Multilevel research strategies characterize contemporary molecular inquiry into biological systems. We outline conceptual, methodological, and explanatory dimensions of these multilevel strategies in microbial ecology, systems biology, protein research, and developmental biology. This review of emerging lines of inquiry in these fields suggests that multilevel research in molecular life sciences has significant implications for philosophical understandings of explanation, modeling, and representation.

Scientific inquiry has led to immense explanatory and technological successes, partly as a result of the pervasiveness of scientific theories. Relativity theory, evolutionary theory, and plate tectonics were, and continue to be, wildly successful families of theories within physics, biology, and geology. Other powerful theory clusters inhabit comparatively recent disciplines such as cognitive science, climate science, molecular biology, microeconomics, and Geographic Information Science (GIS). Effective scientific theories magnify understanding, help supply legitimate explanations, and assist in formulating predictions. Moving from their (...) knowledge-producing representational functions to their interventional roles (Hacking 1983), theories are integral to building technologies used within consumer, industrial, and scientific milieus. -/- This entry explores the structure of scientific theories from the perspective of the Syntactic, Semantic, and Pragmatic Views. Each of these views answers questions such as the following in unique ways. What is the best characterization of the composition and function of scientific theory? How is theory linked with world? Which philosophical tools can and should be employed in describing and reconstructing scientific theory? Is an understanding of practice and application necessary for a comprehension of the core structure of a scientific theory? How are these three views ultimately related? (shrink)

The neuroscience revolution has led many scientists to posit “expansive” or “thinking” brains that instantiate rich psychological properties. As a result, some scientists now even claim you are identical to such a brain. However, Eric Olson has offered new arguments that thinking brains cannot exist due to their intuitively “abominable” implications. After situating the commitment to thinking brains in the wider scientific discussions in which they are posited, I then critically assess Olson's arguments against such entities. Although highlighting an important (...) insight, I show that Olson's objections to the existence of thinking brains fail and that a wider discussion engaging our new empirical findings is actually required in order to resolve the deeper issues. (shrink)

We argue that the mathematization of science should be understood as a normative activity of advocating for a particular methodology with its own criteria for evaluating good research. As a case study, we examine the mathematization of taxonomic classification in systematic biology. We show how mathematization is a normative activity by contrasting its distinctive features in numerical taxonomy in the 1960s with an earlier reform advocated by Ernst Mayr starting in the 1940s. Both Mayr and the numerical taxonomists sought to (...) formalize the work of classification, but Mayr introduced a qualitative formalism based on human judgment for determining the taxonomic rank of populations, while the numerical taxonomists introduced a quantitative formalism based on automated procedures for computing classifications. The key contrast between Mayr and the numerical taxonomists is how they conceptualized the temporal structure of the workflow of classification, specifically where they allowed meta-level discourse about difficulties in producing the classification. (shrink)

Reliability and external validity are two fundamental values that pose incompatible constraints on neurobiological experiments. The more reliability an experimental result achieves, the less external validity it earns, and vice versa. In this article, I propose an externalist interpretation of external validity: the external validity of an experimental result depends not only on how much complexity is built into an experimental design, but also on the relationship between the experimental result and other related experiments. This externalist interpretation, which explains how (...) a neurobiological experiment can be reliable and externally valid simultaneously, suggests a new way to understand the epistemology of neurobiological experimentation. (shrink)

Biologists seems to hold two fundamental beliefs: Organisms are organized into levels and the individuals at these levels differ in their properties. Together these suggest that there will be massive multiple realization, i.e. that many human psychological properties are multiply realized at many neurobiological levels. This paper provides some documentation in support of this suggestion.

