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 Replies to “Ubiquitin: a challenge for evolutionary theory?”

  1. dazz dazz
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    says:

    gpuccio, you insist on affirming I have nothing, and I may not have much, but I think the challenge I presented you deserves some attention:

    You calculate your information based on conservation and functional constraints of certain protein sequences, right? so if you think you’ve found a protein that, being highly conserved in vertebrates grants the conclusion that such a sequence is functionally specified for vertebrates and there’s no gradual path to such protein from pre-vertebrates (what you call an informational jump), that means that there can’t be a gradual pathway from pre-vertebrates to vertebrates.

    I know you laughably claim you’re not interested in explaining life, just “functional information”) but if you were intellectually honest you would at least consider telling us how do you envision this weird scenario where hosts of pre-vertebrates are giving birth to vertebrates, and how can you possibly defend the existence of “barriers” to small gradual change while accepting stupidly large changes as perfectly feasible

  2. Erik
    Ignored
    says:

    Corneel:
    gpuccio@UD

    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?

    What are you saying here? That Darwin’s theory (of evolution by natural selection) can do just fine without common descent? That common descent has no essential role in it?

    But natural selection is the irreducible core of Darwin’s theory, right?

  3. Corneel Corneel
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    says:

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

    Yes, I got that. But how did you calculate the 10^50 evolutionary trials? And the 100k bit jumps?

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

    Which yeast? I strongly doubt this is the case by the way, because there are quite some eukaryotes with smaller genomes. So how do you know?

  4. John Harshman John Harshman
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    says:

    Erik: What are you saying here? That Darwin’s theory (of evolution by natural selection) can do just fine without common descent? That common descent has no essential role in it?

    But natural selection is the irreducible core of Darwin’s theory, right?

    Yes, yes, and no. Darwin had two main theories: common descent, to explain the pattern of variation among species, and natural selection, to explain the origin of adaptive features. Common descent happens with or without natural selection, and natural selection happens even if common descent is only a short-term phenomenon within species. They both explain different sorts of data.

  5. Erik
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    says:

    John Harshman: They both explain different sorts of data.

    They explain different parts of the same framework. Darwin deduced common descent because of natural selection, did he not?

    I don’t see how you can easily part with either one of them. They are both integral to evolution as conceived by Darwin.

  6. Corneel Corneel
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    says:

    Erik: What are you saying here? That Darwin’s theory (of evolution by natural selection) can do just fine without common descent? That common descent has no essential role in it?

    Correct. Natural selection is an explanation of how adaptations arise.

    Erik: But natural selection is the irreducible core of Darwin’s theory, right?

    Darwin presented both the idea of descent with modification and of natural selection in his Origin. Not sure which one you would consider the core, but natural selection is certainly the idea that is most relevant to our discussions on ID, as it negates the need for the Designer.

  7. Corneel Corneel
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    says:

    ninja’d

  8. Corneel Corneel
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    says:

    gpuccion@UD

    That’s correct. But my point was simply that in that case (that neither you nor I believe to be true) the neo-darwinian process could certainly happen, but it would not be the explanation of the functional information that makes species different.

    How could the neo-darwinian process happen without becoming responsible for part of the variation in functional information among species?

  9. dazz dazz
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    says:

    Erik: I don’t see how you can easily part with either one of them. They are both integral to evolution as conceived by Darwin.

    You could easily part with one of them if the evidence showed it’s wrong.
    It’s science, not Bible studies where one assumes absolute inerrancy

  10. Entropy Entropy
    Ignored
    says:

    Corneel:
    Not sure which one you would consider the core, but natural selection is certainly the idea that is most relevant to our discussions on ID, as it negates the need for the Designer.

    Hum. Sorry, but no. “The Designer” would not make it into the scene even if we didn’t know anything about natural selection. Magical beings in the sky belong to the fantasy section, not to the scientific one.

    The correct position when confronted with something we cannot explain is “I don’t know.” Not “God-did-it.”

    I understand you might agree with me, but care should be taken not to appear to buy into creationist’s poor mentality.

  11. Corneel Corneel
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    says:

    Entropy: Hum. Sorry, but no. “The Designer” would not make it into the scene even if we didn’t know anything about natural selection. Magical beings in the sky belong to the fantasy section, not to the scientific one.

    Well, let’s not forget that the Designer did make it onto the scene in early nineteenth century England, where Natural Theology was a respectable scientific tradition (if you will call it that). Times have been a-changing.

  12. Entropy Entropy
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    says:

    colewd to DNA_Jock,
    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.

