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?
Could I request members exercise a little restraint, please. Thanks in advance! 🙂
dazz quotes a comment from gpuccio at Uncommon Descent:
Well, let’s give gpuccio credit for making some specific claims of when “Design” events occur. Punctuated Design! I wonder if he can be persuaded to explain how “Design” happens. Is it, as Behe once went so far as to remark, “Poof”? How can we establish when such events have occurred? What differentiates them (or are they the same as) from miracles? If so, how on Earth can anyone suggest this idea is worthy of scientific consideration?
Show me your interface, gpuccio!
colewd is so unreachable I’ve had to put him on ignore. Nothing anybody can say will make any difference with that one unless they can disprove that “atoms were designed”.
Atoms were designed.
Atoms just happened, and weren’t designed.
What difference does that make? And there’s the problem. The ID proponents think it makes a huge difference. But, from a scientist’s point of view it makes no difference at all. And that’s why ID is not science.
Neil Rickert,
If I were to make the claim that Atoms are irreducibly complex would that make a difference:-)
1. Since they take their clues from something as small as humanity to “infer” design, then they have a huge problem right then and there.
2. Nobody can calculate a probability without a good understanding of the variables. Therefore the calculations are far from being convincing that natural phenomena could not do what they have actually done.
3. It’s enough that we’re so small to understand that taking the clues from us is making it appear as if we’re above nature, when we’re obviously, pathetically, dependent of this huge nature around us, not only to exist, but just to be able to do anything we do, including our ability to design. That looks a lot like designers and design depend on nature, and not the other way around. IDiots put the cart before the horse. Starting to see the deep philosophical problem here?
Alan Fox,
It is worth scientific consideration because it is the only known challenge to Darwinian theory. Your points are valid that it is limited but it is what it is.
The fact than on one has made any detailed challenge to gpuccio is telling. There are real problems with the claims made about evolution.
No, I cannot see how that would make a difference. “Irreducible complexity” is supposed to be an argument about gradual change. Nobody has suggested that atoms came about by gradual change.
This is not arguing against the designer, this is arguing against the poor philosophical grounds of ID. Why would you want the “designer” untouched and unexamined if not to get away with such basic philosophical problems? Are IDiots taking their clues from humanity or not? You admitted so, therefore, it’s fair to check what those designers are like in order to check if the “design” “inference” is philosophically and scientifically sound. They only check for one little detail: ability to design. I prefer not to ignore those other details because I want to be sure that what I’m getting is an actual explanation, not poor wishful thinking.
As I have explained time and again, It is a legitimate reason. Whether it points to ignorance or not is inconsequential to the failed nature of the ID travesty. I prefer, a billion times, to conclude that I don’t know something, than to make a fool out of myself.
Well, how do we do that? What do we look for? How does a design event happen? It’s a bit flippant but say God decides to have a bit of fun and join in a soccer game. The attacking team approach the goal, the winger crosses but too far from the centre-forward. God takes his chance and blasts the ball into the net. What do we observe? An event without a cause – a violation of the laws of motion (and the second law of thermodynamics). Is that the sort of event we should be looking for? What would a design event look like if not a miracle?
For example, when the designer intervenes does the resulting change happen in a specific living organism, or is it a germ line change that is only passed to a descendant?
I might as well in fact ask you Alan, as you might give me an answer. No ID/Cist ever has 😛
I have to rule out God as designer, as an omnipotent, omniscient, omnipresent entity would surely get it right first time and hence it must be something else! But hang on, if God gets it right first time, what’s left for any subordinate designer to do? I’m stumped!
ETA clarity
It’s interesting how gpuccio insists, adamantly, that ID is not a god-of-the-gaps argument. Next he says that the whole point of ID is to evaluate the limits of RV + NS. If from the “limits” of RV + NS (however poorly or richly calculated), you “conclude” that god-did-it, it’s classic god-of-the-gaps. I’m sorry, but it is.
