Rasmus Grønfeldt Winther

Two controversies exist regarding the appropriate characterization of hierarchical and adaptive evolution in natural populations. In biology, there is the Wright-Fisher controversy over the relative roles of random genetic drift, natural selection, population structure, and interdemic selection in adaptive evolution begun by Sewall Wright and Ronald Aylmer Fisher. There is also the Units of Selection debate, spanning both the biological and the philosophical literature and including the impassioned group-selection debate. Why do these two discourses exist separately, and interact relatively little? We postulate that the reason for this schism can be found in the differing focus of each controversy, a deep difference itself determined by distinct general styles of scientific research guiding each discourse. That is, the Wright-Fisher debate focuses on adaptive process, and tends to be instructed by the mathematical modeling style, while the focus of the Units of Selection controversy is adaptive product, and is typically guided by the function style. The differences between the two discourses can be usefully tracked by examining their interpretations of two contested strategies for theorizing hierarchical selection: horizontal and vertical averaging

There are two fundamentally distinct kinds of biological theorizing. "Formal biology" focuses on the relations, captured in formal laws, among mathematically abstracted properties of abstract objects. Population genetics and theoretical mathematical ecology, which are cases of formal biology, thus share methods and goals with theoretical physics. "Compositional biology," on the other hand, is concerned with articulating the concrete structure, mechanisms, and function, through developmental and evolutionary time, of material parts and wholes. Molecular genetics, biochemistry, developmental biology, and physiology, which are examples of compositional biology, are in serious need of philosophical attention. For example, the very concept of a "part" is understudied in both philosophy of biology and philosophy of science. ;My dissertation is an attempt to clarify the distinction between formal biology and compositional biology and, in so doing, provide a clear philosophical analysis, with case studies, of compositional biology. Given the social, economic, and medical importance of compositional biology, understanding it is urgent. For my investigation, I draw on the philosophical fields of metaphysics and epistemology, as well as philosophy of biology and philosophy of science. I suggest new ways of thinking about some classic philosophy of science issues, such as modeling, laws of nature, abstraction, explanation, and confirmation. I hint at the relevance of my study of two kinds of biological theorizing to debates concerning the disunity of science

August Weismann is famous for having argued against the inheritance of acquired characters. However, an analysis of his work indicates that Weismann always held that changes in external conditions, acting during development, were the necessary causes of variation in the hereditary material. For much of his career he held that acquired germ-plasm variation was inherited. An irony, which is in tension with much of the standard twentieth-century history of biology, thus exists – Weismann was not a Weismannian. I distinguish three claims regarding the germ-plasm: (1) its continuity, (2) its morphological sequestration, and (3) its variational sequestration. With respect to changes in Weismann’s views on the cause of variation, I divide his career into four stages. For each stage I analyze his beliefs on the relative importance of changes in external conditions and sexual reproduction as causes of variation in the hereditary material. Weismann believed, and Weismannism denies, that variation, heredity, and development were deeply intertwined processes. This article is part of a larger project comparing commitments regarding variation during the latter half of the nineteenth century.

I analyze the importance of parts in the style of biological theorizing that I call compositional biology. I do this by investigating various aspects, including partitioning frames and explanatory accounts, of the theoretical perspectives that fall under and are guided by compositional biology. I ground this general examination in a comparative analysis of three different disciplines with their associated compositional theoretical perspectives: comparative morphology, functional morphology, and developmental biology. I glean data for this analysis from canonical textbooks and defend the use of such texts for the philosophy of science. I end with a discussion of the importance of recognizing formal and compositional biology as two genuinely different ways of doing biology – the differences arising more from their distinct methodologies than from scientific discipline included or natural domain studied. Ultimately, developing a translation manual between the two styles would be desirable as they currently are, at times, in conflict.

Geographic Information Science (GIS) is an interdisciplinary science aiming to detect and visually represent patterns in spatial data. GIS is used by businesses to determine where to open new stores and by conservation biologists to identify field study locations with relatively little anthropogenic influence. Products of GIS include topographic and thematic maps of the Earth’s surface, climate maps, and spatially referenced demographic graphs and charts. In addition to its social, political, and economic importance, GIS is of intrinsic philosophical interest due to its methodological richness and because it is an instructive analogue to other sciences. This chapter works towards a philosophy of GIS and cartography, or PGISC. In particular, it examines practices of classifying geographic space, objects, and relations. By focusing on the use of natural kinds in data modeling and map generalization practices, I show how the making and using of kinds is contextual, fallible, plural, and purposive.

