Gpuccio: Functional Information Methodology

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.

As for the confusion of homology with similarity, that seems common among molecular biologists, not just Gpuccio.

Bad idea. Taxonomic ranks are arbitrary and taxa of the same rank can’t be considered equivalent. Even as a starting point.