In what follows, I will give examples of the sorts of step that can be taken towards spelling out the intuition that, after all, good models might be true. Along the way, I provide an outline of my account of models as ontologically and pragmatically constrained representations. And I emphasize the importance of examining models as functionally composed systems in which different components play different roles and only some components serve as relevant truth bearers. This disputes the standard approach that (...) proceeds by simply counting true and false elements in models in their entirety and concludes that models are false since they contain so many false elements. I call my alternative the functional decomposition approach. (shrink)

How can we explain the intentional nature of an expert’s actions, performed without immediate and conscious control, relying instead on automatic cognitive processes? How can we account for the differences and similarities with a novice’s performance of the same actions? Can a naturalist explanation of intentional expert action be in line with a philosophical concept of intentional action? Answering these and related questions in a positive sense, this dissertation develops a three-step argument. Part I considers different methods of explanations in (...) cognitive neuroscience (Bennett & Hacker’s philosophical, conceptual analysis; Marr’s three levels of explanation; Neural Correlates of Consciousness research; mechanistic explanation), defending ‘mechanistic explanation’ as a method that provides the necessary tools for integrating interdisciplinary insights into human action. Furthermore, a dynamic, explanatory mechanism allows the assessment of the impact of learning and development on expert action in a valuable way that other methods don’t. Part II continues by scrutinizing several cognitive neuroscientific theories of learning and development (neuroconstructivism; dual-processing theories; simulation theory; extended mind/cognition hypothesis), arguing for the complex interactions between different types of processing and different action representations involved in expert action performances. Moreover, according to our discussion of a particular ‘simulation theory’ these interactions can be influenced in several ways with the use of language, allowing an agent to configure a specific action representation for performance at a later stage. The results of Parts I and II are then applied in Part III to a parallel discussion of philosophical analyses of intentional action (discussing i.a. Frankfurt, Bratman, Pacherie and Ricoeur) and cognitive neuroscientific insights in it. Both approaches are found to converge in emphasizing the importance for an expert to develop stable patterns of actions that comply maximally not only with his intentions, but also with his motor expertise and with situational conditions. Consequently, his actions – automatic, or not – rely on this ‘sculpted space of actions’. (shrink)

In this article we use a hybrid methodology to better understand the skilful performance of sports teams as an exemplar of distributed cognition. We highlight key differences between a team of individual experts and an expert team, and outline the kinds of shared characteristics likely to be found in an expert team. We focus on the way that shared knowledge contributes to expert team performance. In particular, we suggest that certain kinds of shared knowledge and shared skill, potentially developed through (...) a team’s history of playing and training together, facilitate successful coordination. These kinds of shared knowledge and skill may be less developed in a team of experts without a shared history. Exploring the expert performance of sports teams informs our understanding of distributed cognition and collaboration more generally and creates avenues for further philosophical and empirical investigation. (shrink)

In this article, I argue that the use of scientific models that attribute intentional content to complex systems bears a striking similarity to the way in which statistical descriptions are used. To demonstrate this, I compare and contrast an intentional model with a statistical model, and argue that key similarities between the two give us compelling reasons to consider both as a type of phenomenological model. I then demonstrate how intentional descriptions play an important role in scientific methodology as a (...) type of phenomenal model, and argue that this makes them as essential as any other model of this type. (shrink)

The many-faced relationship between chemistry and physics is one of the most discussed topics in the philosophy of chemistry. In his recent book Reducing Chemistry to Physics. Limits, Models, Consequences, Hinne Hettema conceives this relationship as a reduction link, and devotes his work to defend this position on the basis of a “naturalized” concept of reduction. In the present paper I critically review three kinds of issues stemming from Hettema’s argumentation: philosophical, scientific and methodological.

Naive physics beliefs can be systematically mistaken. They provide a useful test-bed because they are common, and also because their existence must rely on some adaptive advantage, within a given context. In the second part of the commentary we also ask questions about when a whole family of misbeliefs should be considered together as a single phenomenon.

It is argued that Reiss (2012) fails to refute attempts to resolve the paradox of false explanatory models. His article fails to provide an articulate conception of what exactly the presumed paradox is, it suffers from uncontrolled ambiguities and inconsistencies, and it fails to adequately address accounts of economic models that might contribute to reconciling their apparent falsehood and explanatoriness. Some details in my account of how apparently false models may explain are clarified.

In this chapter I investigate the kinds of changes that psychiatric kinds undergo when they become explanatory targets of areas of sciences that are not “mature” and are in the early stages of discovering mechanisms. The two areas of science that are the targets of my analysis are cognitive neuroscience and cognitive neurobiology.

