A prominent ID supporter at UD, gpuccio, has this to say:
My simple point is: reasoning in terms of design, intention and plans is a true science promoter which can help give new perspective to our approach to biology. Questions simply change. The question is no more:
how did this sequence evolve by some non existent neo darwinian mechanism giving reproductive advantage?
but rather:
why was this functional information introduced at this stage? what is the plan? what functions (even completely unrelated to sheer survival and reproduction) are being engineered here?
Gpuccio references actual biology in his writings and is one of the few at UD that do, and as such I’m prepared to take him at his word that the ID project is now ready to move from simply determining design to answering the questions he posed:
- why was this functional information introduced at this stage?
- what is the plan?
- what functions (even completely unrelated to sheer survival and reproduction) are being engineered here?
If any ID supporter would like to provide a specific example with answers for those 3 points for discussion that would be perfect.
Gpuccio’s OP concludes:
The transition to vertebrates was a highly engineered process. The necessary functional information was added by design.
In response I simply repeat back the question what is the plan?
What is the probability of another sequence of 10 particular but dissimilar rolls, coming up? The same as 10 of the same in a row.
Indeed. Do you believe there is such a thing as truly random dice?
https://xkcd.com/221/
This always seems to confuse some people. If the dice are fair, then ANY sequence of 10 rolls is going to be highly improbable, and all will be equally improbable. I think people tend to find ordered sequences (according to some ordering scheme in their minds) as being somehow inherently less likely. For example, they might consider a lottery number selection of 1-2-3-4-5-6 as being less likely than a more “random-looking” sequence.
What would be suspicious is if the same sequence were rolled twice.
Hey colewd, what kind of nuclear proteins do you study and how do you study them?
I’m interested and curious
Yeah I’d like to hear more about those supposedly harder to evolve nuclear proteins too.
OMagain,
gpuccio @UD
Yeah, I’ve discussed protein sequence space ad nauseam too. But up it crops, over and over and over.
OMagain,
gpuccio@UD
Hahaha! This is funny. I’m quite sure gpuccio will not appreciate how funny that is. ‘Deleterious in the right environment’ indeed.
Pooch is counting on God to provide the ‘deleterious’ environment when needed.
I would note that intelligently designed proteins that are ‘naturally selectable’ appear to be a bit thin on the ground. Unless one simply declares all functional proteins to be designed.
Random peptides have, incidentally, been shown to successfully replace knockouts for multiple functions in vivo, with absolutely no connection between the algorithm used to subset peptide space and the peptide replaced. But I guess, unless one releases them into the wild and gets a brand new pathogenic strain out of it, it’s inconclusive on the ‘selectable’ question!
colewd,
Could you relate this to biology in some way? While you are doing so, don’t forget the possibility that the first ‘improbable’ result was copied, loads.
Since I typically disagree with gpuccio, it’s good when I occasionally find something to agree with him about.
I think his criticism of Flint’s statement is valid. He writes:
Pooch is right, and another way to see that is to recognize that a sequence repeated twice consecutively is equivalent to a single sequence of twice the length. All such sequences are equiprobable under a uniform distribution.
What makes certain results suspicious is something other than their improbability as individual sequences. I addressed this topic in the following OP:
A resolution of the ‘all-heads paradox’
gpuccio destroys the core of his own argument and does not seem to notice:
gpuccio responds to the above comment by repeating some earlier comments he already made and asking me to read his OP on natural vs unnatural selection.
He re-emphasizes the point that the result was generated by ’rounds of intelligent selection’. It’s almost as if he’s ignored every post made on this thread.
gpuccio, you obviously have the time to comment on my posts rather than the more specific more technical rebuttals others have made. Why is that?
For example, are all functional proteins designed?
Yes, gpuccio, rounds of intelligent selection are only possible in a peptide space that is connected – where weak function can be tuned by [some kind of] selection to improve. Why is this possible in an experimental setup, yet not in nature? It’s not as if the people are picking the sequences most likely to improve. They are simply assaying for the chosen function, then subsetting the peptide library on that basis, mutating and repeating.
This, further, has medical application. By applying the thing-that-doesn’t-work-in-nature, by a remarkable stroke of luck it does work in other arenas.
