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?

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

  1. Joe Felsenstein: Does gpuccio really buy into that?One could as easily say that if, by a carefully and intelligently designed algorithm, we can make a reasonably successful simulation of erosion of soil, that this proves that erosion occurs by intervention of an Intelligent Designer.

    Proving that there’s really nothing too stupid for ID.

    Glen Davidson

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  2. Joe Felsenstein: Does gpuccio really buy into that?

    Yep.

    Joe Felsenstein: One could as easily say that if, by a carefully and intelligently designed algorithm, we can make a reasonably successful simulation of erosion of soil, that this proves that erosion occurs by intervention of an Intelligent Designer.

    I wouldn’t be too surprised if he answered that you’re finally getting it.

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  3. Entropy,

    I thought you were being hard on him at first (I didn’t pay much attention to your “conversation” with him), and then I got a response from him where he didn’t comprehend anything I wrote, not even the fact that he would need to back up his premises rather than merely repeat them.

    Even KF gets the fact that he needs to back up his claims, even though his “standards” for doing so are hideously reductive. So, as annoying as KF is, and as meaningless as ‘trillions of examples of functional complexity having been designed’ is, he’s still a cut above GP.

    It’s sad that we seem to feel the need to come up with a hierarchy of the mental capacities of these dolts, but perhaps it’ll be useful in dealing with them. KF and GP will never learn any more than JoeG and BA77 will, but KF gets some of the basics of science in the abstract (if hardly understanding how to do it without absurd reductionism), while the other three are really just meandering flotsam and jetsam whenever the issue is empiricism.

    The weird thing is that GP writes his OPs as if he has some understanding of science–and then you challenge any of his numerous fallacies and made-up premises. At that point he’s really just blithering ID presuppositions with little or no understanding of what one actually wrote.

    Glen Davidson

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  4. Joe Felsenstein,

    Does gpuccio really buy into that? One could as easily say that if, by a carefully and intelligently designed algorithm, we can make a reasonably successful simulation of erosion of soil, that this proves that erosion occurs by intervention of an Intelligent Designer.

    Gpuccio is discussing experimental intervention not the generation of a software algorithm. If the phrase “Go Huskies” was in the erosion of soil someone from Washington might infer design. From Berkeley, not so much 🙂

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  5. GP pretending to be above name-calling:

    (A couple of names follow, names of friends, and of course I will not report them here, because of course I don’t agree, and because I don’t want to contribute, even indirectly, to name calling)

    GP lying his ass off while name-calling:

    gpuccio@UD,

    You can think as you like, but I am rather sure of the reason: those who defend neo-darwinism are completely dogmatic about it, and cannot accept the obvious failure of their theory. Unfortunately, the worldview implications overcome the scientific attitude.

    You should avoid making these kinds of statements. I know you get something similar from this side of the fence, but just remember: those with religious inclinations abound on your side. So in trying to denigrate people on “the other side,” you end up denigrating most of those who agree with you. Even if they don’t “get a clue.”

    Again, you misunderstand me. I was not retaliating because I am badly treated at TSZ (although I am). I was expressing a thought that is very inportant for me.

    I agree that there are a lot of people whose worldview implications overcome the scientific attitude, on both sides. And I was not trying to denigrate people.

    I have said often that I respect faith commitments, of all kinds, including of course those of atheists. I have no problem with that.

    I only ask that those commitments be kept as under control as possible when a scientific discussion takes place.

    In my statement, I was not referring to generic people who defend neo-darwinism, but rather to scientists, to people who have a role as science makers, and therefore have greater responsibility.

    IOWs, I was denouncing a general cognitive bias of modern science, in particular biology. You will of course disagree, but that idea is very serious, and has not the intention to denigrate individual people, but rather to point to a serious error of modern thought.

    That said, I am usually very tolerant of the faith commitments of people. But, when the discussion requires it, I just point to the overlap between faith and science, to make my point. I have done that with people on your side, and with people on my side. As respectfully as possible.

    There’s almost nothing honest there, as the dumbass lies over and over again with charges he couldn’t pretend had any kind of backing beyond the sheer falsity of ID.

    That’s it, he just inverts the truth. The people without faith commitments have faith commitments, the dogmatists are the open-minded, the open-minded (not that all on the science side are, of course, but the side with the open-minded and not-stupid, not-ignorant, is the science side) are the dogmatists. True, he’s probably deluded and stupid enough to believe this, but the point is that he both calls names and does so without having any kind of basis for it.

