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 thoughts on “Ubiquitin: a challenge for evolutionary theory?

  1. gpuccio’s latest comment reminds me of a hostage note cut from the newspaper.

    He’s carried on that great UD tradition of highlighting words and phrases like “major challenge”, complexity, “integrated stress response”, “an unanticipated role”.

    He notes:

    Emphasis mine

    .
    Yes, indeed….

    Dual or multiple roles seem to be the rule in this intricate network of networks!

    Er, yeah. Sounds like brilliant design to me. Sounds like it is both easy to maintain and easy to make changes to. Er, not!

    They are ooinh and ahhing over what would get you a failing mark at programmer school. And engineering school.

    The word complex appears 200 times on that page as of that comment. But you want individual components to do simple things and those components acting in tandem doing complex things. Not a mish mash of multi layered complexity where it means one thing reading forwards and another backwards and upside-down too, as so impresses BA77. But who designs like that? Only one system that I can think of…..

    But the more complex the better, as that means it’s less likely evolution coulda done it. They just ain’t been listening the past 20 years or so….

  2. gpuccio:

    Dual or multiple roles seem to be the rule in this intricate network of networks!

    OMagain:

    Er, yeah. Sounds like brilliant design to me. Sounds like it is both easy to maintain and easy to make changes to. Er, not!

    They are ooinh and ahhing over what would get you a failing mark at programmer school. And engineering school.

    Gpuccio is making the same error as Sal, who sees Rube Goldbergish systems in biology as evidence of design, when in fact they are exactly the opposite.

    Neither Pooch nor Sal understands good design principles. Pooch at least has the excuse that he’s pontificating in an area outside of his expertise. Sal, on the other hand, claims to have been an engineer earlier in his career. If so, he really should know this stuff.

  3. ET@UD
    Too funny, “entropy” is now in full meltdown mode. It thinks that just because Darwin didn’t use the words blind and mindless processes that he wasn’t talking about them!

    What I think is that you’re too stupid to understand that I’m not a religiously inclined idiot like you. Here it goes again:

    If what you mean is evolution, as in the natural biological phenomena, then say evolution. Don’t talk about “blind watchmakers” as if Dawkins was some kind of prophet. Don’t project your religious stupidity onto others.

    I hope this time you try and exercise some reading comprehension.

    ET@UD
    Earth to entropy- that is all Darwin talked about. Natural selection is both blind and mindless.

    No kidding! And that makes it mandatory that I should know every fucking metaphor and analogy by every person who ever wrote about evolution? I think not. Again, the religious inclinations are all yours ET. Stop projecting.

    ET@UD
    Darwin sought to remove teleology from biology, ie design without a designer.

    No he didn’t. He just understood a way in which natural phenomena could do things that previously were more mysterious. If that “removed teleology” is not Darwin’s fault. That’s just what the many avenues of evidence he studied pointed to. You should learn the difference between figuring something out and aiming to some end like removing teleology. For example, when I started reading Darwin’s origin of species I was seeking to have a laugh at his expense. Instead I found out why he was convinced about evolution and started to get convinced myself. I figured something out (with a lot of help from what was presented in the book). I wasn’t seeking to remove teleology from anything.

    ET@UD
    You don’t have any knowledge nor intellectual honesty. You don’t even know what is being debated. ID is NOT anti-evolution.

    I don’t remember saying that ID was anti-evolution. I read gpuccio’s comments defending common ancestry. It would be stupid of me to say that he’s anti-evolution. You, on the other hand, lack the intellectual honesty to look at my comments as they are. You just assume too much and talk out of your ass.

    ET@UD
    Clearly you are just an ignorant troll who has found a happy home among other ignorant trolls.

    Says the ignorant idiot who couldn’t read my first two comments for comprehension. What about this: next time you want to kiss gpuccio’s ass, instead of calling the apparent opponent “willfully ignorant” without so much as looking at what gpuccio quoted, you just cheer at gpuccio? That way you won’t look like a stupid drooling ass-kissing fool writing about people they never interacted with.

    ET@UD
    Ignorance and dishonesty. No one claims the design inference from mere complexity. Grow up

    No of course not. It’s not as if gpuccio’s most recent comment was all about complex intricate networks with multiple roles and all.

  4. ET@UD
    Oh my. Entropy is a special case of pathetic. Strange that I don’t have any religious inclination just a passion for reality.

    You have a strange way of demonstrating your passion for reality. By imagining that I follow Dawkins and Coyne as if they were some kind of prophets. By “answering” my comments without reading them for comprehension. By defending a position that’s all about an imaginary being. Sure ET, sure. That’s clear passion for reality.