Perhaps it’ll help if I ask
Why is this possible in an experimental setup, yet not in nature?
as gpuccio seems keen to talk to me. Not sufficiently keen to talk here, but keen nonetheless.
I will repeat myself.
Having a human person stand next to the test tube isn’t going to make function magically more prevalent in amino acid sequence space. There does not emanate magical function-creating beams from human bodies into test-tubes such that the proteins inside can suddenly do things they are not supposed to.
It doesn’t matter at all whether humans are doing the selecting. The function is there regardless of who or what is selecting it. The fact that the function is there to select means sequence space is largely connected by functions.
A human being being within a few meters of the test tube isn’t going to make ATP binding suddenly appear where it would not be if the human stepped further away. Gpuccio’s excuse couldn’t be any more ridiculous even if he tried.
gpuccio?
Similar objections were raised against Lenski’s LTEE. As if researchers were picking the winners!
This is gpuccio’s summary of what gpuccio asked me to read:
It seems that proteins don’t reproduce like organisms do, therefore all experiments are invalid.
This is just absurd:
OMagain,
Remaining in a pool drawn from a wider protein library is reproductive success [eta – given that these pools form the next generation, mutated]. The distinctions between artificial and natural scenarios are … artificial. All that is fundamentally required for selection is heritable variation. The medium of inheritance is immaterial.
The comments by Zachriel are worth reading.
gpuccio also said,
And that seems to be the heart of it for him.
As always. Zachriel’s patience continues to inspire.
ATP binding is a naturally selectable function. Countless critical regulatory elements and core metabolic enzymes have ATP binding pockets necessary for their current function. If tomorrow all the ATP binding capacity of Gpuccio’s cells disappeared, he’d die in less than a minute (and if he doesn’t have children already, his reproductive success would go to zero).
But as I wrote already earlier, we can forget about Keefe and Szostak if it makes Gpuccio feel better, and start talking about other similar types of experiments, such as Hayashi et al 2006, where the selection criterion was the capacity of a bacteriophage to infect a bacterium, using a randomized ~140 amino acid protein subdomain. So the reproductive success here was that of a bacteriophage. That’s textbook natural selection. What’s Gpuccio’s excuse going to be now?
So the peptide space is grudgingly accepted to be rich in ‘function’ – defined as showing up in some assay for that function – but poor in ‘naturally selectable function’? How has that been determined? You can’t just look at the space and declare it so. It renders all the ooga-booga probability calculations (and all effort spent addressing them) a waste of time, since selection is entirely context dependent. There is no information regarding it anywhere in protein space.
Since it seems that UD is a safe haven for gpuccio’s ideas and most of the discussion is taking place here, I encourage you to again invite him to join us.
Many of the participants here are banned at UD and still others are unwilling to participate in a forum where their comments may be edited or deleted at the whim of the site’s owner. TSZ does not alter or delete comments nor does it ban people arbitrarily. If gpuccio really wants an open discussion of his ideas, TSZ is a far superior venue.
gpuccio,
It appears to be simply the lack of any step by step pathway that is detailed enough for gpuccio that determines if a protein is designed. Presumably were such a pathway provided to his satisfaction it would only render that particular protein available to natural selection without intelligent design. The rest would remain designed.
Presumably he also asserts that arches are not possible due to the lack of a now-gone support structure.
gpuccio, 259
260,
261
262,
What relevant frequency demonstrates that Intelligent Design is the only possibility gpuccio? Is that a sufficiently technical question? Think carefully before you answer I would suggest.
Gpuccio@UD
Good grief! ID of organismal proteins – how non-conjectural is that? Or is gpuccio of the “ID is not a science” school?
This is hilarious. Gpuccio is making a designer of the gaps-argument. Where we lack a sufficiently detailed phylogeny, that’s where the designer acted.
This is hilarious. That’s not his argument.
Obviously doing a column extraction is the method by which ATP binding is detected. There’s zero grounds for a belief the protein in question can’t bind ATP in vivo.
What Gpuccio fails to address is why ATP binding even exists where he seems to insinuate it shouldn’t. That’s what he keep trying to argue, that something functional was found because the whole thing is “artificial”, rather than “natural”. A synthetic distinction in the first place, since the principles of intermolecular binding are the same everywhere: shape and electromagnetic attraction.