    And he can’t see the dishonesty and hypocrisy of such a massive set of claims that are quite transparently (to anyone above UD mentality, at least) contrary to the truth. Just because he’s too ignorant, stupid, and dogmatic not to know better hardly helps, as all it does is demonstrate how thoroughly false people like him really are.

    Glen Davidson

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  6. GP completely missing the point again that he needs good evidence, not his rambling incomprehension, in order to intelligently claim that something is a code.

    Look, I don’t know how to explain it to you, but I will try just the same.

    In all my reasonings, I use the word “symbol”, and “symbolic code” exclusively to mean what I have included in my definition, that you can find in explicit form at comment #590.

    “A semiotic system is a system which uses some form of symbolic code.

    A symbolic code is a code where something represents something else by some arbitrary mapping.”

    It’s very simple, and objective, It has nothing to do with all your philosophical “arguments”.

    It’s a problem of the structure of the system. Either it uses a symbolic code (an arbitrary mapping that is not explained by laws, but depends on the internal configuration of the system) or it doesn’t.

    The genetic code uses an arbitrary mapping. The mapping is solved by the 20 aatRNA synthetases.

    The Ubiquitin code uses an arbitrary mapping. The mapping is solved by the specific Ubiquitin Binding Proteins, which link the ubiquinated target to the appropriate outcome.

    What’s so difficult in that, that you cannot understand it?

    The simple point is that semiotic systems (in the sense defined) are never observed to arise in non design systems. It’s as simple as that.

    It’s easy to understand that you utterly lack the ability not to put your assumptions into your claims, no matter how devoid of proper evidence they are. And my “philosophical ‘arguments'” just happen to be about the fact that you can’t even imagine how it is important that there be evidence for your delusional claims. More specifically, they’re about not taking the part as the whole, a distinction that eludes GP’s dimwitted brain.

    There is nothing about codes being arbitrary that makes them symbolic, you simpleton. All you ever do is use the typical ID cant to blither around until you think you’ve made some point about the “ubiquitin code” when you haven’t done a damned thing to show that it is symbolic in the least. My “philosophical ‘arguments'” that you’re too stupid to understand are about causality vs. your blinkered assumptions about what constitutes a symbol.

    But GP was too dumb to understand it before, so I don’t have much point in going over it again in much detail. What I wrote and he quoted, in part, was:

    take the definition of a symbol, which includes a representational relationship, and make the leap to ubiquitin tags being symbols simply because they have a similar causal relationship (or actually worse, he says that they indicate an outcome, however ambiguous that is–but it seems based on the causal relationship). Without apparently even realizing that the definition of the symbol depended upon representation, not upon causal outcomes, let alone “indicating” anything to anybody or anything before science discovered the relationship.

    Later, dolt that he is, he wrote:

    A symbolic code is a code where something represents something else by some arbitrary mapping.”

    It’s very simple, and objective, It has nothing to do with all your philosophical “arguments”.

    And further:

    Either it uses a symbolic code (an arbitrary mapping that is not explained by laws, but depends on the internal configuration of the system) or it doesn’t.

    This is where he simply assumes that because a symbolic code uses arbitrary mapping, that a code with arbitrary mapping means that it’s a symbolic code. He can’t imagine how I can’t see it, and I can’t imagine how he’s so ignorant and dull that he doesn’t know the difference between “some” and “all.” As in, some codes with arbitrary mapping are symbolic, which does not mean that all codes with arbitrary mapping are symbolic. A crucial bit of logic that escapes him as certainly as the fact that he has the burden of proof for his own claims escapes him.

    He can’t even think that because a symbolic code represents something else by some arbitrary mapping, that it is possible that a code could have arbitrary mapping sans actual representation. He can’t imagine that the category of arbitrary mapping could be larger than the category of symbolic arbitrary mapping, because he’s too logically challenged to understand parts and wholes.

    And he probably is above most of the cretins at UD, without being able to recognize the difference between the categorical and the universal, at least in this matter. ID is a very dismal “science” indeed.

    Glen Davidson

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  7. colewd:
    The evidence is an organism with a spliceosome and an approximate date for the origin of this organism. We also have preservation of the Prp8 sequence through out all eukaryotic life which shows time differences.

    I fail to see how this shows that the information was added in 100k bit jumps. There must have been literally billions of ancestral generations preceding the “origin” of eukaryotes (as determined by fossil evidence? You reject phylogenetic methods, right?), so the spliceosome could have easily evolved by small additions at a time.