    ET@UD
    And it doesn’t have any clue as to what Darwin’s point was.

    Of course I know what Darwin’s points were. Seems more like you just don’t like the idea that Darwin came to his own conclusions without seeking to “remove teleology from biology.” Of course, I should have imagined this from you. After all, you project your religious inclinations onto others, no wonder you’d reverse-project your seeking to “move teleology into biology” onto Darwin, rather than accepting that “teleology in biology” was a philosophical blunder that shouldn’t have been there in the first place.

    ET@UD
    If evolution is by design then it is very different from what Darwin and his followers (all evolutionary biologists) are talking about. That means one has to be clear about what type of evolution one is talking about. That you are too dim to understand that exposes your dishonesty.

    That you cannot convey the idea without imagining that we have read every book by Dawkins is the problem here. If you want to be clear, then be clear, talk about evolution as understood by [most] scientists, or about evolution by natural means, for example. Anything that doesn’t assume that I share your idiotic religious inclinations would do.

    ET@UD
    And finally there is a huge difference between mere complexity and “complex intricate networks”. You are willfully ignorant and it shows.

    This looks a lot like a laughable, grasping at straws, pathetic attempt to save face. Either way, the willful ignorance is all yours. I didn’t write “mere complexity.” That was you.

    ET@UD
    Good luck with that. And good luck trying to demonstrate that the ubiquitin system evolved by means of natural selection, drift or any other blind and mindless processes. And yes that is what evolutionism demands.

    Evolutionism? You cannot help yourself, can you? You have to project your stupid religious inclinations onto others.

    What makes you think that I need to demonstrate that the ubiquitin system evolved? Do you really think it’s me who has something to demonstrate? While I’d be interested in the history of this and many other biological phenomena, the poor philosophical and poor scientific foundations of ID are enough for me to reject ID. I don’t need to have answers for everything. It’s enough to understand the problems with your position.

  5. gpuccio@UD writes:

    ET:

    Thank you for the updates.

    In case some real argument emerges on that side, please let me know. 🙂

    I was starting to give gpuccio the benefit of the doubt, and then he calls ET’s bullshit “updates.” Oh shit.

  6. This is just gpuccio’s version of FMM’s “hide behind the ignore button” strategy.

    If Pooch depends on “ET” for updates — or pretends to depend on him — then he has an excuse for not responding to refutations of his arguments. “Oh, I didn’t see it — ET didn’t “update” me on it.” As if Pooch were unable to read this thread for himself.

    It’s a shame we have such cowardly opponents.

  7. ET@UD
    Right, uh-huh. You used the word “complexity” all by itself. And that, my ignorant opponent, is mere complexity.

    No you poor illiterate grasping-at-straws fool, that’s any complexity.

    ET@UD
    Entropy seems to think it is my fault that I know more about evolutionism than it does.

    I don’t know anything about “evolutionism.” Since you’re so inclined to religious stupidity, I’m not surprised that you would.

    ET@UD
    Because I have read more evolutionary literature by more authors that is somehow a knock against me.

    What’s a knock against you is your expectation that I should know Dawkins and Coyne’s writings, and that I should care about them. Again, that’s your stupid religious inclinations talking. Also, given your inability to read my comments for comprehension, your “reading” of evolutionary literature cannot be very impressive.

    ET@UD
    Wow. And yes evolutionism is correct as it is based on faith and not science.

    That you cannot conceive of accepting scientific evidence as it comes, rather than twist it to tell the ID bullshit, doesn’t mean that everybody thinks the way you do.

    It would be so easy for you to just stop presenting yourself as a pretentious religious ass-hole, yet there you are, doing exactly what I said you do: projecting your stupid religious inclinations onto others.

    ET@UD
    If you had the science you would just post it

    What the hell are you talking about now? The science about what? Evolutionism? That’s your thing, not mine. It’s you who believes in a religious evolution controlled by your imaginary friend.

    P.S. Ironic that gpuccio is counting on an illiterate buffoon like yourself for “updates.”

  8. keiths: It’s a shame we have such cowardly opponents.

    It’s interesting that gpuccio was first begging for comments “from the other side,” then he won’t read the comments. Who can understand that kind of mentality?

  9. Recent Pooch:

    1) Functional complexity beyond some appropriate threshold (500 bits will do in all contexts) clearly allows a design inference.

    2) Irreducible complexity multiplies the functional complexity of the individual components of the system.

    3) Semiosis is a feature that by its same form is never found in non design systems, and clearly points to design.

