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?

0

906 thoughts on “Ubiquitin: a challenge for evolutionary theory?

  1. colewd:
    Design is an explanation on its own.

    No it isn’t.

    colewd:
    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.

    Very different scenario. In the murder case, we know the kinds of agents that can perform a murder. We can point to several possible candidates. We can point to the same thing happening before. There’s no point where we have to philosophize backwards, ignore the normal characteristics of murderers, etc.

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

    That cannot be done unless the existence of some beings capable of designing flagella could be established. Given that you don’t have that, the best course of action would be to try and check, as much as possible, for knowable candidate phenomena. Answers will come partial, perhaps, but they will come. Due course it to try and establish things based on what can be tested. gathering as much information as you can. Trying new tests, etc. But leaving it at “I don’t believe this can evolve or arise naturally, therefore design” is just lame. Anthropomorphizing the phenomena to call it “semiosis” and then conclude “design!” out of an obvious anthropomorphism is also just lame (as if nobody had ever anthropomorphized natural phenomena before!).

    0
  2. colewd,

    And just because you seemed to miss it, here it goes 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.

    0
  3. From the OP:

    Gpuccio hints at the complexity of the system and the “semiotic” aspects. It seems like another god-of-the-gaps argument.

    It either is or it isn’t a “god of the gaps” argument. If you think it is, make your case.

    Wow, look at the complexity! How could this possibly have evolved! Therefore ID!

    That’s not his argument.

    0
  4. Mung: That’s not his argument.

    That’s exactly what it is. Just look at all his stupid negative proclamations like “x bits of functional information are off limits for RV+NS, therefore design”

    Textbook god of the gaps, argument from ignorance topped by the “ubiquitin” burden shift: “falsify it by showing RV+NS can do it”

    Yawn

    0
  5. John Harshman: John Harshman
    March 21, 2018 at 4:20 pm

    TomMueller: Still would like your take on the PNAS paper

    John Harshman: Seems fine to me, but I don’t see its relevance to the OP.

    Hi John

    Until this OP, I was unaware there was a controversy juxtaposing two models called “concerted evolution” vs “birth-and-death evolution” as alternative explanations for highly conserved gene family protein sequences.

    Two points actually,

    1 – Gpuccio’s invocation of god of the gaps is clearly specious given these two alternative mechanisms are available.

    2 – I am in no position to evaluate the cogency of the PNAS article suggesting that one mechanism is a better explanation than the other – i.e. “concerted evolution” vs “birth-and-death evolution” – in the particular case of ubiquitin

    Ergo my original question asking others more expert than I to explain

    0
  6. TomMueller: I am in no position to evaluate the cogency of the PNAS article suggesting that one mechanism is a better explanation than the other – i.e. “concerted evolution” vs “birth-and-death evolution” – in the particular case of ubiquitin

    That at least is simple. Concerted evolution would homogenize synonymous sites, while divergence in duplicated segments would not. They find the latter.

    0
  7. TomMueller: 1 – Gpuccio’s invocation of god of the gaps is clearly specious given these two alternative mechanisms are available.

    Could you point me to where gpuccio invokes God in his OP?

    0
  8. dazz,

    That’s exactly what it is. Just look at all his stupid negative proclamations like “x bits of functional information are off limits for RV+NS, therefore design”

    His argument is about a lack of evolutionary resources to perform a search beyond x bits. Total evolutionary resources available are around10^40.

    0
  9. dazz: Textbook god of the gaps, argument from ignorance…

    Well, which is it? Or do you think “argument from ignorance” and “god of teh gaps” is the same thing. Since you seem to have the textbook handy, please explain how his argument is a god of the gaps argument.

    Alan, Tom, and dazz, all claiming “god of the gaps” and all without a lick of support other than their own say so. What is this site coming to.

    0
  10. Mung,

    Could you point me to where gpuccio invokes God in his OP?

    First, nice to have you back.
    Second, do you think most the evolutionists realize that they are arguing against straw-men?

    0
  11. TomMueller,

    1 – Gpuccio’s invocation of god of the gaps is clearly specious given these two alternative mechanisms are available.

    Available to do what?

    0
  12. John Harshman: That at least is simple. Concerted evolution would homogenize synonymous sites, while divergence in duplicated segments would not. They find the latter.

    Hi again John

    Forgive me if my lack of insight is beginning to try your patience – but I remain confused.

