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. dazz:
    BTW, I’m almost certain that ET guy at UD is our beloved Frankie the toaster repair man

    There is no “almost” about it. He admitted to being banned here. He has also been demonstrating a month long meltdown at AtBC, still defending his claim that Frequency = Wavelength.

  2. Acartia: There is no “almost” about it. He admitted to being banned here. He has also been demonstrating a month long meltdown at AtBC, still defending his claim that Frequency = Wavelength.

    LOL

  3. Neil Rickert,

    Great. In that case, you should be able to accept that evolution is the designer.

    Sure. RMNS is a potential designer but the evidence is overwhelming that it would fail to make the micro machines we observe in the cell.

    How are you defining “intelligence”?

    As I see it, intelligence has to do with the quality of ones pragmatic judgments. And evolution is a system based on pragmatics (biological systems finding ways to survive).

    Survival is part of intelligence but I would not say it describes all aspects of intelligence. One of the strongest pillars of the design argument is identifying the cause of genetic information. Intelligence can create information as it can generate translatable symbols into meaning or function. This is one of gpuccio’s arguments which he articulated to me recently at UD.

  4. colewd: Sure. RMNS is a potential designer but the evidence is overwhelming that it would fail to make the micro machines we observe in the cell.

    By “the evidence is overwhelming”, I think you mean that you don’t actually have any evidence.

    One of the strongest pillars of the design argument is identifying the cause of genetic information.

    Yes, that’s one of your strongest arguments — because you don’t actually have any arguments.

    Children learn by trial and error. You see that as due to intelligence. Biological populations learn by trial and error. You ought to be seeing that as due to intelligence — the intelligence of evolving populations.

  5. Neil Rickert,

    By “the evidence is overwhelming”, I think you mean that you don’t actually have any evidence.

    The first evidence appeared with the discovery of DNA. Then the transcription and translation mechanism that showed that cellular proteins (micro machines) were made from coded information in DNA. Since this mechanism requires original genetic information the design inference was proposed as an alternative explanation.

    Yes, that’s one of your strongest arguments — because you don’t actually have any arguments.

    The evolutionary community has been responding to design arguments for the last 30 years. This would be hard if they don’t exist 🙂

    Biological populations learn by trial and error. You ought to be seeing that as due to intelligence — the intelligence of evolving populations.

    What do you mean by biological populations learn by trial and error?

  6. colewd: One of the strongest pillars of the design argument is identifying the cause of genetic information.

    That’s pretty sad, since it doesn’t identify the cause of genetic information at all.

    It even takes pains to disclaim its presupposition of the identity of the cause.

    Glen Davidson

  7. GlenDavidson,

    That’s pretty sad, since it doesn’t identify the cause of genetic information at all.

    I understand this is your opinion but I think the argument has merit.

  8. colewd: The first evidence appeared with the discovery of DNA. Then the transcription and translation mechanism that showed that cellular proteins (micro machines) were made from coded information in DNA. Since this mechanism requires original genetic information the design inference was proposed as an alternative explanation.

    Why can’t those things evolve?

  9. Since this mechanism requires original genetic information

    I have a mechanism that will produce original genetic information without intelligent design type guidance. Put genetic material into the mechanism, out comes genetic material with new original genetic information present.

    colewd, what test will you apply to the output of my claimed mechanism such that you will determine if original genetic information has actually been added or not?

  10. Looks like we have a few (all too funny) hypothesis from gppucio:

    JVL:

    “ONLY during that time? No design implementation before or since?”

    No, of course! That was just one example.

    So, let’s be more complete.

    The design for LUCA (OOL) took place on our planet, more or less between 4 billion years ago and 3.5 billion years ago.

    The design for eukaryotes is still less well localized, probably about 2 billion years ago.

    The main design for metazoa and the basic phyla took place, very likely, at the Cambrian explosion.

    For the transition to vertebrates, I have already given an estimate.

    The design for the transition to mammals took place about 100 million years ago.

    The design for the transition to humans took place in the last few million years.

    These are just some of the major events.

    But, as I have always said, each time that a new protein superfamily appears in evolutionary history, that is an act of design. And we have about 2000 different protein superfamilies.

    So, is design continuous? No. The acts of design are punctuated, and they correspong to the rather sudden appearance of big amounts of new functional information that is added to what already exists. They are acts of engineering, limited in time, but occurring thorughout natural history.

    Is that clear enough?

    The ‘cats-giving-birth-to-dogs’ crap all over again. Can you believe it?

  11. For the transition to vertebrates, I have already given an estimate.

    Why have any sort of transition at all?

  12. colewd:
    Adapa,

    What selection feedback from the environment?

    The mechanism Darwin identified over 150years ago.