    Therefore it is not possible to know how many variants would work just as well, and we cannot know how many other protein families could have done the work. Please think about it.

    colewd to DNA_Jock,
    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?

    If not all of the sequence space has been explored, nobody can know if this is an optimized “condition,” or a suboptimal “condition” (even if it might be a local “peak”). Even more, if exploration has be minimal, the best explanation here is that there’s plenty of potential ways in which things would have worked.

    That’s my answer to your comment. Now, don’t you find it interesting that gpuccio says that very little sequence space can be explored, yet, to justify his BLAST-bit-score “inferences” of “functional information,” he assumes that quite-a-bit-if-not-the-whole sequence space has been explored?

    If you don’t understand think about this: How many random mutations would be needed to only leave the “functionally-important” bits of information in the compared protein sequences? Given that, how much sequence space would have been explored?

    Think about it.

  13. Entropy Entropy
    Ignored
    says:

    Corneel: Times have been a-changing.

    Indeed. Hopefully we’ve learned from our mistakes.

  14. Entropy Entropy
    Ignored
    says:

    Erik: They explain different parts of the same framework. Darwin deduced common descent because of natural selection, did he not?

    I really don’t know in which order this happened in Darwin’s mind, but I think that what he did was to put two and two together.

  15. keiths keiths
    Ignored
    says:

    Erik,

    They explain different parts of the same framework. Darwin deduced common descent because of natural selection, did he not?

    No. In fact, common descent had been proposed by Darwin’s paternal grandfather Erasmus long before Charles came up with the idea of natural selection.

  16. dazz dazz
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    says:

    gpuccio @ UD: The detection of a jump just means that there is a huge and rather quick increase in specific functional information. In the particular case of the transition to vertebrates, it happens in the relative time window of about 30 million years. For TRIM62, for example, that jump is of 681 bits.

    This is all we can say from the analysis of the homologies.

    OK, so this transition could have happened gradually you say. Now all those gradual changes obviously happened in functional DNA. That means that each of those small changes could have been naturally selected, because they would produce differential fitness. Don’t you think?

    The consideration that such a jump is well beyond the powers of a neo-darwinian modle derives from many other arguments.

    1) No generation of more than 500 bits has ever been observed to arise in a non design system (as you know, this is the fundamental idea in ID).

    I’m sorry, but I’m not interested in your FI red herring nor any negative arguments. Please don’t pretend we haven’t addressed your math, so let’s stick to what actually might have happened OK?

    Is there evidence that the transition from pre-vertebrates to vertebrates happened? Yes, I’m sure you will agree. If it happened gradually, then only sequences very close to each other were produced at each step, making every step trivially attainable and naturally selectable. Your barriers are only in your imagination.

    All of that in 30 million years, through a ladder that obviously does not exist

    Wait a minute, if the ladder doesn’t exist, then we’re back to saltationism: if the ladder is not there, it’s not there for NS NOR the designer! besides, you keep telling us irreducible complexity is another marker of “design” (nobody knows why, except for your proclamations based on negative arguments), so I must insist:

    Saltation yay or nay?

    You’re between a rock and a hard place buddy:

    The barriers are not to the change, but to the mechanism.

    There’s absolutely no reason to believe there’s a “barrier” to RV+NS if it’s possible to traverse the transition one step at a time (just as regularly observed), and if it’s impossible, then you have to come to terms with the fact that you’re a special creationist in the weird form of hilarious saltationism

    Design can easily generate a lot more.

    I’ve never seen a single act of design producing a single DNA change. Since your FI calculations are based on DNA sequence, I can confidently affirm that I’m on firmer grounds when I say you have absolutely nothing to show for your work. No theory, no evidence, no nothing.

  17. Erik
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    says:

    Corneel: Darwin presented both the idea of descent with modification and of natural selection in his Origin. Not sure which one you would consider the core, but natural selection is certainly the idea that is most relevant to our discussions on ID, as it negates the need for the Designer.

    In every theory there must be an irreducible core. I’m asking about yours from you. An atheist who says his atheism doesn’t depend on whether God exists is an interesting phenomenon.

    Similarly an evolutionist who gives up the idea that related species evolved from a common ancestor. If there’s no common ancestor, then what is it that evolved so that there should be a theory of evolution?

  18. Corneel Corneel
    Ignored
    says:

    Erik: In every theory there must be an irreducible core. I’m asking about yours from you. An atheist who says his atheism doesn’t depend on whether God exists is an interesting phenomenon.

