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?
It’s even more ambitious! For evolution by common descent with modification by natural selection to be correct, there has to be an unbroken line of descent between every extant and extinct organism via viable intermediates back to the last universal common ancestor. That’s a lot to shoot at.
But as others have said, so far there’s no better explanation for the evidence we see.
I only reasonable meaning that I could gather from your words were that it is not possible to have a hierarchy of designers and designed entities. And if that is the case I do not follow your logic.
I look forward to your clarification.
There’s no equal explanation for the evidence that we see.
Anything else is ad hoc, including any “evolution by design.”
Glen Davidson
True enough. And “Intelligent Design” doesn’t qualify as an explanation at all!
It’s pretty much necessary that all Eucarya be cousins. Bananas, humans, and so forth.
It’s still possible that abiogenesis occurred more than once.
dazz quotes gpuccio:
It’s not like we haven’t been over this before.
Sigh.
Between this and colewd’s awesome riposte:
Entropy:
colewd:
I think we have distilled the inanity.
But no survivors survive from any but the event with survivors. Of course the universe could be teeming with life, too.
> is.number(639467265010436782y3952223904758)
Error: unexpected symbol in “is.number(639467265010436782y3952223904758”
Rebooting universe
Corneel,
Lovely data on the promiscuity of the E3 ligases. That pretty much deep-sixes colewd’s argument.
I am also enjoying gpuccio’s false dichotomy between “change one AA at a time” and shuffling protein domains, like there’s nothing possible in between. Then, “I’ll focus exclusively on the former, because the math is less impossible…” add a nice dollop of personal incredulity and hey presto, we’re there: Evolution is impossible!
In living things, all the existing numbers open the safe. Some variations on the number also open the safe.
Thanks, but I think most credit goes to Entropy. I just followed up on his lactate dehydrogenase example 🙂
It’s more like we have a 150 digit string that opens the safe, and some digits can be changed to other digits and still open the safe.
Not just that, but after a digit has changed, DIFFERENT digits can be changed and still open the safe.
Depends on what you mean by survivors. Genes might survive being ingested.
No need to reboot the universe, Corneel, since “639467265010436782y3952223904758” is clearly designed.
The probability that a randomly generated 32-element alphanumeric string would contain one (or fewer) letters is 1.33e-16.
Well, that or he’s not using a German keyboard.
I’m going to go with “designed”.
</creationist>
I get a message that it’s installing updates now. Buckle up guys, some weird shit is about to happen
DNA_Jock,
Im sorry Jock, how many different molecules does a single E3 have to bind with? How many E3 configurations are there?
Alan Fox,
There are two explanations one is mis leading and other is not.
-built by blind unguided processes
-designed
One helps you understand biology the other misleads you. If you study disease and the deregulation of the ubiquitin system as a cause only one will make sense to you.
That’s right!
And that’s why drug developers focus exclusively on the non-design explanation!
Remember, they are not tied to the Darwinist omerta, they just care about making money.
colewd,
I’m very sorry, Bill. but how many different E3 sequences could bind to each target? How many potential E3 configurations are there?
YOU are the one who is trying to put a number on this. Well, you are pretending that the number is one, and then sticking your fingers in your ears, I guess.
DNA_Jock,
You were trying to declare victory and go home with one piece of data.
Are you ready to make a real argument that the paper that Corneel referenced really shows that the ubiquitin system is evolvable?
DNA_Jock,
Some have been but as they clear this nonsense out of their minds real progress is being made like the discovery of the ubiquitin system and how its deregulation causes many known human diseases.
Entropy wrote:
CharlieM replied:
I understood Entropy to be referring to the bootstrap problem: it is our universal experience that designers are made out of meat.
Arguing that designers are necessary to create the first animal is, therefore, problematic.
Hence all the finessing about disembodied intelligences, which have never, I think you will agree, been observed to do anything.
Try reading my comment for comprehension. I was not declaring victory, merely pointing out that your argument doesn’t hold water. At all.
So we are back at “don’t know”.
Regarding researchers working on ubiquitin, you wrote:
LOL
Really? You’re claiming that the researchers uncovering the ubiquitin system are assuming that the system was designed?
Citations, please.
I can say with some certainty that Hugh Pelham and Mariann Bienz reckon it’s the result of evolution.
DNA_Jock,
You made an unsupported assertion. You have not shown at all that my argument doesn’t “hold water”. The promiscuity of the U3 proteins on to a single substrate does not even begin to address my argument to Entropy. How about other substrates, how about binding ATP, Ubiquitin, U1 and U2. You have made an argument from ignorance. Get educated.
DNA_Jock,
Is this the paper you are talking about? Where is the evolution of ubiquitin system discussed?
colewd has a specific, single example of where assuming “design” supposedly “helped” him discover something in his work. I think that’s what he’s referring to.
The simple fact is that if simply “assuming Intelligent Design” was more productive in science it would have never stopped being done.
OMagain,
You are right on this one. What I discovered from bottom up research is that cell division (also stem cell) and vascular growth were controlled by the ubiquitin system. The same system that was initiating a tumor, by increasing transcription rates through loss of control, was also causing it to metastasize by building a bridge to the blood stream. Understand biology is partially about understand system “design”.
Cancer researches are making progress by understanding this “design”. This helped initiate the introduction of proteasome inhibitors for multiple myeloma.
