Ubiquitin: a challenge for evolutionary theory?

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

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

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

and later:

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

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

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

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

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

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

  1. gpuccio,

    I am really surprised, I must say, that a person who seems to understand very well the importance of functional information (see his comment “April 8, 2018 at 8:31 pm” at TSZ, and my comment #796 here) can at the same time misunderstand so blatantly what functional information is (see my comments #828, #831, #847 and #882 here).

    Don’t you see the irony there? Given you have to reference 4 comments how can you complain about people misunderstanding what you mean by functional information. Why don’t you just create a PDF and upload it to a free service like this: http://freepdfhosting.com/ then you can just link to a single document rather then expecting people to follow a breadcrumb trail?

    Then when people are talking about your particular brand of information then can reference it’s definition directly, and so can you, without all that typing and confusion.

    In fact, once you have that document you could perhaps pass it around your friends @ UD and ask them if they can spot any mistakes or suggest any improvements. Once you do that, you can just put up a new version of the PDF and then reference that instead of the older versions.

    Over time your efforts on UD will become the reference for your particular brand of what functional information is.

    Who knows where such a path might lead, eh?

  2. Rumraket: What is the haystack in this analogy? Please elaborate.

    IT’s in the farm, so first you have to stumble across the farm holding the haystack holding the needle.

  3. Mung: IT’s in the farm, so first you have to stumble across the farm holding the haystack holding the needle.

    Yeah as I thought you weren’t making sense.

  4. DNA_Jock: Is this your standard content-free snark…

    Yes. But it least I wasn’t being snarky about another commenter. And I wasn’t sure why you were trying to drag me in to someone else’s argument/claim.

    I think to say whether something is rare or not we’d have to agree on what “rare” means and how to establish “rarity.”

    Is there a statistical definition of “rare” or “common” that everyone is using?

  5. Rumraket: Yeah as I thought you weren’t making sense.

    Yet someone else brought up needles and haystacks and you ask me what the haystack stands for. Why not ask Alan?

  6. keiths: Instead of wasting your time coming up with idiotic arguments for design, why not read Arrival of the Fittest? It discusses this topic in detail.

    Yes, it helped convince me of an underlying design.

  7. Mung: Yet someone else brought up needles and haystacks and you ask me what the haystack stands for. Why not ask Alan?

    Because in his analogy it was obvious it corresponds to the sequence space.

    So since you are insinuating the analogy implies design, I wanted you to explain how the sequence space implies design. That’s effectively what you said. Since there is a sequence space, that implies design. Which seems to me nonsensical, so you either need to explain why a sequence space implies design, or alternatively tell me if you think the haystack is something other than sequence space.

  8. Origines @ UD

    The Skeptical Zone’s winning arguments — part I:
    OMagain: Please feel free to go into detail regarding these “severe limits” and how you have determined that they exist at all.

    Origines then quotes gpuccio:

    I have dedicated two whole OPs and long following discussions to the limits o NA and RV, with a lot of detail.
    Here they are:
    What are the limits of Natural Selection? An interesting open discussion with Gordon Davisson

    And:
    What are the limits of Random Variation? A simple evaluation of the probabilistic resources of our biological world
    Please, feel free to read them and to comment. I will answer.

    Sure, I do have a question. In one of those OPs you say

    It means, for example, that any sequence with 160 bits of functional information is, by far, beyond any reasonable probability of being the result of RV in the system of all bacteria in 4 billion years of natural history, even with the most optimistic assumptions.

    So my question is, can you give me an example of a specific biological sequence with 160 bits of functional information and explain how you know that sequence is functional? I assume that you know what it does, otherwise how do you know it’s functional information.

    And can you then give me another sequence with around half, or 80, bits of functional information and explain how you know it is functional information?

    I’ll then present to you a similar sequence. You can then presumably tell me if it’s actually functional information and if so how many bits it contains?

    If you are not able to do that not, why not? It seems to follow logically from your claims.

    Those are my questions. KTnxBi.

  9. Gpuccio’s two comments about Wagner in the UD thread:

    Frankly, I could never find anything credible in what Wagner says.

    And:

    Wagner is beyond any sense.

    I do hope Pooch will explain the basis for his judgments.

  10. Hum. So, apparently Origenes missed some stuff in trying to make a summary of sorts.

    Entropy: Examining a few organisms, and comparing them to a few other, apparently less complex, ones, and concluding that information has increased, rather than reorganized, is quite a hasty conclusion.