Albert Einstein once made the following remark about "the world of our sense experiences": "the fact that it is comprehensible is a miracle." (1936, p. 351) A few decades later, another physicist, Eugene Wigner, wondered about the unreasonable effectiveness of mathematics in the natural sciences, concluding his classic article thus: "the miracle of the appropriateness of the language of mathematics for the formulation of the laws of physics is a wonderful gift which we neither understand nor deserve" (1960, p. 14). At least three factors are involved in Einstein's and Wigner's miracles: the physical world, mathematics, and human cognition. One way to relate these factors is to ask how the universe could possibly be structured in such a way that mathematics would be applicable to it, and we would be able to understand that application. This is roughly Wigner's question. Alternatively, the way of the mathematical naturalist is to argue that we abstract certain properties from the world, perhaps using our bodies and physical tools, thereby articulating basic mathematical concepts, which we continue building into the complex formal structures of mathematics. John Stuart Mill, Penelope Maddy, and Rafael Nuñez teach this strategy of cognitive abstraction, in very different manners. But what if the very concepts and basic principles of mathematics were built into our cognitive structure itself? Given such a cognitive a priori mathematical endowment, would the miracles of the link between world and cognition (Einstein) and mathematics and world (Wigner) not vanish, or at least significantly diminish? This is the stance of Stanislas Deheane and Elizabeth Brannon's 2011 anthology, following a venerable rationalist tradition including Plato and Immanuel Kant.

Multiculturalism requires sustained and serious philosophical reflection, which in turn requires public outreach and communication. This piece briefly outlines concerns raised by the philosophy of multiculturalism and, conversely, multiculturalism in philosophy, which ultimately force us to reconsider the philosopher’s own role and responsibility. I conclude with a provocative suggestion of philosophy as /public diplomacy/. (As this is intended to be a piece for a general audience, secondary literature is only referred to in the conclusion. References gladly provided upon request.)

Darwin's ideas on variation, heredity, and development differ significantly from twentieth-century views. First, Darwin held that environmental changes, acting either on the reproductive organs or the body, were necessary to generate variation. Second, heredity was a developmental, not a transmissional, process; variation was a change in the developmental process of change. An analysis of Darwin's elaboration and modification of these two positions from his early notebooks (1836-1844) to the last edition of the /Variation of Animals and Plants Under Domestication/ (1875) complements previous Darwin scholarship on these issues. Included in this analysis is a description of the way Darwin employed the distinction between transmission and development, as well as the conceptual relationship he saw between heredity and variation. This paper is part of a larger project comparing commitments regarding variation during the latter half of the nineteenth century.

Paradoxically, explorers of the territory of consciousness seem to be studying consciousness out of existence, from inside the field of "consciousness studies". How? Through their love of the phenomenon/process, they have developed powerful single models or lenses through which to understand consciousness. But in doing so, they also seek to destroy the other /equally useful/ lenses. Our opportunity lies in halting the vendettas and cross-speakings/cross-fire. The imploration is to stop the dichotomous thinking and pernicious reification of single models, and instead search for divisions of labor, complementarities, and legitimate redescriptions among the various extant models. In other words, what would happen if we reimagined the conceptual classifications of the various models of consciousness, classifications based on general philosophical dichotomies (e.g., representational/non-representational and individualist/non-individualist), as a variety of compatible and even complementary perspectives on the same complex phenomenon and process? What would happen if rather than dig in our heels vis-à-vis our favorite theory of consciousness, at the exclusion of all the others, we saw our perceived enemy as an actual, indeed necessary, friend-in-waiting? What would it take to see a battlefield as a collaborative opportunity, to see a promising pluralism rather than an endless state space of conflict?

