Ubiquitin: a challenge for evolutionary theory?

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

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

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

and later:

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

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

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

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

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

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

  1. Bill Cole via Corneel:
    Gpuccio was simulating AA substitutions and Jock changes the argument to nucleic acid (substitutions). A simple straw-man fallacy. Thoughts?

    So now 372944389420147 is an AA sequence? Systematically changing each position in order is a simulation?

    By the way, I understand all right, Bill. I am not struggling at all with gpuccio’s bullshit. So stop talking about my depth of understanding to that imbecile. You have no idea yourself, therefore you’re in no position to judge.

  2. Corneel,

    I never attack people on anything else than their arguments, but if gpuccio wants to pretend that he is a math genius he’d better live up to it.

    How do know he was not just framing the argument which he will win eventually anyway? I am the one who made the error.

  3. colewd,

    Don’t be so hard on yourself, Bill. While being condescending, gpuccio made a math error, and when I pointed it out, you piled on with more condescension. There’s no ‘ad hominem’ going on, I think you misunderstand the meaning of the phrase.
    Now that you’ve seen that you were both wrong, it’s simple enough to say “Oh, I did not see that, silly me.” and move on. Like dazz did.
    Although blaming the people who corrected your error is a mite uncharitable.
    The sad thing is that this pattern gets repeated again and again. gppuccio has not raised any idea that I did not deal with in 2014. Hence my lack of interest in covering the same ground yet again.

  4. Rumraket: At this stage I have to wonder what the hell you think a cause, or an explanation even is.

    You think that chance is a cause. I know that it isn’t. Perhaps you ought to explore how chance can possibly be a cause of anything and after having done so change your mind.

  5. colewd:
    How do know he was not just framing the argument which he will win eventually anyway? I am the one who made the error.

    Maybe you’re the one who made that error. But gpuccio made the “mistake” of exemplifying with systematic changes, while pretending it to pass for what random mutations would do. Yet he claims that I’m the one who doesn’t understand combinatorics.

    Framing the argument my ass. That would require the guy to understand the depth of the problems he’s facing, and he doesn’t. He doesn’t even understand the mistakes he’s making in something as simple as the probability of touching every site randomly, let alone in what would be required to get synonymous sites saturated. I saw a few comments at UD (I shouldn’t have), and guess what? He doesn’t seem to understand what saturated means either.

    Do you want to know what I’m starting to suspect? I suspect that gpuccio presented a systematic change in that 15 digit number because he thinks that his audience doesn’t understand the problem at all. So he gave you some candy just to keep you happy. I think he’s deceiving you because he knows that you think he knows it all. So, whatever he says you’ll accept unquestionably.

  6. Mung: Quite the contrary. It is the materialists with their fallacy of simplicity that are the misguided ones.

    It must have been simple enough at the beginning for it to have occurred by blind dumb luck. There’s no evidence for it, of course. But the evidence just doesn’t matter.

    Rumraket: Also, there is no actual level of complexity that would make it impossible to occur by blind dumb luck.

  7. DNA_Jock,

    DNA_Jock
    April 19, 2018 at 7:44 pm
    Ignored
    dazz quotes gpuccio: For simplicity, I will make 15 substitution in the 15 different sites. This is not a requisite, of course, but it makes the explanation easier. I will also go in order, always for the sake of clarity.

    The original sequence and the final sequence have completely diverged. No homology is any more detectable. We have saturation:

    Okay, given what he’s trying to explain, that’s a truly horrendous error.

    Here’s a tip, folks.
    At one mutation per site, 36% of the sites will be unchanged.
    At three mutations per site, 5% of the sites will be unchanged.
    Ironically, this was another thing I tried to explain to him in 2014.
    It’s e^-n
    And he’s lecturing us on combinatorics.
    ROFL

    This is not a requisite, of course, but it makes the explanation easier.

    This is his statement. He was intentionally simplifying the problem to make his point.

    You call it a math error? You either mis represented the argument or did not understand it.

    All that being said I understand he did “tweak” Entropy and you were trying to defend him.

    There’s no ‘ad hominem’ going on, I think you misunderstand the meaning of the phrase.

    You don’t see one example of attacking the person?

    By the way, I understand all right, Bill. I am not struggling at all with gpuccio’s bullshit. So stop talking about my depth of understanding to that imbecile.