    I do not understand how the homogenization of synonymous sites would ever result high conservation across species.

    I must be missing something here.

    0
  13. colewd: Second, do you think most the evolutionists realize that they are arguing against straw-men?

    Strawmen soaked in oil of red herring and set ablaze. Don’t forget those.

    0
  14. Entropy,

    And just because you seemed to miss it, here it goes 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). And just because you seemed to miss it, here it goes 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.. 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.

    You are invoking the logical fallacy of creating a straw-man argument. Until you clear your head of this you will not understand this argument. The argument is simply making observation of design in nature and not some grand claim about a designer.

    Trying to explain the only designers they can point to, as designed, is very poor philosophy and very poor science

    Again this is not part of the argument. If it was why do you think it is poor philosophy?

    0
  15. Mung:
    From the OP:

    It either is or it isn’t a “god of the gaps” argument.

    It is a “god-of-the-gaps” argument. A classic case! A textbook example!

    If you think it is, make your case.

    The argument, as far as it goes, is evolutionary theory fails to explain the origins of the ubiquitin system, therefore “Design”. It’s both “god-of-the-gaps” and a default (to “Design”) argument.

    That’s not his argument.

    What is his argument, then?

    0
  16. Perhaps – my reading comprehension is declining with age. When wading through gpuccio’s meandering musings – especially in his comments – he repeatedly claims that his rendition of the Ubiquitin Story CANNOT be explained by neo-Darwinism/Natural Selection/Evolution.

    His obtuse references to ” semiosis” are clearly code for “creationism” scratch that ID – scratch that … you fill in the blank

    0
  17. Mung: Well, which is it? Or do you think “argument from ignorance” and “god of teh gaps” is the same thing. Since you seem to have the textbook handy, please explain how his argument is a god of the gaps argument.

    Alan, Tom, and dazz, all claiming “god of the gaps” and all without a lick of support other than their own say so. What is this site coming to.

    See my previous comment. What alternative argument is gpuccio offering for the origin of the ubiquitin system, other than “Design!”? Just a link will do.

    0
  18. Mung: Well, which is it? Or do you think “argument from ignorance” and “god of teh gaps” is the same thing. Since you seem to have the textbook handy, please explain how his argument is a god of the gaps argument.

    Alan, Tom, and dazz, all claiming “god of the gaps” and all without a lick of support other than their own say so. What is this site coming to.

    A “God of the Gaps” argument is a specific type of argument from ignorance. For example, when a creationist says “Science can’t recreate abiogenesis in the laboratory, therefore it can’t have happened, they are implying that a gap in our knowledge, otherwise called ignorance, justifies belief in a supernatural origin of life.

    0
  19. Alan Fox,

    It is a “god-of-the-gaps” argument. A classic case! A textbook example!

    You have invoked a straw-man in your mind by translating design to God. When you do this you fail to understand the argument and your criticisms are useless.

    The argument has weaknesses but “God of the gaps” is not one of them.

    If we found a “design enzyme” in the cell that could be a mechanism of ID. A “design enzyme” is not God.

    0
  20. colewd:
    dazz,

    His argument is about a lack of evolutionary resources to perform a search beyond x bits.Total evolutionary resources available are around10^40.

    Yeah, that nonsense. Look, the closest he is to making a positive design hypothesis is when he claims that some mutations are directed or designed. He concedes some mutations are random. So how many design resources are available if those are a subset of the total probabilistic resources he calculated assuming all mutations are random? Well, obviously the answer is LESS RESOURCES.

    Fricking hilarious. Now I know the answer to that obvious fact will be some appeal to the power of “design” vs “random processes” and all that shit, but hey, fact remains, his own “logic” tells us that there are less than 160.3 bits / 37 specific amino acids available to design stuff.

    Oh, and still no positive case for design beyond the all too cute God poking molecules to direct mutations. U mad? Yes, I mentioned God and we all know the first rule of IDiocy is to refuse to admit it’s god what they have in mind, but you’re not getting off the hook by being dishonest about your intentions and motivations

    0
  21. colewd:
    Alan Fox,

    You have invoked a straw-man in your mind by translating design to God.

    Possibly. God is a meaningless concept to me, so I have difficulty with the intricacies of the plaiting.

    When you do this you fail to understand the argument and your criticisms are useless.