This article began as a review of a conference, organized by Gerhard Schlosser, entitled “Modularity in Development and Evolution.” The conference was held at, and sponsored by, the Hanse Wissenschaftskolleg in Delmenhorst, Germany in May, 2000. The article subsequently metamorphosed into a literature and concept review as well as an analysis of the differences in current perspectives on modularity. Consequently, I refer to general aspects of the conference but do not review particular presentations. I divide modules into three kinds: structural, developmental, and physiological. Every module fulfills none, one, or multiple functional roles. Two further orthogonal distinctions are important in this context: module-kinds versus module-variants-of-a-kind and reproducer versus nonreproducer modules. I review criteria for individuation of modules and mechanisms for the phylogenetic origin of modularity. I discuss conceptual and methodological differences between developmental and evolutionary biologists, in particular the difference between integration and competition perspectives on individualization and modular behavior. The variety in views regarding modularity presents challenges that require resolution in order to attain a comprehensive, rather than a piecemeal and fragmentary, evolutionary developmental biology.

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 explored using a recent exchange between two groups of mathematical modelers in plant biology. Scientific debate can arise from different modeling philosophies.

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. *Received November 2006; revised March 2009. †To contact the author, please write to: Philosophy Department, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064; e‐mail: [email protected].

Although epistasis is at the center of the Fisher-Wright debate, biologists not involved in the controversy are often unaware that there are actually two different formal definitions of epistasis. We compare concepts of genetic independence in the two theoretical traditions of evolutionary genetics, population genetics and quantitative genetics, and show how independence of gene action (represented by the multiplicative model of population genetics) can be different from the absence of gene interaction (represented by the linear additive model of quantitative genetics). The two formulations converge with weak selection but not with strong selection or, for multiple loci, when the aggregated interaction terms are not negligible. As a result of the different formulations of gene interaction, the presence or absence of linkage disequilibrium,/D/, does not necessarily indicate the presence or absence of fitness epistasis. Indeed, linkage disequilibrium is generated in ‘additive’ models in quantitative genetics whenever two (or more) loci experience simultaneous selection. As a research strategy, it is often practical, for theoretical or experimental reasons, to minimize gene interaction by assuming independence of gene action in regard to fitness, or by assuming linear additive effects of multiple loci on a phenotype. However, minimizing the role of epistasis in theoretical investigations hinders our understanding of the origins of diversity and the evolution of complex phenotypes.

Two families of mathematical methods lie at the heart of investigating the hierarchical structure of genetic variation in Homo sapiens: /diversity partitioning/, which assesses genetic variation within and among pre-determined groups, and /clustering analysis/, which simultaneously produces clusters and assigns individuals to these “unsupervised” cluster classifications. While mathematically consistent, these two methodologies are understood by many to ground diametrically opposed claims about the reality of human races. Moreover, modeling results are sensitive to assumptions such as preexisting theoretical commitments to certain linguistic, anthropological, and geographic human groups. Thus, models can be perniciously reified. That is, they can be conflated and confused with the world. This fact belies standard realist and antirealist interpretations of “race,” and supports a pluralist conventionalist interpretation.

Tom Stoppard’s 1966 play (and 1990 movie) /Rosencrantz and Guildenstern are Dead/ is a metatext – as a text, it interprets, builds upon, and refers to another text, Shakespeare’s Hamlet. Similarly, David N. Reznick’s /The Origin then and now: An interpretative guide to the Origin of Species/ (Princeton UP, 2010) is also a metatext. In this review, I turn to the history of science to evaluate whether Reznick’s book shares three families of virtues with Stoppard’s play: (i) brevity and precision, (ii) intrigue and appeal, and (iii) a genuine value-add to the original.

A scientific explanatory project, part-whole explanation, and a kind of science, part-whole science are premised on identifying, investigating, and using parts and wholes. In the biological sciences, mechanistic, structuralist, and historical explanations are part-whole explanations. Each expresses different norms, explananda, and aims. Each is associated with a distinct partitioning frame for abstracting kinds of parts. These three explanatory projects can be complemented in order to provide an integrative vision of the whole system, as is shown for a detailed case study: the tetrapod limb. My diagnosis of part-whole explanation in the biological sciences as well as in other domains exploring evolved, complex, and integrated systems (e.g., psychology and cognitive science) cross-cuts standard philosophical categories of explanation: causal explanation and explanation as unification. Part-whole explanation is itself one essential aspect of part-whole science.