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)

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)

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)

The scope and nature of reductionist explanation in quantum physics is analyzed, with special attention being paid to the situation in quantum physics.

In what sense are the activities and properties of components in a mechanism explanatorily relevant to the behavior of a mechanism as a whole? I articulate this problem, the problem of constitutive relevance, and I show that it must be solved if we are to understand mechanisms and mechanistic explanation. I argue against some putative solutions to the problem of constitutive relevance, and I sketch a positive account according to which relevance is analyzed in terms ofrelationships of mutual manipulability between (...) the behavior of a mechanism as a whole and the properties and activities of its components. My account is a causal-mechanical account in the sense that it is a particular expression of the idea that constitutive explanation is a matter of showing how an explanandum phenomenon is situated within the causal structure of the world. It is thus offered as a rival to epistemic (argument-centered) and psychological accounts of interlevel explanation. (shrink)

Most philosophical accounts of emergence are incompatible with reduction. Most scientists regard a system property as emergent relative to properties of its parts if it depends upon their mode of organization-a view consistent with reduction. Emergence is a failure of aggregativity, in which ``the whole is nothing more than the sum of its parts''. Aggregativity requires four conditions, giving powerful tools for analyzing modes of organization. Differently met for different decompositions of the system, and in different degrees, the structural conditions (...) can provide evaluation criteria for choosing decompositions, ``natural kinds'', and detecting functional localization fallacies, approximations, and various biases of vulgar reductionisms. This analysis of emergence and use of these conditions as heuristics is consistent with a broader reductionistic methodology. (shrink)

Not all models are explanatory. Some models are data summaries. Some models sketch explanations but leave crucial details unspecified or hidden behind filler terms. Some models are used to conjecture a how-possibly explanation without regard to whether it is a how-actually explanation. I use the Hodgkin and Huxley model of the action potential to illustrate these ways that models can be useful without explaining. I then use the subsequent development of the explanation of the action potential to show what is (...) required of an adequate mechanistic model. Mechanistic models are explanatory. (shrink)

The new mechanists and the autonomy approach both aim to account for how biological phenomena are explained. One identifies appeals to how components of a mechanism are organized so that their activities produce a phenomenon. The other directs attention towards the whole organism and focuses on how it achieves self-maintenance. This paper discusses challenges each confronts and how each could benefit from collaboration with the other: the new mechanistic framework can gain by taking into account what happens outside individual mechanisms, (...) while the autonomy approach can ground itself in biological research into how the actual components constituting an autonomous system interact and contribute in different ways to realize and maintain the system. To press the case that these two traditions should be constructively integrated we describe how three recent developments in the autonomy tradition together provide a bridge between the two traditions: (1) a framework of work and constraints, (2) a conception of function grounded in the organization of an autonomous system, and (3) a focus on control. (shrink)

It is widely assumed that functional and dispositional properties are not identical to their physical base, but that there is some kind of asymmetrical ontological dependence between them. In this regard, a popular idea is that the former are realized by the latter, which, under the non-identity assumption, is generally understood to be a non-causal, constitutive relation. In this paper we examine two of the most widely accepted approaches to realization, the so-called ‘flat view’ and the ‘dimensioned view’, and we (...) analyze their explanatory relevance in the light of a number of examples from the life sciences, paying special attention to developmental phenomena. Our conclusion is that the emphasis placed by modern-day biology on such properties as variability, evolvability, and a whole collection of phenomena like modularity, robustness, and developmental constraint or developmental bias requires the adoption of a much more dynamic perspective than traditional realization frameworks are able to capture. (shrink)

Completeness is an important but misunderstood norm of explanation. It has recently been argued that mechanistic accounts of scientific explanation are committed to the thesis that models are complete only if they describe everything about a mechanism and, as a corollary, that incomplete models are always improved by adding more details. If so, mechanistic accounts are at odds with the obvious and important role of abstraction in scientific modelling. We respond to this characterization of the mechanist’s views about abstraction and (...) articulate norms of completeness for mechanistic explanations that have no such unwanted implications. _1_ Introduction _2_ A Balancing Act: When Do Details Matter? _3_ The Norms of Causal Explanation _4_ The Norms of Constitutive Explanation _5_ Salmon-Completeness _6_ From More Details to More Relevant Details _7_ Non-explanatory Virtues of Abstraction _8_ From Explanatory Models to Explanatory Knowledge _9_ Mechanistic Completeness Reconsidered _10_ Conclusion. (shrink)