    Evolutionary theory is neither a religion nor a single concept. It is a framework in which several explanations are fit together to explain various aspects of biodiversity. Common descent explains the hierarchical distribution of derived characters among species. Natural selection explains how adaptations arise. The two explanations interface because natural selection explains some of the modification in “descent with modification” but neither explanation relies on the other being true.

    Erik: Similarly an evolutionist who gives up the idea that related species evolved from a common ancestor. If there’s no common ancestor, then what is it that evolved so that there should be a theory of evolution?

    I am not giving up anything. As far as I am concerned, common ancestry of all organisms on earth is a proven fact. But some creationists / IDers (including gpuccio) seem to be under the impression that, if common descent were proven to be false, the whole edifice of evolutionary biology would come tumbling down. Not so.

  19. Erik
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    says:

    Corneel: But some creationists / IDers (including gpuccio) seem to be under the impression that, if common descent were proven to be false, the whole edifice of evolutionary biology would come tumbling down. Not so.

    The question is: If common descent were proven to be false, then what is still left of evolutionary biology? Given no common descent, what is it that evolves/evolved? What is “evolutionary” about that leftover biology? Yes, you would still have biology, but how can you call it “evolutionary biology”?

    When you remove “There is no God”, do you still have atheism?`When you remove “There is God”, do you still have theism? No, you don’t.

  20. Corneel Corneel
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    says:

    gpuccion@UD

    So, the range of homology for any protein with the human form (that, as explained many times, I use as a probe here) is from 0 to about 2.2. OK?

    Come again? The variable you plot in your graphs is bound between zero and 2.2? Then of course there is not going to be a linear relationship between time since divergence and your measure of conserved functional information. The data in you plot suffer from scaling effects, and you will always observe an information jump around intermediate values!

    I am not sure what you mean by “an exponential phase”.

    Since your data are bound by an upper and lower limit, the fitted curve will assume a sigmoid shape, just like dose-response curves do. Sigmoid curves have three phases: an initial exponential phase, a transitional phase and a plateau phase. The exponential phase is the part where you believe your Designer has been busy, but you will always observe an exponential phase in any curve that uses the entire range, regardless of whether there really were injections of information. What you need to show is that the steepness of the curves is larger then what would be excepted under constant substitution rate.

    See what I mean?

  21. dazz dazz
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    says:

    Bill Cole @UD. He is making the assumption that all functional mutations are selectable. Amazing

    What I’m saying is that mutations that happened, can happen. It’s not rocket science! So was the transition to vertebrates gradual or not?

    Did the fitness landscape allow for that gradual evolution or are those protein functions far and apart (islands of function) in the landscape?

    You guys like simple and obvious arguments, so there’s one for you right there:

    1) if the landscape is smooth: no barrier to RV+NS and your house of cards crumbles down.

    2) If islands of function then saltationism, irrespective of mechanism

    Take your pick!

    Then maybe, for extra lulz, we can discuss the transition to chimps / humans where there are no “jumps” whatsoever

  22. Corneel Corneel
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    says:

    Erik: The question is: If common descent were proven to be false, then what is still left of evolutionary biology? Given no common descent, what evolves/evolved? What is “evolutionary” about that leftover biology? Yes, you would still have biology, but how can you call it “evolutionary biology”?

    What is your definition of evolution?
    Here is one that is often used: “population changes in allele frequency with time”. As I see it, as long as there are populations in which heritable changes are occurring, you will have use for evolutionary biology.

    Erik: When you remove “There is no God”, do you still have atheism?`When you remove “There is God”, do you still have theism? No, you don’t.

    Common descent is not the god of evolutionary biologists. It is an explanation for certain patterns we observe in the distribution of traits among species. Will you please stop comparing evolutionary biology with atheism or religious denominations? I suspect that is the reason for your confusion.

  23. Corneel Corneel
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    says:

    dazz: Then maybe, for extra lulz, we can discuss the transition to chimps / humans where there are no “jumps” whatsoever

    Heh heh, I noticed that too. gpuccio’s plot only run to 100 MYA. I suspect no “information jumps” could be found after that time. Perhaps if we ask nicely, gpuccio would be kind enough to include Pan troglodytes in his graphs and we could discuss the implications of those findings with his fellow IDers?

  24. dazz dazz
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    says:

    Corneel: Heh heh, I noticed that too. gpuccio’s plot only run to 100 MYA. I suspect no “information jumps” could be found after that time. Perhaps if we ask nicely, gpuccio would be kind enough to include Pan troglodytes in his graphs and we could discuss the implications of those findings with his fellow IDers?