    Then enlighten me. Expand on “Design”. What is the “Design” argument?

    The argument has weaknesses but “God of the gaps” is not one of them.

    Are you referring to gpuccio’s exposition on ubiquitin?

    If we found a “design enzyme” in the cell that could be a mechanism of ID.A “design enzyme” is not God.

    If? I don’t do hypotheticals. Is there a “design enzyme”? How do you know?

    0
  22. gpuccio at UD, quoted by dazz: 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.

    Not the extra weasel-words “new original”. Because it has been shown many times that natural selection can put complex functional information into the genome, and this has been discussed here at TSZ and also at Panda’s Thumb many times.

    But add the “new original” and you have the ability to deny that any complex functional information isn’t “new” enough and/or “original” enough to qualify.

    0
  23. Latest from gpuccio

    OK, here is how I see things.

    a) Semiosis is an independent indicator of design, because it is a formal feature which, for its same nature, is incompatible with any non design interpretation. That’s because no system which cannot have any understanding of the siubjective experience of meaning can really generate a symbolic code.

    However, even codes have different levels of complexity, and in that sense, the more complex a code is, the stronger is its power as an indicator of design.

    So, let’s say that semiosis has a double aspect, as an indicator of design:

    a1) A formal aspect, that is the presence of a symbolic code, which is common to all semiotic systems.

    a2) A quantitative aspect, that is the functional complexity linked to the implementation of the code (which is a specific subset of functional complexity), which can differ from a semiotic system to another.

    So, all symbolic codes are indicators of design, but the higher their specific functional complexity, the better.

    b) Functional complexity and Irreducible complexity are more connected, and independent from semiosis. A protein can be (and usually is) functionally complex even if its function is not symbolic.

    The relationship between functional complexity and irreducible complexity is more subtle.

    Let’s say that functional complexity referes usually to individual functional units, while irreducible complexity refers to some set of functional units, each of them functionally complex, which irreducibly sooperate to implement a function.

    So, let’s say that a specifi set of E1-E2-E3 enzymes contributes to ubiquinate some specific target protein.

    Each of the three enzymes has a “local” function in relation to the ubiquitination process, and a functional complexity which can be measure in relation to that local function.

    However, the individula local functions are useless if the whole process is not there, because the treu utility of the process is the final ubiquitination of the target protein. And of course we can add the specific deubiquitinating enzyme which contributes to ensure the correct regulation of the target protein, and other possible factors involved (phosphorylation processes, and so on).

    The simple truth is that if any of those component is lacking, the regulation of the target protein is no more a regulation.

    So, the regulation of the target protein is the true function which is useful (and therefore could be in principle the object of NS).

    So, let’s say that we have the functional complexitiesof the following proteins in relation to their local function (these are just fictional numbers):

    E1 580 bits
    E2 600 bits
    E3 950 bits
    DUB 730 bits

    The functional complexity of the whole system, if it is irreducibly complex, will be the product of those complexitis (that is the sum of the bit values). In this case, 2360 bits (if I am not wrong).

    That is a lot more of the individual functional complexities, because these are exponential values.

    Of course, some component can be shared between different systems. In the case of ubiquitin, for example, the E1 component is almost always the same. But we have seens that the E2 and E3 components provide great specificity, and can be rather unique for each system, or for a small subset of systems.

    So, irreducible complexity is a property which enhances exponentially the functional complexity of the individual components.

    Of course, the presence at the same time of all three features:

    a) High functional complexity of many individual proteins which

    b) form an irreducibly complex system which

    c) works at least in part by a semiotic code

    certainly adds greatly to the final design inference.

    That’s why the ubiquitin system is such a treasure for ID!
    Thoughts, anyone? Bedtime for me!🙂

    0
  24. gpuccio : Semiosis is an independent indicator of design, because it is a formal feature which, for its same nature, is incompatible with any non design interpretation.

    Stopped reading right there. It’s amazing how otherwise intelligent people, are incapable of noticing how full of shit they are.

    0
  25. Mung at UD

    It’s the “I don’t have an argument” of the gaps argument.

    Burden shift? I mean, I have some idea of how evolutionary theory works. I’ll concede it may be considered incomplete, subject to revision due to new evidence emerging, limited in its range and so on… but “Design”? It’s a sham. You don’t even need it with Betsy de Vos in charge.

    What is the point?