    But I suppose that our friends at TSZ are not interested in those arguments.

    We’re not interested in such delusions, true. But, more importantly, they’re not arguments, just IDist wishful thinking (OK, #2 is true, but banal).

    They really do learn very bad habits of thinking from their pseudoscience. In practice, ID is little more than a means of inducing the Dunning-Kruger effect for the sake of belief in ID.

    Glen Davidson

  10. gpuccio also still insists that we don’t have an argument and repeats:

    In my view, instead, my argument is that there are three different markers that are linked to a design originn and therefore allow empirically a design inference

    Those three features are:

    a) Functional complexity (the one I usually discuss, and which I have quantitatively assessed many times in detail)

    b) Semiosis (which has been abundantly discussed by UB)

    c) Irreducible complexity

    We’ve argued to death that’s not how science is done, but hey, we don’t have an argument. Case closed I guess

  11. gpuccio@UD
    1) Functional complexity beyond some appropriate threshold (500 bits will do in all contexts) clearly allows a design inference.

    As I said, they just point to complexity and think that makes their absurd imaginary friend real.

    They compound it with misunderstood information theory and misapplied bit scores, but, in the end, it reduces to their inability to understand how could nature do something, therefore god-did-it. Same old god-of-the-gaps in disguise.

    gpuccio@UD
    2) Irreducible complexity multiplies the functional complexity of the individual components of the system.

    So this is but insistence on point number 1.

    gpuccio@UD
    3) Semiosis is a feature that by its same form is never found in non design systems, and clearly points to design.

    “Semiosis” is your inability to understand the concept, the problem, and the subjectivity, of anthropomorphism. You look at a system described in human terms (naturally, since it’s humans doing the describing), and take the metaphors and analogies to heart: therefore semiosis! It’s like ET’s problem with “teleology in biology,” which is yet another example of anthropomorphism.

    gpuccio@UD
    But I suppose that our friends at TSZ are not interested in those arguments.

    I don’t know about others here, but I’m interested. Not in the way you’d wish though, since I understand the problems with those arguments. I’m interested more in the sense of wondering if you’d understand why I’m not impressed. I understand why you’re impressed though:

    1. You really think that talking about 500 bits is impressive and beyond nature.

    I can explain to you why I find that unconvincing. If it was impossible for nature to put that amount of information together, then it would be impossible for designers to put that amount of information together. How so? Well, in order for designers to put that amount of information together, energy flow is necessary. Putting information together consists on “transforming” energy flow into patterns. We don’t produce available energy. We’re completely dependent on nature for that. So, claiming that a designer is necessary to produce “information,” seems a lot like putting the cart before the horse.

    At the same time, enormous amounts of energy flow transforming into patterns happen all the time regardless of designers. So 500 bits? A joke for natural processes. Natural phenomena have energy flows to spare. So unimaginable, so unmanageable, so out of reach to any designers, that it makes the bits claim pathetic. Ants would be more justified in claiming that all the volcanoes in the planet cannot move as much material as a single ant colony.

    2. You really think that irreducible complexity adds to the bits “problem.”

    See above.

    3. You might have never thought of the problem of anthropomorphism, or you think that’s an obvious inference, rather than an inclination from the fact that you’re human.

    That might be your true handicap. I have to warn you though, that convincing someone like me that your anthropomorphisms are anything but, might be a titanic task.

  12. ET@UD,

    “By the way you have all of the power to refute our design inference. All you have to do step up, do the work and demonstrate materialistic, stochastic (non-telic) processes can produce what we say is intelligently designed.”

    You’re seriously misinformed.

    1. Nobody has produced a way to demonstrate non-“materialistic” processes. So, of course, anything in science will be about “materialistic” processes.

    2. The philosophically appropriate approach to understand nature is to assume non-telic processes.

    3. “Stochastic” is not the same as “non-telic.” Natural phenomena can have directions without being “telic.” Gravitation is a very obvious example.

    Oh, but you say that you don’t have to do anything but poo-poo the design inference with your ignorance. So much for science…

    Again with your illiteracy. No you poor buffoon, I don’t need to poo-poo the design “inference.” Again, all I have to do is understand the problems with it.

  13. ET@UD,

    Entropy was too afraid to join this site. Now I understand why.

    Sure. because I must be as illiterate as you to think that nobody can come here and take a look. Stop projecting your stupidity onto others!

  14. Pathetic ET@UD:

    They are wondering why I don’t relay their alleged refutations

    Wondering? Nah. I think you cannot relay them because you’re too stupid to understand them in the first place.

