Reification is to abstraction as disease is to health. Whereas abstraction is singling out, symbolizing, and systematizing, reification is neglecting abstractive context, especially functional, historical, and analytical-level context. William James and John Dewey provide similar and nuanced arguments regarding the perils and promises of abstraction. They share an abstraction-reification account. The stages of abstraction and the concepts of “vicious abstractionism,” “/the/ psychologist’s fallacy,” and “the philosophic fallacy” in the works of these pragmatists are here analyzed in detail. For instance, in (...) 1896 Dewey exposes various fallacies associated with reifying dualistic reflex arc theory. The conclusion prescribes treatments (pluralism and assumption archaeology) for de-reifying ill models (i.e., universalized, narrowed, and ontologized models) in contemporary scientific fields such as cognitive science and biology. (shrink)

Analytical categories of scientific cultures have typically been used both exclusively and universally. For instance, when styles of scientific research are employed in attempts to understand and narrate science, styles alone are usually employed. This article is a thought experiment in interweaving categories. What would happen if rather than employ a single category, we instead investigated several categories simultaneously? What would we learn about the practices and theories, the agents and materials, and the political-technological impact of science if we analyzed (...) and applied styles, paradigms, and models simultaneously? I address these questions in general and for a specific case study: a brief history of systematics. (shrink)

Pragmatism and the correspondence theory of truth are longtime foes. Nevertheless, there is an argument to be made that pragmatists must embrace truth as correspondence. I show that there is a distinctive pragmatic utility to taking truth to be correspondence, and I argue that it would be inconsistent for pragmatists to accept the utility of the belief that truth is correspondence while resisting the premise that this belief is correct. -/- In order to show how pragmatists can embrace truth as (...) correspondence, I develop a kind of alethic pluralism, which treats pragmatist truth as theoretically fundamental to truth as correspondence. This theoretical fundamentality of pragmatist truth allows the pragmatist to conditionally accept truth as correspondence for certain discourses without falling prey to the typical pragmatist objections to correspondence. This pluralist account of truth thus allows pragmatists to concede that, for certain domains of discourse, truth is correspondence, without thereby betraying their pragmatist principles. (shrink)

One of the reasons why GMOs have met public resistance in the past is that they are perceived as “unnatural”. The basis for this claim has, in part, to do with crossing species boundaries, which is considered morally objectionable. The emergence of CRISPR is sometimes argued to be an ethical game-changer in this regard since it does not require the insertion of foreign genes. Based on an empirical bioethics study including individual interviews and focus groups with laypeople and other stakeholders, (...) this article analyses the normative role of appeals to naturalness in discussions about the moral acceptability of using CRISPR in salmon farming. It discusses two dimensions of naturalness found in the material– living by species-specific nature and being unaffected by humans– and argues that these dimensions put down criteria for the application of CRISPR that lead to a conflict between our moral duties towards the farmed salmon and those we hold towards the wild salmon as a threatened species. It also points to a paradox which is likely to gain traction with further climate change and biodiversity loss, namely that while nature, understood as that which is unaffected by humans, is presented as an ideal, conserving nature in its pristine state may rely on technology and human intervention. (shrink)

How regular do mechanisms need to be, in order to count as mechanisms? This paper addresses two arguments for dropping the requirement of regularity from the definition of a mechanism, one motivated by examples from the sciences and the other motivated by metaphysical considerations regarding causation. I defend a broadened regularity requirement on mechanisms that takes the form of a taxonomy of kinds of regularity that mechanisms may exhibit. This taxonomy allows precise explication of the degree and location of regular (...) operation within a mechanism, and highlights the role that various kinds of regularity play in scientific explanation. I defend this regularity requirement in terms of regularity’s role in individuating mechanisms against a background of other causal processes, and by prioritizing mechanisms’ ability to serve as a model of scientific explanation, rather than as a metaphysical account of causation. It is because mechanisms are regular, in the expanded sense described here, that they are capable of supporting the kinds of generalizations that figure prominently in scientific explanations. (shrink)

This year’s topic is “Genomics and Philosophy of Race.” Different researchers might work on distinct subsets of the six thematic clusters below, which are neither mutually exclusive nor collectively exhaustive: (1) Concepts of ‘Race’; (2) Mathematical Modeling of Human History and Population Structure; (3) Data and Technologies of Human Genomics; (4) Biological Reality of Race; (5) Racialized Selves in a Global Context; (6) Pragmatic Consequences of ‘Race Talk’ among Biologists.