    Then the “summary” of gpuccio’s “answer”:

    A procedure and a conclusion that I have never done or stated.[GPuccio]

    What Origenes “missed”:


    I have not examined “a few organisms”. I have taken the whole human proteome, and blasted it against the proteome of a few representative groups of organisms. So, when I say that the homology of Pricke1 (the whole protein), Q96MT3, has a functional information jump of 689 bits in vertebrates,

    So, he hadn’t examined “a few organisms,” he had examined “a few groups of organisms.” All against just humans. Hum. Oh, and he has concluded that information has increased. Didn’t he say that he did neither?

    Can you check what he said above?

    A procedure and a conclusion that I have never done or stated.[GPuccio]

    Hum. So, he didn’t check a few organisms because he has a special definition for few, and he didn’t conclude that there was increases in information, but he has concluded that there’s “jumps” in information.

    I find that to be very interesting. More importantly, I find it interesting that Origenes missed that. Cannot judge Origenes too harshly though, gpuccio buried that within lots of complains about the part where I said “apparently less complex,” and that I hadn’t read about his magnificent and amazingly informative, if impractical, definition of functional information. A definition he then proceeds to ignore in exchange for differences in BLAST-bit-scores (to be fair, he tries to justify this, not very satisfactorily, but he should not complain that I’m not impressed by his definition, or that I’m not using it, if he cannot use it himself, right?).

    ETA: Either way, gpuccio evaded the point by focusing on semantic details. Something he seems to be fond of.

  11. Origenes contiinues:

    Entropy: You, however, think that just pointing to complexity will make your absurd imaginary friend into a reality.

    Let’s see that summary:

    In my view, instead, my argument is that there are three different markers that are linked to a design originn and therefore allow empirically a design inference (that is the basic concept in ID, and I have discussed it many times in all its aspects).

    Three! OK, let’s see them.

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

    Oh, pointing to complexity, as I said.

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

    Oh! the “difference” is that they compound that pointing with an equivocation. Maybe that’s it. But wait, there’s more!

    c) Irreducible complexity

    Ah! Pointing to complexity again. Who knew?

    In my OP I have discussed in detail a specific biological system where all those three aspects are present. Therefore, a system for which a design inference is by far the only reasonable explanation. [GPuccio]

    So, I stand corrected, they think that pointing to complexity, twice, and compounding that with an equivocation will make their absurd imaginary friend into a reality.

    My apologies for the misunderstanding.

  12. Entropy,

    I haven’t read Andreas’ book. Is it any good?

    It’s very good — engagingly written and well worth reading. It’s also a major headache for IDers, particularly those who are fond of “islands of function” arguments.

    Is it true that he gets into some kind of Platonism?

    Yes, Wagner is a Platonist, but the arguments he makes regarding evolution don’t depend on that.

    Just as a non-Platonist can agree with the math in a book written by a Platonist mathematician, a non-Platonist can agree with the biology in Wagner’s book. The Platonism is secondary.

  13. OMagain: Origines @ UD

    The Skeptical Zone’s winning arguments — part I:

    Teehee, what’s this!?! A collage of out-of-context quotes in three parts meant to puff up the big man’s ego? Origenes even quotes CharlieM as if he was making some point contra gpuccio, when Charlie was actually addressing me.

    Yo, great summary, Origenes. Don’t forget to include your own killer quote, which instantly demolished gpuccio’s 1000+ word argument immediately preceding it.

  14. gpuccio@UD

    bill cole:

    Yes, of course.

    I will include some more discussion about that in my next OP.

    Will that be reposted here at TSZ?

    I think you might agree that the discussion of your OP has greatly benefited from the input from the TSZ participants. I appreciate that some of the ehhh… unflattering responses might deter you, but I would argue that that is greatly outweighted by having your ideas exposed to some substantial criticisms that you would never receive at UD.

  15. Corneel:
    Teehee, what’s this!?! A collage of out-of-context quotes in three parts meant to puff up the big man’s ego?

    Yes. Exactly. However, in the third one, Origenes managed to put together the parts where gpuccio confidently and adamantly claims that affinity has nothing to do with it (complex functions, to which I answered that maybe gpuccio thinks that proteins work by protein telepathy), and that copies don’t add functional information, therefore shooting himself in the foot.

    Corneel:
    Origenes even quotes CharlieM as if he was making some point contra gpuccio, when Charlie was actually addressing me.

    Wasn’t that funny?

    Corneel:
    Yo, great summary, Origenes. Don’t forget to include your ownkiller quote, which instantly demolished gpuccio’s 1000+ word argument immediately preceding it.

    I saw that. Spectacular!

  16. Origenes quoting goes on.

    Entropy: Scientists have understood for quite a while that information arises from the dynamics between energy flows and the nature of physical/chemical “entities.”