According to Joshua Alexander, philosophers use intuitions routinely as a form of evidence to test philosophical theories but experimental philosophy demonstrates that these intuitions are unreliable and unrepresentative.1 According to Herman Cappelen, philosophers never use intuitions as evidence (despite the vacuous sentential leader ‘intuitively’) and experimental philosophy lacks a rationale for its much-touted existence.2 That two books are diametrically opposed on methodology in philosophy is not noteworthy. But eyebrows might be raised at such contradictory accounts of the phenomenology of philosophical (...) inquiry. What is it that (analytic) philosophers do? Why is it so difficult to achieve consensus on the professional activities in which we engage? (shrink)

This chapter provides an introduction to the study of the philosophical notions of mechanisms and causality in biology and economics. This chapter sets the stage for this volume, Mechanism and Causality in Biology and Economics, in three ways. First, it gives a broad review of the recent changes and current state of the study of mechanisms and causality in the philosophy of science. Second, consistent with a recent trend in the philosophy of science to focus on scientific practices, it in (...) turn implies the importance of studying the scientific methods employed by researchers. Finally, by way of providing an overview of each chapter in the volume, this chapter demonstrates that biology and economics are two fertile fields for the philosophy of science and shows how biological and economic mechanisms and causality can be synthesized. (shrink)

What does it look like when a group of scientists set out to re-envision an entire field of biology in symbolic and formal terms? I analyze the founding and articulation of Numerical Taxonomy between 1950 and 1970, the period when it set out a radical new approach to classification and founded a tradition of mathematics in systematic biology. I argue that introducing mathematics in a comprehensive way also requires re-organizing the daily work of scientists in the field. Numerical taxonomists sought (...) to establish a mathematical method for classification that was universal to every type of organism, and I argue this intrinsically implicated them in a qualitative re-organization of the work of all systematists. I also discuss how Numerical Taxonomy’s re-organization of practice became entrenched across systematic biology even as opposing schools produced their own competing mathematical methods. In this way, the structure of the work process became more fundamental than the methodological theories that motivated it. (shrink)

Traditional accounts of the role of learning in evolution have concentrated upon its capacity as a source of fitness to individuals. In this paper I use a case study from invasive species biology—the role of conditioned taste aversion in mitigating the impact of cane toads on the native species of Northern Australia—to highlight a role for learning beyond this—as a source of evolvability to populations. This has two benefits. First, it highlights an otherwise under-appreciated role for learning in evolution that (...) does not rely on social learning as an inheritance channel nor “special” evolutionary processes such as genetic accommodation (both of which many are skeptical about). Second, and more significantly, it makes clear important and interesting parallels between learning and exploratory behaviour in development. These parallels motivate the applicability of results from existing research into learning and learning evolution to our understanding of the evolution of evolvability more generally. (shrink)

This article compares causal and constitutive explanation. While scientific inquiry usually addresses both causal and constitutive questions, making the distinction is crucial for a detailed understanding of scientific questions and their interrelations. These explanations have different kinds of explananda and they track different sorts of dependencies. Constitutive explanations do not address events or behaviors, but causal capacities. While there are some interesting relations between building and causal manipulation, causation and constitution are not to be confused. Constitution is a synchronous and (...) asymmetric relation between relata that cannot be conceived as independent existences. However, despite their metaphysical differences, the same key ideas about explanation largely apply to both. Causal and constitutive explanations face similar challenges (such as the problems of relevance and explanatory regress) and both are in the business of mapping networks of counterfactual dependence—i.e. mechanisms—although the relevant counterfactuals are of a different sort. In the final section the issue of developmental explanation is discussed. It is argued that developmental explanations deserve their own place in taxonomy of explanations, although ultimately developmental dependencies can be analyzed as combinations of causal and constitutive dependencies. Hence, causal and constitutive explanation are distinct, but not always completely separate forms of explanation. (shrink)

The paper discusses how systems biology is working toward complex accounts that integrate explanation in terms of mechanisms and explanation by mathematical models—which some philosophers have viewed as rival models of explanation. Systems biology is an integrative approach, and it strongly relies on mathematical modeling. Philosophical accounts of mechanisms capture integrative in the sense of multilevel and multifield explanations, yet accounts of mechanistic explanation have failed to address how a mathematical model could contribute to such explanations. I discuss how mathematical (...) equations can be explanatorily relevant. Several cases from systems biology are discussed to illustrate the interplay between mechanistic research and mathematical modeling, and I point to questions about qualitative phenomena, where quantitative models are still indispensable to the explanation. Systems biology shows that a broader philosophical conception of mechanisms is needed, which takes into account functional-dynamical aspects, interaction in complex networks with feedback loops, system-wide functional properties such as distributed functionality and robustness, and a mechanism’s ability to respond to perturbations. I offer general conclusions for philosophical accounts of explanation. (shrink)