Yes, more than satisfied with the points that have been made regarding gpuccio’s assertions.
Let’s see: NeilR JohnH, JoeF, AlanF, GlenD, FairWitness, and Entropy to just name a few. His argument is one based on our ignorance of the details of what transpired 2-4 billion years ago.
As John stated how do you ‘prove’ or demonstrate something cannot evolve? How would you go about making a probability argument when you lack the details of the variables?
JoeF makes a great point on his, guccio’s, criteria for falsification “new original” information being added to the genome via known evolutionary processes. Which of course ignores the basic tenent of the known evolutionary process of exploring neighboring sequence space not the entire potential sequence space. Gpuccio rejects the evidence that new information has been found in the genome of e-coli in the LTEE where the mutations necessary for aerobic citrate metabolism has evolved.
Of course we still need the how, when, where, and who for the design hypothesis to be viable. Over 30 years, by your account, and still ID is stuck at the same place.
Have you figured out the bone fusion in bird embryonic development yet? Or are you still in denial that it happens?
It couldn’t be any more obvious, but hey, we’re just deluded “materialists” who accept evolutionary dogma uncritically, so what do we know. That kind of projection of theirs is also so mind bogglingly stupid, SMFH
Entropy,
I completely agree but if you say the quantity of genetic information observed is evidence of design it is not “God of the gaps”.
Well there goes gpuccios dFSCI right down the drain. Have you informed him of this observation?
PeterP,
His argument is based on information jumps in proteins that correspond with the age animals in the fossil record. He is looking at DNA and protein sequences and how information has increased over time.
You cannot prove a negative but you can show that the result in not likely the Neo Darwinian mechanism.
If I copy information have I created new information? I don’t think it is unreasonable to say no.
This is a valid criticism. The theory is limited.
If your ready to demonstrate this I am all eyes and ears.
PeterP,
“It is not means” it is not a God of the gaps argument.
Nope, it’s non existent. Gawd did it won’t cut it. Try again
Alan Fox,
None of this is required. When design looks like the best explanation, as it does for the flagellum, acknowledge it as the best explanation for that application. When you can experimentally validate the evolutionary mechanisms against specific complex multicellular life the design inference goes away for that application.
dazz,
Still addicted to logical fallacies:-)
Still incapable of articulating a positive theory, or even googling “logical fallacy”?
heh
When it can be demonstrated to be the best explanation it should be acknowledged. A bunch of IDists blathering that it looks designed means absolutely nothing.
The effectively false dilemma again. Design is not a default, except to disingenuous pseudoscientists. We don’t have to show any evolutionary mechanisms to note that you do not have and never have had a bit of good evidence for ID. You never demonstrate the kind of match-up between function and need, regardless of ancestry, that characterizes honest design identification. You never explain the bizarre (for design) adaptations, like the fusion of ancestral bird wing “bones” (and can the snarky bullshit, deal with the issues if you ever want respect) into rigid structures, you just move on to the same old creationist tripe that exists only for the ignorant and the dishonest.
See, real science explains things. ID explains nothing, all we ever get are stupid people assuming that the flagellum “must have been designed” for no adequate causal reason at all, then the stupid recourse to the false dilemma yet again. Same as it ever was, stupid shit from ignorant people who believe the people who tell them the most pleasing lies.
Glen Davidson
Is the ‘information’ derived from sequencing the genomes of organism found 2-4 billion years ago or based on extant organisms genomic sequencing? If he isn’t looking at the genomes of the organisms from 2-4 billiion years ago he is merely asserting that which he doesn’t know is true or not.
nonsense. Do you think you can’t prove there isn’t a elephant in my bathtub?
but I’ll indulge you anyway. How do you make the determination that the result is not likely the result of a ‘neo darwinian’ mechanism?
Do you think copying is all that occurred in the LTEE with the development of aerobic citrate metabolism?