    I admit that this point is hard to get across to someone who has never seriously read about statistical mechanics/thermodynamics. However, if someone’s arguments hinge on understanding information, then I’d expect a minimal amount of knowledge in that direction. However, it seems like gpuccio didn’t even glance at any of that stuff. Gpuccio’s ignorance about that, and many other things became much more apparent later on (as I will show when I progress through Origenes’ “summaries”).

    Complex functional information? Really? Examples, please.

    Yes. Even that shit. Examples? I gave a few: rocks sorted by size next to the ocean, our solar system, a meteorite impact sorting minerals into “veins,” of course, all kinds of life forms too (I know how you’d complain about this inclusion, but you’d be too much of a hypocrite if you complained, and maybe you should continue reading until you get the point, I doubt you’re about to do that, mostly due to your incompetence/lack of background preparation to deal with these themes). Maybe you need to read about Maxwell’s demon, entropy/energy/information, etc. However, their scenarios are too simple, and you might miss the point because they don’t talk about molecular biology, but aboiut sorting atoms, but the connection between energy and information (the information “needed” to sort those atoms, or “functional” information if the function is sorting atoms) is right there, and the transformation of chemical energy into heat during life processes shows that the same principles are at work there too.

    If scientists “have understood” such a thing “for quite a while”, it will not be difficult for you to give examples. Do it. [GPuccio]

    I did. By this point I’m just repeating myself. See above.

    More fun later.

  17. Origenes quotes continue,

    Entropy: For example, a substrate that it never encounters in its environment. However, once the correct substrate is found, it looks rather obvious in the efficiency / specificity of the enzyme towards it, compared to the “wrong” substrate. Where does all of this lead? To the realization that enzyme activities are not as perfect as presented in kinder-garden biochemistry, that they range in potential towards substrates other than their “normal” ones, and that, thus, there’s such a thing as “ladders” of specificity available for enzyme evolution. Not only that, after understanding this issue, it seems rather obvious.

    It is important to note that Origenes quoted this, right after gpuccio asks for examples about energy and information, rather than gpuccio’s “challenge” to give him a hint that there’s naturally selectable “ladders” of function available for natural selection.

    There is nothing obvious in this confused fuss.

    It looks rather obvious to me. I re-checked it and it still looks rather obvious and clear. Enzymes have profiles of efficiency taking different substrates, therefore suggesting the existence of ladders of activity available for natural selection. That was the “challenge.” Mission accomplished, except that I didn’t count on your incompetence / ignorance / unwillingness to get the point. I can do nothing in that respect. Learning the appropriate biochemistry is up to you. I’m not your teacher. This is but a blog. Go hit the books and stop pretending that I’m too blame for your ignorance and incompetence.

    You must explain how some new complex functional protein, for example a new protein superfamily, can arise by gradual steps, each of them giving an increase of function.

    Oh, attempting to move the goal posts? Nah! Not you! You wouldn’t!

    Or at least why we should believe that it is possible.

    Oh, so just a hint will do? For a moment there I thoght … Anyway, I gave you that and more. That you’re too ignorant to get something that simple is beyond me. After all, you’re talking so confidently, close to the point of arrogance, about ubiquitin, and complexes, etc, that I thought you’d have some minimal understanding. Now I know you have to hit the books. Go ahead and do that, instead of proudly showing off your ignorance as if that was a good reason to reject my answer.

    You only make generic and confused statements about enzymes. What is your point? [GPuccio]

    Sigh! If you wanted to convince me that you’re clueless about molecular biology and biochemistry, you could have said that. then I would have saved my answer and suggest a few courses you could take in order to be prepared for a discussion you invited, but you’re too ignorant to handle.

    (more of gpuccio’s proudly displayed ignorance and incompetence later)

  18. gpuccio at UD comments (here) of me that

    I am really surprised, I must say, that a person who seems to understand very well the importance of functional information (see his comment “April 8, 2018 at 8:31 pm” at TSZ, and my comment #796 here) can at the same time misunderstand so blatantly what functional information is (see my comments #828, #831, #847 and #882 here).

    I understand Hazen and Szostak’s concept of functional information well, as they were very clear about that. I understand William Dembski’s “complex specified information” (in Dembski’s 2002-2007 arguments) as well as the altered version in his 2005-2006 paper.

    May I assume that gpuccio has not redefined “functional information” from Hazen and Szostak? Is there some reason to discard their definition?

    PS: I will be away from the keyboard, mostly, over the weekend — hope that by Monday gpuccio has cleared that up.

