    Gpuccio addresses his final remarks to me!

    To Alan Fox, I have not much to add. He has his ideas, but I don’t agree with him. We could engage in a long debate about the foundations of science, of ID and of epistemology, but frankly I don’t see the intellectual basis for that, judging from his repeated statements.

    I agree. I don’t see much future in a discussion on ID as science. It fails the hypothesis test in not having one. First find your hypothesis, then get back to me! 🙂

    Just one simple note: if you look at my definition of design (which is in perfect accord with the general use of the word, and is the only one which makes sense for ID), the environment (the niche) cannot design. Indeed I define design as a process where specific forms are first represented subjectively in a consciousness, and then outputted to some material object.

    Do you think microevolution happens? As an MD, you must have a view on antibiotic resistance. What changes a bacterial strain develops resistance to an antibiotic? It’s the niche, in my view. Low dose exposure allows a selection of individuals with mutations beneficial *to survival* in a low dose environment. Natural (or artificial, if you need to make that distinction if in a lab environment) selection. The niche has designed a resistant bacterium. “Environmental design” is just another way of saying “natural selection”.

    You can find that definition, and some more considerations, in my first OP here: Defining Design
    Therefore, environment cannot design, because environment is not a conscious agent and has no subjective representations.

    …and yet it happens. Well, at least I and the overwhelming majority of biologists do. You don’t think species are immutable, do you? I hear even Young Earth Creationists accept microevolution these days.

    I also strongly disagree with this statement:

    “What is there to say about the science? You have to accept the primary research at face value, unless you can repeat experiments or question the methodology or conclusions.”

    Not so. Even if you accept the experiments, the methodology and the conclusions can always be questioned. That is the most important role of scientists: to evaluate critically the methodology and conclusions of what is published.

    I agree. My comment was a bit rushed. Repeating other’s experiments is a great test of the reliability of data.

    But these are only a few aspects about which I disagree with you. There are many more, even more important.

    I suspect the point of science where I disagree with you most strongly is you appear to be claiming that ID is a scientific endeavour, in some way supported by what you have written about ubiquitin. I remain unimpressed. There is no theory or hypothesis of ID that is scientific or testable. ID is not science.

    So, Alan, I would say: let’s stop it here. My idea was to discuss my ideas about the ubiquitin system, not to face the usual stereotypes about ID.

    My OP at TSZ directed at you was prompted by your remarks about no ID skeptics wanting to engage with you. I gave you some reasons.

    Thanks for responding. Good luck finding in your designer one day! 🙂

    ETA*

  24. GlenDavidson
    Ignored
    says:

    colewd:
    GlenDavidson,
    No, you showed me speculation that bird bones fused.

    Are you utterly lacking in shame? I showed you bones that exist in early bird embryos that fuse into fewer bones, over and over again. You just say anything, don’t you? You don’t care how false your claims are.

    The speculation was based on the assumption that evolution is true.

    No, it was the evidence that it occurs. Your false claims notwithstanding. They aren’t dumbasses who deny evolution, they’re simply working with the evidence.

    No one in there right mind would believe that 9 bones fused into 4 without an a-priori commitment to a speculative inference.

    Bullshit.

    But the point is that not only in the past were there more bones, bird wings start with more “bones” that even now have to fuse in order to produce more rigid strucutures. Your shameless denial of the facts notwithstanding.

    You believe this fusion occurred based on your extreme bias and denial that the grand claims of evolution are wild speculation.

    I think you’re too clueless even to recognize what I’m saying, it’s not that bone fusion did occur, it’s that much of it still occurs.

    You not only need to learn science, you need to learn how to read. The bone fusion occurs today, it’s a stupid way to design birds. It’s what evolution is stuck doing, because of the inheritance of past characters that were different. Like I wrote before, it’s also common throughout vertebrates, so that we undergo fusion of bones that were useful as articulated parts in the past and are no longer.