    He has some hilarious ad-hoc stuff for those “special” transitions. I’ve quoted one here that I should have preceded with a warning that it may make you facepalm yourself unconscious and produce potentially irreversible brain damage

  25. Corneel Corneel
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    says:

    gpuccion@UD

    But, as shown in my OP, the most amazing amount of specific functional information is to be found in the 600+ E3 ligases: each of them is highly specific for one or for a group of targets.

    I definitely make a case for them starting with TRIM62 as an example.

    I am not familiar with this gene and have only some superficial knowledge of the ubiquitin system, so you will need to help me out here:

    From online databases I have gathered that TRIM62 (tripartite motif containing 62) also known as DEAR1 is a member of the family of E3 ubiquitin-protein ligases. It is a known tumor suppressor gene and a regulator of cell polarity.

    So what are the complex protein functions that you need to be deconstructed? Is it the the ubiquitin-protein transferase activity? Or perhaps you meant the substrate specificity (SMAD3 seems to be an inmportant substrate). If the latter, how is the substrate specificity conceptionally going to be any different from that of Entropy´s example?

    And look, I have already deconstructed the function of TRIM62 into two simpler steps. We are of to a good start 🙂

  26. Erik
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    says:

    Corneel: What is your definition of evolution?

    This is not about me at all. It’s entirely about you.

    Corneel:
    Here is one that is often used: “population changes in allele frequency with time”.

    “Often used” that turns up 0 (zero) results in Google? Why not something that is used more often than this?

    Corneel: Will you please stop comparing evolutionary biology with atheism or religious denominations? I suspect that is the reason for your confusion.

    I’m placing the components of theories in front of you just to show that when you remove the components you have no theory left.

    Common descent is the evolutionary component of evolutionary biology. Without it you will have simply biology.

    https://en.wikipedia.org/wiki/Evolutionary_biology “Evolutionary biology is the subfield of biology that studies the evolutionary processes that produced the diversity of life on Earth, starting from a single common ancestor.”

    Maybe this is a bit too basic for you. You have evolved far above and away from this.

  27. petrushka
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    says:

    gpuccio via dazz: 1) No generation of more than 500 bits has ever been observed to arise in a non design system (as you know, this is the fundamental idea in ID).

    Gpuccio persists in the comical assumption that change adding information.

    But the inescapable fact is that in the absence of environmental change, all populations are fit. It exists; it lives; therefore, it is fit. If the population changes due to accumulation of genetic mutations, it is still fit. There is no rational basis to assert that the change is due to added information. It is simply change.

    Darwinian selection simply means that some changes are fixed in populations more quickly than others. Darwin assumed that some changes confer a reproductive advantage, and this is probably true, but this phenomenon is not a necessary part of evolution.

  28. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    The assertion that “No generation of more than 500 bits has ever been observed to arise in a non design system (as you know, this is the fundamental idea in ID)” ignores that natural selection can put any number of bits of functional information into the genome.

    So the argument only has force when there is not (yet) any natural selection. Very simple models of population genetics can show large numbers of bits of functional information ending up in the genome. See for example this post here at TSZ. Or my article refuting Dembski (here). And I’m scarcely the only person to have made that point.

  29. dazz dazz
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    says:

    Joe Felsenstein:
    The assertion that “No generation of more than 500 bits has ever been observed to arise in a non design system (as you know, this is the fundamental idea in ID)” ignores that natural selection can put any number of bits of functional information into the genome.

    So the argument only has force when there is not (yet) any natural selection.Very simple models of population genetics can show large numbers of bits of functional information ending up in the genome.See for example this post here at TSZ.Or my article refuting Dembski (here).And I’m scarcely the only person to have made that point.

    Is there any merit to CSI that makes it worth it to show that NS can add it to the genome? Am I missing something Joe?

  30. Corneel Corneel
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    says:

    Erik: This is not about me at all. It’s entirely about you.

    Wrong. It is about your misunderstanding of the significance of common descent for evolutionary theory. That is why I need to know what you mean by “evolutionary”.

    Erik: “Often used” that turns up 0 (zero) results in Google? Why not something that is used more often than this?

    Boy, you suck at googling 🙂 A few seconds gave me this:

    Microevolution is the change in allele frequencies that occurs over time within a population

    and this

    Since evolution is a change in allele frequencies in a population over generations, a population in Hardy-Weinberg equilibrium is, by definition, not evolving.

    True, I did not literally quote a web source but I assumed you could handle a little paraphrasing.

    Erik: Common descent is the evolutionary component of evolutionary biology. Without it you will have simply biology.

    https://en.wikipedia.org/wiki/Evolutionary_biology “Evolutionary biology is the subfield of biology that studies the evolutionary processes that produced the diversity of life on Earth, starting from a single common ancestor.”