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. (shrink)

Leuridan (2010) argued that mechanisms cannot provide a genuine alternative to laws of nature as a model of explanation in the sciences, and advocates Mitchell’s (1997) pragmatic account of laws. I first demonstrate that Leuridan gets the order of priority wrong between mechanisms, regularity, and laws, and then make some clarifying remarks about how laws and mechanisms relate to regularities. Mechanisms are not an explanatory alternative to regularities; they are an alternative to laws. The existence of stable regularities in nature (...) is necessary for either model of explanation: regularities are what laws describe and what mechanisms explain. (shrink)

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. (shrink)

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. (shrink)

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. (shrink)

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. (shrink)

The Formalist tradition in late-scholastic philosophy has gone unnoticed in standard historiography. This article’s overall objective is to add the Formalist tradition to what we know about Renaissance philosophy. I first show how the Formalist tradition was born out of some innovative considerations of hierarchies of distinctions in the wake of the Franciscan John Duns Scotus’s teaching on the formal distinction in the beginning of the fourteenth century (especially Francis of Meyronnes’s model of four distinctions and Petrus Thomae’s more elaborate (...) doctrine of seven kinds of distinctions). I then trace how Formalist literature developed from being an exclusively Franciscan affair to becoming a much more widespread phenomenon. Thus, from the decades up to 1500 and onwards, authors from various late-scholastic schools (Thomism, Lullism, Averroism, and others) produced Formalist literature, i.e., treatises on multiple kinds of distinctions. I highlight particularly how one Franciscan philosopher of the sixteenth century, Jean Du Douet, proposed to view the Formalist preoccupation with distinctions as a discipline in its own right, a proper scientia formalitatum. I finally argue that while this proposal met with dismissive reactions, Du Douet’s idea does in fact reflect the role Formalism played in the scholastic curriculum in the late sixteenth century, at least in Franciscan milieus. (shrink)

A map is not its territory. Taking a map too seriously may lead to pernicious reification: map and world are conflated. As one family of cases of such reification, I focus on maps exuding the omphalos syndrome, whereby a centred location on the map is taken to be the world navel of, for instance, an empire. I build on themes from my book _When Maps Become the World_, in which I analogize scientific theories to maps, and develop the tools of (...) assumption archaeology and integration platforms. Here I argue that excavating assumptions helps fill cartographic silences, showing the limitations of perspectives often at war. Furthermore, integrating perspectives permits resisting imperial central or master images. A worthwhile future project would be a repository of world-navel maps, critically annotated with cultural context and imperial information. Mutual understanding may result from such an integration platform, perhaps implemented online or in a museum. (shrink)

An increasing vaccine hesitancy among parents, which has resulted in insufficient rates of immunization, provides reason to reconsider childhood vaccination practices. Studies suggest that parents' decision-making process concerning whether to vaccinate their child is highly influenced by cognitive biases. These biases can be utilized to increase vaccination uptake via changes in the choice context. This article considers childhood vaccination programmes, which involve children being vaccinated in school or daycare unless their parents actively ‘opt out’. We suggest that such programmes reconcile (...) parents' decisional authority and vaccination duties. First, opt-out childhood vaccination based in schools or daycare centres are not disrespectful of parental authority. Second, the programme aligns the default setting with a moral obligation to vaccinate one's child that most parents have. (shrink)

Scientists use models to understand the natural world, and it is important not to conflate model and nature. As an illustration, we distinguish three different kinds of populations in studies of ecology and evolution: theoretical, laboratory, and natural populations, exemplified by the work of R.A. Fisher, Thomas Park, and David Lack, respectively. Biologists are rightly concerned with all three types of populations. We examine the interplay between these different kinds of populations, and their pertinent models, in three examples: the notion (...) of “effective” population size, the work of Thomas Park on /Tribolium/ populations, and model-based clustering algorithms such as /Structure/. Finally, we discuss ways to move safely between three distinct population types while avoiding confusing models and reality. (shrink)

Over the last decades, science has grown increasingly collaborative and interdisciplinary and has come to depart in important ways from the classical analyses of the development of science that were developed by historically inclined philosophers of science half a century ago. In this paper, I shall provide a new account of the structure and development of contemporary science based on analyses of, first, cognitive resources and their relations to domains, and second of the distribution of cognitive resources among collaborators and (...) the epistemic dependence that this distribution implies. On this background I shall describe different ideal types of research activities and analyze how they differ. Finally, analyzing values that drive science towards different kinds of research activities, I shall sketch the main mechanisms underlying the perceived tension between disciplines and interdisciplinarity and argue for a redefinition of accountability and quality control for interdisciplinary and collaborative science. (shrink)