But Gpuccio needs keep the banner of a somehow invalidated experiment flying whatever it takes, rather than simply concede that his views of sequence space have been falsified. So if humans did the selecting by using some kind of human technology, the rules are suddenly different.
Yes, ATP binding exists in natural proteins too. It operates on the same principle, an ATP binding motif that structurally fits the ATP molecule, and a mutual electromagnetic attraction between the atoms in the protein and the atoms in the ATP molecule.
There is no difference whatsoever between an artificially evolved ATP binding protein or a natural ATP binding protein. They both have an ATP binding motif. They may be different in sequence, but the method by which ATP binds is the same. No amount of obfuscation is going to make this go away.
If the capacity for binding ATP is tied to a key metabolic enzyme for example (and it is, in ATP synthase), then that enzyme, if mutated to a weak binding capacity, would have an impact of reproductive success, because the ATP synthase would be only weakly functional, if at all. So there’s clearly an in vivo selectable function in ATP binding.
Yes it is, the function is part of countless natural proteins. Lots of allosteric regulation is done by ATP binding.
A protein that has a binding pocket for ATP, changes it conformation and as a consequence it’s (for example) enzyme active site access is altered such that activity is reduced, or totally inhibited. Or the same thing happens to regulatory elements that bind DNA, they have a binding pocket for a key stretch of DNA and one for ATP. ATP binds the ATP binding motif and the protein changes conformation, such that it lets go of the DNA.
So yes, ATP binding is a naturally selectable function. It will remain a naturally selectable function no matter how many synthetic excuses and red herrings Gpuccio can invent to save his warm, abiding religious faith about protein sequence space, from falsification.
That is entirely possible, yes. Context dependent of course, as always. There is a context in which some organism could use an allostericly ATP regulated enzyme or genetic regulatory element, and there is some in which it could not. It doesn’t have to be universally beneficial in every and all biological contexts (in the same way the Polar bear’s fur isn’t universally beneficial in all biological contexts), to be a naturally selectabe function.
The answer isn’t no.
Yes, I’ve read basic biochemistry and molecular biology where evidently you have not. I know of how enzymes work and how gene regulation work. ATP binding motifs are ubiquitous in life for those purposes.
Which is the key fact taht remains to be explained, if as Gpuccio insists, protein sequence space is largely void of function. If a random 140 amino acid peptide could be immediately mutated into orders of magnitude increased function, this implies both that there is function all around the initial peptide in sequences space, and that it is naturally selectable.
Indeed, the fact that a totally random 140 amino acid sequence, utterly unrelated to the deleted D2 domain, had a low level of infectivity to begin with, implies the infectivity function is extremely easy and almost ubiquitous in protein sequence space.
With a sequence pool of between 10 and 10^6 sequences, only allowed to change by substitutions.
Which is irrelevant in the first place, because whether the function is lower than wild-type or not, the fact is the function is there and has a demonstrable effect on reproductive success.
Simply but, if Gpuccio is right, the function simply shouldn’t be there. Gpuccio’s main thesis has always been that sequences space is largely devoid of any functions and that most of it is straight up nonfunctional, such that one can’t move around in it and maintain any function, that it is basically some obscure, very far apart and small islands of isolated function.
The fact that there’s a long way to the wild type from here is immaterial. The function is good enough to allow the phage to infect E coli.
The fact that the very first pool of random sequences were immediately functional is a problem to explain for Gpuccio, if the sequence space should be mostly dead. What colossal luck the reasearchers must have had, to just so happen to start the experiment at a functional area in a largely dead sea, right? It’s funny how this is a consistent result with these kinds of experiments. It’s almost like sequence space is actually replete with function.
It is utterly irrelevant that the seqeunce has no homology to the wild-type. The interconnectedness of sequence space does not mean all sequences should be homologous, obviously.
The important fact is that there is a selectabe function closeby, which means this area of sequence space isn’t lethally nonfunctional in a vast area. In fact this just argues that the same basic function exists in multiple locations in sequence space and with relatively few mutations, something that functions well enough to allow reproduction to continue can be reached.
You don’t seem to appreciate what is meant by sequence space being connected. It doesn’t mean you can move from any arbitrary point in the space to any other arbitrary point as if it is one long slope of selection, and end up with a homologous sequence to the wild-type in the end. Rather, what is meant is that there is usually always something functional nearby, not that the particular instance (such as the wild-type D2 domain) of the function in question can always be reached.