    P.S. I’m leaving ET alone. He has nothing to offer but projection of his imbecility onto others, and an astounding inability to read for comprehension.

  15. Entropy:
    Pathetic ET@UD:

    Wondering? Nah. I think you cannot relay them because you’re too stupid to understand them in the first place.

    P.S. I’m leaving ET alone. He has nothing to offer but projection of his imbecility onto others, and an astounding inability to read for comprehension.

    For the record, ET is YEC Joe Gallien AKA “Frankie” who was permanently banned at TSZ for posting porn. The guy has the IQ of a moldy turnip.

  16. keiths,

    He seems to be suggesting that he’s also J-Mac.

    ETA: Maybe it’s just that too many creationists become parodies of themselves and each other.

  17. Entropy:

    He seems to be suggesting that he’s also J-Mac.

    Link?

    Neither is very bright, but there are also a lot of differences. I’m almost certain they’re not the same person.

  18. gpuccio

    One point where some non universal descent could be found is LUCA, which could have been a pool of different organisms.

    The point where some non-universal descent could be found is in the the last universal common ancestor. Sure thing, pal.

  19. colewd: Return to UD and you will see my answer.

    Thanks for making the UD-thread slightly more interesting by introducing some real discussion instead of all the tedious back-patting. I appreciate that you are one of the few IDers here willing to stick his neck out. Still, you and gpuccio are not consistently committing to your positions.

    bill cole:

    “I think Michael Behe said it best when he said that common descent in itself is not that important. It’s explaining new genetic information thats important.”

    gpuccio: That is certainly true! 🙂

    No, that is patently false. You are having your cake and eating it too. The “information jumps” that gpuccio introduces in his OP critically rely on the different genes he is comparing being homologs, i.e. on common descent being true. If he is unwilling to defend this, he must also drop that argument.

  20. gpuccio,

    Do you agree that my arguments here about the biology of the ubiquitin system do show that it is a system that exhibits huge amounts of complex functional information, semiosis and irreducible complexity?

    Perhaps if you were to quantify “huge” you might get an answer.

    ET responding to me asking “who designs like that?”:

    Whoever needs to, duh

    Well, ET, care to name a single person who needs their designs to be complex multilayered interlocking messes?

    In other words ET, what designers are you familiar with that design in such a way?

  21. gpuccio,

    I certainly believe that “explaining new genetic information” is the really important thing. And I use CD to demonstrate that only design can explain it.

    But you can replace “design” with “unicorns” and it does not change the explanation at all!

    In that entire thread you have simply made the argument that there is genetic information to be explained, not actually demonstrated that “design” explains it in a different way to saying “unicorns” designed it.

    In a sense, the information is written by the designer (ID point of view)

    That seems to be the sum total “explanation” on that thread.

    And in any case, gpuccio throws his entire argument under the bus:

    And there is a specific rationale for that: systems which do not include the intervention fo a conscious intelligent designer cannot harness information towards a specific function, because they can rely only on RV and, if there is reproduction, NS. Those mechanisms have severe limits, and cannot go beyond simple results in generating functional information. IOW,s they can generate simple functional information, but never complex functional information (a general threshold of 500 bits will be more than enough in all cases).

    Please feel free to go into detail regarding these “severe limits” and how you have determined that they exist at all.

    What stops “simple functional information” becoming “complex functional information” over time?

    In short, gpuccio has noted that RV+NS can do everything he claims for his designer but not above some arbitrary level. Only the designer can act above “that level”.

    Just a pity that they are unable to actually demonstrate any of this.

    Funny how gpuccio accepts common descent, the power of evolution (under a certain level) but they still all think he’s actually arguing in favour of ID. All that will happen is that at some point gpuccio will have a realisation that his arbitrary level is just that, entirely arbitrary, and vanish from the ID scene.

  22. gpuccio@UD
    I think I do, but it will certainly help to look at your explanations, rather than simply imagine! 🙂

    That’s why I explained. If only you had read the whole comment you’d have some idea.

  23. gpuccio seems to be willing to read answers now, and he asked me explicitly, so here it goes:

    gpuccio@UD:
    Before going to your arguments, I would like to clarify an important aspect.

    My OP here, and almost all the following discussion, is about specific biological issues, with the purpose of showing that:

    The ubiquitin system is a biological system that exhibits huge amounts of complex functional information, semiosis and irreducible complexity.

    I know that was your aim.

    gpuccio@UD:
    You, like all your colleagues, have not touched that point in any way, as far as I can understand.