This chapter examines the philosophical discussion concerning the relationship between time, memory, attention, and consciousness, from Locke through the Scottish Common Sense tradition, in terms of its influence on James' development of the specious present doctrine. The specious present doctrine is the view that the present moment in experience is non punctate, but instead comprises some nonzero amount of time; it contrasts with the mathematical view of the present, in which the divide between past and future is merely a point (...) or a line with no thickness. The anonymous source for the term 'specious present' is revealed as a retired businessman-turned-amateur philosopher. The more likely source for the idea itself is a little-known philosopher, Shadworth Hollway Hodgson, who was not merely a significant influence on James but also on Husserl's development of the tripartite account of internal time consciousness. I conclude by demonstrating how James' changing views on the relationship between concepts and experience meant that by the later period of his writings, including those in which he develops his own views on pragmatism, James would have not merely noted the contrast between a mathematical conception of the present and our actual experience of it, he would have taken a further step and condoned the thick experience of the present as demonstrating the inadequacy of the intellectualized mathematical characterization. (shrink)

A finer-grained delineation of a given explanandum reveals a nexus of closely related causal and non- causal explanations, complementing one another in ways that yield further explanatory traction on the phenomenon in question. By taking a narrower construal of what counts as a causal explanation, a new class of distinctively mathematical explanations pops into focus; Lange’s characterization of distinctively mathematical explanations can be extended to cover these. This new class of distinctively mathematical explanations is illustrated with the Lotka-Volterra equations. There (...) are at least two distinct ways those equations might hold of a system, one of which yields straightforwardly causal explanations, but the other of which yields explanations that are distinctively mathematical in terms of nomological strength. In the first, one first picks out a system or class of systems, finds that the equations hold in a causal -explanatory way; in the second, one starts with the equations and explanations that must apply to any system of which the equations hold, and only then turns to the world to see of what, if any, systems it does in fact hold. Using this new way in which a model might hold of a system, I highlight four specific avenues by which causal and non- causal explanations can complement one another. (shrink)

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]. (shrink)

Even though the evidence‐based medicine movement (EBM) labels mechanisms a low quality form of evidence, consideration of the mechanisms on which medicine relies, and the distinct roles that mechanisms might play in clinical practice, offers a number of insights into EBM itself. In this paper, I examine the connections between EBM and mechanisms from several angles. I diagnose what went wrong in two examples where mechanistic reasoning failed to generate accurate predictions for how a dysfunctional mechanism would respond to intervention. (...) I then use these examples to explain why we should expect this kind of mechanistic reasoning to fail in systematic ways, by situating these failures in terms of evolved complexity of the causal system(s) in question. I argue that there is still a different role in which mechanisms continue to figure as evidence in EBM: namely, in guiding the application of population‐level recommendations to individual patients. Thus, even though the evidence‐based movement rejects one role in which mechanistic reasoning serves as evidence, there are other evidentiary roles for mechanistic reasoning. This renders plausible the claims of some critics of evidencebased medicine who point to the ineliminable role of clinical experience. Clearly specifying the ways in which mechanisms and mechanistic reasoning can be involved in clinical practice frames the discussion about EBM and clinical experience in more fruitful terms. (shrink)

In this field guide, I distinguish five separate senses with which the term ‘mechanism’ is used in contemporary philosophy of science. Many of these senses have overlapping areas of application but involve distinct philosophical claims and characterize the target mechanisms in relevantly different ways. This field guide will clarify the key features of each sense and introduce some main debates, distinguishing those that transpire within a given sense from those that are best understood as concerning distinct senses. The ‘new mechanisms’ (...) sense is at the center of most of these contemporary debates and will be treated at greater length; subsequent senses of mechanism will be primarily distinguished from this one. In part I of this paper, I distinguish two senses of the term ‘mechanism’, both of which are explicitly hierarchical and nested in character, such that any given mechanism is comprised of smaller sub-mechanisms, in turn comprised of yet smaller sub-sub-mechanisms and so on. While both of the senses discussed here are anti-reductive, they differ in their focus on scientific practice versus metaphysics, in the degree of regularity they attribute to mechanisms, and in terms of their relationships to the discussions of mechanisms in the history of philosophy and science. (shrink)