I argue for a manipulationist-mechanistic framework for content-NCC research in the case of visual consciousness (Bechtel 2008; Neisser 2012). Reference to mechanisms is common in the NCC research. Furthermore, recent developments in non-invasive brain stimulation techniques (NIBS) lend support to a manipulationist standpoint. The crucial question is to understand what is changed after manipulation of a brain mechanism. In the second part of the paper I review the literature on intentionalism, and argue that intervention on the neural mechanism is likely (...) to change the intentional content of consciousness. This urges us to shift from content-NCC to what I call “intentional mechanisms”. Such mechanisms, it is argued, should be understood as neural prerequisites of conscious visual experience. (shrink)

Mechanisms are said to consist of two kinds of components, entities and activities. In the first half of this chapter, I examine what entities and activities are, how they relate to well-known ontological categories, such as processes or dispositions, and how entities and activities relate to each other (e.g., can one be reduced to the other or are they mutually dependent?). The second part of this chapter analyzes different criteria for individuating the components of mechanisms and discusses how real the (...) boundaries of mechanisms are. (shrink)

Methodological reductionists practice ‘wannabe reductionism’. They claim that one should pursue reductionism, but never propose how. I integrate two strains in prior work to do so. Three kinds of activities are pursued as “reductionist”. “Successional reduction” and inter-level mechanistic explanation are legitimate and powerful strategies. Eliminativism is generally ill-conceived. Specific problem-solving heuristics for constructing inter-level mechanistic explanations show why and when they can provide powerful and fruitful tools and insights, but sometimes lead to erroneous results. I show how traditional metaphysical (...) approaches fail to engage how science is done. The methods used do so, and support a pragmatic and non-eliminativist realism. (shrink)

Most philosophical debate over mental causation has been concerned with reconciling commonsense intuitions that there are causal interactions between the mental and the physical with philosophical theories of the nature of the mental that seem to suggest otherwise. My concern is with a different and more practical problem. We often confront some cognitive, affective, or bodily phenomenon, and wonder about its source – its etiology or its underlying causal basis. For instance, you might wonder whether your queasiness due to something (...) you ate, or whether it is just nervousness, or whether your aunt’s memory loss is a neurological problem or a psychological response to trauma. Such questions attempt to localize the causes of a phenomenon at some level in the complex multi-level systems that we human animals are. In this paper I will attempt to tease out the sense of level implicit in such questions, and to show how it is related to current mechanistic accounts of levels. I will argue that the explanation of our practices of level attribution is deeply pragmatic. Such attributions are often attempts to locate the causes of problems, and to identify interventions that could solve those problems. (shrink)

According to one large family of views, scientific explanations explain a phenomenon (such as an event or a regularity) by subsuming it under a general representation, model, prototype, or schema (see Bechtel, W., & Abrahamsen, A. (2005). Explanation: A mechanist alternative. Studies in History and Philosophy of Biological and Biomedical Sciences, 36(2), 421–441; Churchland, P. M. (1989). A neurocomputational perspective: The nature of mind and the structure of science. Cambridge: MIT Press; Darden (2006); Hempel, C. G. (1965). Aspects of scientific (...) explanation. In C. G. Hempel (Ed.), Aspects of scientific explanation (pp. 331–496). New York: Free Press; Kitcher (1989); Machamer, P., Darden, L., & Craver, C. F. (2000). Thinking about mechanisms. Philosophy of Science, 67(1), 1–25). My concern is with the minimal suggestion that an adequate philosophical theory of scientific explanation can limit its attention to the format or structure with which theories are represented. The representational subsumption view is a plausible hypothesis about the psychology of understanding. It is also a plausible claim about how scientists present their knowledge to the world. However, one cannot address the central questions for a philosophical theory of scientific explanation without turning one’s attention from the structure of representations to the basic commitments about the worldly structures that plausibly count as explanatory. A philosophical theory of scientific explanation should achieve two goals. The first is explanatory demarcation. It should show how explanation relates with other scientific achievements, such as control, description, measurement, prediction, and taxonomy. The second is explanatory normativity. It should say when putative explanations succeed and fail. One cannot achieve these goals without undertaking commitments about the kinds of ontic structures that plausibly count as explanatory. Representations convey explanatory information about a phenomenon when and only when they describe the ontic explanations for those phenomena. (shrink)