    Oooh, an argumentum ad wikipedium. What can I say? Did you actually read beyond the first sentence of that lemma? I don’t think so. Here comes the second sentence:

    These processes include natural selection, common descent, and speciation.

    Hey, see? It does not just involve common descent but also natural selection and speciation. You might want to read all the other sentences as well.

    Erik: Maybe this is a bit too basic for you. You have evolved far above and away from this.

    Hell no. I love going over the basics … again … and again… and again. So are you going to tell me what you believe is the focus of study of evolutionary biology?

  31. DNA_Jock
    Ignored
    says:


    colewd
    wrote

    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.

    In addition to Entropy’s excellent points [in particular the point that “it is not possible to know how many variants would work just as well, and we cannot know how many other protein families could have done the work.” which is unassailable, and deep-sixes any attempt to calculate p(T|H) ] I would add:
    You are confusing three relevant, but different, “explorations”.
    Consider, as an example, Highly Specified Protein #1 (HSP1) say, the traditional ATPase that earned John Walker his Nobel.
    Exploration one: the exploration that originally led to the production and initial optimization of HSP1. This occurred sometime before LUCA, and is therefore not accessible to traditional phylogenetic methods.
    Exploration two: the exploration, around the local optimum, that has occurred since LUCA. This exploration is restricted to a tiny fraction of sequence space.
    Exploration three: what scientists do. They discover and analyze genes and gene products. This exploration is biased. The massive source of bias is that 99.9% of the research is done on EXTANT genes and gene products. (There are two other biases of note: the tendency to first analyze the version that is most readily accessible, and then after that, to only publish on exceptions to the rule. )
    I have yet to come across a creationist who is able to understand the massive effect that the “we only get to analyze that which survived” bias has on our thinking.
    The debate is around exploration one, the origin of function.
    Sadly, exploration two is what Durston, and gpuccio (and kf, bless his log p(T|H)-innumerate cotton socks) are looking at when they point out how little sequence variation there is in HSP1, and how vanishingly unlikely it is that a random search over an equiprobable landscape would have arrived HERE. This is utterly irrelevant. They make a second error (as Entropy noted) when they fail to consider non-traditional ATPases (Nina et al).
    To understand exploration one, we have to rely on in vitro evolution experiments such as Hayashi et al 2006 and Keefe & Szostak, 2001. The former also demonstrates that explorations one and two are quite different. Gpuccio is aware of this: in fact it was he who provided me with the link to Hayashi – see here.
    You may have heard of hill-climbing algorithms. Personally, I prefer my landscapes inverted, for the simple reason that, absent a barrier, a population will inexorably roll downhill to greater fitness. So when you ask:

    How did it get into this optimized condition which shows a highly specified AA sequence?

    I reply
    It fell there. And now it is stuck in a crevice that tells you nothing about the surface whence it came. Your design inference is unsupported.

  32. Neil Rickert
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    says:

    Erik: If common descent were proven to be false, then what is still left of evolutionary biology? Given no common descent, what is it that evolves/evolved?

    Suppose that life originated 1000 times. And suppose that there has been massive horizontal gene transfer. It could be that all life is descended from that group of 1000 original forms, but that there is no single common ancestor. How would that be a problem for evolutionary biology?

    When you remove “There is no God”, do you still have atheism?

    Yes, of course you still have atheism. For most atheists, their atheism is just the lack of any belief that there is a god. Their atheism does not require a belief that there isn’t any god. Atheism need not be anti-theism.

  33. dazz dazz
    Ignored
    says:

    gpuccio @ UD, “A lot of evidence, however, is for some saltation, definitely (see Gould and Eldredge”

    Punctuation is NOT saltation, please get your facts straight.

    OK, one thing at a time, if you tell us that possibly there’s a gradual pathway for evolution (by design), then you have a few statements you need to retract ASAP:

    1) Island of function in protein sequence space
    2) Microevolution can’t accumulate small steps to produce macroevolution

    Oh, you tell me that some “engineering” might have happened in non functional DNA to one day get activated. Okay, we observe that, your abscibing it to “design” is super cute and all, but smart move anyway!