    Cards on the table! Can you (or anyone with a straight face) explain to me the theory from “Design”. I’ll even do a James Tour and buy them lunch! (Not in Trèbes, though).

    0
  26. Joe Felsenstein: Not the extra weasel-words “new original”.Because it has been shown many times that natural selection can put complex functional information into the genome, and this has been discussed here at TSZ and also at Panda’s Thumb many times.

    But add the “new original” and you have the ability to deny that any complex functional information isn’t “new” enough and/or “original” enough to qualify.

    Yeah, and of course by “new original” he must mean something ridiculous like producing a complex system or a “new, original” organism in a few generations or in one fell swoop, which is of course a walk in the park for their awesome Designer!

    I’m calling this crocoducks or Jeebus, from now on

    0
  27. Alan Fox: a) Semiosis is an independent indicator of design, because it is a formal feature which, for its same nature, is incompatible with any non design interpretation. That’s because no system which cannot have any understanding of the siubjective experience of meaning can really generate a symbolic code.

    Of course it’s not a symbolic code, it’s a chemical code that works by chemical interactions. Genetics was long understood to be a code prior to the understanding of DNA’s form and function. Just read Schroedinger’s book What is life?, which, by the way, was claimed by at least one biologist not to have anything new in it that was good (meaning that the code idea presumably goes back earlier). It makes sense, because the proteins that DNA codes themselves are comprised of chains of specific amino acids, and a sequential code would manage that quite well, and would also be capable of storing enormous amounts of data.

    Basically, Gpuccio’s just word-lawyering there. Call the “semiosis” a formal feature and the DNA code a symbolic code, and you automatically have something produced by intelligence. We’re well aware that. If we let them make it all up as they wish, we can only conclude that it was all designed. But it’s illegitimate assumption to the hilt, and we can’t agree to such nonsense at all.

    Glen Davidson

    0
  28. colewd:
    You are invoking the logical fallacy of creating a straw-man argument. Until you clear your head of this you will not understand this argument. The argument is simply making observation of design in nature and not some grand claim about a designer.

    Wait a minute, are you saying that when they talk about something being designed, it doesn’t mean there must have been a designer doing such design?

    If that’s not what you’re saying, then what straw-man am I building? Be very clear.

    me:

    Trying to explain the only designers they can point to, as designed, is very poor philosophy and very poor science

    colewd:

    colewd:
    Again this is not part of the argument. If it was why do you think it is poor philosophy?

    No? Then where are they talking their “clues” as to what would look like “design” if not from humanity?

    Here again in case you misunderstood something. Please read very carefully:

    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. (Bolded part added for good measure.)

    0
  29. Alan Fox,

    Then enlighten me. Expand on “Design”. What is the “Design” argument?

    That some thinks in nature are best explained by an intelligent cause. The bacterial flagellum is an example. A multi protein complex the allows bacteria to move through liquid by way of a rotary motor.

    The motor is built with around 100k nucleotides of DNA sequences. This information will not only express the required 30 proteins in order it will express the assembly proteins to build it which a bacteria can do every 20 minutes.

    The two areas that point to intelligent cause or design are the highly functional and efficient rotary motor and the genetic information (DNA sequences) that build it.

    Bill: The argument has weaknesses but “God of the gaps” is not one of them.

    Alan: Are you referring to gpuccio’s exposition on ubiquitin?

    .

    Yes. I have not yet seen gpuccio make a God of the gaps argument. He is also well schooled on proteins and the historical leaps in functional information. His ops are very well thought out and always educational.

    If? I don’t do hypotheticals. Is there a “design enzyme”? How do you know?

    One “design” system is the adaptive immune system which engineers antibodies for new invading bacteria or viruses.

    0
  30. Entropy,

    Wait a minute, are you saying that when they talk about something being designed, it doesn’t mean there must have been a designer doing such design?

    Exactly. Evidence of design….full stop. This is how Behe thinks about it and how Gpuccio thinks about it.

    0
  31. gpuccio: “I would really want that someone from the other side had the courage of addressing the real arguments. Someone who had the clarity of saying: no, you are wrong because our theory can explain the things that you describe and analyze, and I will show you the reasons why.”

    gpuccio, you’re NOT EVEN WRONG because your “arguments” are not actual (scientific) explanations. You’re just an arrogant, pedantic asshole with a bag full of the usual creotard fallacies.