    I did touch at least one, I explained that the semiosis you see is but an anthropomorphism.

    gpuccio@UD:
    You have rather repeatedly discussed the more genral issue:

    Are functional complexity, irreducible complexity and semiosis markers of design?

    Because that’s the important problem. You can spend your life calculating information, being very careful about it, making your assumptions explicit, etc, and none of that will solve your main problems.

    gpuccio@UD:
    Which is a completely different issue, that I gave for granted in the present OP, having discussed it many times and in great detail previously, even with you TSZ guys.

    Then why would you want feedback from anybody “on the other side”? If you’re assuming that you have solved all the philosophical and scientific problems of ID, then you don’t need any feedback on the ubiquitin or any other examples you might want to present. All you need to do is go on and present them, keep feeling astounded about the complexity of it all, and claim that’s evidence for ID. You have no use for my feedback at all.

    gpuccio@UD:
    OK, I will discuss it again here.

    But before that, I would like to ask you an explicit question about what you did not touch:

    Do you agree that my arguments here about the biology of the ubiquitin system do show that it is a system that exhibits huge amounts of complex functional information, semiosis and irreducible complexity?

    1. Complex functional information: no. Your definition presumes knowing how many “rocks” can be used as “hatchets” (if I remember correctly). Since you are examining but the one that evolved, you cannot know how many things could have worked just as well. Then, well, you assume quite a bit about the amount of conservation being more than just representative of the amount of divergence, to call it instead “added [functional] information.” (I know that you try and justify the assumption, but no space right now to get there. I can do that later if you’re interested. No point if all I might get is ET making a fool out of himself.)

    2. Semiosis: no. That’s but anthropomorphism.

    3. Irreducible complexity: no. I see your lists, and there’s plenty there where things could vary/miss a component, and the “subsystem” would still work.

    gpuccio@UD:
    OK, I will not wait for your answer (but I would definitely appreciate an answer). So, I will go on to comment on your points.

    Answer given, if incomplete on point 2, just because you’d appreciate it.

  24. OMagain: Well, ET, care to name a single person who needs their designs to be complex multilayered interlocking messes?

    In other words ET, what designers are you familiar with that design in such a way?

    ID does not do “ how”.

  25. Gpuccio’s refusal to answer the saltationist challenge is duly noted.

    Instead he doubles down on his fallacious BS:

    Functional complexity beyond some appropriate threshold (500 bits will do in all contexts) clearly allows a design inference.

    This is an old and fundamental point, I would say the foundation itself of ID

    heh

  26. gpuccio @ UD

    Corneel at TSZ:

    Before going on with Entropy, I would like to give a couple of quick answers to your two posts.

    You do read TSZ. That is excellent. I found this communication by proxy quite a hassle.

    I have no special preference about LUCA being one organism or a pool of organisms. I was just mentioning that both theories exist in the scientific literature.

    No, you were trying to suggest that the three domains of life had independent origins, or at least keeping that option open by inserting lots of “I don’t knows” and “maybes”. And then, Bill and you decided that it was a trivial matter and that we should focus on the source of the new genetic information. However, as I have been pointing out to Bill, one of the arguments you put forward (information jumps) requires common descent to be true at taxonomic levels much lower than LUCA, so I don’t agree that this is “not that important”.

    It is absolutely true that my argument here relies on common descent. I have clarified that I believe in common descent, and that I assume it for my biological resonings.

    But there is more. I have defended Common Descent in detail and with the best arguments that I can think of. see my comments here, #525, 526, 529, 534, 538 and 546. What can I do more than that?

    If others, like Bill Cole, still have doubts, I can only respect their opinion, which is what I do with everyone after having clarified what I think.

    I am very happy that you promote common descent and (a limited form of) natural selection on UD, because if you were to succeed in persuading your ID friends, it would allow us to move on to more interesting discussions than “everything related to evolution must be false”. That is why I am annoyed by your reluctance to emphasize that common descent is required for some of the arguments you made. If Bill Cole would be correct in his presupposition that common descent is false than that would collapse the “information jump” argument. I would think you would be bothered by that, but apparently you are not.

    But it is also true that, if CD were not true (just a mental hypothesis, beware!) then the only explanation for the homologies in proteins would be common design. That’s not what I believe, but it is a true and reasonable consideration.

    And there you go again. Why did you add that? Where did your unwavering defense of CD go? No, it is not a “true and reasonable consideration” because it lacks a plausible mechanism to generate the observed patterns, such as the consistency of the neutral substitution rate with time since divergence and of course the nested hierarchy.