  19. Goodness me!
    G Puccio must have retired from medical practice judging by his new OP at Uncommon Descent. I see he adds in a comment

    Anyone can post [Gpuccio’s Opening Post at UD], or parts of it, at TSZ. There is no copyright, it is public domain.

    and mentions he’s finding it harder to follow comments at TSZ as the length of this thread increases. I think a new OP to discuss gpuccio’s post might be an idea. I suspect Professor Felsenstein will be too busy but maybe Entropy, Corneel, Rumraket, OM or others participating would like to start one.

    ETA On starting to read Gpuccio’s post I see he addresses DNA_Jock, so perhaps DNA_Jock is best qualified, if he has the time.

  20. Joe Felsenstein,

    May I assume that gpuccio has not redefined “functional information” from Hazen and Szostak? Is there some reason to discard their definition?

    I don’t think he is hung up on the definition. He is trying to establish a way to measure it using living organisms.

    From listening to your lecture it appears that you have been aware of this issue for 40 years.

    You and gpuccio have been talking over each other at this point and maybe thats the best we can do for the time being. He is frustrated because you appear to be evasive. Tom posting your lecture is a clue why you are walking so carefully through this discussion.

    It appears that although you don’t completely agree with what Demski has concluded about functional information you do see value.

    Do you see value in the work gpuccio is doing?

    Were you the first to attempt a model of energy/information flow through living organisms?

  21. Alan Fox: I suspect Professor Felsenstein will be too busy but maybe Entropy, Corneel, Rumraket, OM or others participating would like to start one.

    ETA On starting to read Gpuccio’s post I see he addresses DNA_Jock, so perhaps DNA_Jock is best qualified, if he has the time.

    Anybody on this yet?

  22. Corneel: Anybody on this yet?

    Gpuccio’s giant post is about Texas sharpshooters and such. I have made no comments about the TSS issue. So it will not be me who posts a new thread on that. I do want to start a new thread on my questions to gpuccio about how gpuccio defines Functional Information. But there is obviously no time for that right now as just the typing alone will be taking up all of gpuccio’s time.

    So I’ll hold off on that until the sharpshooting subsides some. So one of you folks please go ahead.

  23. I am not a fan of this trying to conduct a conversation by “shouting over the fence”, for a number of reasons.
    +It’s inefficient.
    +It’s an invitation to dissembling – decontextualize opponents’ points pastiche their arguments.
    +It is something of a breach of the peanut gallery rule guideline.
    +It fails to capture a record of the conversation – even worse given that the two sites have different clocks.
    So, given those caveats, if gpuccio had generated some new arguments since he and I last discussed this, I would have been torn.
    But he hasn’t, so I am not.
    The ONLY novelty that he has introduced is the ‘green bricks’ scenario, which is merely a re-working of the “there’s something special about parts of the wall , that tells me where to paint” argument, that I recognized and addressed three and a half years ago (post #586).

    He does score some own goals, however:
    He seeks to correct me when I refer to ATP synthase as “ATPase”:

    “ATP synthase (rather than ATPase)”

    LOL
    ATP synthase was originally identified as an ATPase, and named as such. It’s “functional specification” was originally the REVERSE reaction. Whenever I refer to the ATPase, I am poking fun at your TSS error.
    He resurrects Paley’s timepiece. His alternate ways of achieving this function include (to pad the numbers) a digital watch, which is a category error, but he omits the water clock and the candle clock. (Cue “not meant to be exhaustive list” whining) No, that’s the point: your ignorance or lack of attention is leading you to underestimate the number of other possible ways of achieving any function. Thank you for that example.

    Back when gpuccio and I originally discussed this, he was terribly eager for me to concede that post-hoc specifications were not ALWAYS invalid, which I was happy to do, although I did note that you cannot calculate a probability off a post-hoc specification.
    I also pointed out that one can make p(T|H) arbitrarily small by making the post-hoc specification more and more precise. Now there is a counter-argument to this, and I hoped gpuccio would come up with it. Instead he argued that if you make the spec too precise then your exemplar will no longer reside within the spec. I thought that I must be misunderstanding his position, as this is just too stupid for words, but no, he has repeated this objection in his 9,000+ word post. Ack!

    Readers are welcome to re-read the ground gpuccio and I covered in 2014. I would point them to my posts #148, #556, #586, #621, and #720. (in total, that’s 64% less reading than gpuccio’s latest opus…) in particular his live demonstrations of indulging in the TSS over lottery winners and the Alveolata ATP synthase.
    If anyone genuinely believes that gpuccio has raised an issue that was not addressed in that conversation, and they are willing to discuss that here, they are welcome to do so.
    I’m not interested in a playing a game of telephone.

