John Harshman- Still Ignorant about Nested Hierarchies

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John Harshman may be good at what he does but he definitely does not understand nested hierarchies. For one a phylogeny is not a nested hierarchy. For another Linnaean taxonomy is based on the premise of a Common Design and has nothing to do with descent with modification.

Harshman spews:

The support is simple: a nested hierarchy is exactly what we would expect from common descent (with branching).

That is false as every population has the chance of branching. That would mean that after only a few generations you would have the working of a mess.

It’s not what we expect from separate creation of species, which is what you mean by “common design”. 

Again, Linnaean taxonomy was predicated on a common design.

Phylogenetic analysis does not form a nested hierarchy. See Knox paper-  “The use of hierarchies as organizational models in systematics”, Biological Journal of the Linnaean Society, 63: 1–49, 1998.

And by the way, any pattern is determined by the mechanisms involved. Seeing that you don't know what the mechanism is that can transform populations of prokaryotes into a eukaryotes you can't even get your tree started.