A user's guide to the tree of life

2005

I have taught a course on the diversity of life almost every year that I have had university teaching appointments. Even as a graduate student I taught or assisted in such courses. Through that period, the appreciation for the diversity of life within the biology curriculum has waxed and waned. Moreover, the subject itself has undergone considerable change from 1970 to the present. At first, all of life was divided into plants (Botany) and animals (Zoology). This dichotomy seemed natural and went all the way back to the time of Aristotle (384-322 BCE). Such was my training in college and graduate school. The first courses that I taught on biological diversity as a new professor was called Plant Diversity and covered all living things that were not considered animals. Someone else taught zoology. Then, the five-kingdom system finally took hold and the course evolved into something called Plants, Protists, and Fungi, which was similar to Plant Diversity but incorporated the animal-lik...

Cladistics, 2013

Recent commentary by Costello and collaborators on the current state of the global taxonomic enterprise attempts to demonstrate that taxonomy is not in decline as feared by taxonomists, but rather is increasing by virtue of the rate at which new species are formally named. Having supported their views with data that clearly indicate as much, Costello et al. make recommendations to increase the rate of new species descriptions even more. However, their views appear to rely on the perception of species as static and numerically if not historically equivalent entities whose value lie in their roles as "metrics". As such, their one-dimensional portrayal of the discipline, as concerned solely with the creation of new species names, fails to take into account both the conceptual and epistemological foundations of systematics. We refute the end-user view that taxonomy is on the rise simply because more new species are being described compared with earlier decades, and that, by implication, taxonomic practice is a formality whose pace can be streamlined without considerable resources, intellectual or otherwise. Rather, we defend the opposite viewpoint that professional taxonomy is in decline relative to the immediacy of the extinction crisis, and that this decline threatens not just the empirical science of phylogenetic systematics, but also the foundations of comparative biology on which other fields rely. The allocation of space in top-ranked journals to propagate views such as those of Costello et al. lends superficial credence to the unsupportive mindset of many of those in charge of the institutional fate of taxonomy. We emphasize that taxonomy and the description of new species are dependent upon, and only make sense in light of, empirically based classifications that reflect evolutionary history; homology assessments are at the centre of these endeavours, such that the biological sciences cannot afford to have professional taxonomists sacrifice the comparative and historical depth of their hypotheses in order to accelerate new species descriptions.

An Outline of a Conceptual Framework for Contemporary Biological Systematics, 2023

Biological systematics, exploring the structure of taxonomic diversity (TD), needs a proper conceptualization that would (a) make it complying with certain universal criteria of scientificity and (b) take into account specificity of its studied object. This article outlines a possible conceptual framework for this natural science discipline based on the ideas of contemporary conceptualism. One of the most fundamental of them includes a concept of cognitive situation shaped by three interrelated basic components-ontic, epistemic, and subjective. Its core position is taken by a taxonomic theory (TT) being a conceptual construct resulted from a "summative" effect of all three components and designed for studying TD. The general TT is shown to be composed by a hierarchically arranged array of partial TTs of various levels of generality, and this construct serves as a conceptual justification of taxonomic pluralism. Several kinds of partial TTs are suggested to recognise, viz., ontology-and epistemology-oriented, aspect-and object-based, etc. The aspect-based TTs are of special importance as the conceptual foundations of particular research programs in systematics. The object-based partial TTs are shown to be implemented by concepts of species and homology. A large-scale relation between taxonomic theory and nomenclature is briefly considered.

PLoS biology, 2018