Rasmus Grønfeldt Winther

Character Analysis in Cladistics: Abstraction, Reification, and the Search for Objectivity

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.

Realism, Antirealism, and Conventionalism about Race

This paper distinguishes three concepts of “race”: bio-genomic cluster/race, biological race, and social race. We map out realism, antirealism, and conventionalism about each of these, in three important historical episodes: Frank Livingstone and Theodosius Dobzhansky in 1962, A. W. F. Edwards’s 2003 response to Lewontin’s 1972 paper, and contemporary discourse. Semantics is especially crucial to the first episode, while normativity is central to the second. Upon inspection, each episode also reveals a variety of commitments to the metaphysics of race. We conclude by interrogating the relevance of these scientific discussions for political positions and a post-racial future.

Schaffner’s Model of Theory Reduction: Critique and Reconstruction*

Schaffner’s model of theory reduction has played an important role in philosophy of science and philosophy of biology. Here, the model is found to be problematic because of an internal tension. Indeed, standard antireductionist external criticisms concerning reduction functions and laws in biology do not provide a full picture of the limits of Schaffner’s model. However, despite the internal tension, his model usefully highlights the importance of regulative ideals associated with the search for derivational, and embedding, deductive relations among mathematical structures in theoretical biology. A reconstructed Schaffnerian model could therefore shed light on mathematical theory development in the biological sciences and on the epistemology of mathematical practices more generally.

Evo-devo as a Trading Zone

Evo-Devo exhibits a plurality of scientific “cultures” of practice and theory. When do these cultures act—individually or collectively—in ways that actually move research forward, empirically, theoretically, and ethically? When do they become imperialistic, in the sense of excluding and subordinating other cultures? This chapter identifies six cultures—three styles (mathematical modeling, mechanism, and history) and three paradigms (adaptationism, structuralism, and cladism). The key assumptions standing behind, under, and within each of these cultures are explored. Characterizing the internal structure of each is necessary for understanding how they collaborate or compete, and how they are fragmented or integrated, in the rich interdisciplinary trading zone (Galison 1997) of Evo-Devo. Evo-Devo is an important example of how science can progress through a radical plurality of perspectives and cultures.

Prediction in Selectionist Evolutionary Theory

Selectionist evolutionary theory has often been faulted for not making novel predictions that are surprising, risky, and correct. I argue that it in fact exhibits the theoretical virtue of predictive capacity in addition to two other virtues: explanatory unification and model fitting. Two case studies show the predictive capacity of selectionist evolutionary theory: parallel evolutionary change in E. coli and the origin of eukaryotic cells through endosymbiosis.

Mathematical modeling in biology: philosophy and pragmatics.

Philosophy can shed light on mathematical modeling and the juxtaposition of modeling and empirical data. This paper explores three philosophical traditions of the structure of scientific theory – Syntactic, Semantic, and Pragmatic – to show that each illuminates mathematical modeling. The Pragmatic View identifies four critical functions of mathematical modeling: (1) unification of both models and data, (2) model fitting to data, (3) mechanism identification accounting for observation, and (4) prediction of future observations. Such facets are here explored using a recent exchange between two groups of mathematical modelers in plant biology. Scientific debate can arise from different philosophies of modeling.

Introduction: from a philosophical point of view.

The six articles of this section of the special issue explore philosophical questions of comparative biology, very broadly construed. Under this category, I place systematics, classification, and historical Darwinian evolutionary theory. Classic epistemic and metaphysical questions of comparative biology include: Are species natural kinds or individuals? What are the proper units of the biological hierarchy(ies) pertinent to evolution and classification? What is the fundamental relation between the Tree of Life and the Linnean Hierarchy? Why was Darwin’s (putative?) focus on variational rather than typological thinking so revolutionary? How does phylogenetic inference and reasoning work? Moreover, how should it work? How are parts of complex historical systems individuated? What would a historically sensitive notion of the biological function of structures, behaviors and characters look like? These questions have been investigated from a philosophical point of view at least since the seminal work of philosophers who started analytical philosophy of biology during the 1960s and 1970s, including David Hull, Michael Ruse, Elliot Sober, and William Wimsatt. Biologists such as Richard Lewontin, Ernst Mayr, and Stephen J. Gould have also contributed significantly to setting the question agenda on these matters. We find ourselves today at a dizzying time in biological research. Astounding data-driven progress is being made in a variety of broad biological fields including: (1) genomics, proteomics, and systems biology, (2) biodiversity and ecology, and (3) evolutionary developmental biology (‘‘evo-devo’’). This is not the place to substantiate the reality and depth of these research fields; I trust that that is clear and present to the reader. However, this is a place to argue that each of these growth fields relies heavily—if not explicitly, then certainly implicitly—on comparative biology. Briefly consider the following questions for each area: How do we investigate and discover the function of a particular gene or molecule? We perform a comparative analysis of that gene sequence or molecular structure across a range

Introduction: Genomics and philosophy of race

Philosophy of race has become a multi-faceted subfield of philosophy, drawing on philosophy of biology, metaphysics, philosophy of language, ethics, and political philosophy. Race cuts across disciplinary lines within philosophy. Moreover, disciplines outside philosophydincluding population genetics, anthropology, sociology, and educationdhave much to contribute to discourse about race. A persistent danger of interdisciplinary conversation is that of talking past each other. For instance, scholars in different disciplines have distinct race concepts and use local intellectual machinery to address questions about race. One simple way to address these issues is to have the relevant parties meet each other frequently and repeatedly. But there are some barriers to this strategy. It requires openness, patience, and charity from the participants, and physical proximity is an important consideration. We realized that our own geographic regiondthe San Francisco Bay Areadprovided the necessary concentration of open, patient, and charitable scholars from many disciplines interested in race. During the 2013e2014 academic year, our group of biologists, philosophers, and social scientistsmet for twoworkshops (Stanford, UC Davis) and a public conference (UC Santa Cruz) to discuss a variety of concerns surrounding genomics and race. As a group we shared a commitment to thinking critically about how theoretical population genetics and genomics conceptualize andmodel certain constructs, such as “populations,” which, in turn, are deemed by some to be “races,” as theoretical achievements move from a circumscribed biological domain out to the general public. Therewas of course not complete agreement, but we benefited tremendously from learning from each other. Indeed, we believe the papers in this special issue are evidence that we are now a group of philosophically-informed scientists and scientifically-informed philosophers.