The ‘theory; is stillborn.
So your answer is ‘no, I haven’t understood the evidence presented to me’. That’s sad.
Enter gpuccio’s “universal probability bound”
he’s got bits of info, logarithms and the whole nine yard. Oh my, we’re done
He cannot know if information has increased or decreased over time unless he had access to all life existing at any given moment. Examining a few organisms, and comparing them to a few other, apparently less complex, ones, and concluding that information has increased, rather than reorganized, is quite a hasty conclusion.
And that’s a problem just at the life level. To better calculate if any changes in information have occurred, he’d have to check the organizational and energetic levels of the whole planet at each period of time.
On the side of science, guess what? there’s calculations of energetic flow through our planet, and guess what again? There’s much more than enough to sustain evolutionary changes. Orders of magnitude more. Information is not a problem for nature, it’s more of a problem for creationists to understand.
The information “argument” is bound to fail regardless, because, once you understand the fundamentals, such as the link between energy flow and information, and realize also of the anthropomorphisms embedded in the argument, you’re left realizing too that even human design, again, the place where IDiots pretend to get their clues from (as if), have never ever worked independently of that very energy flow. So, information content doesn’t lead anywhere but towards the question of energy. That question is solved, and nobody is any closer to concluding that “intelligent” design is a properly scientific answer to the history of life.
(Besides the obvious philosophical problems associated with the mere idea.)
Let’s suppose so. That still cannot discount that other natural phenomena, besides the neo-Darwinian mechanisms, can contribute to evolution. For example, the roles of sub-obtimal events, historical accumulations of successful sequences, etc.
It is unreasonable to say no. The only way you could reasonably say no, would be if the copying didn’t require energy to be produced. Guess what? No copy has ever been produced that didn’t require energy.
PeterP,
I am confused where you get the 2-4 billion years. He is looking at multicellular life.
With examples like the flagellum where there appears to require lots of information prior to selective advantage.
No there were also snps but I have not looked at the data recently. The copied transcription factor allowed for transcription of the transporter protein under aerobic conditions. Are you at all concerned that after 30 years no novel enzymes evolved?
As the Zen master said we will see:-)
No, I don’t understand the evidence. I look forward to the education.
Entropy,
I have left him a post at UD. I think we are working with different definitions of information and will spin our wheels until we can sync up on a definition.
I don’t think you’re working with a definition at all.
keiths:
colewd:
Gpuccio made a stupid argument, Bill. Nothing about being a “trained medical doctor” prevents him from doing so, obviously. So stop idiotically repeating “trained medical doctor”, as if those were magic words that could convert dumb arguments into effective ones.
Hey, looks like you suffered a deletion mutation in your copy.
The semiotic aspect is the only new thing (to me) in this thread. Could you explain how that argument works? As I understand it, it takes some molecular patterns to be symbolic representations of downstream effects (e.g. a codon is a symbol for a specific amino acid, or an ubiquitin tag is a symbol for the fate of the tagged protein). That looks like an exotic version of the design analogy to me.
Is that correct?
Easy. Because people make experiments and then describe phenomena the best way they could (obviously from a human perspective), they’re caught on analogies and metaphors. Given that creationists don’t understand the problem of anthropomorphisms, they are caught by the analogies and metaphors and take them to heart, thereby deriving the conclusion that there’s “semiosis” in natural phenomena.
In summary: it’s anthropomorphisms built over the foundation of more anthropomorphisms. There’s nothing new about it.
Yes, “semiosis = (look! it’s a like a code!)”, “functional information = (look! it’s complex!)” and all that stuff are nothing more than red herrings concocted to avoid addressing the real processes, to sound sciency and to beg the question for design without actually advancing any kind of design theory with any kind of explanatory power.
How does semiosis, FI or design explain a single biological fact? Who knows and who cares
When you really don’t care about explaining anything causally, but only want to say that things are designed, you just latch onto labels that sound “designed.” So, “it’s a code, it’s symbolic, it’s semiosis, it’s functionally complex.”