Evolutionary systems biology (ESB) aims to integrate methods from systems biology and evolutionary biology to go beyond the current limitations in both fields. This article clarifies some conceptual difficulties of this integration project, and shows how they can be overcome. The main challenge we consider involves the integration of evolutionary biology with developmental dynamics, illustrated with two examples. First, we examine historical tensions between efforts to define general evolutionary principles and articulation of detailed mechanistic explanations of specific traits. Next, these (...) tensions are further clarified by considering a recent case from another field focused on developmental dynamics: stem cell biology. In the stem cell case, incompatible explanatory aims block integration. Experimental approaches aim at mechanistic explanation while dynamical system models offer explanation in terms of general principles. We then discuss an ESB case in which integration succeeds: search for general attractors using a dynamical systems framework synergizes with the experimental search for detailed mechanisms. Contrasts between the positive and negative cases suggest general lessons for achieving an integrated understanding of developmental and evolutionary dynamics. The key integrative move is to acknowledge two complementary aims, both relevant to explanation: identifying the space of possible dynamic states and trajectories, and mechanistic understanding of causal interactions underlying a specific phenomenon of interest. These two aims can support one another in a joint project characterizing dynamic aspects of evolving lineages. This more inclusive project can lead to insights that cannot be reached by either approach in isolation. (shrink)

The machine conception of the organism (MCO) is one of the most pervasive notions in modern biology. However, it has not yet received much attention by philosophers of biology. The MCO has its origins in Cartesian natural philosophy, and it is based on the metaphorical redescription of the organism as a machine. In this paper I argue that although organisms and machines resemble each other in some basic respects, they are actually very different kinds of systems. I submit that the (...) most significant difference between organisms and machines is that the former are intrinsically purposive whereas the latter are extrinsically purposive. Using this distinction as a starting point, I discuss a wide range of dissimilarities between organisms and machines that collectively lay bare the inadequacy of the MCO as a general theory of living systems. To account for the MCO’s prevalence in biology, I distinguish between its theoretical, heuristic, and rhetorical functions. I explain why the MCO is valuable when it is employed heuristically but not theoretically, and finally I illustrate the serious problems that arise from the rhetorical appeal to the MCO. (shrink)

The concept of mechanism in biology has three distinct meanings. It may refer to a philosophical thesis about the nature of life and biology (‘mechanicism’), to the internal workings of a machine-like structure (‘machine mechanism’), or to the causal explanation of a particular phenomenon (‘causal mechanism’). In this paper I trace the conceptual evolution of ‘mechanism’ in the history of biology, and I examine how the three meanings of this term have come to be featured in the philosophy of biology, (...) situating the new ‘mechanismic program’ in this context. I argue that the leading advocates of the mechanismic program (i.e., Craver, Darden, Bechtel, etc.) inadvertently conflate the different senses of ‘mechanism’. Specifically, they all inappropriately endow causal mechanisms with the ontic status of machine mechanisms, and this invariably results in problematic accounts of the role played by mechanism-talk in scientific practice. I suggest that for effective analyses of the concept of mechanism, causal mechanisms need to be distinguished from machine mechanisms, and the new mechanismic program in the philosophy of biology needs to be demarcated from the traditional concerns of mechanistic biology. (shrink)

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)

Reduction and reductionism have been central philosophical topics in analytic philosophy of science for more than six decades. Together they encompass a diversity of issues from metaphysics and epistemology. This article provides an introduction to the topic that illuminates how contemporary epistemological discussions took their shape historically and limns the contours of concrete cases of reduction in specific natural sciences. The unity of science and the impulse to accomplish compositional reduction in accord with a layer-cake vision of the sciences, the (...) seminal contributions of Ernest Nagel on theory reduction and how they strongly conditioned subsequent philosophical discussions, and the detailed issues pertaining to different accounts of reduction that arise in both physical and biological science (e.g., limit-case and part-whole reduction in physics, the difference-making principle in genetics, and mechanisms in molecular biology) are explored. The conclusion argues that the epistemological heterogeneity and patchwork organization of the natural sciences encourages a pluralist stance about reduction. (shrink)