Mechanistic models in molecular systems biology are generally mathematical models of the action of networks of biochemical reactions, involving metabolism, signal transduction, and/or gene expression. They can be either simulated numerically or analyzed analytically. Systems biology integrates quantitative molecular data acquisition with mathematical models to design new experiments, discriminate between alternative mechanisms and explain the molecular basis of cellular properties. At the heart of this approach are mechanistic models of molecular networks. We focus on the articulation and development of mechanistic (...) models, identifying five constraints which guide the articulation of models in molecular systems biology. These constraints are not independent of one another, with the result that modeling becomes an iterative process. We illustrate the use of these constraints in the modeling of the mechanism for bistability in the lac operon. (shrink)

One way that scientifically recognized properties are multiply realized is by “compensatory differences” among realizing properties. If a property G is jointly realized by two properties F1 and F2, then G can be multiply realized by having changes in the property F1 offset changes in the property F2. In some cases, there are scientific laws that articulate how distinct combinations of physical quantities can determine one and the same value of some other physical quantity. One moral to draw is that (...) in such cases we have the multiple realization of a single determinate, “fine grained” property instance that is exactly similar to another instance. As simple as this moral is, it has ramifications for a number of recent discussions of multiple realization in science. Taken collectively, these ramifications indicate that multiple realization by compensatory adjustments merits greater attention in the philosophy of science literature than it has hitherto received. (shrink)

I argue that examining the explanatory power of the hypothesis of extended cognition (HEC) offers a fruitful approach to the problem of cognitive system demarcation. Although in the discussions on HEC it has become common to refer to considerations of explanatory power as a means for assessing the plausibility of the extended cognition approach, to date no satisfying account of explanatory power has been presented in the literature. I suggest that the currently most prominent theory of explanation in the special (...) sciences, James Woodward’s contrastive-counterfactual theory, and an account of explanatory virtues building on that theory can be used to develop a systematic picture of cognitive system demarcation in the psychological sciences. A major difference between my differential influence (DI) account and most other theories of cognitive extension is the cognitive systems pluralism implied by my approach. By examining the explanatory power of competing traditions in psychological memory research, I conclude that internalist and externalist classificatory strategies are characterized by different profiles of explanatory virtues and should often be considered as complementary rather than competing approaches. This suggests a deflationary interpretation of HEC. (shrink)

The question of the ontological status of social wholes has been formative to the development of key positions and debates within modern social theory. Intrinsic to this is the contested meaning of the concept of emergence and the idea that the collective whole is in some way more than the sum of its parts. This claim, in its contemporary form, gives exaggerated importance to a simple truism of re-description that concerns all wholes. In this paper I argue that a better (...) way to test the ontological status of wholes is to ask whether their causal properties can be reduced to the qualities of their parts. If reduction is possible the ontological status of emergent wholes is diminished. A close analysis of William Wimsatt's definition, conceptualisation, and characterisation of emergent phenomena provides an understanding of the relationship between wholes and their parts and suggests, also, that the properties of collective phenomena of a social kind reduce to the activities of people. Social wholes and their parts reside in the same mode (or level) of organisation. This paper concludes by employing Jaegwon Kim's method of ‘functional reduction’ to demonstrate how to reduce the qualities of wholes to those of their parts. (shrink)

Modeling mechanisms is central to the biological sciences – for purposes of explanation, prediction, extrapolation, and manipulation. A closer look at the philosophical literature reveals that mechanisms are predominantly modeled in a purely qualitative way. That is, mechanistic models are conceived of as representing how certain entities and activities are spatially and temporally organized so that they bring about the behavior of the mechanism in question. Although this adequately characterizes how mechanisms are represented in biology textbooks, contemporary biological research practice (...) shows the need for quantitative, probabilistic models of mechanisms, too. In this paper we argue that the formal framework of causal graph theory is well-suited to provide us with models of biological mechanisms that incorporate quantitative and probabilistic information. On the ba-sis of an example from contemporary biological practice, namely feedback regulation of fatty acid biosynthesis in Brassica napus, we show that causal graph theoretical models can account for feedback as well as for the multi-level character of mechanisms. However, we do not claim that causal graph theoretical representations of mechanisms are advantageous in all respects and should replace common qualitative models. Rather, we endorse the more balanced view that causal graph theoretical models of mechanisms are useful for some purposes, while being insufficient for others. (shrink)