    And what does preservation of a protein sequence mean to someone who rejects common descent, exactly? How do you determine “time differences” without any assurance that the sequences in different species started out identical (a fact that naturally follows from common descent)?

    colewd: Recruited? You are agreeing with the design hypothesis? Recruiting needs a recruiter:-)

    It is done by the same chap who does the selecting in natural selection, on his weekends off.

    colewd: How did it originate in yeast? How was the controlled and variable cell division feature evolved before this complex function could benefit the organism?

    The ubiquitin system originated in YEAST?!? This is certainly news to me.

    I don’t know a lot about the ubiquitin system, but the presence of similar systems in archaea tells me a primitive system may have been in place before the last eukaryotic common ancestor appeared on the scene (for those of you accepting common descent). If the primitive eukaryotic ubiquitination system was like the archaean, it was much simpler, for example like this one involving only a few genes arranged in an operon-like cluster:

    An additional striking discovery concerns another archaeal species, Caldiarchaeum subterraneum. The genome of C. subterraneum was sequenced and the existence of a full set of ubiquitin signaling factors was found: one single-copy ubiquitin gene, one ubiquitin activating enzyme (E1), one ubiquitin conjugating enzyme (E2), one RING-type ubiquitin-protein ligase (E3), and one deubiquitinating enzyme related to the proteasome subunit Rpn11 (described below) [14]. Interestingly, these five genes are organized in an operon-like cluster, representing the most simplified genetic arrangement encoding a eukaryote-like ubiquitin signaling system (Figure 2) [14].

    Once such a simple system exists, I imagine it can be easily expanded by other proteins acquiring ubiquitination sites (targets) or ubiquitin recognition motifs. That would require good ol’fashioned random mutations of far less than 100k bits at a time.

    The evidence says that all complex stuff, including spliceosome and ubiquitination, started out simple.

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  8. Passive-aggressive GP whines, moans, and manages to get in his leaden sarcasm:

    Instead, I have really appreciated the long and varied list of insults in this long post: it’s quite a record, and I am proud.

    Wow, don’t you wish you were competent at sarcasm.

    Wouldn’t it be even nicer if you were smart and could actually make intelligent responses to what I wrote? Of course I call you stupid and dishonest, because you’re vastly both, dumbfuck.

    Calling you what you are signals the fact that it’s clear to me now that you’re too dogmatic, ignorant, and dumb even to deal with simple logic, GP. And only you and the dullards who look up to you are dumb enough to think that your passive-agressive, if rather wooden, sarcasm has anything to do with politeness. It’s like you pretending that you’re not name-calling the science side when you falsely accuse them of dogmatic faith, when it’s clear that only you and yours are dumb enough to believe such a farce.

    Glen Davidson

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  9. Puccio: “Either it uses a symbolic code (an arbitrary mapping that is not explained by laws, but depends on the internal configuration of the system) or it doesn’t.”

    Positive cases, positive cases everywhere!

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  10. GlenDavidson:
    I thought you were being hard on him at first (I didn’t pay much attention to your “conversation” with him), and then I got a response from him where he didn’t comprehend anything I wrote, not even the fact that he would need to back up his premises rather than merely repeat them.

    I can stand plain, honest, stupidity, but arrogant and dishonest stupidity? Nope. No tolerance at all.

    The guy has no respect for others, and no respect for himself. No character. All those apparently honest OPs where he presents his “methods,” and the way he tries to justify his assumptions, are not just erroneous, they’re but setting up a spectacle of smoke and mirrors.

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  11. gpuccio@UD

    Me: Alas, not true. Neo-darwinism is the theory of population change through natural selection put on more secure genetic footing than Darwin did. That doesn’t rely on common descent, I fear.”

    gpuccio: This sounds really strange. I have always thought that the step by step darwinian process does require CD.

    Could you explain better how it could take place if CD were not true? I don’t understand.

    Not that it is important, but I am just curious.

    Oops, sorry I missed that. This double thread thing is a nuisance.

    This has come up at TSZ a lot, especially in the common design vs common descent thread that ran for quite a while here. If you ever feel like wading through a 5000+ comments discussion, go right ahead.

    Common descent is the result of two processes:
    1) lineage splitting (cladogenesis)
    2) lineage change (anagenesis)

    Once these two processes are in place, phylogenesis will occur and after some time we have ourselves a neat evolutionary tree with the lineages at the tips being related by common descent. We (that is the “evos” here at TSZ, but in particular John Harshman) have continually stressed that the mechanism of lineage change is completely irrelevant to common descent being true; All evolutionary novelties could be lovingly crafted by the Designer in her super secret laboratory outside time and space, and we would still end up with an evolutionary tree. This you accept, I think.