  27. @gpuccio

    And I have a question about your plots of human conserved functional information against the estimated time since divergence. You use them to infer that information jumps have taken place wherever there appears to be a steep increase in the bit score, is that correct? My question is: what would a plot look like from a protein neutrally evolving at a constant substitution rate? Could you generate such a plot with simulated data?

  28. Gpuccio never backs up his egregious nonsense, like:

    1) Functional complexity beyond some appropriate threshold (500 bits will do in all contexts) clearly allows a design inference.

    3) Semiosis is a feature that by its same form is never found in non design systems, and clearly points to design.

    One could argue about whether anything in life counts as “semiosis,” but I don’t think that definitions are that important. Call it semiosis, as some on our side do.

    Gpuccio just kind of repeats himself, and uses the excuse that some will argue with him over these matters. I don’t care, he needs to show that they actually indicate design, not merely assert it without reason over and over again. I happen to think that too many do follow the IDists down the rathole produced by their illegitimate claims of what indicates design.

    You have to find the marks of design processes in order to infer design, not use Gpuccio’s false dilemma regarding functional complexity. Or his unwarranted assertions about what “semiosis” indicates. What we have in life is a host of features that make no design sense. I’ll just again show an illustration of the non-design found in life:

    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. gpuccio,

    I think I’m going to enjoy our exchange. Only caveat, this week is horrendously busy, which might make my answers come a tad later. But I haven’t forgotten. Deal?

    Entropy

  30. That is what has to be explained. No observed designer is going to make wings by, in part, starting with five digits, keeping three, and fusing together a whole lot of little “bones” into one larger rigid structure. It’s complex all right, but mostly because it is beholden to the dead hand of history. It is made of ancient parts that it inherited, and evolution has few “choices” of what it can do with them, and as in so many cases the fusion of bones is what evolves.

    Yes I know that he believes in evolution, but clearly if you’re going to put in a designer, you’d expect, you know, design, not the jury-rigging of inherited characters that is what evolution is stuck doing.

    That’s what has to be discussed. There’s nothing to discuss regarding the BS about functional complexity and “semiosis,” they’re just nonsense that IDists put out without any regard for standards of evidence.

    Glen Davidson

  31. Gpuccio:

    OK, I have nothing to say about GlenDavidson’s “argument”, because it is not an argument at all.

    https://tinyurl.com/y7kow24a

    Oh, how meaningful. I had written (in part):

    We’re not interested in such delusions, true. But, more importantly, they’re not arguments, just IDist wishful thinking (OK, #2 is true, but banal).

    Of course he didn’t have the decency to quote that there, but only later on when the issue has shifted. Naturally I wasn’t making an argument in response to his non-argument, and, rather than dealing with the fact that he only made assertions and I called him out on that illegitimate practice, he notes that I didn’t make an argument. No, I called for an argument, not the usual baseless claims and endless blather, and instead of an argument I get tu quoque (where it makes no sense) and the usual blather and baseless claims.

    So he says:

    It’s really strange that GlenDavidson says that, because I have made my biological arguments very explicit and everyone can check easily if what I have said is true or not.

    Bullshit, that’s the whole point, you haven’t made arguments, you’ve made the usual evidence-free IDist claims and built a house of cards on that. That’s the continuing problem.

    Glen Davidson

  32. I emailed gpuccio and asked him to come here but for whatever reason he wont. I’m banned at UD and cant take up his challenge there. Maybe ET will persuade him.

    I think its interesting that both sides here insist that they’ve made devastating points that the other side wont even address. I think the way to discuss this is to dig out every assumption and every idea behind a claim and not to move on till its settled or at least thoroughly vetted. We might not convince the other side but I think it would be useful laying the arguments out that way.

  33. This fun bit is from ET, trying to make his idiocy present:

    I can’t name a single person capable of designing a living organism. Can you, OM?

    I don’t know about OM, but no, me neither. So, let’s get this right: ET cannot name a single person capable of designing a living organisms, therefore the living organism was designed! (?) Way to shoot yourself in the foot ET.

    Can you find any evidence that blind and mindless processes can produce the ubiquitin system? No- then stop whining and get to work

    I sure can. I see it every day around me. Ubiquitin systems arising all over the place by processes that have nothing to do with eyes and minds. Contrast that with your admission that you don’t know anybody who can design a life form, and there you go.

  34. RodW: I emailed gpuccio and asked him to come here but for whatever reason he wont.

    Try quantum interfacing

  35. GlenDavidson: Bullshit, that’s the whole point, you haven’t made arguments, you’ve made the usual evidence-free IDist claims and built a house of cards on that. That’s the continuing problem.