    Please explain how this is not an ad hominem attack?

  8. Entropy,

    It’s really time to take a breather and reflect. People are attacking each other and that is not in the spirit of this site. I acknowledged to Jock that you got “tweaked”. I need time to reflect.

  9. colewd,

    1. DNA_Jock didn’t come to my defence. DNA_Jock just explained the difference between random changes and systematic ones.

    2. That’s directly relevant to the discussion, and shows that gpuccio doesn’t know combinatorics (funny that).

    3. An ad hominem is when a person is attacked instead of the argument. Since gpuccio’s arguments and disdain show deep imbecility, it’s not an ad hominem to call gpuccio an imbecile, it’s a conclusion from the quality of his arguments.

    4. Good idea to stop and reflect. I hope you come back a little wiser.

    I hope that helps.

  10. Entropy,

    3. An ad hominem is when a person is attacked instead of the argument. Since gpuccio’s arguments and disdain show deep imbecility, it’s not an ad hominem to call gpuccio an imbecile, it’s a conclusion from the quality of his arguments.

    I love this one:-) “a conclusion from the quality of his arguments”

    You guys are both smart guys only a very smart guy could “spin” an ad hominem like this.

    We agree that genetic information is an important academic endeavor and he is trying to study and measure it. This common ground is real progress.

    Maybe we could travel to Italy someday and have a beer with him and laugh about these exchanges.

  11. Mung: You think that chance is a cause.

    No I don’t.

    Perhaps you ought to explore how chance can possibly be a cause of anything and after having done so change your mind.

    Perhaps you should learn what the words we use mean?

  12. Mung: Mung: Quite the contrary. It is the materialists with their fallacy of simplicity that are the misguided ones.

    It must have been simple enough at the beginning for it to have occurred by blind dumb luck. There’s no evidence for it, of course. But the evidence just doesn’t matter.

    Rumraket: Also, there is no actual level of complexity that would make it impossible to occur by blind dumb luck.

    See, this is yourself using the term you are now complaining isn’t a cause. I never thought it was a cause, rather I thought you meant the term like I meant the term so that’s why I used it; as a placeholder description of some blind and unintelligent physical phenomenon, like the “tornado in a junkyard”.

    It is strange to see you complain about using a term you yourself brought up in the very manner you are now scolding me for using it. It really reveals you have nothing of substance to add here and is just flailing around.

  13. Entropy: 3. An ad hominem is when a person is attacked instead of the argument.

    No, that’s just a personal attack.

    An ad hominem is a fallacy in logic. It basically goes like this:
    Your conclusion can’t be true because you stink. <- That's an ad hominem.

    If person A say to person B “you stink”, that’s not an ad hominem, that’s just a personal insult.

    If person A says to person B “your conclusion is false, and you stink”, that’s also not an ad hominem, that’s an assertion followed by an insult. It might be true that the conlusion is false, and that the person also stinks (not that it is relevant whether person B stinks).

    It only becomes an ad hominem fallacy when the reason for rejecting the argument is some perceived character failing of the person advancing the argument. When it is stated that the conclusion isn’t true BECAUSE the person stinks.

    Sorry for being a pedant here. And don’t get me started on “it begs the question” used incorrectly in place of “it raises the question”. I don’t know, it bothers me every time. 😀

  14. colewd: You call it a math error? You either mis represented the argument or did not understand it.

    Yes, Bill, I called it a math error because it is a math error. You have even conceded as much. I understand his argument, and I have not misrepresented it. I have merely pointed out that he is erroneously over-stating his case. Happens a lot.
    If you want move past assertion and actually argue that the error is immaterial, you are free to do so.
    Meanwhile, I am enjoying the fact that gpuccio’s description of what “scientistists with sense do” is a classic example of improper use of Fisherian statistics. Another math error, albeit a more subtle one. Coming from a Doctor, no less. I’m assuming he’s never been involved in clinical trial design.

    Bill, please learn to distinguish ad hominem (a fallacy) from insult.
    ad hominem:

    gpuccio’s arguments are wrong because gpuccio is an idiot.

    insult

    gpuccio is an idiot because his arguments are wrong.

    Can you see the difference?

    ETA: Ninja’d!

  15. DNA_Jock,

    Can you see the difference?