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

In this paper I offer an analysis of causation based upon a theory of mechanisms-complex systems whose internal parts interact to produce a system's external behavior. I argue that all but the fundamental laws of physics can be explained by reference to mechanisms. Mechanisms provide an epistemologically unproblematic way to explain the necessity which is often taken to distinguish laws from other generalizations. This account of necessity leads to a theory of causation according to which events are causally related when (...) there is a mechanism that connects them. I present reasons why the lack of an account of fundamental physical causation does not undermine the mechanical account. (shrink)

Any successful account of the metaphysics of mechanistic causation must satisfy at least five key desiderata. In this article, I lay out these five desiderata and explain why existing accounts of the metaphysics of mechanistic causation fail to satisfy them. I then present an alternative account that does satisfy the five desiderata. According to this alternative account, we must resort to a type of ontological entity that is new to metaphysics, but not to science: constraints. In this article, I explain (...) how a constraints-based metaphysics fits best with the emerging consensus on the nature of mechanistic explanation. 1Introduction2Renormalizability2.1The first two desiderata: Intrinsicness and productivity2.2The third desideratum: Scientific validity or non-mysteriousness2.3The fourth desideratum: Directionality2.4The fifth desideratum: Perspectival nature of mechanisms3Constraints and Causation3.1Multi-perspectival realism and causal structure3.2Causal structure as laws3.3Causal structures in analytical mechanics: Constraints3.4A metaphysics inspired by analytical mechanics: Constraints as ontologically primitive modal structures4Constraints and Mechanistic Causal Powers 4.1Inter- versus intra-perspectival categories4.2Mechanistic causal powers are grounded by constraints4.3Intrinsicness and constraints4.4Constraints and productiveness4.5Constraints and directionality5Conclusion. (shrink)

Token physicalism is often viewed as a modest and unproblematic physicalist commitment, as contrasted with type physicalism. This paper argues that the prevalence of functional individuation in biology creates serious problems for token physicalism, because the latter requires that biological entities can be individuated physically and without reference to biological functioning. After characterizing the main philosophical roles for token physicalism, I describe the distinctive uses of functional individuation in models of biological processes. I then introduce some requirements on token identity (...) claims that arise from a position on individuation and identity known as sortalism. An examination of biological examples shows that these sortalist requirements cannot be plausibly met due to differences between individuation by functional biological criteria and by physical criteria. Even without assuming sortalism, token physicalism faces the more basic problem of excluding functionally irrelevant detail from the individuation of biological tokens. I close by suggesting that the philosophical roles for token identity are better fulfilled by a notion of token composition, which promotes a hierarchical picture of individuality. (shrink)

Recently, it has been provocatively claimed that dynamical modeling approaches signal the emergence of a new explanatory framework distinct from that of mechanistic explanation. This paper rejects this proposal and argues that dynamical explanations are fully compatible with, even naturally construed as, instances of mechanistic explanations. Specifically, it is argued that the mathematical framework of dynamics provides a powerful descriptive scheme for revealing temporal features of activities in mechanisms and plays an explanatory role to the extent it is deployed for (...) this purpose. It is also suggested that more attention should be paid to the distinctive methodological contributions of the dynamical framework including its usefulness as a heuristic for mechanism discovery and hypothesis generation in contemporary neuroscience and biology. (shrink)

Biological sciences have strived to adopt the conceptual framework of physics and have become increasingly quantitatively oriented, aiming to refute the assertion that biology appears unquantifiable, unpredictable, and messy. But despite all effort, biology is characterized by a paucity of quantitative statements with universal applications. Nonetheless, many biological disciplines—most notably molecular biology—have experienced an ascendancy over the last 50 years. The underlying core concepts and ideas permeate and inform many neighboring disciplines. This surprising success is probably not so much attributable (...) to mathematical and statistical approaches in molecular biology, but rather to the preponderance of qualitative approaches, especially visualization. Visualizations can be afforded by quantitative research, but usually they rely on both, quantitative and qualitative research. I claim the following three features to be responsible for the unceasing zeal for using visualizations: visual representations facilitate reasoning, images can be cognitively processed in a “fast” manner, and abstractions of visual representations prompt conceptual advances. In summary, visualizations have largely contributed to the success of molecular biology by conveying its concepts to other disciplines, and at the same time, eclipsing mere quantitative approaches. However, visualizations also bear the risk of misinterpretation when traversing neighboring disciplines and even more so when pervading nonscientific domains. (shrink)