Wegner, Giuliano, and Hertel (1985) defined the notion of a transactive memory system (TMS) as a group level memory system that “involves the operation of the memory systems of the individuals and the processes of communication that occur within the group (p. 191). Those processes are the collaborative procedures (“transactions”) by which groups encode, store, and retrieve information that is distributed among their members. Over the past 25+ years, the conception of a TMS has progressively garnered an increased interest among (...) social and organizational psychologists, communication scholars, and management theorists (Ren & Argote 2011). But there remains considerable disagreement about how exactly Wegner’s appeal to group memory should be understood. My goal in this paper is contribute to this debate, by articulating more clearly the value of conceptualizing groups as TMSs. This value, I argue, consists in providing us with a blueprint for how to explain group memory in terms of collective information-processing mechanisms. Collective information-processing mechanisms are dependent on, and interact with, the brain-bound information-processing of individuals, but cannot be reduced to the latter. In my analysis, I lean on extant accounts of mechanistic explanation in the philosophy of science (Bechtel & Richardson 1993; Machamer, Darden, & Craver 2000; Wimsatt 2007) that have been used to analyze the explanatory practices of psychology and cognitive neuroscience (Bechtel 2008, 2009). Based on my reconstruction of Wegner’s conceptualization of a TMS, I argue that the reality of emergent group cognition is compatible with its mechanistic explanation. More generally, my analysis shows that group cognition cannot be reduced to individual cognition, while avoiding the false dilemma between “wholism” and “nothing but-ism” which has hampered traditional construals of the “group mind” thesis (Allport 1968). (shrink)

In recent years, the debate on the problem of causal exclusion has seen an ‘interventionist turn’. Numerous non-reductive physicalists (e.g. Shapiro and Sober 2007) have argued that Woodward's (2003) interventionist theory of causation provides a means to empirically establish the existence of non-reducible mental-to-physical causation. By contrast, Baumgartner (2010) has presented an interventionist exclusion argument showing that interventionism is in fact incompatible with non-reductive physicalism. In response, a number of revised versions of interventionism have been suggested that are compatible with (...) non-reductive physicalism. The first part of this paper reconstructs the definitional details of these modified interventionist theories. The second part investigates whether the modification proposed in Woodward (2011) is not only compatible with, but moreover supports non-reductive physicalism. In particular, it is examined whether that newest variant of interventionism allows for empirically resolving the problem of causal exclusion as envisaged by Shapiro, Sober and others. (shrink)

Some relevant distinctions between the notions of complexity, non-linearity, self-organization and emergence are addressed.

Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features (...) of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely “processually equivalent” entities, “processually versatile” entities, and “stabilized” entities. (shrink)

This paper proposes an account of the self as a multilevel system consisting of social, individual, neural, and molecular mechanisms. It argues that the functioning of the self depends on causal relations between mechanisms operating at different levels. In place of reductionist and holistic approaches to cognitive science, I advocate a method of multilevel interacting mechanisms. This method is illustrated by showing how self-concepts operate at several different levels.

In the contemporary life sciences more and more researchers emphasize the “limits of reductionism” (e.g. Ahn et al. 2006a, 709; Mazzocchi 2008, 10) or they call for a move “beyond reductionism” (Gallagher/Appenzeller 1999, 79). However, it is far from clear what exactly they argue for and what the envisioned limits of reductionism are. In this paper I claim that the current discussions about reductionism in the life sciences, which focus on methodological and explanatory issues, leave the concepts of a reductive (...) method and a reductive explanation too unspecified. In order to fill this gap and to clarify what the limits of reductionism are I identify three reductive methods that are crucial in the current practice of the life sciences: decomposition, focusing on internal factors, and studying parts in isolation. Furthermore, I argue that reductive explanations in the life sciences exhibit three characteristics: first, they refer only to factors at a lower level than the phenomenon at issue, second, they focus on internal factors and thus ignore or simplify the environment of a system, and, third, they cite only the parts of a system in isolation. (shrink)

