PhyloCode names are not useful for phylogenetic synthesis
From the post:
Which brings me to the title of this post. In the PhyloCode, taxonomic names are not hypothetical concepts that can be refuted or refined by data-driven tests. Instead, they are definitions involving specifiers (designated specimens) that are simply applied to source trees that include those specifiers. This is problematic for synthesis because if two source trees differ in topology, and/or they fail to include the appropriate specifiers, it may be impossible to answer the basic question I began with: do the trees share any clades (taxa) in common? If taxa are functions of phylogenetic topology, then there can be no taxonomic basis for meaningfully comparing source trees that either differ in topology, or do not permit the application of taxon definitions. (emphasis added)
If you substitute “names” for “taxa” then it is easy to see my point in Plato, Shiva and A Social Graph about nodes that are “abstract concept devoid of interpretation.” There is nothing to compare.
This isn’t a new problem but a very old one that keeps being repeated.
For processing reasons it may be useful to act as though taxa (or names) are simply given. A digital or print index need not struggle to find a grounding for the terms it reports. For some purposes, that is completely unnecessary.
On the other hand, we should not forget the lack of grounding is purely a convenience for processing or other reasons. We can choose differently should an occasion merit it.