You know there are multiple different enzymes in life that catalyze the same reactions, yet are pretty much entirely unrelated as best we can tell?
Why WAS there a function there, for the synthetic sequence to improve? Shouldn’t it have been much, much more likely for the synthetic sequence to have landed in some vast desert of nonfunctionality that could not ever (within reasonable timeframes) have been mutated towards any appreciable level of function?
That’s so cool. In ID, what matters is some silly piece of rethoric with zero real-world application, designed to impress gullible, already convinced religionists, into being flabbergasted by how scientific it sounds to spray words like “information”, “complex” and “specificity” all over the place.
gpuccio,
heh
gpuccio,
What ‘facts’ does ID explain?
gpuccio,
I would remind you of you own claim regarding what questions ID should answer:
In your thread at UD you have not answered a single one of those questions.
All of them.
What we see is what the designer wanted. Done.
That’s what the section I quoted, which he wrote, means.
So there you go Mung, that is what he wrote. If we lack a highly fine-grained phylogeny of the protein in question, it was designed. That’s a textbook designer-of-the-gaps argument.
He does not have to explicitly say “we don’t know – therefore design” to be in effect arguing like that and thus be guilty of the fallacy.
Why doesn’t it, you know, actually predict what design does, like fitting the design to the function, rather than fitting inherited information to the function?
If design predictions (real ones) fit the evidence, we’d all* be IDists.
Glen Davidson
*Those of us here, at least, I’d wager. There could be some holdouts who really could never abide being wrong, but they’d be the counterparts of the IDists.
There is much blather generated to avoid stating it that boldly, since it’s so obviously fallacious when written in that way. But make up a false means of design detection, like Dembski did, and many will think he’s right. Paley, of course, never went for such a false idea, rather he tried to (and failed to) demonstrate that life has the characteristics expected from architects and artificers.
The fact that Paley’s straightforward and intellectually honest (if on the fuzzy side) standard has been abandoned in favor of idiotic claims that design is (normally) detected by elimination of other causes* shows how it really is all designer of the gaps.
Glen Davidson
*I really don’t know if this has ever been done IRL by intellectually honest seekers. But perhaps it has been done in some cases, so long as the design didn’t have to be miraculously complex and beyond present human capabilities.
At UD, colewd complains about the “strawman” of designer of the gaps, then resorts to same in the next paragraph:
Maybe. But that’s what real science does, finds actual problems based on actual constraints. Bogus crap like ID has no problems, as it has no solutions nor the means of getting to any. ID has yet to explain anything meaningfully. Evolutionary theory has problems because it has considerable explanatory resources, while not being able to actually go back and film the evolution of eukaryotes. Real histories of all kinds have problems of information lost to time. Fables, like ID, don’t.
Glen Davidson
Yet Colewd is completely incapable of articulating why.
This is hilarious. That’s not his argument.
Please elucidate his argument then, Mung.
I think this illustrates pretty well why IDiots can’t wrap their heads around the card deck fallacy. Of all the sequences, the selected ones had to be homologous to something in the wild or else don’t count… because they’re not “part of the plan”.
I would say, starting from random sequences and then mutation+selection, getting something that has an homologous in the wild might have suggested teleology… too bad it falsified “islands of functions” instead
Thanks for that insightful clarification Mung. I’m going to go ahead and keep believing you are mistaken until actual clarification is served. If that’s not alright with you I couldn’t give any less of a fuck. You are welcome to start contributing substantially instead of just offering vapid commentary.
This. It’s all they know. You are wrong and that’s it. They never notice they are never right as that’s not what it’s about for them.
Do you think Rumraket has provided an accurate portrayal of the argument?
Here’s gpuccio on the subject:
He denies reasoning from missing data. So either he is contradicting himself or you and your pals here at TSZ are misrepresenting him.
gpuccio:
Who do you suppose he is talking about?
Rumraket even quoted gpuccio as saying:
Then Rumraket went on to ignore everything before that and…
I am perfectly capable of “contributing substantially instead of just offering vapid commentary,” but have to ask myself why should I? Who here really wants honest respectful dialogue?