Odenbaugh and Alexandrova provide a challenging critique of the epistemic benefits of robustness analysis, singling out for particular criticism the account we articulated in Kuorikoski et al.. Odenbaugh and Alexandrova offer two arguments against the confirmatory value of robustness analysis: robust theorems cannot specify causal mechanisms and models are rarely independent in the way required by robustness analysis. We address Odenbaugh and Alexandrova’s criticisms in order to clarify some of our original arguments and to shed further light on the properties (...) of robustness analysis and its epistemic rationale. (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)

A classic analytic approach to biological phenomena seeks to refine definitions until classes are sufficiently homogenous to support prediction and explanation, but this approach founders on cases where a single process produces objects with similar forms but heterogeneous behaviors. I introduce object spaces as a tool to tackle this challenging diversity of biological objects in terms of causal processes with well-defined formal properties. Object spaces have three primary components: (1) a combinatorial biological process such as protein synthesis that generates objects (...) with parts that are modular, independent, and organized according to an invariant syntax; (2) a notion of “distance” that relates the objects according to rules of change over time as found in nature or useful for algorithms; (3) mapping functions defined on the space that map its objects to other spaces or apply an evaluative criterion to measure an important quality, such as parsimony or biochemical function. Once defined, an object space can be used to represent and simulate the dynamics of phenomena on multiple scales; it can also be used as a tool for predicting higher-order properties of the objects, including stitching together series of causal processes. Object spaces are the basis for a strategy of theorizing, discovery, and analysis in biology: as heuristic idealizations of biology, they help us transform inchoate, intractable problems into articulated, well-structured ones. Developing an object space is a research strategy with a long, successful history under many other names, and it offers a unifying but not overreaching approach to biological theory. (shrink)

The concept of hierarchical organization is commonplace in science. Subatomic particles compose atoms, which compose molecules; cells compose tissues, which compose organs, which compose organisms; etc. Hierarchical organization is particularly prominent in ecology, a field of research explicitly arranged around levels of ecological organization. The concept of levels of organization is also central to a variety of debates in philosophy of science. Yet many difficulties plague the concept of discrete hierarchical levels. In this paper, we show how these difficulties undermine (...) various implications ascribed to hierarchical organization, and we suggest the concept of scale as a promising alternative to levels. Investigating causal processes at different scales offers a way to retain a notion of quasi-levels that avoids the difficulties inherent in the classic concept of hierarchical levels of organization. Throughout, our focus is on ecology, but the results generalize to other invocations of hierarchy in science and philosophy of science. (shrink)

This contribution provides an assessment of the epistemological role of scientific models. The prevalent view that all scientific models are representations of the world is rejected. This view points to a unified way of resolving epistemic issues for scientific models. The emerging consensus in philosophy of science that models have many different epistemic roles in science is presented and defended.

This chapter explores a philosophical hypothesis about the nature of (some) probabilities encountered in social sciences. It should be of interest to those with philosophical concerns about the foundations of probability, and to social scientists and philosophers of science who are somewhat puzzled by the nature of probability in social domains. As will become clear below, the chapter is not intended as a contribution to an empirical methodology such as a particular way of applying statistics.

Evo-Devo exhibits a plurality of scientific “cultures” of practice and theory. When are the cultures acting—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, or within each of these cultures are explored. Characterizing the internal structure of (...) the cultures 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. (shrink)