Cora Diamond has criticized capacity-based approaches to determining the moral status of animals, arguing instead that the morally significant fact is that we have relationships to animals as our fellow creatures. This paper explores implications of her approach to fish and the practice of fish farming. Fish differ from most other animals due to their appearances and under-water existence, and it is not obvious that fish belong to our fellow creatures, and – if so – what it means for our (...) treatment of them. In particular: if fish are fellow creatures, can we treat them in the way done in contemporary salmon farming ? Iris Murdoch points out that moral differences are conceptual differences, that is differences in how we see the world. Similarly, Diamond argues that we should not consider ‘animal’ or ‘human’ as biological classifications – they are conceptual configurations that shape the way we think and make sense of the world. In this article, we explore the implication of the fellow creature concept for the case of fish, which challenge our ordinary understandings of companionship with animals. We argue that farmed salmon should be consibdered as a special kind of fellow creatures living in water, and discuss how scientific research on biological features of fish may influence how we see them. We also sketch how Diamond’s approach implies a need for reform of current salmon farming practices. (shrink)

The ocean terrain spanning the globe is vast and complex—far from an immense flat plain of mud. To map these depths accurately and wisely, we must understand how cartographic abstraction and generalization work both in analog cartography and digital GIS. This chapter explores abstraction practices such as selection and exaggeration with respect to mapping the oceans, showing significant continuity in such practices across cartography and contemporary GIS. The role of measurement and abstraction—as well as of political and economic power, and (...) sexual and personal bias—in these sciences is illustrated by the biographies of Marie Tharp and Bruce Heezen, whose mapping of the Mid-Atlantic Ridge precipitated a paradigm shift in geology. (shrink)

Deflationists believe that the question “What is truth?” should be answered not by means of a metaphysical inquiry into the nature of truth, but by figuring out what use we make of the concept of truth, and the word ‘true’, in practice. This article accepts this methodology, and it thereby rejects pluralism about truth that is driven by ontological considerations. However, it shows that there are practical considerations for a pluralism about truth, formulated at the level of use. The theory (...) expounded by this article states that truth is a dual-purpose tool; it can be used as a device for transferring justificatory burdens and, for select areas of discourse, it can also be used as a standard, a norm. This contrast in how truth is used introduces a bifurcation in our discourse that is reminiscent of metaphysical divides traced by more traditional versions of alethic pluralism. However, my pluralism “at the level of use” states that truth is plural solely at the level of use. It is unified at both the conceptual as well as the metaphysical level. At those levels, the theory takes its cue from deflationism. As such, this theory is offered as a midway point and as a potential way forward in the debate between deflationism and pluralism. (shrink)

Levins and Lewontin have contributed significantly to our philosophical understanding of the structures, processes, and purposes of biological mathematical theorizing and modeling. Here I explore their separate and joint pleas to avoid making abstract and ideal scientific models ontologically independent by confusing or conflating our scientific models and the world. I differentiate two views of theorizing and modeling, orthodox and dialectical, in order to examine Levins and Lewontin’s, among others, advocacy of the latter view. I compare the positions of these (...) two views with respect to four points regarding ontological assumptions: (1) the origin of ontological assumptions, (2) the relation of such assumptions to the formal models of the same theory, (3) their use in integrating and negotiating different formal models of distinct theories, and (4) their employment in explanatory activity. Dialectical is here used in both its Hegelian–Marxist sense of opposition and tension between alternative positions and in its Platonic sense of dialogue between advocates of distinct theories. I investigate three case studies, from Levins and Lewontin as well as from a recent paper of mine, that show the relevance and power of the dialectical understanding of theorizing and modeling. (shrink)

I investigate how theoretical assumptions, pertinent to different perspectives and operative during the modeling process, are central in determining how nature is actually taken to be. I explore two different models by Michael Turelli and Steve Frank of the evolution of parasite-mediated cytoplasmic incompatility, guided, respectively, by Fisherian and Wrightian perspectives. Since the two models can be shown to be commensurable both with respect to mathematics and data, I argue that the differences between them in the (1) mathematical presentation of (...) the models, (2) explanations, and (3) objectified ontologies stem neither from differences in mathematical method nor the employed data, but from differences in the theoretical assumptions, especially regarding ontology, already present in the respective perspectives. I use my "set up, mathematically manipulate, explain, and objectify" (SMEO) account of the modeling process to track the model-mediated imposition of theoretical assumptions. I conclude with a discussion of the general implications of my analysis of these models for the controversy between Fisherian and Wrightian perspectives. (shrink)