Extrapolation from a well-understood base population to a less-understood target population can fail if the base and target populations are not sufficiently similar. Differences between laboratory mice and humans, for example, can hinder extrapolation in medical research. Mice that carry a partial or complete human physiological system, known as humanized mice, are supposed to make extrapolation more reliable by simulating a variety of human diseases. But what justifies our belief that these mice are similar enough to their human counterparts to (...) simulate human disease? I argue that, unless three requirements are met in the process of humanizing mice, very little does. My requirements are not meant to provide necessary and sufficient conditions that guarantee a particular outcome. Instead, they serve as a heuristic for guiding scientific judgments involving extrapolation. In developing each requirement, I engage with philosophical issues concerning the nature of model-based science and the mechanistic approach (and its limits) to making generalizations in the life sciences. (shrink)

The goal of this paper is to encourage a reconfiguration of the discussion about typology in biology away from the metaphysics of essentialism and toward the epistemology of classifying natural phenomena for the purposes of empirical inquiry. First, I briefly review arguments concerning ‘typological thinking’, essentialism, species, and natural kinds, highlighting their predominantly metaphysical nature. Second, I use a distinction between the aims, strategies, and tactics of science to suggest how a shift from metaphysics to epistemology might be accomplished. Typological (...) thinking can be understood as a scientific tactic that involves representing natural phenomena using idealizations and approximations, which facilitates explanation, investigation, and theorizing via abstraction and generalization. Third, a variety of typologies from different areas of biology are introduced to emphasize the diversity of this representational reasoning. One particular example is used to examine how there can be epistemological conflict between typology and evolutionary analysis. This demonstrates that alternative strategies of typological thinking arise due to the divergent explanatory goals of researchers working in different disciplines with disparate methodologies. I conclude with several research questions that emerge from an epistemological reconfiguration of typology. (shrink)

In this article, I present two conceptual problems for Craver's mutual manipulability account of constitutive relevance in mechanisms. First, constitutive relevance threatens to imply causal relevance despite Craver (and Bechtel)'s claim that they are strictly distinct. Second, if (as is intuitively appealing) parthood is defined in terms of spatio-temporal inclusion, then the mutual manipulability account is prone to counterexamples, as I show by a case of endosymbiosis. I also present a methodological problem (a case of experimental underdetermination) and formulate two (...) partial, but fallible solutions based on the notions of parthood and synchronicity. (shrink)

This article argues that the basic account of mechanism and mechanistic explanation, involving sequential execution of qualitatively characterized operations, is itself insufficient to explain biological phenomena such as the capacity of living organisms to maintain themselves as systems distinct from their environment. This capacity depends on cyclic organization, including positive and negative feedback loops, which can generate complex dynamics. Understanding cyclically organized mechanisms with complex dynamics requires coordinating research directed at decomposing mechanisms into parts and operations with research using computational (...) models to recompose mechanisms and determine their dynamic behavior. This coordinated endeavor yields dynamic mechanistic explanations. (shrink)

A classification of models of reduction into three categories — theory reductionism, explanatory reductionism, and constitutive reductionism — is presented. It is shown that this classification helps clarify the relations between various explications of reduction that have been offered in the past, especially if a distinction is maintained between the various epistemological and ontological issues that arise. A relatively new model of explanatory reduction, one that emphasizes that reduction is the explanation of a whole in terms of its parts is (...) also presented in detail. Finally, the classification is used to clarify the debate over reductionism in molecular biology. It is argued there that while no model from the category of theory reduction might be applicable in that case, models of explanatory reduction might yet capture the structure of the relevant explanations. (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)