Laws of nature take center stage in philosophy of science. Laws are usually believed to stand in a tight conceptual relation to many important key concepts such as causation, explanation, confirmation, determinism, counterfactuals etc. Traditionally, philosophers of science have focused on physical laws, which were taken to be at least true, universal statements that support counterfactual claims. But, although this claim about laws might be true with respect to physics, laws in the special sciences (such as biology, psychology, economics etc.) (...) appear to have—maybe not surprisingly—different features than the laws of physics. Special science laws—for instance, the economic law “Under the condition of perfect competition, an increase of demand of a commodity leads to an increase of price, given that the quantity of the supplied commodity remains constant” and, in biology, Mendel's Laws—are usually taken to “have exceptions”, to be “non-universal” or “to be ceteris paribus laws”. How and whether the laws of physics and the laws of the special sciences differ is one of the crucial questions motivating the debate on ceteris paribus laws. Another major, controversial question concerns the determination of the precise meaning of “ceteris paribus”. Philosophers have attempted to explicate the meaning of ceteris paribus clauses in different ways. The question of meaning is connected to the problem of empirical content, i.e., the question whether ceteris paribus laws have non-trivial and empirically testable content. Since many philosophers have argued that ceteris paribus laws lack empirically testable content, this problem constitutes a major challenge to a theory of ceteris paribus laws. (shrink)

This essay analyzes and develops recent views about explanation in biology. Philosophers of biology have parted with the received deductive-nomological model of scientific explanation primarily by attempting to capture actual biological theorizing and practice. This includes an endorsement of different kinds of explanation (e.g., mathematical and causal-mechanistic), a joint study of discovery and explanation, and an abandonment of models of theory reduction in favor of accounts of explanatory reduction. Of particular current interest are philosophical accounts of complex explanations that appeal (...) to different levels of organismal organization and use contributions from different biological disciplines. The essay lays out one model that views explanatory integration across different disciplines as being structured by scientific problems. I emphasize the philosophical need to take the explanatory aims pursued by different groups of scientists into account, as explanatory aims determine whether different explanations are competing or complementary and govern the dynamics of scientific practice, including interdisciplinary research. I distinguish different kinds of pluralism that philosophers have endorsed in the context of explanation in biology, and draw several implications for science education, especially the need to teach science as an interdisciplinary and dynamic practice guided by scientific problems and explanatory aims. (shrink)

Humans are capable of understanding an incredible variety of actions performed by other humans. Even though these range from primary biological actions, like eating and fleeing, to acts in parliament or in poetry, humans generally can make sense of each other’s actions. Understanding other people’s actions is called action understanding, and it can transcend differences in race, gender, culture, age, and social and historical circumstances. Action understanding is the cognitive ability to make sense of another person’s action by integrating perceptual (...) information about the behavior with knowledge about the immediate and sociocultural contexts of the action and with one’s own experience. Scholars are increasingly dissatisfied with monodisciplinary approaches to understanding human action. Such one-sidedness can rest upon various motives. For example, “hermeneutic interpretations” of action understanding tend to emphasize historical and cultural influences while overlooking that ultimately such influences depend upon individual cognitive processes. This has provoked criticism of the corresponding assumption that humans are born as a “blank slate” and that culture is solely responsible for all cognitive contents. However, such critique in turn easily slides into an overemphasis on the biology of human nature and a denial of sociocultural influences on cognition (Pinker, 2003). Fortunately, recent interdisciplinary endeavors have shown that an interdisciplinary approach is preferable when investigating complex functions like action understanding. The purpose of this chapter is to propose a “mechanism-based explanation” of action understanding that will provide a theoretical framework for integrating various and often conflicting disciplinary insights. (shrink)

Scientific models share one central characteristic with fiction: their relation to the physical world is ambiguous. It is often unclear whether an element in a model represents something in the world or presents an artifact of model building. Fiction, too, can resemble our world to varying degrees. However, we assign a different epistemic function to scientific representations. As artifacts of human activity, how are scientific representations allowing us to make inferences about real phenomena? In reply to this concern, philosophers of (...) science have started analyzing scientific representations in terms of fictionalization strategies. Many arguments center on a dyadic relation between the model and its target system, focusing on structural resemblances and “as if” scenarios. This chapter provides a different approach. It looks more closely at model building to analyze the interpretative strategies dealing with the representational limits of models. How do we interpret ambiguous elements in models? Moreover, how do we determine the validity of model-based inferences to information that is not an explicit part of a representational structure? I argue that the problem of ambiguous inference emerges from two features of representations, namely their hybridity and incompleteness. To distinguish between fictional and non-fictional elements in scientific models my suggestion is to look at the integrative strategies that link a particular model to other methods in an ongoing research context. To exemplify this idea, I examine protein modeling through X-ray crystallography as a pivotal method in biochemistry. (shrink)