    Vice versa, if common descent were shown not to be true (hey, just a mental hypothesis) for example because all extant species were created independently in the past, then they could still be evolving by the neo-darwinian process of natural selection of beneficial genetic variants. Natural selection is a within-population process, see?

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  12. GlenDavidson,

    You should check what I answered about the symbolic codes and arbitrary mapping, then what he answered back (a link to his full “answer” is there in case you want to see that in context). He shows that either he doesn’t know what “arbitrary” means, or he’s willing to pretend so just to avoid confronting the problems with his bullshit.

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  13. dazz: Puccio: “Either it uses a symbolic code (an arbitrary mapping that is not explained by laws, but depends on the internal configuration of the system) or it doesn’t.”

    By definition, an arbitrary mapping does not depend on “laws.” “Laws” are mathematical descriptions of deterministic phenomena in nature. Idiotucci means the phenomena.

    A symbolic code is not just an arbitrary mapping, but a consciously generated one. Idiotucci holds to arbitrary mapping alone to get away with an equivocation fallacy. Also, here he’s defining nature as being just about deterministic phenomena, while somewhere else he defines it as being just about stochastic events (so that nature alone would not be able to generate “functional” information). His moves depend on what he wants to defend. Of course, arbitrary “mappings” can appear in nature by the combination of “law-like” phenomena and stochastic events.

    It’s equivocation by redefinition.

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  14. gpuccio@UD

    Oh crikey, another comment I missed. Sorry about that. Let’s briefly take on the main points:

    I am not sure I understand. Of course we can plot anything. Let’s see if I understand.

    No, this is not what I meant. Having not worked with bit scores before, I have no intuition for them. I realise they are derived from raw alignment scores, but they receive some transformation. Another thing is: as you travel back in time the sequence similarity will not fall in a linear way, because there will be saturation of AA that were already substituted twice or more.

    Bottom line: I suspect that the plots you make will always produce an exponential phase, even if the substitution rate remains constant. But I cannot test that idea myself. So that’s the reason I asked you: If we were to plot a protein in your graph that evolves at a constant rate, might we not still observe “information jumps”?.

    two simple questions:

    1) Is there any conceptual reason why we should believe that complex protein functions can be deconstructed into simpler, naturally selectable steps? That such a ladder exists, in general, or even in specific cases?

    2) Is there any evidence from facts that supports the hypothesis that complex protein functions can be deconstructed into simpler, naturally selectable steps? That such a ladder exists, in general, or even in specific cases?

    Not sure what you mean by “complex protein functions” seeing as you rejected Entropy’s example of substrate affinity. Could you provide a concrete example?
    I don’t think the human ubiquitin system qualifies, as you can read a few posts above this one, in my answer to Bill cole.

    ETA: link

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  15. Entropy: By definition, an arbitrary mapping does not depend on “laws.” “Laws” are mathematical descriptions of deterministic phenomena in nature. Idiotucci means the phenomena.

    A symbolic code is not just an arbitrary mapping, but a consciously generated one. Idiotucci holds to arbitrary mapping alone to get away with an equivocation fallacy. Also, here he’s defining nature as being just about deterministic phenomena, while somewhere else he defines it as being just about stochastic events (so that nature alone would not be able to generate “functional” information). His moves depend on what he wants to defend. Of course, arbitrary “mappings” can appear in nature by the combination of “law-like” phenomena and stochastic events.

    It’s equivocation by redefinition.

    In another thread at UD, commenter JVL has posted a few links to some bio-logos articles by John Venema like this one

    https://biologos.org/blogs/dennis-venema-letters-to-the-duchess/biological-information-and-intelligent-design-the-curious-world-of-rna-continued

    https://biologos.org/blogs/dennis-venema-letters-to-the-duchess/biological-information-and-intelligent-design-abiogenesis-and-the-origins-of-the-genetic-code

    Those who follow the Intelligent Design literature will know that philosopher and historian of science Stephen Meyer discusses transcription and translation at length in his 2009 book Signature in the Cell. In this book, Meyer attempts to build a case that the “information” we see in living organisms is in fact information in the same sense as a human code or a language. Part of his case involves casting doubt on the RNA world hypothesis, since this hypothesis suggests a material, chemical origin for the genetic code, even if an incomplete one. One of Meyer’s critiques in Signature is that such a hypothesis would have to explain how ribosomes transitioned from using RNA enzymes to using protein ones: Meyer erroneously claims that the enzyme in the ribosome that joins amino acids together is a protein. This is, of course, incorrect, since present-day ribosomes are ribozymes. As we have seen, proponents of the RNA world hypothesis suspected that the ribosome might still be a ribozyme, since its function may have been difficult to transition from an RNA enzyme to a protein one. When, in 2000, the ribosome was definitively shown to be a ribozyme, it was widely seen as a successful prediction for the RNA world position. That Meyer was unaware of this widely-cited and highly-influential work (it would garner the 2009 Nobel Prize in Chemistry, the same year that Meyer’s book appeared) came as quite a surprise to biologists reading Signature, especially given its import for Meyer’s claims.

