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).
- 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.
- 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.
- 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?
A few questions. Is transcribed but untranslated DNA information? Are regulatory sequences information? Why not? By “synchronous” do you mean “synonymous” or something else?
John Harshman,
I agree with you transcribed but not translated would also be information but this is not what he is testing so I am narrowing the definition to focus on the data he is generating. His data shows strong support for significant common descent.
Correction synonymous, thanks.
gpuccio
Since Uniprot’s bit score appears to be some measure of sequence similarity, isn’t he just roughly mapping evolutionary distances? The “information jump” looks an awful lot like nothing else but the deep branching between vertebrates and other metazoans. Or am I missing something here?
The semiotic theory of ID certainly looks like an interesting flavour of the design argument. If I understand gpuccio’s argument correctly, he believes that the ubiquitin tags have a semiotic structure. For example, polyubiquitination of proteins at certain amino acid positions states something like: “This protein badly needs to be degraded”. Sort of like how trees are marked with an “X” when they need to be cut down.
Which seems a strange argument to me. If I turn the key in my car, the engine starts. But the turning of the key is not a “symbol” that gets communicated to the engine. Likewise, it seems to me that the ubiquitination tags are not symbols that get interpreted in any way, but are modifications that set in motion a chain of events due to specific biochemical interactions with proteins in the proteolytic system.
Even Richard Dawkins agrees. Richard Dawkins is an ID theorist minus the designer.
So simply claiming stuff appears designed makes one an ID theorist?
How very telling that you would respond that to a thoughtful comment exploring the nuances of what designing means.
For the IDist the devil is in the detail, so they avoid it at all cost
It’s not like Dawkins could be wrong.
Oh, except they’re saying he’s wrong on all sorts of things. But since this is supposedly an “admission against his interest” (it couldn’t be Dawkins thinking paradoxically, if not very carefully. No!), this is the unquestioned truth. Because it’s all a conspiracy anyhow. Lewontin!
And so ID shows its poisonous pseudoscience yet again. For flat-earthers, it’s a NASA conspiracy, for ancient alien “theorists” it’s a government conspiracy, and for IDists it’s biologists in particular and government in general. Just believe what you’re told, and you can keep track of the fallacies and falseness of ID, just like with other conspiracy theories.
Glen Davidson
It seems to me that the ID always comes first. The Designer supposedly thought it all up symbolically and semiotically, thus when DNA and its transcription and translation equipment were placed into organisms, it was, of course, semiotic. And it’s a code, so you know… Then there’s the purported clincher, that the code is arbitrary (at least as it operates today)–even though it would need to be in order to really work well as a means of storing information.
It’s how they’re supposed to think, and they do it constantly. The religion and ID come first, they can’t just look at the chemistry and ask how it all functions and evolves. For them, it’s automatic to assume an intelligent source and designed status, and to just prop up those assumptions with a few non sequiturs (like the fact that the code is arbitrary vis-a-vis the information stored, which any good code should be). Begin with design assumptions and you end up with design conclusions, like any good IDist would.
Then they look outside of the circle and marvel that “Darwinists” don’t get how it all makes sense. Which it does, it’s just that they start out with unwarranted assumptions.
Glen Davidson
So you two actually haven’t read any Richard Dawkins. This is a good thing, I suppose.
For the record, KN’s idea was, for fear of ID, to deny the appearance of design. Biologists overwhelmingly affirm the appearance of design (and Richard Dawkins goes further than that, all the way to the Blind Watchmaker). ID basically says that if it appears designed, it is designed. ID is wrong of course, which in my opinion takes away the reasons to fear it, but obviously you don’t care what I think, so I’ll just let it be.
So you just repeat the fallacy of argumentum ad verecundiam along with the unwarranted conspiracy BS, and whine that we don’t care what you think.
No, I most certainly don’t, because you rarely argue well, just as you failed to there. Biologists don’t overwhelmingly affirm the appearance of design. Paley’s arguments didn’t resonate well in biology pre-Darwin, because even before evolutionary theory existed there were many known aspects of biology that didn’t seem to make good design sense.
Basically, you used the fallacy of the argument to authority, repeated the BS that the IDiots bleat again and again, ignored our considered points, then wrote the same BS and whined that we don’t care what you think. Try actually thinking, rather than stating pseudoscientific nonsense as if it were truth.
Glen Davidson
Reading the comments in this UD thread gpuccio tries to justify his decision to compute functional information using the totality of sequence space.
Apparently it never occurred to him that, assuming evolution, if you have two distant sequences with some significant homology, precursors all the way down till their last common ancestor must also have (decreasingly) significant homology. But no, he thinks he’s justified in assuming equiprobability of all possible DNA sequences.