    Hey, you think you’ve proved mathematically that RV+NS can’t explain the “functional information” present in life. I’m so sorry you won’t get the recognition you deserve for debunking decades of scientific effort, but rest assured the flying spaghetti monster will reward you for your effort with beer volcanoes and hot strippers

    ETA: and just as I was hitting the submit button I noticed the reference to the FSM might be misinterpreted. I didn’t do that because you’re italian, but because you guys claim ID is not about identifying the designer

    0
  32. TomMueller: I do not understand how the homogenization of synonymous sites would ever result high conservation across species.

    I must be missing something here.

    It’s not high conservation across species that we’re attempting to explain here; it’s high similarity across loci within species. Concerted evolution should affect synonymous sites as well as non-silent sites, while purifying selection should affect only (well, mostly) non-silent sites. The results show that synonymous sites, quite the opposite of showing little variation, are nearly saturated, i.e. randomized between loci.

    0
  33. colewd:
    Exactly. Evidence of design….full stop.This is how Behe thinks about it and how Gpuccio thinks about it.

    Are you seriously saying that if something was designed it doesn’t mean there was a a designer? So, when Behe and gpuccio propose that there’s evidence for intelligent design, they might as well think that’s some spontaneous stuff that just happens to look intelligently designed?

    0
  34. Also:

    colewd:
    Again this is not part of the argument. If it was why do you think it is poor philosophy?

    Entropy: No? Then where are they talking their “clues” as to what would look like “design” if not from humanity?

    Here what I said for reference:

    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.

    0
  35. colewd:
    Entropy,

    Exactly.Evidence of design….full stop.This is how Behe thinks about it and how Gpuccio thinks about it.

    Behe at Kitzmiller:

    A Well, I’ve said that quite a number of times. I think I said that at the beginning of my testimony yesterday, that I think in fact from — from other perspectives, that the designer is in fact God. But if you turn back to page 699, there’s a section entitled, “Is it possible that the designer is a natural entity?” And I won’t quote from it, but I come to the conclusion there that sure it’s possible that it is, but I do not — I myself do not find it plausible.

    http://www.talkorigins.org/faqs/dover/day11pm2.html

    I’ve seen him speak at a religious college, and he was complaining that while design might be considered in science, it won’t be if it’s “supernatural.” And he put up a picture of a Ghostbusters type sign where “Ghosts” is written and a red line crosses it out. He’s less shy about “god did it” in front of audiences that like that message.

    Glen Davidson

    0
  36. Entropy,

    Are you seriously saying that if something was designed it doesn’t mean there was a a designer?

    The “who” is not part of the argument.

    we’d still be stuck with natural phenomena other than intelligence.

    On what basis do you eliminate intelligence as a cause?

    0
  37. IDiots still don’t get it and never will: you don’t get to proclaim what counts as evidence for your theory. That’s a job for the theory itself, but since there’s no such thing the rest is rhetorical BS

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

    Nothing is part of the “argument” because you have none. You have no who, what, where, when or why, just your usual failed analogies, question begging and celebration of your own pathetic ignorance.

    0
  38. colewd: The “who” is not part of the argument.

    Is that what you guys tell your kids? Of course not, if your kids ask who is that designer you have in mind you will tell them it’s sweet little jeebus as you pinch their noses. That’s just to illustrate the stupidity and dishonesty of your position. How can you possibly be so dim to believe you’ll ever convince us that the identity of the designer doesn’t matter to you and your sorry excuse for an argument?

    0
  39. colewd: The “who” is not part of the argument.

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

    On what basis do you eliminate intelligence as a cause?

    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).

    0
  40. Alan Fox:
    Latest from gpuccio

    OK, here is how I see things.

    a) Semiosis is an independent indicator of design, because it is a formal feature which, for its same nature, is incompatible with any non design interpretation. That’s because no system which cannot have any understanding of the siubjective experience of meaning can really generate a symbolic code.

    Hmmm! Two things missing here. What gpuccio means by semiosis in the context of ubiquitin (perhaps he is extending on UB’s claims that the DNA-RNA-protein synthesis system is unevolvable cos semiotics – itself an unsupported assertion) and what he means by “design”. The hoary chestnut of where the designer comes from, where, when and how he/she/it/they act(s) (I’ll give why a pass as unanswerable) is unaddressed.