    If you would learn something you wouldn’t have to fling utterly false accusations, deny what’s right before your eyes, and project your extreme prejudice onto others. But if you’d have to be very different than what you are now in order to learn.

    Glen Davidson

  25. John Harshman John Harshman
    Ignored
    says:

    colewd: What evidence do you have other then fossil similarity and speculation that bird bones are fused bones?

    Leaving aside the point that this is asking for “what other evidence than sight and touch do you have for the elephant in your living room”, have you forgotten already that Glenn made his case using embryological evidence?

  26. John Harshman John Harshman
    Ignored
    says:

    colewd:
    John Harshman,

    Can you give an example of a complex and efficient machine built with unmatched parts outside of biology?

    I don’t understand how “unmatched” got into that sentence or what purpose it serves. Nor do I understand the purpose of the question with or without that word. Please explain.

  27. Mung Mung
    Ignored
    says:

    GlenDavidson: Are you utterly lacking in shame?

    Yes, yes I am.

  28. GlenDavidson
    Ignored
    says:

    I’m going to skip the carpal fusion, which is somewhat confused and not clear in the photos, and just go to digit fusion. I only went for the carpals in the first place because I was sure that some of them fuse, however the fusion isn’t all that obvious in the depiction.

    Here is how part of bird wings develop, fusing bones together that were articulated in their ancestors. Additionally, in (c) you get to see how all five digits develop to a degree, then some disappear:

    Developmental stages of chick wings in dorsal view. (a) Adult wing with three ossified digits. (b) Stage 35 embryo with four chondrified digits. (c) Stage 29 embryo with five mesenchymal digits (From: Galis et al. 2002).

    http://people.eku.edu/ritchisong/554notes1.html

  29. John Harshman John Harshman
    Ignored
    says:

    GlenDavidson:
    I’m going to skip the carpal fusion, which is somewhat confused and not clear in the photos

    Well, now, let’s not skip the carpal fusion entirely. It’s very clear that the semilunate carpal, clearly visible in the chondral form of (b), becomes fused to the carpometacarpus in (a).

  30. GlenDavidson
    Ignored
    says:

    And why would anyone design a bird wing like that, starting out with ancestral parts that disappear, and, rather than starting with a single structure attached to the radius and ulna, a “hand” develops whose bones fuse together? What’s the point from a design standpoint?

    It’s just what evolution is stuck with, however, reworking ancestral characters into what serves at the present.

    Glen Davidson

  31. GlenDavidson
    Ignored
    says:

    John Harshman: Well, now, let’s not skip the carpal fusion entirely. It’s very clear that the semilunate carpal, clearly visible in the chondral form of (b), becomes fused to the carpometacarpus in (a).

    Good point.

    Glen Davidson

  32. Mung Mung
    Ignored
    says:

    GlenDavidson: And why would anyone design a bird wing like that, starting out with ancestral parts that disappear, and, rather than starting with a single structure attached to the radius and ulna, a “hand” develops whose bones fuse together?

    It was an introductory course in bird wing design. The students were just starting out and they didn’t have the advantage of your 20/20 hindsight on how to design a bird wing.

    Tell us again what your experience in bird wing design consists of?

  33. colewd
    Ignored
    says:

    John Harshman,

    Leaving aside the point that this is asking for “what other evidence than sight and touch do you have for the elephant in your living room”, have you forgotten already that Glenn made his case using embryological evidence?

    My eyes work well on this one but they don’t tell me how the elephant is related to the mouse next to it.

    I am ready for Glenn to support his claim with embryological evidence. There are several papers he can cite. I am curious how clearly he can explain the evidence to everyone.

  34. Entropy Entropy
    Ignored
    says:

    colewd:
    The identification of the designer is interesting but not the design argument.

    Then there’s no design argument to make.

  35. colewd
    Ignored
    says:

    Entropy,

    Then there’s no design argument to make.