*facepalm*
While I agree with your diagnosis, I’m forced by my smugness to tell you that you should not misuse those terms. Things are homologous if they share common ancestry. Thus, it’s pretty much dichotomous: either things are homologous or they’re not. What you’re actually talking about is similarity. Significant similarity. Because homology is inferred from similarity far beyond random expectations, people mistake those terms all too frequently.
Entropy,
Thanks for the correction!
Wait, you won’t accept my data as supporting common descent, but you’ll accept his? What’s the difference? And what is “significant common descent” as opposed to “common descent”? Also, what do you mean by “information”?
Could you please, please reread at least once before posting?
You’ve got it right. He’s using BLAST’s bit scores (BLAST is a program for sequence comparison), which are measures of similarity, as measures of added “functional” information.
I’ve always been mystified by gpuccio’s argument. As long as we are analogizing, why isn’t change to the parameters of a program anything other than change? Why is a substitution an addition?
This is a rephrasing of the question, why is change considered progress?
Or, is there an objective measure of genomic complexity? Could such a measure of complexity measure the increase in complexity from say a mouse to a human? Could it do so without access to and reference to the phenotype?
By the way, I seem to remember a paper that concluded that most of the sequence space has indeed been explored, do you guys recall which one?
ETA: http://rsif.royalsocietypublishing.org/content/5/25/953
After reading but the first paragraph of an answer I wrote to our friend Bill Cole, gpuccio wrote the following:
Oh, thanks! That must mean that my comment was of superior quality! Now gpuccio feels like it’s worth trying again! How nice!
But now we’re good, right?
1. I wasn’t answering you, gpuccio (I hope your ego doesn’t suffer from this realization), I was answering Bill Cole.
2. I don’t think that you suffer from some mental illness.
3. Yes. My generosity knows no bounds.
Now I’m wondering if this is some kind of projection. We’re supposed to argue for new-Darwinism? Why? Are we supposed to believe in it religiously? Because I don’t. I don’t feel compelled to defend neo-Darwinism. Not only that, I know too much about evolution to regard it as being just about neo-Darwinism, and, even then, I truly don’t care about defending evolution, let alone from misguided philosophically and scientifically poor arguments like those of the ID crowd. I have said it before: even if the mechanisms we know about didn’t suffice to explain what we see, I would not be any more inclined to trust something as hypocritical, philosophically and scientifically poor as ID. Ignorance is much better than making a fool out of myself. So, thank you, but religiosity belongs to you gpuccio, not to me. Please keep it to yourself.
Oh! So it was projection! Keep the religiosity to yourself gpuccio. Don’t act surprised that I don’t react religiously to your attacks on neo-Darwinism. I don’t recite a credo, you do.
I understand ID “theory” all right. Even when you deny it, your claims tell the very opposite of what you want them to say. They confirm my diagnoses, rather than refute them. You’re right about the second though. I didn’t know what your arguments in particular were until now. Just remember, I was answering Bill, not you.
You get too caught by your rhetoric gpuccio. You made it appear as if you thought it was worth answering at the beginning of your rant, only to end saying that it’s not worth it. Make up your mind.
Thanks. His use of BLAST bit scores seems to introduce some wonky stuff indeed. I looked at some more of his curves of “human conserved functional information” plotted against the estimated time of divergence, and something tells me these are not a linear curves. Looks more like sigmoid curves, don’t they? So should we really be surprised to observe an “information jump” in the exponential phase of the curve? Might that be an artifact of the bit score?
John Harshman,
This is the explanation that got my attention that common descent was involved in forming a wide range of species. We see synonymous mutations that are saturating over long periods of time along with evidence of strong purifying selection. Below is from gpuccio at UD. Ka means non synonymous mutations. Ks means synonymous mutations.
Entropy,
Yes, you and gpuccio have many of the same conclusions but not all. His paper on the spliceosome is very interesting and problematic for Neo-Darwinism. Heavy purifying selection is a double edge sword.
Funny how the title of the thread claims to “defy any non-design explanation” and doesn’t even attempt to advance a design explanation.
gpuccio closes the article with “Whoever can really believe that all this can be explained by some RV + NS model is, IMO, really admirable for his faith in a wrong paradigm”
Just like groundhog day
Please explain why this convinces you of common descent while nothing else does. How far are you now willing to admit common descent goes?
John Harshman,
You never tried to explain common descent because you never had to. Your papers assumed it as almost all evolutionary biology papers do. Sequence similarity does not explain common descent. The nested hierarchy is only weak evidence.
What gpuccio showed is that DNA was mutating but only until purifying selection stopped it due to a deleterious mutation caused by an AA substitution. This showed that a gene was mutating randomly over long periods of time and stopped only by purifying selection. Information additions to the genome appear to be based on the current genome and not whole genome changes per organism. This supports directed common descent.
