Do all deer share a common ancestor?

[Tim]

@Giltil

Clearly, with this astonishing claim, it can be seen that it’s you who have a problem with logic, not Gpuccio.

“Clearly” your astonishment is both idiosyncratic, and misplaced.

“It can be seen” that your conclusion is a non sequitor and thus fallacious.

@Giltil

Well, to my comment that Gpuccio was allowed to express his view on this site in a special, very unusual way, ie through a dedicated thread only open to the scholars frequenting this site, you first reply by saying that it was hardly unusual on this forum. As far as I can tell, it is unusual for since I participate in this forum, it has happened only for two guests, namely Gpuccio and Winston Ewert. I may be wrong. If so, I would welcome any correction on this matter.

Consider yourself corrected then – most recently, this thread was created for discussion of Rope Kojonen’s book, and then restricted to exclude “anonymous/non-academic participants” when he turned up. This did not, in fact, stop Kojonen from getting eviscerated by many of the non-anonymous academic participants.

@Giltil

You also added that it is certainly not an indication that the individual so ‘honored’ is worthy of any credibility. I think your statement here is illogical and that the special way Gpuccio was allowed to express his view is evidence that he was considered here as as a knowledgeable and articulate person with interesting views worth being debated by the best experts on this forum.

Your fallacious argument rests on two false premises:

1. That having a moderated-thread is in some way “special”. Heck, even I got a moderated (“curated”) thread once – for a discussion that I eventually came to the conclusion was a complete waste of bandwidth and time.

2. That being “allowed to express his view” is in some way an indication that his views are credible. Heck, even @colewd is “allowed to express his view” on this forum, and even the replies to him on this thread should give you an indication of how little credibility he has here.

@Giltil

Here are some quotes that make this point taken from the thread where Gpuccio expressed his view on this forum:

These comments are simply boiler-plate ‘welcomes’, and confer no credibility. If you want to see how credible he is here, you need to read further down the thread to see how his ideas held up under scrutiny. It would seem that they were viewed with skepticism that Gpuccio was unable to dispel:

@Faizal_Ali

That conclusion just comes out of nowhere. I fail to see how he has supported his belief that this protein was “engineered”.

@John_Harshman

A few thoughts. First, it seems to me that a simple pairwise comparison is completely inadequate for what he claims to be doing, and using the actual phylogenetic tree, with lots of chordate sequences, would better enable him to do what he seems to be trying to do here very clumsily, which is to estimate the sequences at internal nodes. And also to estimate sequence conservation. More work than clicking on a few buttons in BLAST, but a much better approach. Oh, I see @davecarlson has already mentioned this.

Second, I don’t understand why similarity to the human sequence should estimate functional information. If you started with a tunicate sequence, would you not see something similar, and wouldn’t that show a big information jump on the way to Ciona? I do not, in general, see an argument for relating bitscore to functional information.

@Art

As far as I can tell, the goal is to estimate what gpuccio calls “human conserved FI”, the idea being (as far as I can tell) that large amounts of “human conserved FI” will be suggestive of design. What confuses me is the method that is used to arrive at “human conserved FI”, and how this relates to any parameter that may suggest design.

To illustrate – gpuccio estimates the “human conserved FI” for a given protein by subtracting the bit scores from BLAST comparisons of human, shark, and Saccoglossus (H:S – H:Sa). The problem with this is that one can obtain very different values if one changes the organisms that are plugged into the analysis. For example, replace sharks with chimpanzees (Ch) and one gets much, much larger values. However, also replace Saccoglossus with the mouse (M) and the value for “human conserved FI” (H:Ch – H:M) will be much, much smaller.

To show why this doesn’t make much sense to me, consider instead the Saccharomyces species (cerevisiae and fragilis), and, as an “outgroup” to represent some unicellular predecessor, Plasmodium. Run gpuccio’s calculation (Sc:Sf - Sc:P) and one gets a result that would call for design in the origination of yeasts (probably, for the comparison I present here, the amount of “conserved FI” would be much greater for yeast than for humans when that latter is calculated using chimpanzees and mice).

Thus, as best I can tell, “conserved FI” is little more than a measure of evolutionary relatedness. One can rig the calculation to obtain pretty much any value one wants, and the value would reflect relationships between the three organisms used for the analysis. Nothing more, IMO.

Beyond this, it is not clear to me what the connection is between “conserved FI” and design. I suspect (but would welcome correction) that gpuccio is drawing on the work of Dembski, Axe, Behe, et al. who argue that information, defined as the frequency of occurrence of a functional sequence in sequence space, is suggestive of design when it is high. However, as many, many discussions here on PS have shown, the ID vanguard is wrong when it comes to their ideas about protein functionality and information. This calls into question gpuccio’s use of the term, and the conclusions drawn.

@Art

I may have more later, but for now it should be noted that the bit score from a BLAST search and the informational number of bits used to identify design may be two rather different things. The usage adopted by gpuccio and most ID proponents is just a -log2 transformation of the ratio of functional to all possible sequences. I don’t believe the bit score from a BLAST search is the same thing.

@Rumraket

Whether some protein grew in size during the evolution of some clade or along some branch, or how conserved that protein is in that clade, seems to me to have little to nothing to do with whether it was designed. What am I missing?

@sfmatheson

Speaking only for myself, I don’t think there is any reason to discuss design, or “ID theory,” in this context until the very basic questions asked by @swamidass are addressed. And I would reiterate that asking this question outside of even a basic phylogenetic analysis/approach is futile.

It is not possible to talk meaningfully about “functional information” without these basic foundational tasks being done.

@Rumraket

This is what you should be working to demonstrate. You have now asserted this, so you should proceed to demonstrate the truth of this assertion.

@glipsnort

Be that as it may, this thread is about @gpuccio’s argument, and that argument relies on BLAST bit scores being a good proxy for the defined sense of FI. But they’re not.

@Art

I would note that the bits calculated in this cited essay cannot be equated with bits derived from either BLAST analyses or the equation for FI that has been given above. They are quite completely different, and the calculation in the essay simply does not provide a bit-based estimate of probabilistic resources.

@gpuccio gpuccio, have you ever considered trying to derive expressions that would formalize the relationships between the different information calculations you have presented here? I believe this is possible for the BLAST-FI usages, and a clever mathematical biologist could probably do something similar for the metric you describe in the cited essay. I believe this could be a valuable addition to this field, as it were, and would address a lot of the concerns and confusion that you may see here, or have encountered before.

Etc, etc.