    Not only that, they entertain themselves trying to patch the cards at the top, as if that’d fix the problems with the “foundations.”

  36. [quotes from https://tinyurl.com/yahf9yd2 ]

    You don’t want to discuss functional complexity and semiosis.

    Quit BSing. I wrote: “Gpuccio never backs up his egregious nonsense, like:” Then I quoted your BS about functional complexity and “semiosis.” I didn’t say I don’t want to discuss it, I want you to back up your claims. You really really like to make your strawmen, don’t you?

    If I were a mean guy, I would simply say that I don’t want to discuss your points, those that in your opinion “have to be discussed”.

    If you were a smart guy, you’d just discuss issues instead of pretending that it’s all about what people say. You don’t just get to make things up in science, although you certainly do plenty of that at UD.

    But I am generous (sometimes 🙂 ). So, I will discuss them.

    Well, I wish you would, rather than making your meaningless excuses.

    In general, I never discuss morphologic arguments, if the molecular mechanism is not known. Because it’s at the molecular level that information works.

    It’s at the morphologic level that “selection” works.

    However, it seems that your objection is of the kind: “no designer would do that”.

    Quit making shit up. I wrote: “No observed designer is going to make wings by, in part, starting with five digits, keeping three, and fusing together a whole lot of little “bones” into one larger rigid structure.” [Italics added]

    It’s all about observation, not omniscience. It’s not about someone’s (not mine) claim that “no designer would do that.” You’re repeating the typical ID misrepresentation of the epistemic problem that you have. You don’t have any example of something that makes life, or the sorts of bizarre (in terms of design) adaptations that occur, but instead of recognizing that you’re devoid of the necessary observations to infer design from life, you try to shift the burden to us by pretending that we say “no designer would do that.” How the hell would I know if something might design as stupidly as your “designer”? Present evidence of one that does design that stupidly and I’ll consider it. Lacking that, you really have nothing.

    I don’t agree. The designer of biological objects clearly works under constraint.

    Why? And what evidence do you have of any designer that would work under such constraints, save when, say, our limitations mean that domesticated life can only be changed so much by us. But we’re not the sorts of things that make life from scratch, either.

    that has always been one of my constant points.

    No, that’s another of your evidence-free claims.

    He cannot do all that he likes. He works through common descent, introducing new information when and if possible.

    Does he? So it all looks just like it would if not designed, except where you have decided that it “must have been designed”? Why? Again, why would anyone design like that? Humans wouldn’t. Do you have evidence of any intelligence that would?

    And why doesn’t the “designer” introduce new information from non-interbreeding lineages? Why don’t bats have feathers and bird wings? A human designer would be inclined to include at least some parts from other lineages, while this one oddly follows the limitations of dumb evolutionary processes.

    He also has to do with negative constraints: for example, random mutations.

    Why? Your claim is that he’s supersmart, able to make life from scratch. Why doesn’t he just undo the random mutations? And what evidence do you have for any of this, btw?

    What we see is not th result of some omnipotent design from scratch.

    And yet that’s your claim for the start of life.

    It is the convergence of design under constraints, maybe even of the action of different designers. It is more like adapting some existing code to new requirements, working on what already exists, and doing the best possible.

    Dumb way to design. If you have evidence of designers that design that stupidly, I’m all ears.

    Then you say:

    “Bullshit, that’s the whole point, you haven’t made arguments, you’ve made the usual evidence-free IDist claims and built a house of cards on that. That’s the continuing problem.”

    I have made a lot of arguments, biological arguments, detailed arguments, both here and in the other OPs I have quoted. And you have never addressed them.

    That’s because they’re based on bullshit, like the junk you wrote above, mere claims based on nothing.

    But please, go on that way. So I have one discussant less to be answered.

    Yes, you have utterly failed to back up any claim of yours. So you blame me.

    As far as that goes, it’s clear that you’ll never discuss anything intelligently, and without resort to your many baseless assertions. So who cares if you’re not going to continue to throw BS at the actual issues I that I bring up?

    Glen Davidson

  37. gpuccio said: “He also has to do with negative constraints: for example, random mutations.”

    That’s a tacit admission of defeat right there, unless he’s willing to take back all that crap about “probabilistic resources” being insufficient to produce the observed diversity of life

  38. GlenDavidson,

    It’s at the morphologic level that “selection” works.

    How would selection be involved in producing the ubiquitin system?

