Because the author not so much refutes but rather rejects the logic of the arguments of those he criticises, a response could at best be a rephrasing in different words of what I wrote in the paper that incensed him so. It consequently seemed pointless to write a reply, and indeed I would just refer again to that paper anybody who is interested in arguing about the information content of 'evolutionary' classifications, the feasibility of delimiting taxa based on long branches, and the relevance of a distinction between paraphyletic and polyphyletic taxa.
However, a few days later I picked the manuscript attached to the letter up another time and gave more attention than before to the second half, the one where the author's ire is directed towards the publications of Frank Zachos. There I found a section that motivated me to write something after all; not much, but something, simply because the section in question is so depressingly typical of much of the opposition to phylogenetic systematics:
Another subterfuge is to exempt species from the ban on paraphyly ("the concept of paraphyly does not apply to the species category"), so the "actual common ancestor is (or was) a species, but it does (did) not belong to any supraspecific subdivision of the descendant group" - again a desctructive [sic] (making classification cripple [sic], with millions - one for each "accepted" non-monotypic taxon! - of species "not belonging anywhere") and illogical "convention" designed only to defend the indefensibly harmful dogmaIt contains two claims of interest.
The first is that we have millions of species that under a phylogenetic classification would not belong into any higher taxon. This does not fly because firstly we don't actually have them (do you know which fossil bones belong to the one species that is the most recent common ancestor of all birds? because I don't), and secondly there is no problem with assigning the species to the clade that is descended from it.
But yes, under the unrealistic assumption that we could ever have a 100% certain ancestral species and wanted to confidently treat it as ancestral then it could not be assigned to any of the subclades of the clade whose common ancestor it is. That is how it should be, and there would still be no problem under a rankless phylogenetic classification, although a problem would arise from the Linnean binary species names. The problem is well understood, and it is partly for this reason that some cladists argue for abandoning Linnean ranks.
The second claim is the one that really pushed my button: that the inapplicability of the concept of paraphyly to species is a "subterfuge" and an "illogical convention designed only to defend the indefensibl[e]".
I believe that Willi Hennig's Phylogenetic Systematics is of relevance here, and in particular its chapter II: Tasks and methods of taxonomy. The first figure of that chapter is the original of the following famous diagram which I found on the website of the USA's National Center for Science Education:
Note the difference that Hennig makes between tokogenetic relationships within (sexual) species and phylogenetic relationships between species. Terms ending in -phyly such as monophyly or paraphyly apply to phylogenetic relationships. By their very definition they cannot apply where there is no phylogenetic relationship, in the same way that colour terms like 'red' or 'blue' cannot apply to a sound.
I do not mention this because I believe that whatever Willi Hennig wrote is automatically correct. The uncritical Darwin worship of some 'evolutionary' systematists weirds me out - as if nothing has been discovered and no new argument developed since 1859! Likewise, Hennig's arguments have to be evaluated on their merits, and it would be unsurprising to find that he was wrong about some things.
But this book from 1966 does have some relevance to the claim that cladists only "designed" the non-applicability of paraphyly to species as an "illogical convention" to defend what had become indefensible. Willi Hennig invented phylogenetic systematics, and that convention was there from the start. Indeed calling it merely a convention is utterly misleading; the whole logic of phylogenetic systematics is built on the observation that different classificatory principles apply within and between sexually reproducing species.
Sorry for shouting, but this is important. This distinction is the heart and core of cladism and has been so from the very first minute. Anybody who thinks that the incoherent phrase "but species are paraphyletic" is an argument against phylogenetic systematics operates at the same level as the creationist who asks why, if humans are descended from monkeys, there are still monkeys, or as the physics crank who thinks that his totally unprecedented idea of a flash-light on a train moving at light speed disproves Einstein. One should at least try to obtain a very rough understanding of something before one publicly declares it to be obviously illogical.