Comments on Gpuccio: Functional Information Methodology

Yes, but it is clear @gpuccio has lots and lots of things he wants to tell us about before he gets to the big reveal, if he ever does. You know and I know what a big disappointment that is going to be. But this should prove to be a very enlightening demonstration of how ID’ers think science works.

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Indeed, I have already answered in detail questions #2 and #3. I have also asnwered briefly question #1, but I have to detail. I will do that in next post.

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Can someone explain to me what’s in this graph?

I see three curves, what are they derived from? Are those names of clades on the red dotted line? What’s “cart”? “afro”? “mars”? Should there be a line between them? I’m getting DAP vibes from this.

I get some vague sense that it’s about some proteins that grew in size during their previous 500 million year history in some lineages in some clades. Okay. And?

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I will agree you have written lots and lots and lots of words in response to those questions. As to whether those questions have been answered, I suppose that is up to the individual reader to decide.

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To his credit, he has willingly painted himself into a corner in which his claim could easily be refuted in no uncertain terms. ID Creationists are not usually so willing to do this.

The real test, of course, will be his response to when the refutation is made…

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If any of you scholarly types who are allowed to comment is paying attention here, I would like to know why gpuccio is using the crude measure of pairwise BLAST scores rather than actual reconstruction of sequences on a phylogenetic tree.

Like this: Lee et al. 2013. Rates of Phenotypic and Genomic Evolution during the Cambrian Explosion. Current Biology 23:1889-1895.

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We asked him this too. We are waiting for him to respond. I’m going to give this some more time to play out and then summarize the issues. This will be on the list for sure.

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This is a very strange condition upon which to insist. The issue is whether evolution (which produces only “biological objects”) can produce 500 bits of FI, or whether this can only be produced by “design.” No one is suggesting a third option. So even if you rule out such 3rd options, that does not help resolve the central question in any way.

e.g. If it was demonstrated that the bacteria in the Lenski long-term evolution experiment produced 500 bits of new FI, this would not meet the criteria you are demanding. Yet this would be a clear refutation of your “design” argument.

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I disagree. The search space is going to be dependent on the pre-existing genome, and we simply don’t know enough about genomes 400 million years ago to do this, at least from what I can see. You seem to be assuming that functional sequences emerge de novo from previously non-functional DNA, but this certainly doesn’t have to be the case. There could have been pre-cursor genes that had functional tertiary structures that were then modified through subsequent mutations. That pre-cursor gene could have been lost to history. If there is billions of years of evolution that led to a gene that was one mutation away from finding a novel function, then you would need to factor in those billions of years of evolution into your calculations.

Those approximations are wild guesses, at best. On top of that, your target space needs to incorporate all functional space, not just the function that did evolve. Nature is full of species that found different strategies for adapting to environmental challenges, and I would suggest this extends to the molecular level. For example, intron splicing is just one possible function that could have arisen. A completely different method for dealing with misfolded proteins could have emerged.

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I’d give that post a million likes, if I could.

This is where we see if ID is science or religious apologetics…

[mod edit: this post is in reference to Gpuccio: Functional Information Methodology, the reference was removed when the post was moved to the comments thread]

Just as an FYI if you didn’t know already, you can cut-n-paste a quote from the main thread into a response here to make sure the reference is clear. It’s a lot cleaner than the moderators moving posts over here.

So there we have it, I can not have ten consecutive ancestors according to Gpuccio.

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That’s not as damning to @gpuccio’s claim as the fact that hundreds of different antibodies perform the same function (binding the same antigen) in one person, and hundreds of different ones in another.

@gpuccio’s estimate of target space has no basis in reality.

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We would also have to ask if any observation of evolving function in sequences would be evidence against design, or if these observations would be considered ongoing design. Behe famously stated that if we observed something like the bacterial flagellum evolving in the lab this would disprove design, but he also seemed to walk this back in more recent times. On the face of it, it would seem rather strange that design would suddenly stop, unless there is a theological reason to make this argument.

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if we are talking about sequence space i think that its not true when we are dealing with convergent evolution. at this case we can know what is the chance to get the same function again, since we have evidence for it.

I think you point is powerful especially we see a highly similar sequence re appearing through convergence.

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Posting this comment from UD (link at 69)

Comment 467

(UprightBiPed)

“Note to the “experts” at PS:

You are equivocating on the vast (and very well-documented) difference between what physicists refer to as “physical” or “structural” information, and the semantic information contained in the gene system (the source of specification and control over protein synthesis).

Joshua Swamidass, biological information is semantic and rate-independent, requiring a coordinated set of non-integrable constraints, to be actualized in a non-reversible process. The process itself requires complimentary descriptions in order to be understood. Structural or physical “information”, on the other hand, is purely dynamic and reversible. Clearly, you should know these things, and should not present yourself as an expert on the subject while casually equivocating between these diametrically-opposed meanings. A protein is the product of an encoded description; the position of the stars in the night sky are not. Neither are the locations of islands on the open sea. Neither are weather patterns and tornadoes.”

Forgive the naive question, but how does one measure the increase in FI in a situation where a sequence of junk DNA undergoes neo-functionalization? Would it be treated as if the entire sequence had just popped into existence whole cloth as a new functional element?

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The problem is the inclusion of the latter under the category “semantic” information is the point in question. The large majority of experts who do not accept the creationist argument also do not accept the creationist claim that the physical and chemical interactions of the molecules involved in biological processes are directly analogous to sort of semantic information involved in, say, a written novel or a computer program.

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Yes, I guess that "the chance that a tornado sweeping through a junkyard might assemble a Boeing 747 » is not null. But we would rather not consider this type hypothesis if we are to remain in the domain of science!

There are only 3 causes that can explain an object, i.e., chance, necessity or design. If you can rule out chance or necessity or a combination of both, then design is the explanation and you don’t need to compute the probability of design to draw a design inference. According to ID theory, objects exhibiting high level of FI can’t be produced by chance or by necessity or a combination of both. Therefore, they are designed. This is ID in a nutshell.

As far as biological objects are concerned, I think this is indeed the only real issue here. ID theorists think that as a rule of thumb, most fonctional protein are very rare in the sequence space. If true, ID wins. If wrong, ID may be in trouble. My take is that most functional proteins are very rare in the sequence space. But I will let @gpuccio elaborate on this point if he want.

You are committing here the Texas sharpshooter fallacy.