Although there is increasing recognition that theory and practice in science are often inseparably intertwined, discussions of scientific controversies often continue to focus on theory, and not practice or methodologies. As a contribution to constructing a framework towards understanding controversies linked to scientific practices, we introduce the notion of borrowed epistemic credibility, to describe the situation in which scientists exploit fallacious similarities between accepted tenets in other fields to garner support for a given position in their own field. Our proposal (...) is based on the analysis of a recent controversy in phylogeography, a biological subdiscipline concerned with the study of the historical causes of variation in genetic diversity within species in concrete biogeographical locations. Through a review of the arguments that support the two conflicting phylogeographic schools, we show that ‘theory’ plays essentially no role as a foundation of the controversy, whereas both sides borrow epistemic credibility from sources such as formal logic, similarity of results to those in other scientific areas, the authority of prominent scientists, or the presumed superiority of quantitative vs. verbal reasoning. Our case study underscores the indivisibility of theory and practice and provide a means to re-examine important philosophical issues such as the meaning of inference, rationality, justification, and objectivity in scientific practice. (shrink)

The dangers of character reification for cladistic inference are explored. The identification and analysis of characters always involves theory-laden abstraction—there is no theory-free “view from nowhere.” Given theory-ladenness, and given a real world with actual objects and processes, how can we separate robustly real biological characters from uncritically reified characters? One way to avoid reification is through the employment of objectivity criteria that give us good methods for identifying robust primary homology statements. I identify six such criteria and explore each (...) with examples. Ultimately, it is important to minimize character reification, because poor character analysis leads to dismal cladograms, even when proper phylogenetic analysis is employed. Given the deep and systemic problems associated with character reification, it is ironic that philosophers have focused almost entirely on phylogenetic analysis and neglected character analysis. (shrink)

The history of biological systematics documents a continuing tension between classifications in terms of nested hierarchies congruent with branching diagrams (the ‘Tree of Life’) versus reticulated relations. The recognition of conflicting character distribution led to the dissolution of the scala naturae into reticulated systems, which were then transformed into phylogenetic trees by the addition of a vertical axis. The cladistic revolution in systematics resulted in a representation of phylogeny as a strictly bifurcating pattern (cladogram). Due to the ubiquity of character (...) conflict—at the genetic or morphological level, or at any level in between—some characters will necessarily have to be discarded ( qua noise) in favor of others in support of a strictly bifurcating phylogenetic tree. Pattern analysts will seek maximal congruence in the distribution of characters (ultimately of any kind) relative to a branching tree-topology; process explainers will call such tree-topologies into question by reference to incompatible evolutionary processes. Pattern analysts will argue that process explanations must not be brought to bear on pattern reconstruction; process explainers will insist that the reconstructed pattern requires a process explanation to become scientifically relevant, i.e., relevant to evolutionary theory. The core question driving the current debate about the adequacy of the ‘Tree of Life’ metaphor seems to be whether the systematic dichotomization of the living world is an adequate representation of the complex evolutionary history of global biodiversity. In ‘Questioning the Tree of Life’, it seems beneficial to draw at least four conceptual distinctions: pattern reconstruction versus process explanation as different epistemological approaches to the study of phylogeny; open versus closed systems as expressions of different kinds of population (species) structures; phylogenetic trees versus cladograms as representations of evolutionary processes versus patterns of relationships; and genes versus species as expressions of different levels of causal integration and evolutionary transformation. (shrink)

Molecular methods have revolutionised virtually every area of biology, and metazoan phylogenetics is no exception: molecular phylogenies, molecular clocks, comparative phylogenomics, and developmental genetics have generated a plethora of molecular data spanning numerous taxa and collectively transformed our understanding of the evolutionary history of animals, often corroborating but at times opposing results of more traditional approaches. Moreover, the diversity of methods and models within molecular phylogenetics has resulted in significant disagreement among molecular phylogenies as well as between these and earlier (...) phylogenies. How should this broad and multifaceted problem be tackled? I argue that the answer lies in integrating evidence to infer the best evolutionary scenario. I begin with an overview of recent development in early metazoan phylogenetics, followed by a discussion of key conceptual issues in phylogenetics revolving around phylogenetic evidence, theory, methodology, and interrelations thereof. I then argue that the integration of different kinds of evidence is necessary for arriving at the best evolutionary scenario rather than merely the best-fitting cladogram. Finally, I discuss the prospects of this view in stimulating interdisciplinary cross-talk in early metazoan research and beyond, and challenges that need to be overcome. (shrink)