    Defeating this argument without invoking a straw-man or denying that it is an argument at all is a real challenge.

    Ken Miller who is a very intelligent guy (as you are) had to invoke a straw-man and conflate evidence to challenge Behe. This convinced me that Behe was on to something.

  36. Alan Fox Alan Fox
    Ignored
    says:

    I just noticed this comment in gpuccios thread at UD on ubiquitin:

    The problem with ubiquitin is just that, it is ubiquitous.

    It’s like finding out that grains of sand can fill in any number of holes and declaring you’ve discovered a semiotic system, therefore holes filled with sand are designed.

    But what about the complexity! Well, my measure is 500 grains of sand. 500 grains of functional sand complexity (FSC)is enough to infer design.

    This is why I just can’t take ID arguments seriously.

    Nice try gpuccio.

    Have you always been an ID skeptic, Mung?

  37. Alan Fox Alan Fox
    Ignored
    says:

    Another final reply from gpuccio

    The problem is simple.

    Possibly but it’s solutions that are hard.

    We in ID know that functional complexity, semiosis and irreducible complexity are reliable markers of design. We know that empirical evidence supports that beyond any possible doubt.

    But how do you know? So far, neither gpuccio or anyone else has supported these sorts of assertions with any scientific hypotheses that might be tested.

    I have given my explicit definition of design, and there can be no possible doubt about what I mean by design in my reasonings.

    An operational definition is what you need. Something you can test, not something you can just assert.

    I have given my explicit definition of functional complexity and measured it in many contexts, with a methodology which is objective and reproducible, and that I can defend explicitly.

    It’s meaningless unless you can demonstrate that you can discriminate between, say, sets of data. Dembski’s “explanatory filter” was a pretty diagram, entirely useless as a scientific tool.

    There is a very clear definition of semiosis, and UB has written a lot about that.

    I, among others, urged him to promote his idea on a website. My apologies for contributing to that wasted effort. Writing a paper and offering it for publication might have been a better choice. The let-down would have been swifter and allowed him to move on sooner.

    Behe has written clearly about Irreducible complexity.

    and singularly failed to gain any traction in the scientific community. Debunked on the bacterial flagellum, debunked on chloroqhine resistance.

    So, most of us in ID agree very well about what these concepts are. And we agree that they allow a safe design inference, if correctly applied.

    Hardly a scientific argument!

    Now, an OP like this (ubiquitin) has not the purpose of putting all that in discussion again. It has the purpose to show a well described and clear example of a system in biology that exhibits huge amounts of:

    a) Functional complexity

    b) Semiosis

    c) Irreducible complexity

    Now, what one would expect from a commenter on the other side is some possible criticism about my arguments, IOWs some argument that shows that the ubiquitin system does not exhibit one or all of those features, according to the explicit definitions that have been given.

    Or, alternatively, some recognition that my arguments are correct, and that the ubiquitin system does exhibit the features that I described, but with a reminder that the basic objection remains that those features, for our opponents, do not allow a design detection.

    That would be a reasonable discussion, about the topic of the thread.

    Instead, Alan Fox, who recognizes that he did not know well the subject of ubiquitin, seems to criticize me for describing a system which was discovered by others (???), and for suggesting as a “subtext” that the system points to design.

    Then he and his colleagues go on dismissing the basics of ID, without any reference to the issues in this OP.

    OK guys, we know that you don’t accept ID. No need to remind that each time.

    We have discussed the reasons when possible, and in the end it is clear that there are deep differences in our views about science, about philosophy of science, about scientific methodology, and so on.

    But really, if you cannot address the specific issues in this topic, if you cannot say if you agree or not that the ubiquitin system shows evidence of functional complexity, semiosis, and irreducible complexity, if you don’t even understand what functional complexity or irreducible complexity are (I hope you understand at least what semiosis is), if even if you understood the concepts you would never accept that they are connected to design, if you go on quoting papers that have nothing to do with the issue, only because they include the words “ubiquitin” and “evolution” in their abstract, and so on and so on, then what discussion can we have?

