Categorizing Ideas about Trees: A Tree of Trees

Abstract

The aim of this study is to explore whether matrices and MP trees used to produce systematic categories of organisms could be useful to produce categories of ideas in history of science. We study the history of the use of trees in systematics to represent the diversity of life from 1766 to 1991. We apply to those ideas a method inspired from coding homologous parts of organisms. We discretize conceptual parts of ideas, writings and drawings about trees contained in 41 main writings; we detect shared parts among authors and code them into a 91-characters matrix and use a tree representation to show who shares what with whom. In other words, we propose a hierarchical representation of the shared ideas about trees among authors: this produces a “tree of trees.” Then, we categorize schools of tree-representations. Classical schools like “cladists” and “pheneticists” are recovered but others are not: “gradists” are separated into two blocks, one of them being called here “grade theoreticians.” We propose new interesting categories like the “buffonian school,” the “metaphoricians,” and those using “strictly genealogical classifications.” We consider that networks are not useful to represent shared ideas at the present step of the study. A cladogram is made for showing who is sharing what with whom, but also heterobathmy and homoplasy of characters. The present cladogram is not modelling processes of transmission of ideas about trees, and here it is mostly used to test for proximity of ideas of the same age and for categorization.

Categorizing Ideas about Systematics: Alternative Trees of Trees, and Related Representations

“…Some variables were redundant, while 344 none of them expressed the important distinction between a tree (as in Hennig) and a network 345 However, to allow a direct comparison with the results of FL and to demonstrate the utility of 348 other exploratory methods, we decided not to introduce changes. In one sense it is thus good 349 news that our results confirmed several findings made by Fisler and Lecointre (2013), 350 especially regarding the choice of outgroups, and the presence of minor "clades". Not 351 surprisingly, our Tree 4, the additive one (which may also be conceived as a distance based 352 cladogram, i.e.…”

“…Although Fisler and Lecointre (2013) were skeptical about the usefulness of networks for 397 demonstrating changes of biological thought, we found them to be as meaningful as any tree 398 or ordination scatter plot. 399…”

“…In the present study, we use exactly the same data as used in Fisler and Lecointre (2013, their Table 3): 41 works (OTUs 2 ) described in terms of 91 variables, all of them nominal, with mostly 2, or rarely 3, states (possible values). Nominal variables represent the simplest type of data we can have: by using them the only judgment we can make about the OTUs is whether or not they possess the given variable.…”

“…The data from Table 3 of Fisler and Lecointre (2013) rearranged to follow the three-cluster 494 classification obtained by UPGMA clustering (groups A to C), such that the sequence of 495 writings is in the same order as in the dendrogram of Fig. 2.…”

“…36 These categories are determined in most cases based on a fairly subjective basis, without 37 formal quantitative analyses of the views expressed by designated representatives of these 38 schools. A noted exception is a recent paper by Fisler and Lecointre (2013;abbreviated 39 hereafter as FL) who recognized that ideas in biology may be described in terms of many 40 measurable variables simultaneously, allowing the possibility of objective comparisons. 41 FL selected 41 published works with the purpose to categorize ideas about "phylogenetic" 42 trees and tree-based classifications.…”