Wtf does that even mean?
1 Like
Hi Bill,
Letâs see what Ewert states in the Predictions section of his paper, p. 5:
Addressing the gene family sizes or exact sequences is left to future research.
Do you need me to go into more detail, Bill, or do you now see from Ewertâs own hand that you greatly misunderstood both this discussion and Ewertâs paper?
Best,
Chris
2 Likes
[quote=âcolewd, post:176, topic:8066â]. @Chris_Falter
You said
Sadly, neither of these interesting conjectures make any predictions about distribution patterns of phylogenetic characters, amino acid sequences, or DNA sequences. To his credit, Ewert explicitly recognizes the inability of his model to address sequence data.
I responded
I respectfully disagree. The dependency chart makes a prediction that the data will fall into a pattern that we see in software design called a dependency chart. Winston did some simulations to show this. The problem is right now the sequence data bases are not robust enough to support this work very well.
[/quote]
I misunderstood that your comment was talking specifically about sequences vs the gene families he compared⌠As you can see from my whole quote I realized the sequence data in some of the data bases used is immature.
My only point is that he is building a predictive tool. It will be a better tool when the sequence databases mature. Page 8 has a list of the data bases and when I discussed this with Winston off line he said that he crossed referenced the information in the 8 databases.
How would Ewertâs method be adapted to sequence data if the data bases were âmatureâ?
1 Like
The issue is to accurately represent the gene families. When I scrubbed the data around humans rats mice and chimps the data base had around 100 genes that were uniquely shared with chimps and rats. Some of these genes had very similar sequences in humans. This puts into the doubt that all the 100 genes in the gene family were unique to rats and chimps. I wrote Winston and he acknowledged the issue. Improving the data base will increase the accuracy of the dependency chart.
You didnât scrub the data at all Bill. DNA_Jock posting over at TSZ showed you that claim was all wrong and based solely on annotation errors at HomoloGene.
You commented on the work at TSZ so I know you saw it. Yet here you are repeating a claim you know to be false. What does that make you Bill?
3 Likes
Bill, you are very far out of your depth. What you have just said is that you have no idea how to adapt Ewertâs method to sequence data, and this has nothing to do with the condition of any database. This makes sense, as it would be impossible to adapt the method to sequence data.
2 Likes
Sequence data is a check for if he has isolated gene families correctly.
We are talking about a dependency diagram not a tree as a model for the data. His claim is a dependency diagram is a best fit for the data. He uses the tree as a control for testing his method.
Which DNA_Jockâs analysis showed he did NOT do correctly.
Want to explain why you are completely ignoring all the contradictory data DNA_Jock showed you? Is ignoring contradictory data an honest thing to do?
2 Likes
So you agree, as you originally denied, that the model canât incorporate sequence data, just presence/absence data. If you canât understand the model itâs hard for you to defend it.
1 Like
The same thing is going on with Billâs defense of @gpuccioâs false assumption that sequence conservation correlates with functional information:
âThe simple assumption is that such information, which is not modified by neutral variation in a time span of hundreds of million years, is certainly highly functionally constrained, and is therefore a very good empirical approximation of the value of functional information in a protein.â
This has no basis in reality. It is objectively false. The easiest proteins with which to illustrate its falsehood are sarcomeric (muscle) proteins.
So, Bill, I defined âcorrelationâ for you and you havenât offered a substantive response. Do you really not understand that you can neither support nor falsify a correlation by citing a single item? That correlation is about fitting a line/curve to a lot of those items? And that neither you nor @gpuccio has bothered to do that?
1 Like
I really donât understand the point you are trying to make. Sequences are part of the model by definition as comparing them is a method to determine if genes of different animals are the same.
I donât think your definition is correct. Itâs simply trying to defend your assertion.
the process of establishing a relationship or connection between two or more measures.
STATISTICS
interdependence of variable quantities.
When the sequences are not mutating neutrally we have established a relationship between functional constraint and functional information.
Bill do you understand deeply conserved sequences can vary a great deal in sequence length? If we accept your latest claim you just refuted the ID argument FI can be calculated bases solely on sequence length.
Way to shoot yourself in the foot again big guy! 
1 Like
Yes, but the dependency graph is supposed to explain why there is tree-structure in the presence or absence of certain genes. So sequences, as you note, are only used to determine whether the gene is there or not. They are used to recognize the genes.
It does not explain the patterns in the presence or absence of particular mutations in those genes. It does not explain why they have the sequences that they do in different species. It does not explain why they are even different at all.
2 Likes
No, we have not.
1 Like
Then offer your own definition of âcorrelation,â Bill.
You keep trying to move the goalposts. We are disagreeing about the alleged correlation between sequence conservation (not âfunctional constraintâ) and functional information.
This isnât that complicated. We are discussing the validity of @gpuccioâs assumption. I credit him with admitting that it is merely an assumption, something you appear to be unwilling to do:
âThe simple assumption is that such information, which is not modified by neutral variation in a time span of hundreds of million years, is certainly highly functionally constrained, and is therefore a very good empirical approximation of the value of functional information in a protein.â
https://uncommondescent.com/intelligent-design/the-amazing-level-of-engineering-in-the-transition-to-the-vertebrate-proteome-a-global-analysis/
I am simply pointing out that there is no correlation between sequence conservation and functional information. The assumption is false. This is an objective, empirical statement.
Your lack of interest in the relevant evidence speaks volumes.
1 Like
Thatâs my point exactly. You donât understand any of this.
2 Likes
If that was true, you or one of the other creationist/IDers would have done it long ago, and youâd be referencing or reproducing it, rather than blathering about it. But you arenât, they havenât, and it isnât.
2 Likes
We have Roy. It simply becomes evolutionist denial that it is hierarchal. Just like Rum"s denial that preservation was evidence of correlation of functional information and Harshmanâs denial that sequence data was a method of how gene families were established.
At some point I need to write off your guys in ability to see reality. If ideology is first the facts no longer matter.