    No, I cannot. In both cases you are attacking the person. Lets move to moderation if you want to take this further.

    Yes, Bill, I called it a math error because it is a math error.

    No, it wasn’t and you often make this error of assigning an error by changing the argument.

    Now, let’s say that the sequence is completely neutral, without any functional constraint. And let’s say that I can operate one substitution per site per minute.

    For simplicity, I will make 15 substitution in the 15 different sites. This is not a requisite, of course, but it makes the explanation easier. I will also go in order, always for the sake of clarity.

    So we get, in 15 minutes, the following results (the mutation is in bold):

    1) 572944389420147
    2) 522944389420147
    3) 528944389420147
    4) 528644389420147
    5) 528674389420147
    6) 528672389420147
    7) 528672989420147
    8) 528672959420147
    9) 528672950420147
    10)528672950820147
    11)528672950840147
    12)528672950845147
    13)528672950845847
    14)528672950845817
    15)528672950845812

    The original sequence and the final sequence have completely diverged. No homology is any more detectable. We have saturation:

    372944389420147
    528672950845812

    Now, I will ask a few very simple questions that even Entropy and dazz should be able to answer:

    a) How many different states have we reached?

    (Answer: 15)

    So based on his statement, show me the math error without changing his argument.

    I did make an assumption error based on your calculation.

  16. colewd: So based on his statement, show me the math error without changing his argument.

    Bill,

    The error is in changing those numbers systematically, instead of randomly. Do you really not see the difference? Mutations are not systematic, they’re random. Saturating every synonymous positions, while changing every less-functionally-compromised site, randomly, would require quite a load of mutations. It’s gpuccio who doesn’t understand combinatorics. (He doesn’t seem to understand saturation either if he thinks that total changes in sequence is the same as saturation of synonymous sites.)

    The guy made a fool out of himself by presenting systematic changes instead of random ones, all the while asking a rhetorical question in a condescending tone.

    I think it’s a much better idea for you to take that break.

  17. In all fairness, I do believe gpuccio intentionally simplified the math there. Unfortunately, that only makes him look even worse IMO. He actually thought we were arguing that once all similarity is erased by neutral evolution, the entire sequence space has been explored.

    gpuccio:
    Entropy and dazz seemed to be under the starnge illusion that the simple facts that all sites underwent mutations in some evlutionary time demosntrated that the search space had been traversed. That was a completly senseless idea, and I have made a simple example to make them realize that. That’s all.

    Why would he do that? Well, because he’s so high on himself and his ridiculous “theory” that he actually thinks we need and we’re trying to show that evolution must be able to search the entire space! He just can’t wrap his head around the idea that someone wouldn’t take his shit seriously!

    So the whole math simplification was just him being condescending.

    Hilarious

  18. Entropy,

    The “error” is in changing those numbers systematically, instead of randomly. Do you really not see the difference?

    Did he say he was going to change the numbers randomly? If he did then he would of made a math error. He did not.

    He understands the difference. He used a systematical calculation for simplicity.

    The error was in the “tweak” as without this, the discussion would have had value. Jock, however, did not diffuse it, instead he re “tweaked”.

  19. dazz,

    In all fairness, I do believe gpuccio intentionally simplified the math there. Unfortunately, that only makes him look even worse IMO. He actually thought we were arguing that once all similarity is erased by neutral evolution, the entire sequence space has been explored.

    You are right on this one. So the error is he “tweaked” you guys. Now you just “tweaked” him back. What are you trying to accomplish?

  20. colewd:
    Did he say he was going to change the numbers randomly?If he did then he would of made a math error. He did not.

    He’s supposedly answering my point. In order to answer my point he has to understand the problem. To understand the problem he has to understand random changes. If he understood this, he’d understand that systematic changes don’t go anywhere near my point.

    colewd:
    He understands the difference. He used a systematical calculation for simplicity.

    If he was mistaken enough to try and “answer” my point by using systematic changes, then he didn’t understand. I think he was putting a show for you and his sycophants Bill. If so, he succeeded in that regard. You’re unable to understand the problem even now, after many attempts at explaining it to you.

    colewd:
    The error was in the “tweak” as without this, the discussion would have had value.Jock, however, did not diffuse it, instead he re “tweaked”.