    I wont demand the kind of ridiculous evidence for that design mechanism that you demand for Darwinism, heck, I won’t demand ANY supporting evidence at all

    I’ll just ask, how do you get from pre-vertebrates to vertebrates through that mechanism gradually? You claim there are thousands of proteins involved in the design of vertebrates. Were all those sequences engineered in non functional DNA and activated all at once? Or can you have intermediates with a mix of pre-vertebrate and vertebrate proteins? maybe we should start looking for crocoducks

  34. Erik
    Ignored
    says:

    Neil Rickert: Suppose that life originated 1000 times.And suppose that there has been massive horizontal gene transfer.It could be that all life is descended from that group of 1000 original forms, but that there is no single common ancestor.How would that be a problem for evolutionary biology?

    Positing a thousand common descents does not reduce common descent. It adds more common descents.

    Neil Rickert:
    Yes, of course you still have atheism.For most atheists, their atheism is just the lack of any belief that there is a god.Their atheism does not require a belief that there isn’t any god.Atheism need not be anti-theism.

    So new-borns who have not heard anything about the debate are by default atheists? How about squirrels and nuts? They lack the belief too…

  35. dazz dazz
    Ignored
    says:

    At any rate, gpuccio, you at least conceded that saltationism might be an entailment of your (negative) claims. So props to you for that. Only you and Torley have had the balls to admit it so far. I don’t think it’s just a possibility, it’s simply inevitable: if your claims were right, you would need prevertebrates givng birth to vertebrates. Now I could try to explain how I find there’s a massive barrier to that kind of transitions, but I hope you can figure it out yourself

  36. colewd
    Ignored
    says:

    DNA_Jock,

    You are confusing three relevant, but different, “explorations”.
    Consider, as an example, Highly Specified Protein #1 (HSP1) say, the traditional ATPase that earned John Walker his Nobel.
    Exploration one: the exploration that originally led to the production and initial optimization of HSP1. This occurred sometime before LUCA, and is therefore not accessible to traditional phylogenetic methods.
    Exploration two: the exploration, around the local optimum, that has occurred since LUCA. This exploration is restricted to a tiny fraction of sequence space.
    Exploration three: what scientists do. They discover and analyze genes and gene products. This exploration is biased.

    I understand we are looking at extant proteins but we have the evidence we have. What is the evidence telling us in the case of the three proteins we are talking about?

    There is no evidence of another peak relative to the proteins that make up the complexes. With multi protein complexes the proteins become specifically defined based on the other proteins in the complex. I know you understand this. In the ubiquitin complex case, the E3 protein must bind to E2, ubiquitin and the target protein for destruction or other targets.

    We have no evidence that any exploration has occurred only speculation. We have no evidence of another peak only speculation.

    We have evidence that in its current configuration that exploration is extremely limited.

    This is strong support for the design inference.

  37. colewd
    Ignored
    says:

    dazz,

    Now I could try to explain how I find there’s a massive barrier to that kind of transitions, but I hope you can figure it out yourself

    Is this an argument from personal incredulity? If not, why not?

  38. dazz dazz
    Ignored
    says:

    I missed this:

    gpuccio: “Ah, yes, and you have:

    “If it happened gradually, then only sequences very close to each other were produced at each step, making every step trivially attainable and naturally selectable. ”

    IOWs:

    “If my theory is true, then my theory is true”.”

    What’s your problem with that? if every step in the way was a microevolutionary one, why would you question the adequacy of darwinism as a mechanism?

  39. dazz dazz
    Ignored
    says:

    colewd:
    dazz,

    Is this an argument from personal incredulity?If not, why not?

    Well, I happen to find it hard to believe that an invertebrate could give birth to a vertebrate somehow. Call me hyper-skeptical if you wish, but you must admit it must have been a brick shitting sight.

    Now if you want to convince someone that small changes always reach a point were they can’t accumulate, it’s sort of silly to suggest that many many more small changes happening in one fell swoop would not be problematic at all

  40. GlenDavidson
    Ignored
    says:

    colewd: We have evidence that in its current configuration that exploration is extremely limited.

    This is strong support for the design inference.

    Non sequitur.

    Glen Davidson

  41. colewd
    Ignored
    says:

    dazz,

    Well, I happen to find it hard to believe that an invertebrate could give birth to a vertebrate somehow. Call me hyper-skeptical if you wish, but you must admit it must have been a brick shitting sight.

    You make an interesting argument here and thats why I posted it on UD. We see a massive saltation in genetic information yet how that information got transferred and eventually executed is indeed a mystery.

    On the other hand just because we cannot imagine the saltation event (personal incredulity) does not mean we should turn a blind eye to the genetic evidence.

  42. dazz dazz
    Ignored
    says:

    colewd: On the other hand just because we cannot imagine the saltation event (personal incredulity) does not mean we should turn a blind eye to the genetic evidence.

    No, Bill, no. There’s no genetic evidence for such a ridiculous scenario.