A sample of the biological design hypothesis:
Notice the phrase “control of the system”. The ubiquitin system fits this very well.
Strange. I had seconded Entropy’s argument thus
and pointed out the difference in constraint between optimized proteins and “younger” proteins.
You responded
Corneel’s reference notes:
I noted that this deep-sixes your argument. That’s not an unsupported assertion. It’s a supported assertion. Learn the difference.
You mentioned binding ATP. That’s quite the own goal: we KNOW that there’s multiple ways of doing that.
Did you start out assuming cell division was uncontrolled? Why would the conclusion of “design” not be equally as valid were something else to be controlling those things? What could cell division be controlled by that would not cause you to conclude “design”?
Why have you scare quoted “design” there?
As noted above, did you start out thinking that cell division was uncontrolled and unconstrained?
It always amuses me to ask “which one?” when IDists proclaim that the bacterial flagellum was designed.
Will it be scales or spines tonight Sir?
Silly Billy. You claimed, in reference to the non-design explanation, that
I replied
The pubmed search link was to show you that they are productive in the field.
Do you have any citations for productive researchers who reckon that it is designed? Or were you only referring to yourself? In which case…
DNA_Jock,
You think you have provided evidence that exploration has occurred.
You are contradicting your own argument that current observation tells us nothing about history.
Cornell is explaining E3’s current function. And yes I would guess that binding flexibility would be important to this design as most all nuclear proteins are involved.
Your citation did not support your claim. There are speculative papers on the subject. You can find them with a google search.
OMagain,
No. I started out trying to find out why low blood levels of a small molecule were dramatically increasing cancer risk. I had no idea how cell division was controlled at that time.
DNA_Jock,
This is your straw-man. Why do fell compelled to create one at this point?
Why would the conclusion of “design” not be equally as valid were something else to be controlling cell division? What could cell division be controlled by that would not cause you to conclude “design”?
At that time, had you concluded that cells were designed?
gpuccio:
Pow! Pow!
DNA_Jock,
There you go again. Declare victory and go home with a silly claim that is irrelevant to the discussion. I am going to part here until you can make a serious argument about the evolvability of the ubiquitin system.
It’s kind of the point actually. Multiple ways of doing similar things is the ladder.
OMagain,
Not at that point. It was not relevant to the research as I understood it at the time.
So, was it finding that cell division was controlled that led you to conclude design? If so, why would the conclusion of “design” not be equally as valid were something else to be controlling cell division? What could cell division be controlled by that would not cause you to conclude “design”?
Well, given that multiple different ligases can address the same protein target, and multiple different protein targets can be addressed by each ligase, I think that your claim
is looking unwell.
You’ve suddenly decided that “binding flexibility would be important to this design”. And you think that I am contradicting my own argument? ROFL
OMagain,
You’re looking at the design of a single protein. The adaptive immune system uses hypermutation to create new antibodies. Thats another function that emulates evolution but is specifically designed with a very small substrate (about 10 AA long) which limits the search space. These are specific designed systems that tell us nothing about their origin.
The ladder is one protein making a step by step journey to a new function. How can it do this without falling into the abyss of sequence space unless the ladder is designed?
DNA_Jock,
Where have you or Corneel demonstrated another Peak? You’re continuing to double down on your poor analogy and still have not made progress convincing anyone that the ubiquitin system evolved.
So you’re trying to claim protein binding flexibility is evidence that another peak exists? I have to admit your skill set is impressive trying to escape your own self contradiction.
Maybe your daughter can help you here:-)
You claimed microevolution was “common knowledge and accepted by everyone”. That’s a far cry from a few philosophers noting that species were not fixed. You are also ignoring the fact that these notions were denounced as pagan when Christianity swept over the ancient world.
gpuccio@UD
Oooh excellent. Your sense of humor is much better than ETs 🙂
ETA: will address the other comments later. It’s getting late for me.
gpuccio@UD
It is not entirely surprising to see you packaging both human exceptionalism and personal incredulity into a single sentence. But this argument is neither scientific nor empirical, don’t you agree?
gpuccio@UD
For starters: I don’t believe that the substrate binding domains of all those 600+ E3 ligases are completely unrelated. You better bring some evidence to the table for that claim.
LOL, you make exactly the same 180 degree turn that Bill Cole made at TSZ. What’s that? E3 ligases are not specific but promiscuous? NO! They are flexible, they have multiplicity. If E3 ligases have great specificity then that is evidence of Design, and if they bind a shitload of different proteins then that is also evidence of Design. So what isn’t evidence of Design?
This is so typical of the everything-must-be-designed ID bias. If this is true, then why would the authors consider this a challenge for detecting valid substrates? Better read that part again:
Many of the substrate-ligase interactions detected in vitro do not occur in vivo because the substrate and the ligase are not co-expressed! What the authors are saying is that a large part of the substrate-ligand pairs that were identified are expected to be spurious. That is why the paper has a paragraph dedicated to the validation of the candidates found by high-throughput methods. That completely undermines your claim that all of this is “cross-talk”,”strict control” or “complexity, at the highest level”. Patent nonsense.
And now you need to face up to the fact that the issue of protein promiscuity, as raised by Entropy, is a valid answer to your challenge:
To which the answer now must be “yes” with respect to the substrate specificity of E3 ligases.
Corneel, to gpuccio:
The lame arguments of Pooch and Bill. They aren’t designed, but instead evolve by a series of goalpost moves. 🙂