Creationists use facts like drunks use street lamps, not for illumination, but to prop themselves up. They can’t do much other than latch onto some term that sounds (to them, anyway) like design or intelligence, claim that only intelligence can produce it (and/or evolution can’t), and pound away while claiming that their opponents won’t admit what’s obvious.
Colewd learns from them, avoiding any kind of proper scientific thought.
Glen Davidson
gpuccio has posted a couple of comments at the ubiquitin thread in UD
I’d like to ask him the million dollar question and if he chooses to ignore me, I totally understand. Vincent Torley was kind and honest enough to answer it, and I’m not saying you wouldn’t be if you don’t. But anyway, there it goes:
If you think the transition to vertebrates happened abruptly, not gradually, you only have two alternatives: special creation (considering you’re an ID proponent) or wild saltationism. For all I know you accept common descent, so it must be saltationism. Do you believe it’s reasonable to accept this scenario with invertebrates giving birth to vertebrates? Do you have an estimate on when and where we should expect another of these brick-shitting ID events? Because I want to make sure I’m there to bear witness
Dear gpuccio,
While I will answers your comments a bit later. For now, just a few points:
1. I wasn’t responding to you. I was responding to Bill Cole. I haven’t even read, directly, your OP, or anything else written by you until now.
2. You should have read my comment in its entirety. Taking an isolated paragraph, of course you’d miss a lot of the explanations.
3. I don’t think you’re crazy or deranged. I don’t think that you have some mental illness.
4. I think you’ve assumed way too much about me.
Later!
dazz,
That was a bit painful to read, gpuccio understands much less than he thinks he understands. Thanks for the link.
I was wondering, is gpuccio’s dFSCI different in any way to Dembski’s CSI?
Entropy,
I just read his explanation to me and my description to you was incomplete. Your challenge to my interpretation helped me understand his work more clearly. Thank you.
I let him know your challenge was due to my misunderstanding so I think were good.
I summarized his thesis and am awaiting his feedback or correction to my understanding.
Corneel,
This is new to me too so I will give it my best shot. I think the gold standard for semiotics is the transcription translation mechanism where 4 bits of DNA get translated to a functional protein of 22 bits of amino acids. The translation mechanism, the ribosome, function is pretty clear.
For the ubiquitin system it is less clear as there is no clearly specified translation system I can identify. The “code” is based on how the identified proteins are modified for specific processes like destruction.
Hi dazz,
You might find these links to be of interest:
Money quote from the first link:
Hope that helps.
colewd,
I will answer regardless of the misinterpretations due to the mediation.
Later!
vjtorley,
Thank you Vincent. Much appreciated
vjtorley,
So if I got it right, it’s the same concept, calculated the same way, only that gpuccio’s metric is transformed to bits and refers to functional specifications.
Seems just as redundant and unnecessary as FSCO/I
dazz,
This 2014 comment of mine may help:
keiths,
Yeah, he completely ignores evolutionary processes
Wasn’t that the issue in Dembski’s original formulation of CSI? It debunks tornado-in-a-junkyard as an explanation of proteins, certainly irrelevant to darwinism, or evolution.
A 10 year old can tell you that without the not so fancy math
Heh, I thought you were familiar with the concept because you are so fond of transcription / translation as evidence of design.
Thanks. There indeed appears to be a requirement for a “protocol” to interpret the symbolic code. A function that is fulfilled by ribosomes and tRNAs in translation. I discovered that semiotic theory was already discussed here at TSZ a long time ago (there is a category tag for it in the side bar).
Entropy,
In gpuccio’s research all information means is DNA that is transcribed and translated to protein. Most his work is with protein sequences however with a few proteins he has compared synchronous mutations with non synchronous mutations to test for purifying selection and common descent. Based on his data I think you are right on both accounts.