A reply to ‘Science versus vernacular’: should some taxa of animals and plants be renamed according to ‘indigenous’ practices?

Palma & Heath (2021) have recently commented on our proposal to reinstate indigenous names within the Linnaean system of nomenclature on the basis of their chronological priority. They argue that this challenges rules that have been unquestioned for 250 years. However, we hold that the rules of the various codes of nomenclature are constantly under review. The opinion they prosecute crystallises down, in large part, to one that suggests that because there are pre-existing rules about priority, we should not change these: an argument that involves a degree of circularity. Unfortunately, Palma and Heath misinterpret our proposal throughout much of their discussion. We do not advocate replacing the binomina as is claimed nor do we advocate for name changes where there is no consensus on a given taxon among the people indigenous to the natural distribution of that taxon. Our proposal is that indigenous names can replace the species epithet where there is a consensus on a single indigenous name for a taxon throughout its distribution and where there is demonstrable temporal priority. Without such consensus, species that cover wide distributions and have multiple indigenous names will, under our proposal, remain unchanged in their nomenclature.

Avenues into Integration: Communicating taxonomic intelligence from sender to recipient

“What is crucial for your ability to communicate with me… pivots on the recipient’s capacity to interpret—to make good inferential sense of the meanings that the declarer is able to send” (Rescher 2000, p148). Conventional approaches to reconciling taxonomic information in biodiversity databases have been based on string matching for unique taxonomic name combinations (Kindt 2020, Norman et al. 2020). However, in their original context, these names pertain to specific usages or taxonomic concepts, which can subsequently vary for the same name as applied by different authors. Name-based synonym matching is a helpful first step (Guala 2016, Correia et al. 2018), but may still leave considerable ambiguity regarding proper usage (Fig. 1). Therefore, developing "taxonomic intelligence" is the bioinformatic challenge to adequately represent, and subsequently propagate, this complex name/usage interaction across trusted biodiversity data networks. How do we ensure that senders and recipients of biodiversity data not only can share messages but do so with “good inferential sense” of their respective meanings? Key obstacles have involved dealing with the complexity of taxonomic name/usage modifications through time, both in terms of accounting for and digitally representing the long histories of taxonomic change in most lineages. An important critique of proposals to use name-to-usage relationships for data aggregation has been the difficulty of scaling them up to reach comprehensive coverage, in contrast to name-based global taxonomic hierarchies (Bisby 2011). The Linnaean system of nomenclature has some unfortunate design limitations in this regard, in that taxonomic names are not unique identifiers, their meanings may change over time, and the names as a string of characters do not encode their proper usage, i.e., the name “Genus species” does not specify a source defining how to use the name correctly (Remsen 2016, Sterner and Franz 2017). In practice, many people provide taxonomic names in their datasets or publications but not a source specifying a usage. The information needed to map the relationships between names and usages in taxonomic monographs or revisions is typically not presented it in a machine-readable format. New approaches are making progress on these obstacles. Theoretical advances in the representation of taxonomic intelligence have made it increasingly possible to implement efficient querying and reasoning methods on name-usage relationships (Chen et al. 2014, Chawuthai et al. 2016, Franz et al. 2015). Perhaps most importantly, growing efforts to produce name-usage mappings on a medium scale by data providers and taxonomic authorities suggest an all-or-nothing approach is not required. Multiple high-profile biodiversity databases have implemented internal tools for explicitly tracking conflicting or dynamic taxonomic classifications, including eBird using concept relationships from AviBase (Lepage et al. 2014); NatureServe in its Biotics database; iNaturalist using its taxon framework (Loarie 2020); and the UNITE database for fungi (Nilsson et al. 2019). Other ongoing projects incorporating taxonomic intelligence include the Flora of Alaska (Flora of Alaska 2020), the Mammal Diversity Database (Mammal Diversity Database 2020) and PollardBase for butterfly population monitoring (Campbell et al. 2020).

5. Species and classification

‘Species and classification’ first considers the species problem and the biological species concept. It then discusses phylogenetic systematics, which involves the organization of species into higher taxa. Classification in science raises a deep philosophical issue as all objects can in principle be classified in more than one way. Is there a ‘correct’ way to assign organisms to species, and species to higher taxa? Classification of organisms was traditionally done using the Linnaean system, which served biologists well for years, and elements of it are still used today. However, the rise of evolutionary biology has led to fundamental changes in both the theory and practice of biological classification.

Wars of the Roses

During the latter half of the eighteenth century, opposition to the sexual theory intensified among social and religiously conservative asexualists who felt threatened by the political theories of the Enlightenment. For some, the Linnaean system was a stalking horse for libertinism, radical Jacobinism, feminism and anarchy. They maintained their ideological purity citing philosophical, religious and pedagogical reasons for rejection. Among the opponents were the Marquis de Condorcet, Hans Möller and William Smellie. Lazzaro Spallanzi and Charles Alston tried, but failed, to repeat Camerarius’s experiments. Flowers were so feminized symbolically the idea that most flowers were hermaphroditic seemed perverse, but Mary Wollstonecraft attacked hyper-feminine poetic metaphors for women as inimical to the struggle for equality. Meanwhile, hybridization experiments by Joseph Gottlieb Koelreuter eliminated the last rational objection to the sexual theory and demolished the preformationist theory, in both ovist and spermist versions. Christian Konrad Sprengel laid the foundation for floral ecology.

Behind the Green Door

Chapter 14 explores literary and scientific reactions to the idea of sex in plants. England experienced a fashion for “phytoerotica”: bawdy verse, in which plants represented human genitalia, and classically inspired poetry, in which stamens and pistils were personified as husbands, wives and lovers. The former had little to do with plants. The latter served to teach the Linnaean sexual classification system. In reaction, some botanists rejected both the sexual theory and the Linnaean system. Two camps developed, the “sexualists” and the “asexualists”. J.G. Siegesbeck railed, “[Who] will ever believe that God Almighty should have introduced such…shameful whoredom for the propagation of the reign of plants.” The negative impact of the sexual system on the morals of women became the asexualist’s rallying cry. In 1759, the Pope banned all Linnaeus’s books and ordered them burned. Nevertheless, Erasmus Darwin’s “Loves of Plants,” with its fascinating female plant characters, was a hit.

Taxonomy - for Computers

We explore solutions for identifying and reconciling taxonomic concepts that take advantage of the powers of computational representation and reasoning without compromising the suitability of the Linnaean system of nomenclature for human communication. Using the model of the semiotic triangle, we show that taxonomic names must variously achieve reference to nomenclatural types, taxonomic concepts (human-created theories of taxonomic identities), and taxa (evolutionary entities in nature). Expansion of the reference models into temporally transitioning systems shows that the elements of each triangle, and provenance among elements across triangles, are only identifiable if taxonomic names and concepts are precisely contextualized. The Codes of nomenclature, by mandating identifier (name) reuse but not requiring concept-specific identifier granularity, leave the challenge of framing and aligning the symbol/reference instances to human communicators who have superior cognitive abilities in this regard. Computers, in turn, can process greater volumes of narrowly framed and logically aligned data. Comparative, taxonomically referenced biological data are becoming increasingly networked and reutilized in analyses that expand their original context of generation. If we expect our virtual comparative information environments to provide logically enabled taxonomic concept provenance services, then we must improve the syntax and semantics of human taxonomy making - for computers.