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. (shrink)

This article uses the current post-truth crisis to level a charge against deflationism. It argues that a post-truth society rejects the normativity of truth, thereby deflating truth, by treating disagreements about, say, scientific facts, as mere disagreements of taste. To have substantive disagreements, the notion of truth at stake must be substantive as well. To ward off the perils of post-truth politics, truth must be taken to be more than what deflationists can account for. If we want our disagreements to (...) amount to more than mere differences of opinion, we should have an inflated notion of truth. The article concludes with putting this claim within the context of conceptual engineering. (shrink)

This paper discusses the Uniqueness Thesis, a core thesis in the epistemology of disagreement. After presenting uniqueness and clarifying relevant terms, a novel counterexample to the thesis will be introduced. This counterexample involves logical disagreement. Several objections to the counterexample are then considered, and it is argued that the best responses to the counterexample all undermine the initial motivation for uniqueness.

A key question in the philosophy of logic is how we have epistemic justification for claims about logical entailment (assuming we have such justification at all). Justification holism asserts that claims of logical entailment can only be justified in the context of an entire logical theory, e.g., classical, intuitionistic, paraconsistent, paracomplete etc. According to holism, claims of logical entailment cannot be atomistically justified as isolated statements, independently of theory choice. At present there is a developing interest in—and endorsement of—justification holism (...) due to the revival of an abductivist approach to the epistemology of logic. This paper presents an argument against holism by establishing a foundational entailment-sentence of deduction which is justified independently of theory choice and outside the context of a whole logical theory. (shrink)

Pragmatists are usually very antagonistic toward the correspondence theory of truth. They contend that the evidence-transcendent standard entailed by the theory is antithetical to the pragmatist methodology of elucidating concepts by exposing their practical bearings. What use could truth be to us if it offers a target we cannot even see? After judging the correspondence theory to be in violation of the Pragmatic Maxim, the pragmatist is prone to banishing it to the wastelands of empty metaphysics, where nothing of practical (...) importance could ever grow. This article makes the case that this unjust condemnation must be appealed and overturned. The ground for my case is an argument to the effect that the correspondence conception of truth can be practically advantageous, which provides proof of the fact that, contrary to popular pragmatist belief, the correspondence theory does comply with the Pragmatic Maxim. (shrink)

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. (shrink)

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. (shrink)

In his analysis of “the essential tension between tradition and innovation” Thomas S. Kuhn focused on the apparent paradox that, on the one hand, normal research is a highly convergent activity based upon a settled consensus, but, on the other hand, the ultimate effect of this tradition-bound work has invariably been to change the tradition. Kuhn argued that, on the one hand, without the possibility of divergent thought, fundamental innovation would be precluded. On the other hand, without a strong emphasis (...) on convergent thought, science would become a mess created by continuous theory changes and scientific progress would again be precluded. On Kuhn’s view, both convergent and divergent thought are therefore equally necessary for the progress of science. In this paper, I shall argue that a similar fundamental tension exists between the demands we see for novel insights of an interdisciplinary nature and the need for established intellectual doctrines founded in the classical disciplines. First, I shall revisit Kuhn’s analysis of the essential tension between tradition and innovation. Next, I shall argue that the tension inherent in interdisciplinary research between, on the one hand, intellectual independence and critical scrutiny and, on the other hand, epistemic dependence and trust is a complement to Kuhn’s essential tension within mono-disciplinary science between convergent and divergent thought. (shrink)

I motivate the concept of styles of scientific investigation, and differentiate two styles, formal and compositional. Styles are ways of doing scientific research. Radically different styles exist. I explore the possibility of the unification of biology and social science, as well as the possibility of unifying the two styles I identify. Recent attempts at unifying biology and social science have been premised almost exclusively on the formal style. Through the use of a historical example of defenders of compositional biological social (...) science, the Ecology Group at the University of Chicago from, roughly, the 1930s to the 1950s, I attempt to show the coherence and possibility, if not utility, of employing the compositional style to effect the synthesis of biology and social science. I also relate the efforts of the Ecology Group to those of investigators in the Sociology Department of the University of Chicago. In my conclusion, I discuss the usefulness both of employing the category of styles of scientific investigation in historical and philosophical studies of science, as well as the concept of compositionality in scientific studies. I end the paper with some tentative suggestions regarding the importance of compositionality for an analysis of human society. (shrink)

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.