    The same one you and the IDiots are too stupid to understand or too dishonest to incorporate in your lame arguments.

  13. colewd:
    The “who” is not part of the argument.

    I know. I find that very stupid and philosophically suicidal, but I know they try to not make it about who. But you’re missing the point: Where are they talking their “clues” as to what would look like “design” if not from humanity?

    colewd:
    On what basis do you eliminate intelligence as a cause?

    As my many times repeated question implies, on the basis that the only intelligent designers you can point to are made of the things you are claiming to be the product of intelligent design.

    And once again:

    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 other than intelligence.

  14. Some more entertainment from gpuccio:

    gpuccio:
    Third, there are however a few known human proteins which have no protein counterpart in other primates, as VJ correctly states. These seem to have very good counterparts in non coding DNA of primates.

    So, if we accept these proteins as real and functional (unfortunately not much is known about them, as far as I know), then what seems to happen is that:

    a) The sequence appears in some way in primates as a non coding sequence. That means that no NS for the sequence as representing a protein can take place.

    b) In some way, the sequence acquires a transcription start in humans, and becomes an ORF. So the protein appears for the first time in humans and, if we accept the initial assumption, it is functional.

    Well, if that kind of process will be confirmed, it will be a very strong evidence of design. the sequence is prepared in primates, where is seems to have no function at all, and is activated in humans, when needed.

    The origin of functional proteins from non coding DNA, which is gaining recognition in the recent years, is definitive evidence of design. NS cannot operate on non coding sequences, least of all make them good protein coding genes. So, the darwinian mechanism is out, in this case.

    Priceless

  15. dazz: a) The sequence appears in some way in primates as a non coding sequence. That means that no NS for the sequence as representing a protein can take place.

    b) In some way, the sequence acquires a transcription start in humans, and becomes an ORF. So the protein appears for the first time in humans and, if we accept the initial assumption, it is functional.

    If it looks like an evolutionary process and acts like one, clearly it’s design.

    This just shows how deep into their “design” holes they go when they decide that just anything can be design. They don’t even pretend to find real evidence for design (intelligence going beyond evolutionary limitations), just find evolution co-opting whatever it inherits and call it “design.”

    God put sequences into primates in order to provide humans with ORFs in the future. Designers do that, because that’s what we see in this case (…in mysterious ways).

    Glen Davidson

  16. Entropy,

    Where are they talking their “clues” as to what would look like “design” if not from humanity?

    You are right that is exactly one of the issues that drives the argument along with a lack of probabilistic resources for the Neo Darwinian mechanism.

    This is an argument from analogy which is fair game.

  17. Entropy,

    As my many times repeated question implies, on the basis that the only intelligent designers you can point to are made of the things you are claiming to be the product of intelligent design.

    This is again arguing against the designer which is not part of the argument. It also does not look like a legitimate reason to eliminate a cause as it points to ignorance as the reason.

  18. Adapa,

    The mechanism Darwin identified over 150years ago.

    The same one you and the Idiots are too stupid to understand or too dishonest to incorporate in your lame arguments.

    The bacterial flagellum was unknown 150 years ago. For this mechanism to work you need an advantage that you can get to with available probabilistic resources. The advantage of mobility takes over 30 matched proteins.

  19. GlenDavidson: If it looks like an evolutionary process and acts like one, clearly it’s design.

    This just shows how deep into their “design” holes they go when they decide that just anything can be design.They don’t even pretend to find real evidence for design (intelligence going beyond evolutionary limitations), just find evolution co-opting whatever it inherits and call it “design.”

    God put sequences into primates in order to provide humans with ORFs in the future.Designers do that, because that’s what we see in this case (…in mysterious ways).

    Glen Davidson

    It happened in humans no less, so forget the evidence, how could it not be “design”?

    What really baffles me about these guys is their complete inability to grasp the fundamental mistakes in their reasoning. Hey, no god of the gaps! ID is real!

    gpuccio:
    As you certainly know, the whole point of ID is to evaluate the probabilistic barriers that make it impossible for the proposed mechanism of RV + NS to generate new complex functional information

    LMFAO

    I know gpuccio is a nice guy and all, and I tend to resort to derision or even name calling, but I have no respect for someone who is incapable of noticing there’s no science to all that BS, which is BTW entirely unoriginal (his functional complex information is just another CSI, FIASC/O rehash, his ubiquitin is just another flagellum, origami crane, etc…, his barriers are a knockoff of Behe’s edge of evolution)

    I mean, with every Paley’s watch rehash these guys really think they’ve debunked evolution (again) and the whole scientific community is shutting them down to protect the “mainstream materialistic dogma”. They’re certifiably crazy with clear delusions of grandeur.