In summary, many extant definitions of the niche concept are based on the geometric metaphor which represents the niche as an object embedded in a geometric space. There are several difficulties with this approach; the activities of organisms are not fully described, certain attributes of the functional aspect of the niche are not represented, the life cycles of organisms are not described, and the heuristic value of the concept diminishes with increasing dimensionality.An alternative and complementary approach to the niche is (...) the linguistic metaphor. This approach is based on the explanatory objective to explain the assembly of the ecosystems of successional seres from species pools and abiotic environmental factors. The linguistic metaphor suggests that a theory of ecosystem assembly is a generative grammar that associates particular species with environmental features. The niche of a particular species is defined in terms of the rules of a generative-transformational grammar used to derive an hierarchically organized description of that species. This approach also has conceptual difficulties: (1) empirically testing competence theories and distinguishing possible and impossible objects (e.g. species and ecosystems) are difficult, (2) evolutionary processes are difficult to incorporate, (3) the mathematical tools associated with grammars do not have the range of applicability of the mathematical tools associated with the geometric metaphor, and (4) the productions (hierarchical trees) of a grammar are not easily visualized.The geometric and linguistic metaphors of the niche should be viewed as complementary pictures of the same object. The geometric representation is most adept at describing community dynamics and stability, niche overlap, and organism response to abiotic environments. The linguistic metaphor represents well organism activities, niche dynamics, and ecosystem assembly. (shrink)

The terms “perspectivism” and “perspectivalism” have been the focus of an intense philosophical discussion with important repercussions for the debate about the role of mechanisms in scientific explanations. However, leading exponents of the new mechanistic philosophy have conceded more than was necessary to the radically subjectivistic perspectivalism, and fell into the opposite error, by retaining not negligible residues of objectivistic views about mechanisms. In order to remove this vacillation between the subjective-cultural and the objective-natural sides of mechanisms, we shall raise (...) the question about theory-ladenness over again and interpret it in its connection with the technical–experimental nature of scientific knowledge, as affirming the perspectival character of scientific knowledge: It is because of the character at once theory-laden and practice-laden, i.e. technique-laden, of our putting questions to nature that empirical reality must be investigated from particular perspectives: nature can be known scientifically only from a potentially infinite number of perspectives or theoretical points of view, concretely exemplified by mechanisms or experimental ‘machines’ that allow specific access to specific aspects of sensible reality. (shrink)

Richard Levins’ distinction between aggregate, composed and evolved systems acquires new significance as we recognize the importance of mechanistic explanation. Criteria for aggregativity provide limiting cases for absence of organization, so through their failure, can provide rich detectors for organizational properties. I explore the use of failures of aggregativity for the analysis of mechanistic systems in diverse contexts. Aggregativity appears theoretically desireable, but we are easily fooled. It may be exaggerated through approximation, conditions of derivation, and extrapolating from some conditions (...) of decomposition illegtimately to others. Evolved systems particularly may require analyses under alternative complementary decompositions. Exploring these conditions helps us to better understand the strengths and limits of reductionistic methods. (shrink)

Even though complexity is a concept that is ubiquitously used by biologists and philosophers of biology, it is rarely made precise. I argue that a clarification of the concept is neither trivial nor unachievable, and I propose a unifying framework based on the technical notion of “effective complexity” that allows me to do justice to conflicting intuitions about biological complexity, while taking into account several distinctions in the usage of the concept that are often overlooked. In particular, I propose a (...) distinction between two kinds of complexity, “mechanical” and “emergent”, which can be understood as different ways of relating the effective complexity of mechanisms and of behaviors in biological explanations. I illustrate the adequacy of this framework by discussing different attempts to understand intracellular organization in terms of pathways and networks. My framework provides a different way of thinking about recent philosophical debates, for example, on the difference between mechanistic and topological explanations and about the concept of emergence. Moreover, it can contribute to a proper assessment of metascientific arguments that invoke biological complexity. (shrink)

Recently the functional model of reduction has become something like the standard model of reduction in philosophy of mind. In this paper, I argue that the functional model fails as an account of reduction due to problems related to three key concepts: functionalization, realization and causation. I further argue that if we try to revise the model in order to make it more coherent and scientifically plausible, the result is merely a simplified version of what in philosophy of science is (...) known as mechanistic explanation. Hence, instead of analyzing reduction in philosophy of mind in terms of functional reduction, it should be analyzed in terms of mechanistic explanation. (shrink)