    None at all.

    My position is different. I don’t reject others’ideas out of prejudice or of vague and wrong ideas about the philosophy of science. I reject neo-darwinism for very precise reasons, and I have dedicated a lot of discussion to express those reasons, including my two recent posts about RV and NS and their limits, which are very detailed in terms of biological arguments.

    I don’t reject neo-darwinism saying that it is a darwin-of-the-gaps theory (although it certainly is). I try to make a specific analysis of what it says, and of the reasons why what it says is wrong.

    But our interlocutors seem not to be interested even in that. Their discussions are always vague a priori philosophical rejections of ID, whatever its arguments may be. But, strangely, they are never a defense of their own theory: they never really defend neo-darwinism.

    So, if I say that RV has severe limitations, I would expect from a convinced neo-darwinism an immediate reaction: no, you are wrong! and I will show you why you are wrong.

    Instead, nothing. I have published a table with a very generous computation of the probabilistic resources of our biological scenarios. No reaction. Am I wrong? Am I right? That does not seem to interest neo-darwinist. At most, we can expect something of the kind: but you have not demonstrated that what we say is impossible!

    No active defense. Ever.

    I have published a whole OP where I analyze in detail the known cases of NS, and I argue very specifically about what NS cannot do.

    No active defense. Ever.

    But NS is always invoked when one shows the limitations of RV.

    And neutral variation is always invoked when one shows the limitations of NS.

    And natural selection is invoked again when one shows that neutral variation has the same limitations of RV.

    And so on, and so on.

    Selectionists become neutralists when it is convenient, and neutralists invoke selection when only that option remains.

    What if someone just shows the limitations of both RV and NS?

    No active defense. Ever.

    After all, their theory is a dogma, and why should one actively defend a dogma? Any falsification of the dogma is, of course, a god-of-the-gaps argument. Because who can exclude that some day, in some place, some explanation compatible with the dogma will be found?

    No one. After all, it is possible

    No active defense. Ever. Faith is more than enough, for those who proudly define themselves “skeptics”.

    To attack evolutionary theory, you need an alternative. There is no alternative ID theory. At this moment, you are not even wrong.

  38. GlenDavidson
    Ignored
    says:

    a) Functional complexity

    b) Semiosis

    c) Irreducible complexity

    Now, what one would expect from a commenter on the other side is some possible criticism about my arguments, IOWs some argument that shows that the ubiquitin system does not exhibit one or all of those features, according to the explicit definitions that have been given.

    Or, alternatively, some recognition that my arguments are correct, and that the ubiquitin system does exhibit the features that I described, but with a reminder that the basic objection remains that those features, for our opponents, do not allow a design detection.

    It’s amazing that he thinks we ought to accept his sham criteria for “detecting design,” when the complete bankruptcy of that nonsense is what those of us who want to defend science standards happen to oppose.

    We don’t care if ubiquitin has those aspects at all. What we do care about is that it is patterned according to the limitations of evolutionary processes, and it lacks any meaningful evidence of actually having been designed. The thought processes of IDists are orthogonal to sound empirical investigative standards.

    He is right about one thing, we don’t have anything to discuss if they’re not willing to consider how faulty their whole basis of “design detection” actually is. And they’re really not (including the ones that are here).

    Glen Davidson

  39. Mung Mung
    Ignored
    says:

    Contradict yourself much Glen?

  40. colewd
    Ignored
    says:

    Alan Fox,

    To attack evolutionary theory, you need an alternative. There is no alternative ID theory. At this moment, you are not even wrong.

    Why do you need an alternative theory to attack evolutionary theory? All science should be open to criticism. Why do you feel the need to protect a theory?

    There is no alternative ID theory.

    Your opinion but others disagree.

  41. dazz dazz
    Ignored
    says:

    colewd: Your opinion but others disagree.