  24. The quintessential fallacy of IDcreationism (and Gpuccio’s arguments) is that when we look back in time, the present always looks contingent on a huge number of historical events, each of which were just one among a huge ensemble of theoretically possible different historical trajectories that never happened.

    And because THIS particular chain of history happened, and because THIS particular history is extremely unlikely out of all the possible unrealized histories, surely it must have been a miracle that this is the one that happened.

    The problem with this line of reasoning is it’s completely ad-hoc. Invariably IDcreationists will try to support their “history turned out special” line of reasoning with some sort of probability calculation, which they then compare to some nonsensical “barrier” to unlikelihoods they erect, and then declare that because history is more unlikely than their barrier allows, magicmustadunit.

    But that’s silly, because all sufficiently long historical developments will look unbelievably unlikely after the fact. To pick an example, take one of the lineages in the Long Term Evolution experiment with E coli. In this lineage, over 600 particular mutations have accumulated in the E coli genome over the last 25 years. What is the likelihood of that particular collection of mutations?

    Suppose we travel back in time 25 years to right before Richard Lenski starts the long-term evolution experiment with E coli. Then we ask: “what is the probability that 25 years in the future a set of these particular 600 mutations will have fixed, in the particular order they did, in this particular lineage out of the 12 running in parallel?”

    We do the calculation (and simplify to just look at substitutions), and find that the very fist mutation has a probability of 1 in 4(the number of substitutions) in 4.5 million(roughly the E coli genome size in basepairs).
    So does the next mutation.
    So does the next mutation

    600 times.

    The compound probability of those 600 mutations happening over the next 25 years in that particular lineage of E coli, is (4.5×10^6 x 4)^-600= 1 in 1.457*10^4353.

    One in one point four five seven times ten to the four-thousand three-hundred and fifty third power. An incomprehensibly unlikely event. Yet those 600 particular mutations happened in that lineage. And roughly a similar number in the other eleven lineages running in parallel. And each outcome was different, and they all had roughly the same incredibly low likelihood before they happened.
    What this should show a rational person is that these kinds of ad-hoc probability calculations are meaningless. They don’t tell us whether something could have happened in the past (or what caused it to happen). Mutations accumulate over time, and they are subject to drift and selection. But any long historical sequence of such accumulations is going to look unfathomably unlikely in the future when we look back at them.

    What were the odds that that particular sequence of mutations would have happened? Incomprehensibly low. But since mutations constantly accumulate, and since they are all subject to drift and selection, many years and generations in the future some sequence of them will be the one that has happened.

    Calculating it’s probability will be meaningless. We can’t falsify history with a probability calculation. Otherwise we would be forced to conclude that the Long term evolution experiment (LTEE) did not take place. Or that everything that happens where there were many other possible outcomes is it’s own little miracles. Roll enough dice and you become a miracle machine. Which is obviously ridiculous.

    The kind of thing IDcreationists are trying to achieve with these calculations is a fool’s errand. It doesn’t actually tell us what caused something to happen, whether it was by design, or whether it was just blind chance mutations filtered by drift and selection.

  25. Quickest way to test the isolated islands theory is to do a Long Term Evolution Experiment and see if mutations result in genetic meltdown, or if change continues indefinitely.

    To bad evilutionists won’t put their religion to the test.

  26. DNA_Jock,

    No, that’s the point: your ignorance or lack of attention is leading you to underestimate the number of other possible ways of achieving any function.

    Can you demonstrate that he made the claim of the number of possible ways of achieving function? If not, how can you make the claim he underestimated it?

  27. DNA_Jock,

    Readers are welcome to re-read the ground gpuccio and I covered in 2014. I would point them to my posts #148, #556, #586, #621, and #720. (in total, that’s 64% less reading than gpuccio’s latest opus…) in particular his live demonstrations of indulging in the TSS over lottery winners and the Alveolata ATP synthase.
    If anyone genuinely believes that gpuccio has raised an issue that was not addressed in that conversation, and they are willing to discuss that here, they are welcome to do so.
    I’m not interested in a playing a game of telephone.

    He is making an inference from the preserved sequence of ATP synthase. Alaveolata may have a different pattern and you can make a separate inference from that pattern.

    The only question is if the data from ATP synthase is adequate to make an inference?

    The inference is not by painting a target but it is by comparing one bullet hole pattern to others which demonstrates preservation of the pattern. If all the bullet holes create an arrangement of the words ” Texas sharp shooter” so much the better:-)

  28. colewd:
    Can you demonstrate that he made the claim of the number of possible ways of achieving function?If not, how can you make the claim he underestimated it?