    Riddle me this. why can the designer add tons of mutations to engineer a new protein but can’t do it one at a time on a functional one?

  43. DNA_Jock
    Ignored
    says:

    Nope, colewd,

    Even if all of the claims you make here were supported, the situation still would not differ from what we might expect under an evolutionary scenario. Your claimed absence of evidence is not evidence of absence. And for ATPase, the topic of my conversation with gpuccio, we KNOW that there are other peaks.

    But I am curious – is it really true that there is zero polymorphism in all of the genes in the ubiquitin system? Is it really true that all individual members of the system are present in all species?
    Cuz this is what you are claiming.
    You also have a delightful “lock-and-key” view of protein-protein interactions.

  44. dazz dazz
    Ignored
    says:

    gpuccio: The landscape is certainly not smooth. It is certainly rugged.

    And functions are obviously in islands, as all evidence shows.

    The discussion is at most on how big the islands are.

    Theresore, slatationism in information is the only truth.

    But, as I have tried to explain to you, saltation of information can well be achieved by gradual engineering.

    Or it can be achieved by quick engineering, and therefore with a steep saltation in time.

    See comment #776.

    I can’t see why you see saltation as a problem for ID. It is definitely a problem for your theory, but not for ID.

    You’re missing the point. I’m not talking about saltationism in information, or at the molecular level. I’m saying that your assertions imply wild saltations at the phenotypic/morphological level, and those are HUGE problems for your “theory”.

    Can you address this please:

    dazz: I’ll just ask, how do you get from pre-vertebrates to vertebrates through that mechanism gradually? You claim there are thousands of proteins involved in the design of vertebrates. Were all those sequences engineered in non functional DNA and activated all at once? Or can you have intermediates with a mix of pre-vertebrate and vertebrate proteins?

    You tried to dodge the islands of function problem by proposing that the engineering could happen in non-coding DNA (because gradual engineering of functional proteins destroys islands of function), but you’re still left with the problem of the effect of activating a protein that has undergone massive changes. One would presume, since you also make a huge deal about protein complexes and IC, that activating a single protein at a time won’t do the job (what good is half a protein complex? don’t all the proteins need to be in place to have a functional IC system?).

    In conclusion, upon activation of the newly engineered sequence, you would get an entirely new organism: poof! in one fell swoop!

    Special creationism makes just as much sense: none at all

  45. Erik
    Ignored
    says:

    Corneel: True, I did not literally quote a web source but I assumed you could handle a little paraphrasing.

    Paraphrasing like when you say “evolutionary biology” I should understand that you mean only microevolution?

    Yes, I can handle it. But my point was to show that your level of precision with the terminology of what you (think you are) talking about is not even at high school level. And this point stands.

    You are a bit better than the level of your opponents at UD though, so congrats for that.

    Corneel: Hey, see? It does not just involve common descent but also natural selection and speciation. You might want to read all the other sentences as well.

    Yes, common descent and natural selection and speciation. And why are they mentioned? Because they all belong there and none of them can be taken away. There is no evolutionary biology without them.

  46. Entropy Entropy
    Ignored
    says:

    Bill,

    Any reason why you’re avoiding my comments?

    colewd to DNA_Jock,

    I understand we are looking at extant proteins but we have the evidence we have. What is the evidence telling us in the case of the three proteins we are talking about?

    That there’s three proteins doing some stuff. Perhaps that we haven’t found much variation between them (maybe, I haven’t looked at the sequences myself, maybe they have varied quite a bit).

    colewd to DNA_Jock,
    There is no evidence of another peak relative to the proteins that make up the complexes.

    Not that you can see, maybe.

    colewd to DNA_Jock,
    With multi protein complexes the proteins become specifically defined based on the other proteins in the complex.

    “Become” is the right word. As proteins in a complex evolve their interactions, their efficiencies increase, if the efficiency becomes an important feature for the organism, then the proteins will have less room to move from their current “situation” as their efficiencies increase. That tells you nothing about whether the complex could have evolved, whether any of the component proteins could have been from other protein families, or whether there’s still a lot of sequence “space” to explore. It only tells you that the current situation seems rather set.

    colewd to DNA_Jock,
    I know you understand this. In the ubiquitin complex case, the E3 protein must bind to E2, ubiquitin and the target protein for destruction or other targets.

    See above.

    colewd to DNA_Jock,
    We have no evidence that any exploration has occurred only speculation. We have no evidence of another peak only speculation.