    However, even codes have different levels of complexity, and in that sense, the more complex a code is, the stronger is its power as an indicator of design.

    So, let’s say that semiosis has a double aspect, as an indicator of design:

    a1) A formal aspect, that is the presence of a symbolic code, which is common to all semiotic systems.

    a2) A quantitative aspect, that is the functional complexity linked to the implementation of the code (which is a specific subset of functional complexity), which can differ from a semiotic system to another.

    So, all symbolic codes are indicators of design, but the higher their specific functional complexity, the better.

    All evidence-free assumptions. No science here.

    b) Functional complexity and Irreducible complexity are more connected, and independent from semiosis. A protein can be (and usually is) functionally complex even if its function is not symbolic.

    The relationship between functional complexity and irreducible complexity is more subtle.

    Let’s say that functional complexity referes usually to individual functional units, while irreducible complexity refers to some set of functional units, each of them functionally complex, which irreducibly sooperate to implement a function.

    So, let’s say that a specific set of E1-E2-E3 enzymes contributes to ubiquinate some specific target protein.

    Each of the three enzymes has a “local” function in relation to the ubiquitination process, and a functional complexity which can be measure in relation to that local function.

    However, the individual local functions are useless if the whole process is not there, because the true (?) utility of the process is the final ubiquitination of the target protein. And of course we can add the specific deubiquitinating enzyme which contributes to ensure the correct regulation of the target protein, and other possible factors involved (phosphorylation processes, and so on).

    More assuming conclusions, here. Specificity can be preceded by a system that is less specific.

    The simple truth is that if any of those component is lacking, the regulation of the target protein is no more a regulation.

    If you look at the current end point of an evolutionary pathway, it may look “designed” specifically for the process it regulates, finely tuned. But precursors could be less specific.

    So, the regulation of the target protein is the true function which is useful (and therefore could be in principle the object of NS).

    So, let’s say that we have the functional complexitiesof the following proteins in relation to their local function (these are just fictional numbers):

    E1 580 bits
    E2 600 bits
    E3 950 bits
    DUB 730 bits

    The functional complexity of the whole system, if it is irreducibly complex, will be the product of those complexitis (that is the sum of the bit values). In this case, 2360 bits (if I am not wrong).

    That is a lot more of the individual functional complexities, because these are exponential values.

    Of course, some component can be shared between different systems. In the case of ubiquitin, for example, the E1 component is almost always the same. But we have seens that the E2 and E3 components provide great specificity, and can be rather unique for each system, or for a small subset of systems.

    So, irreducible complexity is a property which enhances exponentially the functional complexity of the individual components.

    Irreducible complexity (we have examples of systems claimed to be IC that have evolutionary explanations) increases exponentially with number of components? Methinks it is your model that is at fault, not reality.

    Of course, the presence at the same time of all three features:

    a) High functional complexity of many individual proteins which [can evolve from precursors with less specificity]*

    b) form an irreducibly complex system which [there are examples of evolutionary pathways refuting claims of IC]*

    c) works at least in part by a semiotic code certainly adds greatly to the final design inference.

    *added by AF.
    Again we have “design inference”. What does it signify? What is/was the mechanism of “design”. How was it implemented? By what or by whom? When and how often? Couldn’t God get it right first time?

    That’s why the ubiquitin system is such a treasure for ID!

    Gpuccio, You’ve written much at Uncommon Descent on the ubiquitin system and how it is an icon of “design”. I still only see wishful thinking – not science. I’m sure if you tried to publish a refined version in a peer-reviewed journal, you would be challenged to put some substance into your evidence-free assertion of a “design inference”.

    0
  41. colewd:

    The “who” is not part of the argument.

    On what basis do you eliminate intelligence as a cause?

    “Intelligence” is a WEASEL WORD used to weasel a god into the discussion.

    Does your god know you are so embarrassed by him that you use a weasel word in place of his name?

    0
  42. colewd:

    Then enlighten me. Expand on “Design”. What is the “Design” argument?

    That some thinks in nature are best explained by an intelligent cause.

    And that’s as far as it ever gets. Who or what is the “designer”? How often does the “designer” act? What mechanisms of action does the “designer” employ?

    The bacterial flagellum is an example. A multi protein complex the allows bacteria to move through liquid by way of a rotary motor.