    No Bill, sorry. The error was with pretending to answer a point just to show that he didn’t understand it. Of course, that was compounded by his condescending tone while making a fool out of himself.

  21. Entropy,

    If he was mistaken enough to try and “answer” my point by using systematic changes, then he didn’t understand.

    For relationship purposes I will concede this point. I think it is quite valid that he underestimated you’re understanding of the issue. Lets take a break and then talk about the root cause of mis understanding.

  22. Dazz@

    dazz: Random sequences rapidly evolve into de novo promoters

    Abstract
    How new functions arise de novo is a fundamental question in evolution. We studied de novo evolution of promoters in Escherichia coli by replacing the lac promoter with various random sequences of the same size (~100 bp) and evolving the cells in the presence of lactose. We find that ~60% of random sequences can evolve expression comparable to the wild-type with only one mutation, and that ~10% of random sequences can serve as active promoters even without evolution. Such a short mutational distance between random sequences and active promoters may improve the evolvability, yet may also lead to accidental promoters inside genes that interfere with normal expression.

    The paper is about “short mutational distances” — it speaks of “only one mutation” and “Substantial promoter activity can typically be achieved by a single mutation in a 100-base sequence …”
    I take it that you are aware of the fact that ID-proponents, like Gpuccio and Behe, have pointed out, often, that such is within the reach of natural selection.

    Therfore, it is not immediately clear why you want me to pass GPuccio this paper.

    Two remarks:
    There is also a lot of artificial selection going on — e.g. “To evolve the de novo expression of the lac genes, we applied selection for the ability to utilize lactose.”
    My concern with this is, as is often the case in these type of studies, that artificial selection takes a crucial step that natural selection cannot take.

    If it is true that “10% of random sequences can serve as active promoters” and for others this function can “typically be achieved by a single mutation”, then I start to suspect that there are other factors involved besides promoters.

  23. Origenes: Two remarks:
    There is also a lot of artificial selection going on — e.g. “To evolve the de novo expression of the lac genes, we applied selection for the ability to utilize lactose.”
    My concern with this is, as is often the case in these type of studies, that artificial selection takes a crucial step that natural selection cannot take.

    If it is true that “10% of random sequences can serve as active promoters” and for others this function can “typically be achieved by a single mutation”, then I start to suspect that there are other factors involved besides promoters.

  24. colewd:
    For relationship purposes I will concede this point.I think it is quite valid that he underestimated you’re understanding of the issue.Lets take a break and then talk about the root cause of mis understanding.

    No worries Bill, I just needed to take a rest. I’m still convinced that gpuccio was being, well, gpuccio. I should not be surprised though. After all, I wrote that I expected him to miss the point, he missed the point. That he was condescending while making a fool out of himself is but one of his character flaws.

  25. gpuccio@UD

    I think instead that the number of expected mutations to change all the sites can be computed by the Coupon collector’s problem formula. See also here:

    https://en.wikipedia.org/wiki/Coupon_collector%27s_problem

    That would give 35 tries for my 15 figures sequence.

    The expected time to complete touching all sites within a sequence of length 15 using the coupon collectors method is 50 mutations.

    But of course, as long as the mistakes are accurate to within 14 orders of magnitude, pointing them out is “irrelevant and ridiculous”.

  26. Origenes:
    There is also a lot of artificial selection going on — e.g. “To evolve the de novo expression of the lac genes, we applied selection for the ability to utilize lactose.”
    My concern with this is, as is often the case in these type of studies, that artificial selection takes a crucial step that natural selection cannot take.

    Here the “artificial selection” consists on having lactose as a carbon source. In other words, having lactose in the growth medium. That’s a good representation of a “natural” situation where there’s a carbon source available, rather than another. This excuse “oh, they were making an experiment! therefore that doesn’t count” is tiresome in its foolishness, and looks a lot like an irrational attempt at missing the point in order to reject a perfectly valid study. So, please stop it. If you want to pretend that ID is scientific, then be honest with yourselves and stop making those kinds of excuses.

    Origenes:
    If it is true that “10% of random sequences can serve as active promoters” and for others this function can “typically be achieved by a single mutation”, then I start to suspect that there are other factors involved besides promoters.