    […]

    I recall reading Meyer’s argument for an arbitrary code when Signature first came out in 2009, and being surprised by it. The reason for my surprise was simple: in 2009 there was already a detailed body of scientific work that demonstrated exactly what Meyer claimed had never been shown.[1] Though Meyer claimed that “molecular biologists have failed to find any significant chemical interaction between the codons on mRNA (or the anticodons on tRNA) and the amino acids on the acceptor arm of tRNA to which the codons correspond” this was simply not the case.

    One hypothesis about the origin of the genetic code is that the tRNA system is a later addition to a system that originally used direct chemical interactions between amino acids and codons. In this hypothesis, amino acids would directly bind to their codons on mRNA, and then be joined together by a ribozyme (the ancestor of the present-day ribosome). This hypothesis is called “direct templating”, and it predicts that at least some amino acids will directly bind to their codons (or perhaps anticodons, since the codon/anticodon pairing could possibly flip between the mRNA and the tRNA).

    So, is there evidence that amino acids can bind directly to their codons or anticodons on mRNA? Meyer’s claim notwithstanding, yes—very much so! Several amino acids do in fact directly bind to their codon (or in some cases, their anticodon), and the evidence for this has been known since the late 1980s in some cases. Our current understanding is that this applies only to a subset of the 20 amino acids found in present-day proteins. In this model, then, the original code used a subset of amino acids in the current code, and assembled proteins directly on mRNA molecules without tRNAs present. Later, tRNAs would be added to the system, allowing for other amino acids—amino acids that cannot directly bind mRNA—to be added to the code.

    The fact that several amino acids do in fact bind their codons or anticodons is strong evidence that at least part of the code was formed through chemical interactions— and, contra Meyer, is not an arbitrary code. The code we have—or at least for those amino acids for which direct binding was possible—was indeed a chemically favored code. And if it was chemically favored, then it is quite likely that it had a chemical origin, even if we do not yet understand all the details of how it came to be. As such, building an apologetic on the presumed future failings of abiogenesis research, when current research already undercuts one’s thesis, seems to me as problematic for Meyer in 2009 as it did for Edwards in 1696. Do unanswered questions remain? Of course. Should we bank on them never being answered? Or would it be more wise to frame our apologetics on what we know, rather than what we don’t know?[2]

    So the “arbitrary” DNA “code” could have had a chemical origin after all

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  16. Also, our narcissistic friend, puccio, who likes to think he’s so exceptional, has of coursed ripped off the whole arbitrary code idea from Meyer, just like he’s borrowed the rest of his unoriginal nonsense.

    No new original information is ever produced by IDiots, how ironic

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  17. Gpuccio has no idea what DNA_Jock is on about when he points out GP’s propension to texas sharp shooting. He of course can’t see the link between that and Glen’s criticism of GP’s failure to explore the aspects of biology that don’t make any sense under any “design” perspective, while focusing exclusively on what he perceives supports his design preconceptions.

    I made a similar point when I called their inability to look at the big picture “the jesus-in-a-bread-toast effect”. They do “science” like they read the bible: they look for a passages in it to bolster some preconceived idea.

    So once they think they’ve found something in biology that seems to support their stupid intuitions (that alleluyah moment that gives them the warm fuzzies), they will staunchly refuse to look elsewhere or consider any other approach to the subject.

    Bellow, a graphic description of their attitude

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  18. Corneel,

    I fail to see how this shows that the information was added in 100k bit jumps. There must have been literally billions of ancestral generations preceding the “origin” of eukaryotes (as determined by fossil evidence? You reject phylogenetic methods, right?), so the spliceosome could have easily evolved by small additions at a time.

    You have 150 bits of trials over 4 billion years and 100k bits of new information just to get the first prototype of the multicellular world.
    I do not reject phylogenetic methods.

    so the spliceosome could have easily evolved by small additions at a time

    150 bits of total evolutionary resources and 100k bits of information. Closer to impossible then easy:-)

    Once such a simple system exists, I imagine it can be easily expanded by other proteins acquiring ubiquitination sites (targets) or ubiquitin recognition motifs. That would require good ol’fashioned random mutations of far less than 100k bits at a time.