    By using an existing protein family for his calculations, gpuccio is implicitly assuming that such family and no other could do that work, and that the extant sequences in the family are the only ones that could have done that work. That’s how he underestimates the number of possible ways of achieving a function.

    You should already understand this. Seems like the very main thing we’ve been discussing here. You even go ahead and talk about it in the next comment you made after the one I’m answering.

  29. colewd:
    He is making an inference from the preserved sequence of ATP synthase. Alaveolata may have a different pattern and you can make a separate inference from that pattern.

    He’s drawing a target around the “bullet holes” represented by some members of a protein family. Since alvealoata have a different sequence, then you can proceed to draw another target around that sequence.

    Are you starting to understand the problem yet?

    colewd:
    The only question is if the data from ATP synthase is adequate to make an inference?

    And the answer is no.

    colewd:
    The inference is not by painting a target but it is by comparing one bullet hole pattern to others which demonstrates preservation of the pattern .If all the bullet holes create an arrangement ofthe words ” Texas sharp shooter” so much the better:-)

    The whole protein family (the related sequences) represents a “cluster of holes” around which gpuccio is drawing those targets. You are missing the reason why it’s called a Texas Sharp Shooter Fallacy, yet you’re describing the “inference” almost in precisely the terms that should allow you to understand the problem.

    You’re making DNA_Jock’s point.

  30. Entropy,

    By using an existing protein family for his calculations, gpuccio is implicitly assuming that such family and no other could do that work, and that the extant sequences in the family are the only ones that could have done that work. That’s how he underestimates the number of possible ways of achieving a function.

    No, you are invoking a straw-man here. His claim is not assuming that no other family can do the work. He is simply measuring the genetic information in bits and comparing it to a limit for design of 500 bits. He is using an evolutionary conserved sequence that all living organisms have.

    The whole protein family (the related sequences) represents a “cluster of holes” around which gpuccio is drawing those targets. You are missing the reason why it’s called a Texas Sharp Shooter Fallacy, yet you’re describing the “inference” almost in precisely the terms that should allow you to understand the problem.

    No, to use the bullet hole analogy he is looking at the scatter plot of the bullet holes and looking at other scatter plots and inferring if the same shooter was responsible.

    The protein family represents a conserved sequence across species.

    And the answer is no.

    i think the answer is yes, but thats what makes a market:-)

    Are you starting to understand the problem yet?

    Yes, all the counter arguments to gpuccio are logical fallacies such as creating a straw-man, ad hominem and appeal to authority. I have to assume that he has the correct position as you, Jock and Rumraket are all smart guys.

  31. DNA_Jock: I am not a fan of this trying to conduct a conversation by “shouting over the fence”, for a number of reasons.
    +It’s inefficient.
    +It’s an invitation to dissembling – decontextualize opponents’ points pastiche their arguments.
    +It is something of a breach of the peanut gallery rule guideline.
    +It fails to capture a record of the conversation – even worse given that the two sites have different clocks.

    @Alan
    What do you think? I don’t mind putting up an OP with a link and a blurb to anchor a new discussion thread, but DNA_Jock is right that this may not be the most productive way to have a discussion (it violates the TSZ guidelinerules as well).
    It looks like gpuccio is hesitant to have this discussion in a venue where the pro-ID side is not dominant. Otherwise he would have simply put up a copy of his OP here and interacted with us directly.

  32. I have upset gpuccio, apparently.

    But it is really shameful that he has not even mentioned my argument that his argument about my argument about the alpha and beta chains of ATP synthase is completely wrong.
    As I have said, the alpha and beta chains of ATP synthase are the same in Alveolata as in all other organisms. So he is wrong, I have clearly said why, quoting the same paper that he linked, and he does not even mention the fact.

    Oh boy, this is awkward. I have not mentioned his 2018 argument because, even if it were correct, it makes his 2014 mistake worse. Let me try to explain.
    Back in 2014, gpuccio aligned the sequences for three [!! and not even the right three!!] F1 ATPases () and noted “Together, they present 378 perfectly conserved aminoacid positions from LUCA to humans, which point to a target space of at least 1633 bits” and “Now, 378 identities after about 4 billion years during which all possible neutral mutations had time to happen mean just one thing: those 378 AAs must be there, and they must be what they are for the molecule to work.”
    A poster “REC” responded, noting the divergence of apicomplexa.
    Gpuccio immediately re-defines his function, writing:

    My argument about those two sequences is about their conservation in a complex molecule. You can scarcely deny that those specific sequences are necessary, with that high level of conservation, to the working of ATP synthase in its common form, and especially the form which utilizes H+ gradients.
    The Apicomplexa paper you link describes a very different complex molecule, made of many different protein sequences, and is a complex example of a different engineering solution. In no way it is in contradiction with the functional specification of the sequences I examined in the traditional ATP synthase complex.