    IDiots disagree, but all you have are negative arguments, made up thresholds and refusals to address the obvious and total lack of explanatory power of “design”.

    So yep, same old crap.

  42. Entropy Entropy
    Ignored
    says:

    colewd:
    Defeating this argument without invoking a straw-man or denying that it is an argument at all is a real challenge.

    No it isn’t. I already explained to you some basic philosophical problems with proposing “design.” So, unless there was evidence for a designer, the explanations must be something else.

    Cherry-picking from something as small and ephemeral as humanity, to try and explain something as big and long-lasting as the history of life on earth, is very bad philosophy, and very bad science (if we could even call it that). Trying to explain the only designers they can point to, as designed, is very poor philosophy and very poor science (if we could even call it that). That, and much more, makes “design” a no starter, no matter how challenging you might think that something is for evolution, we’d still be stuck with natural phenomena.

  43. phoodoo
    Ignored
    says:

    Alan,

    I would like to say…

    But as you know I can’t.

    I am blocked.

    Perhaps this comment will make it through moderation. But I won’t risk the hard work involved in preparing a substantive comment being wasted.

  44. John Harshman John Harshman
    Ignored
    says:

    colewd:
    John Harshman,

    My eyes work well on this one but they don’t tell me how the elephant is related to the mouse next to it.

    Not a reply. I assume you don’t have a real one.

    I am ready for Glenn to support his claim with embryological evidence.There are several papers he can cite.I am curious how clearly he can explain the evidence to everyone.

    It would seem to me that the figures he showed make the argument all by themselves. Not you?

  45. Alan Fox Alan Fox
    Ignored
    says:

    gpuccio ressonds with another final remark.

    [quoting AF in a comment above]

    “To attack evolutionary theory, you need an alternative.”

    This is completely false. Of course a theory can be falsified even if there is no alternative available. Science is about the best explanation, but an explanation that does not work is not an explanation at all.

    Yes, I put that badly (or rather, too briefly). Falsification is a powerful tool when hypothesis testing. But it is a question of degrees of wrongness. If there is only one hypothesis, it may nevertheless be not so wrong as to be discardable until a better hypothesis (more accurate in predictive power, fits the evidence) comes along. Think Newton (not bad at predicting space shots) being supplanted by Einstein (needed for GPS).

    I should have said “to attack evolutionary theory effectively, you need an alternative”.

  46. Neil Rickert
    Ignored
    says:

    phoodoo: I am blocked.

    Perhaps this comment will make it through moderation. But I won’t risk the hard work involved in preparing a substantive comment being wasted.

    You are moderated, not blocked. And I’m pretty sure that you know what’s needed to get of the “moderated” list.

    In any case, substantive comments from you will be approved as soon as we notice them.

  47. colewd
    Ignored
    says:

    Entropy,

    No it isn’t. I already explained to you some basic philosophical problems with proposing “design.” So, unless there was evidence for a designer, the explanations must be something else.

    Design is an explanation on its own.

    In the case of a dead body in the middle of the room there are several possible causes. Isolating the cause to murder is progress but not the end of the investigation.

    Isolating the origin of the bacterial flagellum to design is progress, yet not the end of the investigation.

  48. Acartia Acartia
    Ignored
    says:

    colewd: Isolating the origin of the bacterial flagellum to design is progress, yet not the end of the investigation.

    It’s been over twenty years since Behe “proved” that the flagellum was designed. When is the next part of this investigation going to start?

  49. GlenDavidson
    Ignored
    says:

    Acartia: When is the next part of this investigation going to start?

    It’s been ongoing ever since.

    They’re praying very hard.

    Glen Davidson

  50. dazz dazz
    Ignored
    says:

    gpuccio @ UD:

    ID can be falsified by showing that non design systems can generate new original complex functional information. Of course, nobody has ever been able to show that.

    Won’t even bother looking up an appropriately hilarious gif to respond to that bullshit

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