    Are you proposing less then 150 bits will get you from what I read in your article to a full eukaryotic ubiquitin system? Ok now whats left for the spliceosome? Whats left for the nuclear pore complex? Whats left for chromatin structure? Whats left for intron formation?

    It is done by the same chap who does the selecting in natural selection, on his weekends off.

    I think you should run with this hypothesis:-)

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  19. colewd: You have 150 bits of trials over 4 billion years and 100k bits of new information

    Still parroting puccio’s numerology as if it had any kind of relevance to reality? Nobody cares about that shit Billy. Deal with it

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  20. dazz:
    Also, our narcissistic friend, puccio, who likes to think he’s so exceptional, has of coursed ripped off the whole arbitrary code idea from Meyer, just like he’s borrowed the rest of his unoriginal nonsense.

    No new original information is ever produced by IDiots, how ironic

    With so little intelligence evident, as well.

    Glen Davidson

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  21. Yikes, gpuccio is rocking the self-righteousness these days.

    Even DNA_Jock, who is certainly an intelligent and competent person, went ballistic with me a few years ago simply because I did not agree with his intepretation and use of the “Texas Sharp Shooter” fallacy as a criticism of ID. And he still remembers it.
    And believe me, he was (and is) completely wrong about that issue. If you want, I can explain the details.

    Uh-huh.
    Here’s why I was reminded of that interaction, gpuccio:
    In comment #583, in response to Entropy asking for a definition of functional information, you linked to the whole TSS debacle —
    “An attempt at computing dFSCI for English language.”
    I encourage UDites to read that conversation, and see if they can figure out who was right, who was wrong, and who, err, “went ballistic”.

    LOL

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  22. DNA_Jock,

    Uh-huh.
    Here’s why I was reminded of that interaction, gpuccio:
    In comment #583, in response to Entropy asking for a definition of functional information, you linked to the whole TSS debacle —
    “An attempt at computing dFSCI for English language.”
    I encourage UDites to read that conversation, and see if they can figure out who was right, who was wrong, and who, err, “went ballistic”.

    LOL

    Do you believe that the conservation of ATP synthase over time supports strong purifying selection? If not please explain.

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  23. colewd,

    Not sure what you mean by “strong”, but yes, I think that the conservation of the sequence of the traditional ATPase is indicative of selection.
    Do you agree that the degree of conservation of the sequence of the traditional ATPase tells us precisely nothing about how rare or common such functionality might be in sequence space?
    If not, please explain.

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  24. Probably too late but can I suggest that adding insults to otherwise cogent and convincing rebuttals is counter-productive, allowing gpuccio to dismiss those comments as insulting.

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  25. DNA_Jock,

    Do you agree that the degree of conservation of the sequence of the traditional ATPase tells us precisely nothing about how rare or common such functionality might be in sequence space?

    I disagree. If there is strong purifying selection that says a change of AA is highly deleterious and indicates that high specificity is required for the protein to function properly. If the sequence is preserved over a long period of time that indicates very high specify.

    Why do you think it is a meaningless indicator?

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  26. colewd: You have 150 bits of trials over 4 billion years and 100k bits of new information just to get the first prototype of the multicellular world.

    You will need to explain this. I am not familiar with those numbers.

    colewd: I do not reject phylogenetic methods.

    Apologies. However, you do reject common descent of all eukaryotes, right? We were discussing whether ostriches were a created kind not so long ago.

    colewd: Are you proposing less then 150 bits will get you from what I read in your article to a full eukaryotic ubiquitin system?

    What qualifies as a “full eukaryotic ubiquitin system”? Besides all the ubiquitin systems that eukaryotes have now, of course.

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  27. It’s a bit like stumbling on the theory of relativity then refusing to publish a paper, but instead going and shouting on the street corner at random passers by in the hope that one day a scientist will walk by and stop and listen.

    If they really have proven god made us, then they can spend the rest of their lives spending that Templeton cash “proving” it. But they only have excuses as to why they won’t publish in a venue where their ideas might actually get evaluated fairly.

    Remember that “Intelligent Design” Wiki that attempted to collect everything there was to know about Intelligent Design? Perhaps Joel someone? Some guy who actually genuinely thought there was something to it and tried to actually get organised and do something. And then one day I guess he realised the truth, deleted the site and got on with his life. If anyone has a copy….