Synthetic biology is an umbrella term that covers a range of aims, approaches, and techniques. They are all brought together by common practices of analogizing, synthesizing, mechanicizing, and kludging. With a focus on kludging as the connection point between biology, engineering, and evolution, I show how synthetic biology’s successes depend on custom-built kludges and a creative, “make-it-work” attitude to the construction of biological systems. Such practices do not fit neatly, however, into synthetic biology’s celebration of rational design. Nor do they (...) straightforwardly embody Richard Feynman’s “last blackboard” statement that without creating something it cannot be understood. Reflecting further on the relationship between synthetic construction and knowledge making gives philosophy of science new avenues of insight into scientific practice. (shrink)

Starting from the sixties of the past century theory change has become a main concern of philosophy of science. Two of the best known formal accounts of theory change are the post-Popperian theories of verisimilitude (PPV for short) and the AGM theory of belief change (AGM for short). In this paper, we will investigate the conceptual relations between PPV and AGM and, in particular, we will ask whether the AGM rules for theory change are effective means for approaching the truth, (...) i.e., for achieving the cognitive aim of science pointed out by PPV. First, the key ideas of PPV and AGM and their application to a particular kind of propositional theories - the so called "conjunctive propositions" - will be illustrated. Afterwards, we will prove that, as far as conjunctive propositions are concerned, AGM belief change is an effective tool for approaching the truth. (shrink)

This article aims to show that fundamentality is construed differently in the two most prominent strategies of analysis we find in physical science and engineering today: (1) atomistic, reductive analysis and (2) Systems analysis. Correspondingly, atomism is the conception according to which the simplest (smallest) indivisible entity of a certain kind is most fundamental; while systemism, as will be articulated here, is the conception according to which the bonds that structure wholes are most fundamental, and scale and/or constituting entities are (...) of no significance whatsoever for fundamentality. Accordingly, atomists maintain that the basic entities—the atoms—are fundamental, and together with the “external” interactions among them, are sufficient for illuminating all the features and behaviors of the wholes they constitute; whereas systemists proclaim that it is instead structural qualities of systems, that flow from internal relations among their constituents and translate directly into behaviors, that are fundamental, and by themselves largely (if not entirely) sufficient for illuminating the features and behaviors of the wholes thereby structured. Systemism, as will be argued, is consistent with the nonexistence of a fundamental “level” of nondecomposable entities, just as it is consistent with the existence of such a level. Still, systemism is a conception of the fundamental in quite different, but still ontological terms. Systemism can serve the special sciences—the social sciences especially—better than the conception of fundamentality in terms of atoms. Systemism is, in fact, a conception of fundamentality that has rather different uses—and importantly, different resonances. This conception of fundamentality makes contact with questions pertaining to natural kinds and their situation in the metaphysics of the special sciences—their situation within an order of autonomous sciences. The controversy over fundamentality is evident in the social sciences too, albeit somewhat imperfectly, in the terms of debate between methodological individualists and functionalists/holists. This article will thus clarify the difference between systemism and holism. (shrink)

Although there has been much recent discussion on mechanisms in philosophy of science and social theory, no shared understanding of the crucial concept itself has emerged. In this paper, a distinction between two core concepts of mechanism is made on the basis that the concepts correspond to two different research strategies: the concept of mechanism as a componential causal system is associated with the heuristic of functional decomposition and spatial localization and the concept of mechanism as an abstract form of (...) interaction is associated with the strategy of abstraction and simple models. The causal facts assumed and the theoretical consequences entailed by an explanation with a given mechanism differ according to which concept of mechanism is in use. Research strategies associated with mechanism concepts also involve characteristic biases that should be taken into account when using them, especially in new areas of application. (shrink)

Philosophical accounts of emergence have been explicated in terms of logical relationships between statements (derivation) or static properties (function and realization). Jaegwon Kim is a modern proponent. A property is emergent if it is not explainable by (or reducible to) the properties of lower level components. This approach, I will argue, is unable to make sense of the kinds of emergence that are widespread in scientific explanations of complex systems. The standard philosophical notion of emergence posits the wrong dichotomies, confuses (...) compositional physicalism with explanatory physicalism, and is unable to represent the type of dynamic processes (self-organizing feedback) that both generate emergent properties and express downward causation. (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.