    There’s a “factor,” but it’s not besides promoters, but about promoters. Promoters and binding sites for transcription factors are somewhat short sequences. Because they’re short and can vary, they contain little information (yes, information without any idiotic qualifiers). That makes their probability high, and the evolution of transcriptional regulation a no-brainer. This is low hanging fruit, but perfectly valid, juicy, low hanging fruit.

    There you have it. You can accept the results, learn something, keep yourself honest in this respect, and still hold to your beliefs that evolution-cannot-do-everything-therefore-god-did-it.

  27. Rumraket: See, this is yourself using the term you are now complaining isn’t a cause. I never thought it was a cause, rather I thought you meant the term like I meant the term so that’s why I used it; as a placeholder description of some blind and unintelligent physical phenomenon, like the “tornado in a junkyard”.

    It is strange to see you complain about using a term you yourself brought up in the very manner you are now scolding me for using it. It really reveals you have nothing of substance to add here and is just flailing around.

    I was clearly attributing such a view to materialists, not to myself. And you copped to it. But as long as you’re now walking it back, that’s progress.

    But now we’re left with the fact that at the heart of evolutionary theory is blind chance, where “chance” is just a word expressing our ignorance of the actual underlying causes.

    The inscrutability of the gods.

  28. dazz: Well, because he’s so high on himself and his ridiculous “theory” that he actually thinks we need and we’re trying to show that evolution must be able to search the entire space!

    What would prevent “evolution” from “searching” the entire space? IF you deny that “evolution” can “search” the entire space then you are in essence agreeing with the “islands of function” crowd. Congratulations. You’ll be a Creationist soon.

  29. dazz: Keep mocking your own worldview. You guys are pathetic.

    And deep at the heart of the materialist worldview is a profound ignorance, and being a materialist requires embracing that ignorance.

    How does it feel?

  30. It’s ok dazz. I can see it bothers you. And that’s a good thing.

    Think about it.

  31. It doesn’t bother me at all. Mutations appear to be random with respect to to fitness and evolution has no foresight. I only see creotards getting their knickers in a bunch over that simple fact. I know you guys need to feel like the universe has conspired with the FSM to make you but it is what it is. Deal with it

  32. Mung: What would prevent “evolution” from “searching” the entire space? IF you deny that “evolution” can “search” the entire space then you are in essence agreeing with the “islands of function” crowd. Congratulations. You’ll be a Creationist soon.

    Don’t be silly Mung. The enormous search space means that it’s pretty hard for anything to navigate it completely. The reasonable position here would be that evolutionary processes don’t have to navigate the whole search space in order to work, not that god-did-it.

    Also, the islands of function are not a creationist invention. It’s a conceptual framework produced by actual scientists trying to figure out a way to study how molecules work and evolve.

  33. Mung: I was clearly attributing such a view to materialists, not to myself.

    Of course you were, while having implicitly granted that it is a sensible way to speak.

    It is only when you started having problems you came up with the desperate idea that anyone thinks chance is itself a cause, as opposed to just a way of using mathematics to speak about situations where there are multiple possible outcomes.

    And you copped to it.

    Yeah I’m sorry for assuming you know something about what the words we are using means. I won’t think you aren’t that incredibly ignorant in the future, sorry.

    But now we’re left with the fact that at the heart of evolutionary theory is blind chance, where “chance” is just a word expressing our ignorance of the actual underlying causes.

    The ironic thing is you’re actually describing IDcreationism. At the heart of ID is the word “design” that just expresses a complete ignorance of the underlying causes.

    The inscrutability of the gods.

    Exactly. That is what your position amounts to. A vacuous “design did it” that predicts or explains nothing, and nobody knows why or how or when or where. Hoisted by your own petard.

    This is progress. Now that you have discovered how thoroughly vacuous your position is, you can start to think about ways to improve. And I don’t mind helping.

  34. Mung: What would prevent “evolution” from “searching” the entire space?

    The rate of mutation, the size of populations, the size of the space.

    IF you deny that “evolution” can “search” the entire space then you are in essence agreeing with the “islands of function” crowd.

    The whole concept was invented by Arch-evolutionst Sewall Wright (of neo-Darwinism fame) in 1932. He also argued that in the fitness landscape metaphor, the landscape is dynamic and changes over time, because the environments which ultimately determine the adaptiveness of different phenotypes, also changes.

    Another total own-goal by Mung. 🙂

    Congratulations. You’ll be a Creationist soon.