    I join the conversation, pointing out the irony of what gpuccio just did:

    Another beautiful example of the Texas Sharp-Shooter. You were quite satisfied with your specification of the “ATP synthase”, a nice tight cluster of bullet holes in the wall. Then REC points out a separate cluster of bullet holes, the Alveolata ATP synthase. Immediately you re-define your “ATP synthase” as “ATP synthase in its common form” or “the traditional ATP synthase”, and get out some fresh paint for the recently observed bullet holes, which represent “a very different complex molecule, made of many different protein sequences, and is a complex example of a different engineering solution.”
    [emphasis in original]

    Now, in 2018, gpuccio wants to claim that the F1 subunits do not differ. [He claims this because his pairwise comparison between Tetrahymena and humans yielded 285 identities for F1-alpha and 357 identities for F1-beta.]
    Gpuccio, if this were correct, then this makes your behavior in 2014 WORSE. You didn’t even bother to check where the new cluster of bullet holes were, you immediately reached for the can of fresh paint.
    [But don’t worry, you are probably wrong about that – as REC explained to you in 2014, if you do your alignments properly, there are ZERO conserved residues, and 12 residues that are 98% conserved (this latter statistic may have changed somewhat since then).]
    It is interesting that gpuccio does not realize that his 2018 counter-argument is no help at all. I think that the reason that he cannot understand this is because he thinks we are having a discussion about the wall, and the parts of the wall that are objectively super-special and objectively require paint. We are not. We are having a discussion about the tendency of humans to apply paint in a TSS manner, because they believe that this is the only way it could be.
    “those 378 AAs must be there, and they must be what they are for the molecule to work”
    Indeed.

    Journal club: Muelheip et al 2017 raise an issue for people who like to over-conclude from primary structure conservation:

  33. colewd: He is using an evolutionary conserved sequence that all living organisms have.

    To clarify a technical detail here, the ubiquitin system is not universally conserved. The only universally conserved genes are the central components of the translation system. That is the RNA cores and some of the surface proteins of the large and small ribosomal subunits, the tRNA molecules, the aminoacyl-tRNA enzymes, and a small handful of translation initiators.

    For literally everything else you can think of, for all other genes, some organism somewhere is known to lack them.

  34. His justification for painting the target around something is hilarious: “the propert I am using to recognize the function post-hoc an objective property of the system”

    The property is, the target is the problem, obviously!

    So mind bogglingly stupid

  35. colewd:
    No, you are invoking a straw-man here.His claim is not assuming that no other family can do the work.He is simply measuring the genetic information in bits and comparing it to a limit for design of 500 bits.He is using an evolutionary conserved sequence that all living organisms have.

    There’s a difference between a misunderstanding and a straw-man. So, even if I had misunderstood, I didn’t deform what gpuccio has presented just to make it an easy win. So, not a straw-man. (Are we in ugly terms now?)

    Here you seem to have mixed different problems. One is the “calculation” of “bits,” the other is the assumption that the known variants of a protein family are the only variants that would work, related to this one, the assumption that the sequence-space-explorations represented by such variants are exhaustive at all points of divergence (which would mean that putting together 500 bits is nothing for the evolutionary processes, quite a contradiction that you seem to forget over and over and over), and the other one that only that family would perform the function. In his new OP gpuccio seems to be defending all of them. I’ll see if I have the patience to dig it up later.

    colewd:
    No, to use the bullet hole analogy he is looking at the scatter plot of the bullet holes and looking at other scatter plots and inferring if the same shooter was responsible.

    So he’s assuming that the shooter must be the answer, and drawing the targets around those bullet holes in the name of the shooter. Same problem.

    colewd:
    The protein family represents a conserved sequence across species.

    A somewhat conserved sequence across species, which doesn’t represent the amount of sequence exploration around that particular solution, nor does it represent the only solutions within or without the protein family.

    colewd:
    Yes, all the counter arguments to gpuccio are logical fallacies such as creating a straw-man, ad hominem and appeal to authority.I have to assume that he has the correct position as you, Jock and Rumraket are all smart guys.