  20. OMagain,

    colewd, what test will you apply to the output of my claimed mechanism such that you will determine if original genetic information has actually been added or not?

    First test is to look at the sequence and see if proper start and stop condons exist alone with a transcriptional binding sequence.

    It that is all there then run it through the transcription translation mechanism and see if a functional protein is generated and identify the new function.

  21. dazz,

    I know gpuccio is a nice guy and all, and I tend to resort to derision or even name calling, but I have no respect for someone who is incapable of noticing there’s no science to all that BS, which is BTW entirely unoriginal (his functional complex information is just another CSI, FIASC/O rehash, his ubiquitin is just another flagellum, origami crane, etc…, his barriers are a knockoff of Behe’s edge of evolution)

    Gpuccio is taking Behe and Demski’s concepts and showing additional applications where they apply. He has also added a symbolic argument which is specifically applied to the ubiquitin system.

    Two things that gpuccio are not is unoriginal or uninformed. When you disrespect him you look foolish.

  22. colewd: He has also added a symbolic argument which is specifically applied to the ubiquitin system.

    You don’t get it. The unoriginality is in the type of arguments he makes. The X is a code argument from analogy is most definitely not new and just as fallacious as it was the first time.

    It goes in the form: “This or that looks like something we design (codes, machines…) and only intelligence can do those things”. It’s the same old failed, unscientific negative argument. Stop wasting people’s time please. It’s the sciency equivalent to spotting the face of jesus in bread toasts, guaranteed to be followed by the omnipresent burden shift: “if you don’t agree, show something can produce X without design” which is impossible without a positive case for design to begin with.

    colewd: Two things that gpuccio are not is unoriginal or uninformed. When you disrespect him you look foolish.

    I never said he’s uninformed. He’s just incapable of escaping his fallacious ID state of mind. I think ID is better explained as a psychological condition

  23. gpuccio:

    Well, if that kind of process will be confirmed, it will be a very strong evidence of design. the sequence is prepared in primates, where is seems to have no function at all, and is activated in humans, when needed.

    Why not just put the functional gene in humans, as an intelligent designer would do, and leave the non-functional precursor out of the primates?

    Funny how your designer is such a dedicated evolution mimic.

  24. colewd: Entropy,

    Where are they talking their “clues” as to what would look like “design” if not from humanity?

    You are right that is exactly one of the issues that drives the argument along with a lack of probabilistic resources for the Neo Darwinian mechanism.

    This is an argument from analogy which is fair game.

    Only if it actually was analogous with what humans produce. But humans don’t make anything nearly so derivative of earlier “designs” as evolution actually does, as I’ve pointed out with bird wings and the like.

    That doesn’t change how you drone on ignorantly about how it’s “analogous” anyway. It’s just pathetic how you ignore the vast evidence that runs contrary to your cherished, (proper) evidence-free, beliefs.

    Glen Davidson

  25. dazz,

    I never said he’s uninformed. He’s just incapable of escaping his fallacious ID state of mind. I think ID is better explained as a psychological condition

    This is your opinion Dazz.

    You think people that don’t agree with you are mentally deranged.

    Michael Savage the conservative radio commentator thinks liberalism is a mental disorder. I guess were all a little crazy 🙂

  26. GlenDavidson,

    Only if it actually was analogous with what humans produce. But humans don’t make anything nearly so derivative of earlier “designs” as evolution actually does, as I’ve pointed out with bird wings and the like.

    Isn’t it amazing how the design of the wheel was dropped 1000 years ago.

  27. colewd:
    dazz,

    This is your opinion Dazz.

    You think people that don’t agree with you are mentally deranged.

    Michael Savage the conservative radio commentator thinks liberalism is a mental disorder.I guess were all a little crazy

    It’s not about agreeing with me, it’s about what’s proper science & reasoning skills. I wasn’t expecting you to understand anyway.

  28. dazz,

    It’s not about agreeing with me, it’s about what’s proper science & reasoning skills. I wasn’t expecting you to understand anyway.

    You are talking about a trained medical doctor and you are claiming you understand science and reasoning better then he does. What gives you this level of confidence? Are you really this indoctrinated in evolutionary propaganda?

  29. colewd:
    dazz,

    You are talking about a trained medical doctor and you are claiming you understand science and reasoning better then he does.What gives you this level of confidence?Are you really this indoctrinated in evolutionary propaganda?

    I’m shocked to learn his doctorate in not in numerology

  30. colewd:
    dazz,

    You are talking about a trained medical doctor and you are claiming you understand science and reasoning better then he does.What gives you this level of confidence?Are you really this indoctrinated in evolutionary propaganda?

    we are talking about a general practitioner pontificating on things way outside his area of expertise.