As far as this all extends, I have not thought that through and am hoping more data will shed light on this.
But it’s not a god-of-the-gaps argument I tell you!
Of course not. Cuz he doesn’t mention god, you know.
As usual, that was incomprehensible. I don’t think you understand gpuccio’s argument, and you certainly didn’t understand mine. I still have no idea why you found that argument convincing, unless it was that it affirmed your prior beliefs in design.
John Harshman,
I will check with gpuccio to see if he thinks I understand his argument.
You are right that I don’t understand your argument.
If his bias is similar to yours (support IDers over evolutionists by reflex), then I’m sure he’ll say that you do understand. If you don’t understand my argument, how can you reject it?
John Harshman,
If he does what he has in the past he will make clarifying remarks as I am sure my understanding at this stage is incomplete.
I have not rejected your arguments. I don’t think your argument for the nested hierarchy is strong but you’re understanding of generation of phylogenetic trees is beyond my current understanding so my opinion of your arguments is based on ignorance.
The story continues:
Well, if you didn’t get it, maybe you needed to read the whole thing, rather than just that paragraph. Not only that, if you were familiar with information theory, you’d have at least a hint as to what I was talking about.
I was confronted with that very problem when I started reading your “answers” to Bill. I decided to go “piecemeal.”
Curious that you’d say that, since the problem I was complaining about is, precisely, about analyses of time/place specific increases of information, because they ignore a larger context. It’s like talking about entropy in an open system, but making the analyses as if the system was closed.
OK. So, functional information would be something of a subset of information. That seems to give me more reasons to complain. Anyway, I’m guessing then that we’d need to know what that function is, and the kinds of objects that could be used for that function to be accomplished.
In other words, we have to forget everything we know about physics because gpuccio is talking about a subset of information, and it will look more as if there’s good science in ID if we ignore science (!?).
I doubt that people don’t understand that “simple” idea. I think it’s more that it looks a tiny bit suspicious.
So, I complain about comparing a few organisms to “infer” increases in information, and gpuccio tells me, very-offended-but-also-mockingly, that he made inferences about increases in information, ups, sorry, in functional information, by comparing a few organisms. That’ll teach me!
Not only that, I’m ignoring his “obviously rich, explicit, undeniable, and easy to measure” definition of functional information, but he’s using BLAST bit scores to infer increases in functional information. I thought it was me who was ignoring his definition.
OK, that’s about it for that comment (there’s others). Let’s check where we are:
1. My comment is about ignoring the context when claiming that information has increased.
2. Somehow that indicated that I don’t understand what gpuccio is talking about when he talks about information. I fully confess that was true: I didn’t know what he was talking about. I thought that gpuccio’s arguments were much better than they actually are.
3. Then gpuccio claims, proudly and with derision, that he’s ignoring much more context than I thought when talking about increases in information. Silly me. I apologize gpuccio.
4. Then gpuccio presents a definition of the kind of information he’s talking about, which shows that he’s talking about some subset of information, and that the subset is “defined” as “the information necessary to implement sone explicitly defined function, and is measured in relation to the defined function.” Not only that, gpuccio insists that “Any function can be defined, and the functional information in some object can be measured as linked to that function.”
5. However, instead of working with such definition, gpuccio is working with BLAST bit scores, and assumes that any difference in BLAST bit scores between organisms closer and closer in evolutionary distance (of sorts), represent increases in the very information that we ignore and don’t understand.
6. No functions were defined, and no measurements were made against such functions. Yet, it’s me/us who is making some kind of mistake because we “ignore” what gpuccio means by functional information.
Wow. He’s got me. Now I have to convert … ahem … I mean … to accept the scientific evidence for intelligent design.
There’s more comments by gpuccio around my sinful misunderstanding of his versions of information. I don’t know if I’ll have the time though.
See ya.
Remember this is the guy who said:
The jesus-in-a-bread-toast effect strikes again.
Look, BLAST scores are measured in bits and gpuccio’s FI is also measured in bits, the connection must be there, somewhere
It’s ironic that you didn’t read my comment, yet you think that because gpuccio’s “answer,” which you probably didn’t understand, is copious, it must mean that I’m willfully ignorant.
All I know about some “blind watchmaker” is that such wording is in the title of a book by Richard Dawkins that I didn’t read (and that I have no intention to read). So you can go to hell with your demands for a defence of a book I didn’t read and I don’t care about.
Your opinion about everything concerning evolutionary biology is based on your ignorance. That doesn’t stop you from coughing up some of the silliest anti-science ID dreck though.
Not quite. gpuccio was talking about subsitutions at synonymous sites, which tend to be neutral and are therefore not constrained by purifying selection. Genes always keep acquiring novel mutations of this type. Also you seem to have missed how this relates to the conclusion of homology of genes in different lineages, and how that leads to the conclusion of common descent of species. Need I point out how amusing it is that after all this time, you were convinced of common descent by an argument that you misunderstood, just because it was made by someone who is “ID-friendly”?