    You mean, like speculating that no exploration has occurred? Like speculating that this could not have evolved because you prefer the conclusion that there’s some designer inference to attain?

    colewd to DNA_Jock,
    We have evidence that in its current configuration that exploration is extremely limited.

    For obvious reasons, like what I explained above, and reasons others have explained before.

    colewd to DNA_Jock,
    This is strong support for the design inference.

    Sorry, but there’s no such thing as strong support for the design inference here. There’s an attempt to infer a designer out of ignorance. Nothing more.

    You are also showing a double standard. You’re claiming that there’s little evidence for evolutionary exploration, and conclude that there’s a “designer.” Yet, for the designer side, anything does. How come that for evolutionary processes you want to have all the data in the planet, yet for the design “inference,” it’s enough to you to imagine that a designer did it?

    For example, why not look for evidence that designers can exist without everything you’re claiming to be designed? We have ubiquitin systems. That means that ubiquitin systems cannot be designed, since they’re part of what makes designers. Wouldn’t you need evidence that designers exist that don’t have ubiquitin systems in them? Where’s that evidence?

    Starting to see the double standard and the poor philosophy and poor scientific “grounds” of the designer “inference” yet?

    Please think about it.

  47. dazz dazz
    Ignored
    says:

    One other thing I just noted is that gpuccio, in your proposal for a design mechanism based on duplication-deactivation-tweaking-reactivation, you qualified that engineering sequence as non-coding.

    I’m guessing that’s not a coincidence, you couldn’t have possibly said non-functional DNA because there’s no such thing as junk DNA, right? I mean, you could say that it’s function is to provide a medium to engineer the future protein, but it would still be technically non-functional or junk DNA as understood by mainstream biology.

    More questions spring to mind: is there any evidence that such a process is currently ongoing? any way we can check for non coding DNA being prepared for the next macro-design event with tons of coordinated protein complexes with unique functions being engineered?

  48. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    dazz: Is there any merit to CSI that makes it worth it to show that NS can add it to the genome? Am I missing something Joe?

    In my 2007 article at Reports of the National Center for Science Education (linked in my comment above) I took the position that specified information was meaningful. It was not invented by William Dembski — he noted that Leslie Orgel had first described it. (I also defined an equivalent, “adaptive information” in a paper in 1978). William Hazen and Jack Szostak defined “functional information”, equivalent to specified information in a better defined context.

    These are meaningful (“complex” specified information as used by Dembski is just a certain amount of SI). The flaw in Dembski’s argument is not in use of CSI but in the assertions, and attempted proofs, that natural selection cannot put it into the genome.

    Nevertheless many commenters critical of Dembski’s argument have declared that CSI is meaningless. I disagree strongly. Yes, the amount of specified information is very difficult to measure, but it is meaningful, and there is no doubt that the amount of it in any living form exceeds Dembski’s threshold. The real question is how it got there, not whether the scale is meaningless.

    See the examples in my 2007 article.

  49. Corneel Corneel
    Ignored
    says:

    Erik: Paraphrasing like when you say “evolutionary biology” I should understand that you mean only microevolution?

    You have a hard time understanding that microevolution is something evolutionary biologists study? I hope you are kidding.

    Erik: Yes, I can handle it. But my point was to show that your level of precision with the terminology of what you (think you are) talking about is not even at high school level. And this point stands.

    Nonsense. Look at all three definitions and tell me in what way they differ. They don’t because they all describe the same thing; genetic change within a single population.
    But evolution can be defined in different ways. So if you don’t agree with my terminology, than offer us your definition and we can discuss whether common descent is a necessary part of it.

    Erik: You are a bit better than the level of your opponents at UD though, so congrats for that.

    Haha, was that a compliment? Thanks … I think

    Erik: Yes, common descent and natural selection and speciation. And why are they mentioned? Because they all belong there and none of them can be taken away. There is no evolutionary biology without them.

    I ask again: what should evolutionary biologists be studying, according to you? And why couldn’t they be studying it if different species were unrelated?

  50. dazz dazz
    Ignored
    says:

    Joe Felsenstein,

    Thank you Joe. I was basing my judgment on this article by Richard Wein at talkorigins:

    Dembski devises his own measure of how complex a phenomenon’s configuration is, and calls it specified information (which I’ll abbreviate to SI). He calculates this measure by choosing a specification (as described in 3.1 above) and then calculating the probability of an outcome matching that specification as if the phenomenon was generated by a process having a uniform probability distribution.

    http://www.talkorigins.org/design/faqs/nfl/#csi

    That looks a lot like a formalization of the tornado-in-a-junkyard straw man to me, as Wein argues, but I’ll check your 2007 article

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