While the epistemic significance of disagreement has been a popular topic in epistemology for at least a decade, little attention has been paid to logical disagreement. This monograph is meant as a remedy. The text starts with an extensive literature review of the epistemology of (peer) disagreement and sets the stage for an epistemological study of logical disagreement. The guiding thread for the rest of the work is then three distinct readings of the ambiguous term ‘logical disagreement’. Chapters 1 and (...) 2 focus on the Ad Hoc Reading according to which logical disagreements occur when two subjects take incompatible doxastic attitudes toward a specific proposition in or about logic. Chapter 2 presents a new counterexample to the widely discussed Uniqueness Thesis. Chapters 3 and 4 focus on the Theory Choice Reading of ‘logical disagreement’. According to this interpretation, logical disagreements occur at the level of entire logical theories rather than individual entailment-claims. Chapter 4 concerns a key question from the philosophy of logic, viz., how we have epistemic justification for claims about logical consequence. In Chapters 5 and 6 we turn to the Akrasia Reading. On this reading, logical disagreements occur when there is a mismatch between the deductive strength of one’s background logic and the logical theory one prefers (officially). Chapter 6 introduces logical akrasia by analogy to epistemic akrasia and presents a novel dilemma. Chapter 7 revisits the epistemology of peer disagreement and argues that the epistemic significance of central principles from the literature are at best deflated in the context of logical disagreement. The chapter also develops a simple formal model of deep disagreement in Default Logic, relating this to our general discussion of logical disagreement. The monograph ends in an epilogue with some reflections on the potential epistemic significance of convergence in logical theorizing. (shrink)

I present three reasons why philosophers of science should be more concerned about violations of causal faithfulness (CF). In complex evolved systems, mechanisms for maintaining various equilibrium states are highly likely to violate CF. Even when such systems do not precisely violate CF, they may nevertheless generate precisely the same problems for inferring causal structure from probabilistic relationships in data as do genuine CF-violations. Thus, potential CF-violations are particularly germane to experimental science when we rely on probabilistic information to uncover (...) the DAG, rather than already knowing the DAG from which we could predict the right experiments to ‘catch out’ the hidden causal relationships. (shrink)

Mary Midgley, Iris Murdoch, Gertrude Anscombe and Philippa Foot studied together in Oxford during the war, at a time when most of the men had left the university, leaving it to them for themselves. These unique circumstances where decisive for the fact that they all went on to become successful philosophers and were able to develop their own original philosophical theories, opposing the philosophical dogmas of their time, Midgley later wrote. This claim is the point of departure for this article. (...) It has three purposes: First I try to say something about the circumstances that made it possible to develop such alternatives, and second, I try to say something about what they consist in. Finally, I ask what this story can teach us about inclusion of women in philosophy today. (shrink)

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? (shrink)

The reduction of grounding to causation, or each to a more general relation of which they are species, has sometimes been justified by the impressive inferential capacity of structural equation modelling, causal Bayes nets, and interventionist causal modelling. Many criticisms of this assimilation focus on how causation is inadequate for grounding. Here, I examine the other direction: how treating grounding in the image of causation makes the resulting view worse for causation. The distinctive features of causal modelling that make this (...) connection appealing are distorted beyond use by forcing them to fit onto grounding. The very inferential strength that makes causation attractive is only possible because of a narrow construal of what counts as a causal relation; as soon as that broadens, the inferential capacity markedly diminishes. Making causation suitable for application to grounding spoils what was appealing about causation for this task in the first place. However, grounding need not appeal to causation: causal modelling does not have exclusive claim to structural equation modeling or other formal techniques of modelling structure. I offer a case in favour of a different kind of metaphysical frugality, which tend towards narrow, more restrictive construals of relations like causation or grounding, because then each relation behaves more homogenously. This more homogenous behavior delivers stronger inferential power per relation even though there may be more relations to which one is committed. (shrink)

Humean accounts of laws are often contrasted with governing accounts, and recent developments have added pragmatic versions of Humeanism. This paper offers Mitchell's pragmatist, perspectival account of laws as a third option. The differences between these accounts come down to the role of modality. Mitchell's bottom-up account allows for subtle gradations of modal content to be conveyed by laws. The perspectival character of laws is not an accident or something to be eventually eliminated - it is part of how this (...) modal content is conveyed. I conclude with a discussion of the metaphysical commitments in Humeanism as requiring a perspectiveless view of the manifold from outside, and how Mitchell's situated account is better able to account for the substantive notion of possibility involved in scientific laws. (shrink)

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. (shrink)