Pattern Cladistics and the ‘Realism–Antirealism Debate’ in the Philosophy of Biology

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.

Section: Defending "Pattern Cladistics"mentioning

confidence: 99%

Ronald Brady and the cladists

Ebach

Williams

2019

“…it may have a “just so” aspect). In my personal experience, implementing Rieppel's () approach can lead to counter‐intuitive coding schemes, especially if one were to argue that character state propositions are merely conjectures that require a limited amount of theorizing (for discussion see de Pinna, ; Brady, ; Vergara‐Silva, ).…”

Section: Sequence Of Analytical Stages—from Legacy Character Assemblymentioning

confidence: 99%

Anatomy of a cladistic analysis

Franz

2013

The sequential stages culminating in the publication of a morphological cladistic analysis of weevils in the Exophthalmus genus complex (Coleoptera: Curculionidae: Entiminae) are reviewed, with an emphasis on how early-stage homology assessments were gradually evaluated and refined in light of intermittent phylogenetic insights. In all, 60 incremental versions of the evolving character matrix were congealed and analysed, starting with an assembly of 52 taxa and ten traditionally deployed diagnostic characters, and ending with 90 taxa and 143 characters that reflect significantly more narrow assessments of phylogenetic similarity and scope. Standard matrix properties and analytical tree statistics were traced throughout the analytical process, and series of incongruence length indifference tests were used to identify critical points of topology change among succeeding matrix versions. This kind of parsimony-contingent rescoping is generally representative of the inferential process of character individuation within individual and across multiple cladistic analyses. The expected long-term outcome is a maturing observational terminology in which precise inferences of homology are parsimony-contingent, and the notions of homology and parsimony are inextricably linked. This contingent view of cladistic character individuation is contrasted with current approaches to developing phenotype ontologies based on homology-neutral structural equivalence expressions. Recommendations are made to transparently embrace the parsimony-contingent nature of cladistic homology. 1 The terms "scope" and "scoping" are used herein in the sense of Rieppel (2007a). A properly scoped character or homology is formulated in such a way that it refers precisely to the intended set of taxa -no more (including unintended taxa within or outside of the analysis), and no less (failing to refer to intended taxa). Rieppel (2007a) discusses the effects of scope expansion and restriction (i.e. shifts in taxon sampling schemes) on character codings.

“…This biogeographical approach, especially regarding consilient hypotheses, is a complementary perspective to previous papers concerning realism (e.g. Ruse, 1979;Rieppel, 2007;Vergara-Silva, 2009) and also the lack of empirical foundation (e.g. Kearney and Rieppel, 2006;Rieppel and Kearney, 2007;Assis, 2009) in systematics.…”

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confidence: 91%

“…Although there seems to be no room for prediction in phylogenetic analyses (Rieppel et al., 2006; Rieppel, 2008) and, as said before, instrumentalism advocates hypotheses only as tools to generate predictions, an instrumentalist perspective is a very pervasive approach throughout contemporary systematics. It is conducted in a manner similar to that proposed by the empiricist Bas van Fraassen in the so‐called “constructive‐empiricism” (see Vergara‐Silva, 2009, and references therein). Under the constructive‐empiricism perspective, theories are supposed to provide the greater empirical adequacy among the statements they assemble, no aspect of realism being taken into account.…”

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confidence: 99%

Realism in systematics through biogeographical consilience

Capellari

Santos

2011

There is an overlooked gap between any phylogenetic hypothesis and the natural world shaped by historical evolutionary processes, since the main concern during phylogenetic analyses is solely the search for congruence among characters under a defined criterion. Given a scientific realistic view, however, phylogenetic hypotheses are scientific theories that try to depict the historical series of cladogenetic events among biological entities. In this sense, the challenge is to establish a form of measuring the degree of truthfulness of our phylogenetic hypotheses. Here, we advocate the use of consilient biogeographical hypotheses to recognize the biological meaning of a phylogenetic inference apart from its instrumentalist value. Our proposal is based on the assumption that robust biogeographical hypotheses allows us to be close to the real evolutionary history of taxa. © The Willi Hennig Society 2011.