It would be more accurate to state that Gpuccio’s methodology assumes “that those 800 bits are a good estimator of specific FI” – as we have no evidence that it’s a “good estimator” of anything of the sort.
This is not “design detection” but merely ‘design assumption’ and ‘design assertion’.
It sounds like Gpuccio doesn’t understand what he’s doing. A fine example of the pseudoscience of ID. I can’t imagine why you’re trying to defend it when it dies no credit to you or ID.
“Human specific FI” would - by definition - be in humans alone, so you’re really not making sense here. However Gpuccio’s measure does assume that humans are special because the measure of information is similarity to the human protein. Neutral changes will be counted as information - and if the sequence is highly conserved there will be neutral changes that persist for long periods of time.
It should be clear that Gpuccio’s methodology is not measuring that at all. There’s not even an attempt to measure FI. You ought to know that by now,
Since he doesn’t measure bits of conserved sequence similarity - and they wouldn’t be a good measure of FI if he did his methodology is hopelessly flawed. Again, this is a clear example of pseudoscience.
What does that even mean? How does “human-specific” FI compare to plain vanilla FI? How can he be measuring this quantity of unknown significance and simultaneously claim to be following Szostak’s definition? And now you and Gpuccio admit that he isn’t measuring Szostak’s FI, just the similarity of sequences to human sequences, which is what the rest of us have been saying all along. This does not help your point.
I think you’re right here, and I should have said « Gpuccio made clear several times that he doesn’t estimate the totality of FI, but only vertebrates specific FI. »
Not sure to understand your point here. But no, neutral changes don’t persist for long periods of time.
Then how can he claim it can’t evolve? The closer you get to human, the more human-specific the sequence will become. The canonical human sequence evolved from a not-entirely-human sequence (which was specific to that ancestor), which evolved from one even less so, etc.
Same goes for all the other species-specific variants of the protein. They each evolved from ones less like the present one and ancestral to it. Incrementally over generations.
His method doesn’t work. He’s not really measuring FI, just similarity, and since extant species-specific sequences evolved incrementally from ancestor-specific sequences, he can’t justify any conclusion that the extant sequence couldn’t evolve.
Why don’t you get this? I must reiterate my request to have you explain how measuring sequence-similarity tells you that any extant sequence could not have evolved from some ancestral sequence increasingly dissimilar to it?
Please connect the dots. Explain how the similarity between two sequences becomes proportionally less and less with increasing time since their common ancestor, implies the extant sequence couldn’t have evolved incrementally from that common ancestor. And further, how this implies the last common ancestral squence in turn could not have evolved from some other sequence possibly performing some other function?
If you’re going to say you can infer design by ruling out evolution, and that you can rule out evolution with these similarity measures, you need to do a lot of work you haven’t done. You’ve just assumed what we are asking you to explain.
It still makes zero sense.
Why not? Please show your math.
Exactly.
Espistasis can lock in changes that were initially neutral. In the genetic background, specific mutations are neutral, but then when they have occured, further mutations can “lock in” those neutral mutations such that further changes to those residues are deleterious.
Yes, they can - if the sequence is highly conserved. If only a few changes to a sequence are possible, change will be rare - whether it is neutral or beneficial.
No, you were right the first time. He measures human-specific FI if he measures any sort of FI. The problem with that is that human-specific FI makes no sense, and he doesn’t measure FI anyway, just the degree of similarity of some protein sequence to a human sequence. The great scientific discovery Gpuccio has made, in fact his only discovery, as encapsulated in the two figures posted here, is that the more closely related a taxon is to humans, the more similar its proteins are likely to be to human proteins. This is cargo cult science at its finest.
Who is Gpuccio? Any sort of CV or Bio?
I can see a few things. His name is Giuseppe Puccio. He’s not a DI fellow, he has several articles on Zombie Uncommon Descent, but no information about him in them, and he comes up only once in a search of Evolution News, as a commenter on a blog. And there are lots of Giuseppe Puccios on line, so no idea which if any is “gpuccio”.
No, he measures vertebrate specific FI. At last, this is my understanding. Let’s see. Imagine that by measuring the sequence similarities of protein A between pre-vertebrates and human, you end up with only 10% similarities . Then you measure the similarities of the same protein between cartilaginous fish and human and end up with 75% similarities. Does it means that the totality of the 25% that doesn’t match aren’t necessary for the function of the human or the shark protein? Of course not, for some of the differences will certainly result from functional divergence, ie divergence due to different functional specificities in the two organisms. So no, Gpuccio doesn’t measure human specific FI but rather vertebrates specific FI.
First, that isn’t FI at all. Since he claims to be using Szostak’s definition, none of that fits Szostak’s definition. And any unexpressed other definition he may be actually using wouldn’t make any sense either.
Second, he’s not doing any multispecies comparisons, just pairwise comparisons with human sequences. So “vertebrate specific”, which would presumably require sampling a bunch of different vertebrates for a mass comparison, isn’t a thing.