    But that’s kind of the point I suspect. Anyone who actually thinks there is something to ID seems to quickly run out of steam as far as actual science goes.

    They quickly turn to the manufacturing of excuses as to why they won’t publish their revolutionary work via peer reviewed outlets and then they start writing that book!

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  28. colewd,

    Because the fraction of total sequence space that is explored by mutations to an optimized protein is a tiny, tiny fraction of the total sequence space. You guys keep pointing out how effing yuge the sequence space is. Sampling an infinitesmial fraction of it tells you bugger all about the remainder.

    Do you guys not even pay attention to your own arguments?

    Imagine a 80aa protein motif.
    It’s optimized (this matters) so mutation can perhaps explore three steps away from the optimum, 1520 nearest neighbours, 2.3 million two steps away, 3.5 billion three steps away.
    but 1.2 x 10 ^104 members of the space, so you’re only explore one 10^95 th of the space.

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  29. Alan Fox: Probably too late but can I suggest that adding insults to otherwise cogent and convincing rebuttals is counter-productive, allowing gpuccio to dismiss those comments as insulting.

    And they wonder why they get banned at UD, lol.

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  30. Alan Fox:
    Probably too late but can I suggest that adding insults to otherwise cogent and convincing rebuttals is counter-productive, allowing gpuccio to dismiss those comments as insulting.

    No matter how cogent and convincing our rebuttals, gpuccio will dismiss them. He has shown unwillingness to read courteous answers for comprehension. So insults, no insults, it makes no difference. He’s just receiving the adjectives he worked so hard to earn.

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  31. colewd:
    Why do you think it is a meaningless indicator?

    Because it only tells you the story about a single protein family, and maybe the extent of the sequence space it might have “explored” (as DNA_Jock explains). That there’s one protein family doing the work doesn’t mean that no other protein family could have done the same work. It could have been another, or another, or another, or another, or another.

    In other words, variants within a single protein family cannot inform you about how many variants of the family might work, they can only tell you about the limitations of what the evolution of the family “has explored.” They cannot tell you anything about how many unrelated protein families could have done the job either.

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  32. Entropy: So insults, no insults, it makes no difference. He’s just receiving the adjectives he worked so hard to earn.

    He may have earned the insults, but they rally onlookers to his side. They permit him to concentrate on how unfairly he was treated, rather than on the weakness of his arguments.

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  33. colewd: 150 bits of total evolutionary resources

    What does this number mean?

    What is “150 bits of total evolutionary resources”?

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  34. DNA_Jock,

    I enjoyed your explanations at UD about the post-facto specifications quite a bit. Might have been wasted on the intended interlocutor, but I appreciate a good explanation any time.

    Which Kahneman’s book were you talking about?

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  35. Entropy: Because it only tells you the story about a single protein family, and maybe the extent of the sequence space it might have “explored” (as DNA_Jock explains). That there’s one protein family doing the work doesn’t mean that no other protein family could have done the same work. It could have been another, or another, or another, or another, or another.

    In other words, variants within a single protein family cannot inform you about how many variants of the family might work, they can only tell you about the limitations of what the evolution of the family “has explored.” They cannot tell you anything about how many unrelated protein families could have done the job either.

    Or maybe life would be very different if evolution had produced some other protein families with different functions, right? I find the topic “replaying the tape of life” fascinating

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  36. dazz: Or maybe life would be very different if evolution had produced some other protein families with different functions, right? I find the topic “replaying the tape of life” fascinating

    I find that topic fascinating as well. 🙂

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  37. dazz: Or maybe life would be very different if evolution had produced some other protein families with different functions, right? I find the topic “replaying the tape of life” fascinating

    This issue seems to be recycled endlessly. We can cast our knowledge across past organisms in all their fantastic variety, and we STILL presume that what happened to evolve was what could ONLY have evolved. So we perpetually fall into the error of trying to calculate the probability of THIS (organism, character, mechanism, etc.) occurring, instead of the probably of anything evolving that works for any useful purpose.

    I see life like God’s Own Kaleidoscope, producing an endless and infinite realization of potentials while always bound by the broad limits of biology. Which seems to render such probability calculations moot.

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  38. The best response to the Texas Sharpshooter ploy is silence. It doesn’t merit a response. Perhaps a hundred years ago it needed to be addressed, but no now.

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  39. Alan Fox:
    Probably too late but can I suggest that adding insults to otherwise cogent and convincing rebuttals is counter-productive, allowing gpuccio to dismiss those comments as insulting.

    hin

    Adding truth that is contrary to ID allows GP to dismiss rebuttals and to repeat his mindless drivel yet again. While he repeats his unsupported and false accusations against “neo-darwinists.”