    Linus Pauling, a winner of two Nobel prize winner, went off the rails with his claims about vitamin C and cancer. If someone with his credentials could be so wrong what makes you think gpuccio is immune in his thinking/claims about evolution?

    reminds me of the Salem Hypothesis:

  31. And we can add Billy’s argumentum ad verecundiam to the long list of classic creationist fallacies

  32. PeterP,

    Linus Pauling, a winner of two Nobel prize winner, went off the rails with his claims about vitamin C and cancer. If someone with his credentials could be so wrong what makes you think gpuccio is immune in his thinking/claims about evolution?

    He can be wrong but so can Dazz.

    Gpuccio makes detailed arguments where Dazz generally makes unsupported claims. Dazz trying to claim the high ground on understanding science is beyond ridiculous.

  33. dazz,

    ad verecundiam

    Exactly Dazz. This is the logical fallacy you were committing along with unsupported claims.

  34. PeterP,

    we are talking about a general practitioner pontificating on things way outside his area of expertise.

    Can you support this claim?

  35. colewd:
    dazz,

    Exactly Dazz.This is the logical fallacy you were committing along with unsupported claims.

    It’s not a logical fallacy and it wasn’t me who brought up credentials.
    You’re not equipped to understand stuff, Billy, even the simplest of things

  36. colewd, to dazz:

    You are talking about a trained medical doctor and you are claiming you understand science and reasoning better then he does.

    Take a look at this stupid argument from your “trained medical doctor”, Bill:

    gpuccio:

    Well, if that kind of process will be confirmed, it will be a very strong evidence of design. the sequence is prepared in primates, where is seems to have no function at all, and is activated in humans, when needed.

    Do you see the obvious mistake? I explained it above:

    Why not just put the functional gene in humans, as an intelligent designer would do, and leave the non-functional precursor out of the primates?

    Funny how your designer is such a dedicated evolution mimic.

  37. dazz,

    It’s not a logical fallacy and it wasn’t me who brought up credentials.

    You claimed he did not understand science. On what basis did you make that claim? Are you really this clueless?

  38. colewd:
    dazz,

    You claimed he did not understand science.On what basis did you make that claim?Are you really this clueless?

    You could go back and try reading for comprehension, but you will fail as you always do.

  39. keiths,

    Why not just put the functional gene in humans, as an intelligent designer would do, and leave the non-functional precursor out of the primates?

    Funny how your designer is such a dedicated evolution mimic.

    You made a reasonable counter argument. So what?

  40. dazz,

    It’s not about agreeing with me, it’s about what’s proper science & reasoning skills. I wasn’t expecting you to understand anyway.

    This doesn’t look like Spanish. Were you not attacking his science and reasoning skills?

  41. colewd:
    PeterP,

    Can you support this claim?

    What is there to dispute? Are you claiming he has credentials outside of his medical degree?

    I’ve never seen him mention any expertise other than his medical degree. I’m willing to admit an error once you demonstrate to me that he does hold degrees (MS or PhD) in any field other than medicine. Until you do that I’ll go by what he has stated and make my judgements based on that knowledge.

  42. colewd:
    dazz,

    This doesn’t look like Spanish.Were you not attacking his science and reasoning skills?

    Any objections? on second thought, keep it to yourself. I know from experience you’re not worth anyone’s time

  43. PeterP,

    I’ve never seen him mention any expertise other than his medical degree. I’m willing to admit an error once you demonstrate to me that he does hold degrees (MS or PhD) in any field other than medicine.

    Why don’t you read his ops and make a judgement on his comprehension of protein function.

    You just admitted making a statement you cannot support. Your attempt at a burden shift is duly noted.

  44. dazz,

    I know from experience you’re not worth anyone’s time

    There you go again. Dazz the “ad verecundiam” kid.

  45. colewd: You just admitted making a statement you cannot support. Your attempt at a burden shift is duly noted.

    His, gpuccio’s, own claims are what I based my assessment on…following the evidence where it leads and all that. What more support do I need other than the words from is keyboard. I duly note that you appear to be unable to provide anything to refute my conclusion.

    colewd: Why don’t you read his ops and make a judgement on his comprehension of protein function.

    Why would you think I haven’t read his screeds? The points of contention are not in protein function but his assertions of their evolution or in his case, the lack there of. Others have already pointed out the erroneous nature of his claims so no need to repeat them here just look upthread in case you missed them.

  46. PeterP,

    Why would you think I haven’t read his screeds? The points of contention are not in protein function but his assertions of their evolution or in his case, the lack there of. Others have already pointed out the erroneous nature of his claims so no need to repeat them here just look upthread in case you missed them.

    So you are completely satisfied with the counter arguments to gpuccio’s claims so far? Who has made the most compelling argument in your opinion?

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