    What was that about looking at the beam in thy own eye? What about you checked gpuccio’s strategies? Arguing by dictionary while missing the point, pretending not to know what the word “arbitrary” means, after using the word a million times for his argument (he didn’t like the implication against his argument, so he wants a demonstration that the word he uses means what it means, go figure), assuming that he’s right from the very beginning (using circular logic), but then getting angry if I mention that life forms do all this stuff by themselves with no designer interventions anywhere to be seen, asking for a minimal reason why we could believe that there’s “ladders” of function available for evolution, only to then reject the reasons by pretending first not to understand them, then claiming that affinities have nothing to do with protein functions (holy crap!!!), long etc.

    Check also how, when convenient, he changes position. For example, in the OP about ubiquitin, he talks about copies of ubiquitin adding to the complexity of the system, but if I mention copies, then copies don’t add any information. Isn’t that interesting? He can use whatever he wants to claim “design,” but we better keep away from any of it.

    Check the guy as if he was arguing against your position. Then tell me with an honest face that we’re the ones with the fallacies.

  36. Entropy,

    There’s a difference between a misunderstanding and a straw-man. So, even if I had misunderstood, I didn’t deform what gpuccio has presented just to make it an easy win. So, not a straw-man. (Are we in ugly terms now?)

    I did not claim you intended to do this but misrepresenting your opponents claim is a straw-man aside from intent.

    that putting together 500 bits is nothing for the evolutionary processes, quite a contradiction that you seem to forget over and over and over),

    I think the evidence goes against this claim. I have not forgotten the claim.

    A somewhat conserved sequence across species, which doesn’t represent the amount of sequence exploration around that particular solution, nor does it represent the only solutions within or without the protein family.

    I agree that it does not represent the only solution however the evidence of preserved sequences is strong indication of genetic information. Finding this information through a evolutionary search is highly unlikely.

    gpuccio’s discussion of the Hayashi paper.

    bill cole at #38 and 42:

    The Hayashi paper is about function retrieving. So, it is not about a completely new function.

    They changed one domain of the g3p protein of the phage, a 424 AAs long protein necessary for infectivity, with a random sequence of 139 AAs.

    The protein remained barely functional, and that’s what allows them to test RV and NS: the function is still there, even if greatly reduced. The phage can still survive and infect.

    An important point is that fitness is measure here as the natural logarithm of infectivity, therefore those are exponential values.

    If you look at Fig. 2, you can see that the initial infectivity is about:

    e^5 = 148

    Their best result is about:

    e^14.8 = 2,676,445

    That’s why they say that they had an increase in infectivity of about 17000 folds.

    (the numbers are not precise, I am deriving them from the Figure).

    However, the wildtype has an infectivity of about:

    e^22.4 = 5,348,061,523

    which is about 2000 times greater (from 2.6 millions to 5.3 billions).

    So, they are still far away from the function of the wildtype, and they have already reached stagnation.

    Moreover, if you look at the sequences at the bottom of the same Figure, you can see that the best result obtained has no homology to the sequence of the wildtype. As the authors say:

    “More than one such mountain exists in the fitness landscape of the function for the D2 domain in phage infectivity. The sequence selected finally at the 20th generation has ?=?0.52 but showed no homology to the wild-type D2 domain, which was located around the fitness of the global peak. The two sequences would show significant homology around 52% if they were located on the same mountain. Therefore, they seem to have climbed up different mountains.”

    Entropy

    Check the guy as if he was arguing against your position. Then tell me with an honest face that we’re the ones with the fallacies.

    So far TSZ is committing the bulk of the fallacies and that is an indicator of argument quality. Were all human and the tide can turn.

  37. Rumraket,

    To clarify a technical detail here, the ubiquitin system is not universally conserved.

    The TSS argument is based on ATP synthase.

  38. The alpha and beta subunits from F-type ATP synthases that gpuccio is obsessing about belong to a big family of haxameric helicases.

    They are WILDLY divergent in sequence over the diversity of life, and many of them are involved in other processes and functions that have nothing to do with ATP synthase/ATPase. Besides the structural similarities, they all seem to be involved in many different forms of DNA or RNA nucleotide/ribonucleotide processing (such as unwinding of double stranded DNA or RNA), of which NTP hydrolysis or synthesis as observed in ATP synthase, is just one among these many different functions.

    So not only are they divergent in sequence in ATP synthase machines, versions of the structure is part of many other functions besides ATP hydrolysis and synthesis. Which evolved from which, or do they all derive from a common ancestral function different from any present one? We don’t know. But we know that both the sequence and functional space of hexameric helicases goes well beyond the ATP synthase machinery.

    Their capacity to function as an RNA helicase could be hinting at an RNA world role.

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