    You know, it’s one thing to say that insults don’t help (arguable, if not indubitable), it’s another to pretend that there’s anything but intellectual dishonesty to be had from GP and almost everyone else at UD.

    Glen Davidson

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  40. dazz: So the “arbitrary” DNA “code” could have had a chemical origin after all

    Very interesting stuff.

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  41. dazz:
    Also, our narcissistic friend, puccio, who likes to think he’s so exceptional, has of coursed ripped off the whole arbitrary code idea from Meyer, just like he’s borrowed the rest of his unoriginal nonsense.

    No new original information is ever produced by IDiots, how ironic

    As for most of them, apparently including GP, they just know what the other IDiots say.

    No understanding of science and scientific inference, just a blind faith in various texts, including ID texts.

    Glen Davidson

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  42. Puccio responds to Entropy acknowledging that

    By definition, an arbitrary mapping does not depend on “laws.” “Laws” are mathematical descriptions of deterministic phenomena in nature.

    just to tell us a bit later that:

    it [the genetic code] is arbitrary. Its [potentially chemical] origin is all another matter.

    How could it be arbitrary if it originated by means of known chemical laws?
    This reeks of anticipation of the need to jump into another potential gap: if it originated chemically, but the later addition of tRNA made it look arbitrary, then that’s where “design” will be

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  43. GlenDavidson: As for most of them, apparently including GP, they just know what the other IDiots say.

    No understanding of science and scientific inference, just a blind faith in various texts, including ID texts.

    Glen Davidson

    I predict in 20 years these clowns will have some 100 + long acronym.

    Ultra
    Specified
    Quasi
    Conserved
    Para
    Symbolic
    Deffo
    Semiotic
    Prolly
    FunctionallyConstrainedButAlsoArbitrarillyFineTunedAndNowThatNoOnesPayingAttentionIllJustPadThisCrapWithRandomOopsNoWayNoRandomDarwinistStuffHereSorryBoutThatJeebusSavesPraiseTheLawd

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  44. Flint: This issue seems to be recycled endlessly. We can cast our knowledge across past organisms in all their fantastic variety, and we STILL presume that what happened to evolve was what could ONLY have evolved. So we perpetually fall into the error of trying to calculate the probability of THIS (organism, character, mechanism, etc.) occurring, instead of the probably of anything evolving that works for any useful purpose.

    I see life like God’s Own Kaleidoscope, producing an endless and infinite realization of potentials while always bound by the broad limits of biology. Which seems to render such probability calculations moot.

    Too true. They don’t even try to make a positive case, and in pulling their negative arguments against “Neo-Darwinism” they slip their own stupid teleological assumptions making it all a ridiculous straw man.

    It’s unbelievable, they will go out of their way to deny the contribution of NS to proclaim that randomness won’t get you to some after the fact target, when obviously, if there’s anything in Darwinism that might make history repeatable it’s precisely the regularity of NS.

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  45. OMFG, I’m having a blast reading some UD threads. I’m in the one where Keiths and DNA_jock press Kairosfocus to calculate p(T|H) and he insists the correct term is log p(T|H).

    Looks like I missed the golden days of IDiot comedy.

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  46. Corneel,

    You will need to explain this. I am not familiar with those numbers.

    If you say 150 bits that means 2^150 as the number of evolutionary trials or around 10^50.

    Apologies. However, you do reject common descent of all eukaryotes, right? We were discussing whether ostriches were a created kind not so long ago.

    I am open on common descent. I am also open on special creation as I don’t think we know how diverse life forms emerged.

    What qualifies as a “full eukaryotic ubiquitin system”? Besides all the ubiquitin systems that eukaryotes have now, of course.

    The ubiquitin system found in yeast is the most “primitive system we can observe”.

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  47. DNA_Jock,

    Because the fraction of total sequence space that is explored by mutations to an optimized protein is a tiny, tiny fraction of the total sequence space.

    In the case you were discussing with GP the two units contained 13 proteins. What we observe now is little change between organisms whose mutation rates and ages are variable. You are making the case that over the long time the total sequence space was not explored and I agree. No matter what the condition age and mutation rate we can only explore a fraction of the sequence space.

    The case qpuccio is making is that we are observing it in an optimized condition. How did it get into this optimized condition which shows a highly specified AA sequence?

    The inference is design.

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  48. To anyone participating here: good luck getting Bill to explain or clearly state anything.

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