When scientists use a taxon name like Mammalia, it is important that they talk about the same thing. But, what does it mean to be the same thing in different phylogenetic hypotheses? And, how is taxonomic reference maintained across hypotheses? Here, we discuss the differences between real and hypothetical clades, and how such a distinction relates to the sameness problem. Since hypotheses influence how we perceive things and pursue science, we find it important to have a functioning nomenclatural system for clades as perceived in phylogenetic hypotheses. As a solution to the sameness problem for such clades, we argue that a taxon name does not primarily refer to a single clade that somehow mirror the reality of branches in the tree of life. Instead we suggest that a taxon name refers to a set, or natural kind, of counterfactual and reconstructed clades.

Om relationen mellan biologin idag och Linnés klassificeringssystem

Recent developments in biological nomenclature suggest advantages of phylogenetic alternatives to more traditional Linnaean approaches. My aim is to discuss some fundamental aspects underlying biological nomenclature in general and phylogenetic nomenclature in particular. A basic assumption, in both traditional and phylogenetic nomenclature, is that taxon names can and should be defined. From the ontological view of individuality I question this view and argue that taxon names only refer since no defining properties are involved for particular clades. Even if we accept the idea that a taxon is a natural kind with a historical essence, and thus has defining properties, I see problems of definitions from an epistemological and inferential point of view. Our conceptualization of phylogeny is dependent on our hypotheses. Therefore, definitions based on discarded hypotheses are problematic. Instead, each new and accepted hypothesis should form the basis of our conceptualization. Another theme in this paper is what should count as the same taxon under different hypotheses. Can a phylogenetic definition guarantee that a name always refers to the same taxon under different hypotheses? I argue that this is questionable. I conclude by suggesting that we need to rethink the role of definition, sameness, and stability in nomenclature. Rethinking these concepts, I believe, will shed some new light on biological nomenclature. My conclusions strongly favor a phylogenetic approach to nomenclature but also suggest that we, besides some practical problems, still have many interesting theoretical and philosophical aspects to take into account.

In this paper I draw attention to the concepts of content and ancestry in phylogenetic nomenclature. I argue that these concepts are tightly linked and that they cannot be separated as suggested by Bryant and Cantino [Biol. Rev. 77 (2002) 39] in their recent response to a critique of phylogenetic nomenclature. In addition, I argue that the basic assumption in phylogenetic nomenclature that a taxon-name always refers to the same ancestor or ancestry is questionable.

In the present paper I argue that the two systems of phylogenetic nomenclature hitherto proposed represent, in a generalized sense, two different philosophies for how science develops and progresses. The phylogenetic system of definition. initially proposed by de Queiroz and Gauthier [Syst. Zool. 39 (1990) 307], and later labeled PSD, is typically Popperian in the 'sense that science progresses toward truth by An accumulation of knowledge. Phylogenetic definitions of taxon names are assumed to adapt automatically to each new hypothesis of phylogeny, thereby reflecting better and better hypotheses. The phylogenetic system of reference proposed by Harlin [Zool. Scr. 27 (1998a) 381], on the other hand, is more Kuhnian, because it is built on the idea that successive hypotheses are incommensurable (and thus not cumulative) and that taxon names might be equalled with low-level paradigms.