Moving Past the Systematics Wars

How Phenograms and Cladograms Became Molecular Phylogenetic Trees

Tree diagrams are the prevailing form of visualization in biological classification and phylogenetics. Already during the time of the so-called Systematist Wars from the mid-1960s until the 1980s most journal articles and textbooks published by systematists contained tree diagrams. Although this episode of systematics is well studied by historians and philosophers of biology, most analyses prioritize scientific theories over practices and tend to emphasize conflicting theoretical assumptions. In this article, I offer an alternative perspective by viewing the conflict through the lens of representational practices with a case study on tree diagrams that were used by numerical taxonomists (phenograms) and cladists (cladograms). I argue that the current state of molecular phylogenetics should not be interpreted as the result of a competition of views within systematics. Instead, molecular phylogenetics arose independently of systematics and elements of cladistics and phenetics were integrated into the framework of molecular phylogenetics, facilitated by the compatibility of phenetic and cladistic practices with the quantitative approach of molecular phylogenetics. My study suggests that this episode of scientific change is more complex than common narratives of battles and winners or conflicts and compromises. Today, cladograms are still used and interpreted as specific types of molecular phylogenetic trees. While phenograms and cladograms represented different forms of knowledge during the time of the Systematist Wars, today they are both used to represent evolutionary relationships. This indicates that diagrams are versatile elements of scientific practice that can change their meaning, depending on the context of use within theoretical frameworks.

Against unifying homology concepts: Redirecting the debate

The term "homology" is persistently polysemous, defying the expectation that extensive scientific research should yield semantic stability. A common response has been to seek a unification of various prominent definitions. This paper proposes an alternative strategy, based on the insight that scientific concepts function as tools for research: When analyzing various conceptualizations of homology, we should preserve those distinguishing features that support particular research goals. We illustrate the fruitfulness of our strategy by application to two cases. First, we revisit Lankester's celebrated evolutionary reappraisal of homology and argue that his analysis has been distorted by assimilation to modern agendas. His "homogeny" does not mean the same thing as modern evolutionary "homology," and his "homoplasy" is no mere antonym. Instead, Lankester uses both new terms to pose a question that remains strikingly relevant-how do mechanistic and historical causes of morphological resemblance interact? Second, we examine the puzzle of avian digit homology, which exemplifies disciplinary differences in homology conceptualization and assessment. Recent progress has been fueled by the development of new tools within the relevant disciplines (paleontology and developmental biology) and especially by increasing interdisciplinary cooperation. Conceptual unification has played very little role in this work, which instead seeks concrete evolutionary scenarios that integrate all the available evidence. Together these cases indicate the complex relationship between concepts and other tools in homology research.

Pattern Without Process: Eugen Smirnov and the Earliest Project of Numerical Taxonomy (1923-1938)

The progress towards mathematization or, in a broader context, towards an increased "objectivity" is one of the main trends in the development of biological systematics in the past century. It is commonplace to start the history of numerical taxonomy with the works of R. R. Sokal and P. H. A. Sneath that in the 1960s laid the foundations of this school of taxonomy. In this article, I discuss the earliest research program in this field, developed in the 1920s by the Russian entomologist and biometrician Eugen (Evgeniy Sergeevich) Smirnov. The theoretical and methodological grounds of this program are considered based on the published works of Smirnov as well as some archival sources. The influence of Smirnov's evolutionary (mechano-Lamarckian) convictions on the development of this project of "exact systematics" is analyzed as well as the author's attempts to establish a novel concept of "mathematical essentialism" in animal taxonomy. The probable causes of the failure of Smirnov's project are viewed from both externalist and internalist perspectives, including the opposition to the use of quantitative methods in biology by some of the Lysenkoist ideologists in the USSR. A brief comparison of Smirnov's research program with that developed 40 years later by Sokal and Sneath is provided.

Ronald Brady and the cladists

Ronald Brady was the first philosopher to defend pattern cladistics as an independent scientific field. That independence was achieved through the decoupling of biological systematics from phylogenetics--that is, inferred evolutionary processes (e.g. character transformation). Brady saw parallels between biological systematics and Wolfgang von Goethe's Morphology, an empirical scientific field that incorporates human observation and perception to discover coherent morphological structures. Goethe's Morphology and pre-Darwinian systematics were independent from evolutionary narratives, a tradition that continued into the 20th Century through the work of biologists such as Agnes Arber. Most importantly, Brady provided the philosophical and historical foundations to an independent systematics by demonstrating the links between phenomenology, Goethe's Morphology and comparative biology.

Coordinating dissent as an alternative to consensus classification: insights from systematics for bio-ontologies

The collection and classification of data into meaningful categories is a key step in the process of knowledge making. In the life sciences, the design of data discovery and integration tools has relied on the premise that a formal classificatory system for expressing a body of data should be grounded in consensus definitions for classifications. On this approach, exemplified by the realist program of the Open Biomedical Ontologies Foundry, progress is maximized by grounding the representation and aggregation of data on settled knowledge. We argue that historical practices in systematic biology provide an important and overlooked alternative approach to classifying and disseminating data, based on a principle of coordinative rather than definitional consensus. Systematists have developed a robust system for referring to taxonomic entities that can deliver high quality data discovery and integration without invoking consensus about reality or "settled" science.

Animal Behavior, Population Biology and the Modern Synthesis (1955-1985)

This paper examines the history of animal behavior studies after the synthesis period. Three episodes are considered: the adoption of the theory of natural selection, the mathematization of ideas, and the spread of molecular methods in behavior studies. In these three episodes, students of behavior adopted practices and standards developed in population ecology and population genetics. While they borrowed tools and methods from these fields, they made distinct uses (inclusive fitness method, evolutionary theory of games, emphasis on individual selection) that set them relatively apart and led them to contribute, in their own way, to evolutionary theory. These episodes also highlight some limitations of "conjunction narratives" centered on the relation between a discipline and the modern synthesis. A trend in conjunction narratives is to interpret any development related to evolution in a discipline as an "extension," an "integration," or as a "delayed" synthesis. I here suggest that this can lead to underestimate discontinuities in the history of evolutionary biology.

Background knowledge: the assumptions of pattern cladistics

This paper reviews the ontogeny of pattern cladistics from the 1970s and 1980s, rebuts criticisms by contemporary anti-cladists, and endeavours to clarify persistent misunderstandings about the philosophical foundations of the approach.