    Like the fathers of the neo-Darwinian synthesis of evolution were?

  35. Hi, just drifting in on the ether waiting for a job to run … I liken ubiquitin to the https:// tag on URLs. It has become embedded in many systems because … well, evolution. Any from an enormous set of possibilities would have done at the outset, but once one or a few proteins started to bind specifically to this tag, it became non-negotiable. Many structural and signalling proteins are much more highly conserved than any enzyme, for this reason. Far more sequences would do the job, but they get pinned in place by the things that bind them, rather than their own merits.

    Ho ho Silver … awaaaay! (who was that masked man?).

  36. Mung: IF you deny that “evolution” can “search” the entire space

    I’m Brian and so’s my wife!

  37. J-Mac, to Allan:

    Are you going to finally explain the gender evolution? How many genders are there? I got many…

    J-Mac has many genders.

  38. gpuccio @UD responds saying the paper about the evolution of promoters, wait for it, supports ID and “correctly” uses his principles!

    Poor Puccio, he didn’t even get a citation in the references of the paper. How evil of those evil evilutionists.

    Of course he doesn’t even mention “islands of function” there, but wait! he found the word “design” in the paper! Praise Jeebus. LMFAO

    https://uncommondescent.com/intelligent-design/defending-intelligent-design-theory-why-targets-are-real-targets-propabilities-real-probabilities-and-the-texas-sharp-shooter-fallacy-does-not-apply-at-all/#comment-656758

    https://uncommondescent.com/intelligent-design/defending-intelligent-design-theory-why-targets-are-real-targets-propabilities-real-probabilities-and-the-texas-sharp-shooter-fallacy-does-not-apply-at-all/#comment-656791

  39. Oh, and look at this:

    ORIGINAL PAPER:

    We began by building three such strains, each one carrying a different random sequence upstream to the lac genes (termed RandSequence1, 2, and 3). We observed that none of these strains could utilize or grow on lactose because they could not express the lac genes (Supplementary Fig. 1). This experimental observation was therefore consistent with the expectation that a random sequence is unlikely to be a functional promoter.

    […]

    ~10% of random 103 bp serve as promoters without evolution

    What would gpuccio quote from that? This, no more, less:

    To broadly represent the non-functional sequence space, we used random sequences (generated by a computer) with equal probabilities for all four bases

    This experimental observation was therefore consistent with the expectation that a random sequence is unlikely to be a functional promoter.

    Holy quote mining batman!

  40. Hahahaha oh my lard. How can anyone be that uncommonly dense?

    Gpuccio’s response basically amounts to complaining that there’s someone flipping the coin. It’s now no longer about whether it is likely to flip a particular sequence of heads or tails. He’s now complaining that because a computer was used to flip the coins, this somehow qualifies as design.

    Nobody can be that dumb. Nobody. This is FANTASTIC!

  41. Rumraket,

    I’m ashamed that I was treating that IDiot with respect. He’s gone into full fundamentalist apologetics mode. Total Stupidity. Not even worth responding.

  42. And the expectations are of course met: some creo asks puccio in despair: “Is the promoter paper about what is called microevolution?”

    Puccio steps up to comfort him: “Yes, definitely.

    A functional transition of 1 nucleotide + 1 nucleotide optimization is much simpler than, say, penicillin resistance, where you need 1 AA + a few AA optimization.

    One AA is 4.3 bits of information, while one nucleotide is only 2 bits.

    So, this is really a simple transition.”

    See? Case closed! E-Coli is still E-Coli! No new original gazillion nats (oops, heresy) I mean bitz of superspecificespialidociousinformation!!!11!

    They’re just following puccio’s lead! How can you not see that?: “they are implicitly speaking of functional information: the set of functional sequences, that will implement the function of providing a promoter. This is pure ID theory.”

  43. Holy crap guys, check this out too

    Puccio: “By the way, have you noticed that the paper is about computing, by experiment and math, the probabilities of generating one specific functional target, even if a simple one?

    Is the paper fatally flawed as an example of TSS fallacy? Didn’t the reviewers understand that?”

    HAHAHAHAHAHA, That’s just priceless!
    Why doesn’t Puccio let them know they’re doing it wrong by not dividing 1 by the totality of the search space like he does?

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