Third, much of what you say here is word salad. What’s the point of the comparison between humans and “pre-vertebrates” (dubious term)? You bring it up and then immediately drop it. If some differences are due to functional diverence (unlikely to be true for most proteins, incidentally), what does that have to do with vertebrate FI? Just a mass of confused verbiage there.
All gpuccio measures is the similarity of various protein sequences to human protein sequences, one at a time. I will also point out that sharks are not the vertebrates most distant from humans either. What happened to lampreys and hagfish?
You are conducting a cargo cult defense of cargo cult science.
He doesn’t claim that.
Agree. I was wrong when I said that Gpuccio measures human specific FI for in reality he measure vertebrate specific FI.
Again, he doesn’t claim that extant sequences couldn’t evolve.
Although maybe a theoretical possibility, there is no trace of this imaginary scenario. And without evidence, I have reasons to doubt any such scenario, especially when considering the difficulties associated with them.
Then what was the point of that whole “500 bits” stuff if not to show the protein couldn’t evolve and therefore design?
Have you checked?
You have no more reason to doubt the ancestral protein evolved than you have to doubt the extant ones did. Are these reasons going to be a re-hash of all the same stuff previously debunked too?
You have provided no evidence that “Gpuccio’s analysis” of a purported “jump of functional information” has anything to do with this thread’s stated topic of “design detection”.
You have likewise provided no evidence that Gpuccio’s idiosyncratic graphs provide a reasonable approximation of Szostak’s definition of functional information, that being:
−log2 of the probability that a random sequence will encode a molecule with greater than any given degree of function.
Lacking evidence on both these points, I would point out that discussion of Gpuccio’s claims is woefully off-topic on this thread.
Gpuccio had this weird argument that if the FI for some function(performed by some class of proteins, say) was 500 bits or more, then it couldn’t evolve, because then sequences capable of performing the function would be incredibly rare in sequence space and thus evolution would not be expected to be able to find them. And then supposedly he could infer design because evolution is the only other game in town. Something to that effect.
The whole argument hinges on this idea that evolution must happen on one of these extremely rare sequences by a lucky guess. It is essentially built into the argument as an assumption that these rare sequences can’t be incrementally evolved towards through some alternative route where sequences have other, or simpler/more likely functions.
Gilbert is trying to get out of this by putting the burden of proof on us to show, for any given example of a protein function, that there are such indirect routes to the protein in question. There are some few cases where scientists have done that, but he can just play the “but what about this example?” game (with millions of uncharacterized protein sequences in the databases there will always be proteins who’s entire, or plausible histories and origins, haven’t been experimentally characterized.) Ultimately the argument comes down to not being able to prove evolution can do it to his satisfaction and if we can’t, “intelligent design” gets an automatic pass (nothing needs to be proven about this, to design proponents, it’s just assumed designers can do basically anything.)
Edit: Here is where Gpuccio states the if 500 bits or more → design argument:
So @Giltil is just wrong. This is what Gpuccio’s “FI method” is supposed to be doing. Finding examples of “big information jumps” of “500 bits or more” and through that ruling out evolution so you can infer design (by magically just knowing).
Intelligent design by revelation. In ID proponent land, designers design stuff by magically just knowing how to make something. If functional solutions are unfathomably rare in sequence space, designers can just wish them up by just knowing how to make something that can perform a particular function.
This whole thing all the rests of us had to do with learning and being taught and benefiting from thousands of generations of accumulated knowledge and experience. Interacting with the world, feedback, and gaining experience through that interaction. Nah forget it. Design is this mystical ability to gain the knowledge to solve a problem by magical revelation.
Magic. Design is literal magic to them. If by some argument with dubious premises a learning process can’t figure out how to solve a problem, then a magical instantiation of just knowing musta dun it. POOF
Don’t ever fall for this idea that the inference to design includes alien but ultimately material or naturalistic designers. Those would have had to learn stuff too to be able to design. Which just pushes the problem back a step. Those aliens would have had to originate too somehow. And sooner or later we’re into the design-by-magically-just-knowing “theory” of Intelligent Design.
This isn’t something that ever occurs in reality though. You can’t just magically know the solution to a long random password. This is what they are proposing intelligent design is, though. They have this probability argument that passwords can’t be randomly guessed because it would be extremely unlikely. And they can’t be evolved towards of course. So there must be this thing that magically just knows what the passwords are, and designs stuff by wishing the correct magically known things into existence.
That’s the essence of ID.
A corollary of this has to do with the common objection that the mere conduct of a scientific experiment amounts to intelligent interference that disqualifies the attendant scientific conclusions. For example, Ann Gauger on this board implied that scientists can telekinetically “guide” mutational outcomes, and thus that the uses of selection in genetics and evolutionary studies were invalid.
Of course, in such a world, it would be impossible to conduct scientific research. This is because diametrically-opposed hypotheses could both be confirmed by the scientists testing the hypotheses. If they want the hypothesis to be true, then their telekinetic powers would will the results to the proper outcome.
Which he ensures will never happen by ignoring the evidence.