    The motor is built with around 100k nucleotides of DNA sequences. This information will not only express the required 30 proteins in order it will express the assembly proteins to build it which a bacteria can do every 20 minutes.

    Are you not familiar with work questioning the unevolvability of bacterial flagella? (Note, plural. There is variation in known examples of flagellar propulsion systems.) Here’s an old article in New Scientist that’s not too technical. Nick Matzke has written stuff on the pathway of evolvability from the type III secretory pore. And, the separate kingdom of prokaryotes, Archaea, have organisms with their own completely unrelated version. Why didn’t the “designer” just use one design for both?

    The two areas that point to intelligent cause or design are the highly functional and efficient rotary motor and the genetic information (DNA sequences) that build it.

    “…point to intelligent causes…” How so? Just saying “intelligent cause or design” is not informative. I challenge you, or any advocate for “Intelligent Design” to go beyond the mere utterance of the phrase.

    0
  43. Alan Fox,

    And that’s as far as it ever gets.

    Yes, and this is the weakness of the argument.

    Are you not familiar with work questioning the unevolvability of bacterial flagella?

    Yes I have looked at these including Nick’s. They fall a hair short of explaining how a complex micro machine can be built by an e coli bacteria every 20 minutes. What we have here is the organization of 100k nucleotides that can mass produce mobility in bacteria. If the type 111 is indeed an interim or ATP synthase is an interim that explains very little about the flagellum’s origin.

    Given all the work that has been done by evolutionary biologists to attempt to counter the flagellar design argument I would say that the argument is real in the minds of some evolutionary scientists.

    0
  44. colewd:
    Alan Fox,

    Given all the work that has been done by evolutionary biologists to attempt to counter the flagellar design argument I would say that the argument is real in the minds of some evolutionary scientists.

    It’s important to real scientists only in they feel the need to counter the lies and disinformation being pushed on the lay public by ID-Creationists.

    0
  45. Alan Fox,

    What’s more, of these 23 proteins, it turns out that just two are unique to flagella. The others all closely resemble proteins that carry out other functions in the cell. This means that the vast majority of the components needed to make a flagellum might already have been present in bacteria before this structure appeared.

    It is statements like this in the counter argument that show what an enormous challenge Behe has put forth. “Closely resemble” does help the counter argument. The components need to be matched, which requires modification of DNA code.

    I think gpuccio is right on how you would created a probability calculation for randomly generating an irreducibly complex structure.

    0
  46. colewd: It is statements like this in the counter argument that show what an enormous challenge Behe has put forth. “Closely resemble” does help the counter argument. The components need to be matched, which requires modification of DNA code.

    Why? We only see the living tips of the twigs on the branches of the history of life on Earth. The whole point of biochemical evolution is to examine and propose plausible pathways that allow evolution of specificity and complexity in small steps. Life has had four billion years to evolve and for almost all of that, no direct evidence of ancestral biochemistry and physiology remains. The comparisons we can make among extant organisms, the circumstantial evidence if you like, however, do give us many plausible evolutionary pathways.

    0
  47. Alan Fox,

    Life has had four billion years to evolve and for almost all of that, no direct evidence of ancestral biochemistry and physiology remains. The comparisons we can make among extant organisms, the circumstantial evidence if you like, however, do give us many plausible evolutionary pathways.

    Billions of years and populations translate to less then 10^50 trials. How do you build the flagellum in less then 10^50 trials? Given Szostak’s number for binding (10^11 trials) you can’t build more then 4 proteins that can bind with each other let alone perform a specific function.

    The comparisons we can make among extant organisms, the circumstantial evidence if you like, however, do give us many plausible evolutionary pathways.

    This is an assertion. If you have all the evolutionary resources in the history of life dedicated to forming a flagellum you will probably fail. I think plausible should be changed to highly unlikely.

    0
  48. colewd:
    Alan Fox,

    Billions of years and populations translate to less then 10^50 trials.How do you build the flagellum in less then 10^50 trials?

    Selection feedback from the environment. Same as the last dozen times you made the same dumbassed “it’s too improbable!!” argument.

    0
  49. BTW, I’m almost certain that ET guy at UD is our beloved Frankie the toaster repair man

    0
  50. Adapa,

    Selection feedback from the environment. Same as the last dozen times you made the same dumbassed “it’s too improbable!!” argument.

    What selection feedback from the environment?

    0

Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.