What is directed common descent? What is being directed to where?
Well put!
Entropy,
BTW. How can he not see that BLAST scores would be meaningless if evolution needed to traverse the entire sequence space with all sequences being equiprobable? It’s so fucking obvious that one wouldn’t expect any kind of similarity above random if that was the case, ugh!
Corneel,
No, your conclusion is in error. The reason I thought this data was interesting is because I had already thought of this method of validating his hypothesis of purifying selection which was key to his information argument. The evidence is in a dated and timed post to gpucccio. You can go on UD and see the conservation.
After additional thought I don’t think this data is as strong of support for additional common descent as I originally thought. I will have this conversation with gpuccio and see how it shakes out.
Corneel
This is the result of new genetic information that is causing diversity of living organisms.
You do that, and let us know how it went. Since gpuccio’s way of detecting “conserved functional information” critically relies on common descent, I certainly look forward to you telling him that this line of argumentation is flawed because there is no common descent.
This cannot be your answer. New genetic information is also causing divergence of lineages in plain vanilla common descent. Why is the “directed” necessary?
Why discuss things with an ignorant troll who avoids the same evidence that you do?
Oh wait, I guess I just answered my own question.
Glen Davidson
I doubt that the similarities extend beyond what I explained to you about synonymous and non-synonymous substitutions a while ago. By the way, it’s a bit sad to suspect that you accepted that because gpuccio mentioned them, rather than because of my magnificent and patient explanations.
Really? All I saw was “hey! this is very complex–insert misused/misunderstood sequence comparison tools and lots of claims and assumptions–therefore god-did-it!”
Don’t you find it curious that gpuccio claims that the whole of sequence space can be easily explored in a couple hundred million years? He says it differently, of course. He says that the time is enough to “erase” any “homology” between sequences (“homology” is the wrong term), leaving only the “functional information”-related parts of a sequence.
I’d think that the double edged sword is in his misuse of sequence comparison tools, and his over-exitement about the meaning he wants to give to those results. In his excitement he shot himself in the foot. “Hey! It’s safe to assume that the whole sequence space can be explored in a few hundred million years! Therefore the “functional information” is unexplainable!”
Ah, now I see you borrowed the term from gpuccio. He also uses the phrase “guided common descent”. I hope that you, unlike him, realize that “directed” is a completely superfluous adjective. Seeing how you have been given to understand a gazillion times that the cause of divergence among lineages is irrelevant to the conclusion of common descent.
BTW are you going to answer his question ?
I trust that you are going to pelt him with random gene loss and Sal’s flower.
Corneel,
BTW are you going to answer his question ?
Return to UD and you will see my answer.
Yes, according to the updated definition that separates out mechanism.
???
That’s always been the definition of common descent. It’s the one I’ve been using consistently while trying and failing convince you of common descent. So why haven’t you noticed until now? Everyone but you can see that it’s because you’re getting it from an IDer. (Which is a little puzzling, since Michael Behe told you the same thing with no result.)
Common descent is a category of mechanisms. It could be reproduction, or it could be the transfer of specific information.
That’s why we can see the effects of common descent in both organisms and in languages, despite the fact that all of the mechanisms of descent and modification differ.
Your inability to see it seems to relate both to your unwillingness to admit that those you disparage for disagreeing with you are right, and ineptitude.
Glen Davidson
I saw it. I am curious what gpuccio will reply. Just for clarity: Did you really suggest that sometimes a genome gets replaced wholesale by a new copy? Like an upgrade?
RL intervened. Have there been developments?
Totally clueless? Interesting. Let’s see.
I read three books by Darwin (not Dawkins). Incidentally, that was the way I learned that creationists had been lying to me about evolution. Regardless, in none of those books did Darwin mention a blind watchmaker. If what you mean is evolution, as in the natural biological phenomena, then say evolution. Don’t talk about “blind watchmakers” as if Dawkins was some kind of prophet. Don’t project your religious stupidity onto others.
So you think I need to read the words of yet another person I could not care less about? You call me clueless and you couldn’t get a clue?
I’m ignorant of what Dawkins and Jerry have written. You’re ignorant that I don’t hold a religion.
I have enough knowledge and intellectual honesty to notice the profound problems with “intelligent design.” You, however, think that just pointing to complexity will make your absurd imaginary friend into a reality. I’d call that clueless. What was that about “the beam in thy own eye, you hypocrite”?
Do you have anything to offer to the discussion, or you just babble and drool over whatever gpuccio presents?
If that’s from JoeG (aka Frankie, aka ET@UD), then you should consider it high praise.