  39. Corneel,

    No, that is patently false. You are having your cake and eating it too. The “information jumps” that gpuccio introduces in his OP critically rely on the different genes he is comparing being homologs, i.e. on common descent being true. If he is unwilling to defend this, he must also drop that argument.

    Gpuccio agrees with you here where I do not. I will address it again with Gpuccio. All you need for information jumps is to show change in species that adds information rich sequences.

    How you determine how information rich they are is based on translated amino acid counts and the required specificity to the AA sequence. If an AA sequence is preserved historically that is evidence of purifying selection. This along with the number of AA in the sequence tells us the information count in bits.

    Gpuccio is on very solid ground with his 500 bit limit as most everyone here would admit that a random process cannot perform this search. If you ask about selection the proper question is evidence of an interim sequence. The challenge with the ubiquitin system is that it controls cell division rates which is mission critical to multicellular life.

  40. ET unwittingly lets gpuccio know what he really thinks:

    But get your research published and maybe someone will care

  41. OMagain:

    ET unwittingly lets gpuccio know what he really thinks:

    But get your research published and maybe someone will care

    Too funny. ET/Joe G is the personification of the phrase “own goal”.

  42. Origenes, at UD:

    I remember someone named Keiths, who made similar jaw-dropping arguments. When you point out to him that physical processes on their own cannot produce e.g. a spaceship, he would counter that intelligent design is also unable to do it. Amazing stuff.

    Um, no. That bears no resemblance to any argument I have made.

    But why try (and fail) to refute my arguments when you can just make shit up instead? Right, Origenes?

  43. Origenes at UD,

    Entropy: If it was impossible for nature to put that amount of information together, then it would be impossible for designers to put that amount of information together.

    Origenes: I remember someone named Keiths, who made similar jaw-dropping arguments. When you point out to him that physical processes on their own cannot produce e.g. a spaceship, he would counter that intelligent design is also unable to do it. Amazing stuff.

    If you wanted to display your ignorance of information theory and of the relationship between information and energy, then you succeeded. It might be better if you left adults continue their discussion.

    Entropy: “How so? Well, in order for designers to put that amount of information together, energy flow is necessary. Putting information together consists on “transforming” energy flow into patterns.”

    Origenes: Hmmm. So?

    So you continue reading the whole comment to see if you understand, and if not, then you ask for clarifications, or, if too shy for that, you leave the discussion to those who can handle it.

    Entropy: “We don’t produce available energy. We’re completely dependent on nature for that.”

    Origenes: Yes. But why is our specific situation relevant? We are neither the designers of earth’s life nor the universe, now are we?

    So ID is not a scientific endeavour, but a religious argument? All the times they’ve insisted that they take their clues from what human designers do they were lying? I didn’t know that. Thanks for the clarification. I’m a bit sad because of the lies, but well, I should have known. ID looked so suspicious. Man I should stop being so naïve.

  44. Someone pass on to gpuccio that I cant post at UD. I’ve been banned. And I have no more email addresses that I can use to start a new account!

  45. ET at UD,

    ET: Can you find any evidence that blind and mindless processes can produce the ubiquitin system? No- then stop whining and get to work

    Entropy: I sure can. Ubiquitin systems arising all over the place by processes that have nothing to do with eyes and minds.

    ET: Question-begging cowardice. Nicely done

    There’s no question begging. Those systems are produced by processes that have nothing to do with eyes and minds. This is clear and undeniable evidence if you know how to look at it. But, given your inability to read for comprehension, I’m not wasting time in explaining it to you.

    Also, of course I knew you’d charge me with question begging. So I have a question: are you saying that to explain life I cannot use life? If so, where do you get your “clues” as to what designers are able to do? If you take that from human design, then I’d say two things:

    1. Then you’re “question begging” in the very way you’re imagining that I’m question begging (again, what was that about the beam in thy own eye, you hypocrite?).

    2. Then you’re back to shooting yourself in the foot, since no human designer that you know about can design life forms.

  46. RodW,

    Someone pass on to gpuccio that I cant post at UD. I’ve been banned. And I have no more email addresses that I can use to start a new account!

    Done

  47. RodW:

    Someone pass on to gpuccio that I cant post at UD. I’ve been banned. And I have no more email addresses that I can use to start a new account!

    Gpuccio,

    I know your little fingers are fastened tightly onto Mama Arrington’s skirt, but there comes a time when little boys need to become big boys and venture out into the world.

    The discussion can proceed freely here, but not at UD. Be brave and come here, where RodW isn’t censored. Mama Arrington will still be there at UD. You can always go running to her if TSZ becomes too scary for you.

Leave a Reply