Chemical kinds are generally treated as having timelessly fixed identities. Biological kinds are generally treated as evolved and/or evolving entities. So what kind of kind is a biochemical kind? This article defends the thesis that biochemical molecules are clustered chemical kinds, some of which—namely, evolutionarily conserved units—are also biological kinds. On this thesis, a number of difficulties that have recently occupied philosophers concerned with proteins and kinds are shown to be either resolved or dissolved. 1 Introduction2 Conflicting Intuitions about Kinds (...) of Proteins3 Against Permissive Pluralism4 Against Nominalism, Toward a Duality of Kinds5 Biological Kinds, Chemical Kinds, and Their Relations6 Implications for Biological Individuals7 Implications for Monism and Scientific Practice. (shrink)

Philosophers’ traditional emphasis on theories, theoretical modeling, and explanation misguides research in philosophy of science. Articulating and applying core theories is part of scientific practice, but it is not the essence of scientific practice. Insofar as science has an essence, it is to systematically investigate and learn about what is not yet understood. This lecture analyzes genetics to articulate a broad-practice-centered approach to philosophy of science. It concludes by arguing that this approach can lead to richer, deeper, and more useful (...) philosophies of science, philosophies that can better inform science policy and the public’s understanding of science. (shrink)

Microstructuralism in the philosophy of chemistry is the thesis that chemical kinds can be individuated in terms of their microstructural properties (Hendry in Philos Sci 73:864–875, 2006 ). Elements provide paradigmatic examples, since the atomic number should suffice to individuate the kind. In theory, Microstructuralism should also characterise higher-level chemical kinds such as molecules, compounds, and macromolecules based on their constituent atomic properties. In this paper, several microstructural theses are distinguished. An analysis of macromolecules such as moonlighting proteins suggests that (...) all the forms of microstructuralism cannot accommodate them. (shrink)

Different chemical species are often cited as paradigm examples of structurally delimited natural kinds. While classificatory monism may thus seem plausible for simple molecules, it looks less attractive for complex biological macromolecules. I focus on the case of proteins that are most plausibly individuated by their functions. Is there a single, objective count of proteins? I argue that the vagaries of function individuation infect protein classification. We should be pluralists about macromolecular classification.

In this article I address the issue of the ontological conditions of possibility for a naturalistic notion of emergence, trying to determine its fundamental differences from the atomist, vitalist, preformationist and potentialist alternatives. I will argue that a naturalistic notion of ontological emergence can only succeed if we explicitly refuse the atomistic fundamental ontological postulate that asserts that every entity is endowed with a set of absolutely intrinsic properties, being qualitatively immutable through its extrinsic relations. Furthermore, it will be shown (...) that, ironically enough, this metaphysical assumption is implicitly shared by all the above mentioned alternatives to Emergentism. The current article concludes that the notion of organization by itself is not enough, and that ontological emergence can only be justified by assuming a relational ontological perspective that, in opposition both to atomism and holism, defends that the existence-conditions, the identity and the causal behavior of any emergent systemic property can only be conceived, and explained, as constructed by and through specific networks of qualitatively transformative relational processes that occur between the system’s components and between the system and its environment. Additionally, I try to explain how one can make sense of the idea that an emergent phenomenon is both dependent on, and autonomous from, its emergence base. (shrink)

This paper proposes an integrated-structure notion of interlevel emergence, from a dynamic relational ontological perspective. First, I will argue that only the individualist essentialism of atomistic metaphysics can block the possibility of interlevel emergence. Then I will show that we can make sense of emergence by recognizing the formation of structures of transformative and interdependent causal relations in the generation and development of a particular class of mereological complexes called integrated systems. Finally, I shall argue that even though the emergent (...) structural attributes of such systems are not micro-determined nor micro-reducible, they can still be accounted for by an interlevel integrative neo-mechanistic form of explanation. (shrink)

It has long been held that the structure of a protein is determined solely by the interactions of the atoms in the sequence of amino acids of which it is composed, and thus the stable, biologically functional conformation should be predictable by ab initio or de novo methods. However, except for small proteins, ab initio predictions have not been successful. We explain why this is the case and argue that the relationship among the different methods, models, and representations of protein (...) structure is one of integrative pluralism. Our defence appeals to specific features of the complexity of the functional protein structure and to the partial character of representation in general. We present examples of integrative strategies in protein science. 1. Introduction2. Partiality of Representation3. Protein Functional Complexity4. Modelling Protein Structure4.1 Integrating ab initio and experimental models4.2 Integrating multiple experimental models5. Conclusion. (shrink)

ABSTRACT It has long been held that the structure of a protein is determined solely by the interactions of the atoms in the sequence of amino acids of which it is composed, and thus the stable, biologically functional conformation should be predictable by ab initio or de novo methods. However, except for small proteins, ab initio predictions have not been successful. We explain why this is the case and argue that the relationship among the different methods, models, and representations of (...) protein structure is one of integrative pluralism. Our defence appeals to specific features of the complexity of the functional protein structure and to the partial character of representation in general. We present examples of integrative strategies in protein science. _1._ Introduction _2._ Partiality of Representation _3._ Protein Functional Complexity _4._ Modelling Protein Structure _4.1_ Integrating ab initio and experimental models _4.2_ Integrating multiple experimental models _5._ Conclusion. (shrink)

The inapplicability of variations on theory reduction in the context of genetics and their irrelevance to ongoing research has led to an anti-reductionist consensus in philosophy of biology. One response to this situation is to focus on forms of reductive explanation that better correspond to actual scientific reasoning (e.g. part–whole relations). Working from this perspective, we explore three different aspects (intrinsicality, fundamentality, and temporality) that arise from distinct facets of reductive explanation: composition and causation. Concentrating on these aspects generates new (...) forms of reductive explanation and conditions for their success or failure in biology and other sciences. This analysis is illustrated using the case of protein folding in molecular biology, which demonstrates its applicability and relevance, as well as illuminating the complexity of reductive reasoning in a specific biological context. (shrink)

Following Kripke and Putnam, the received view of chemical kinds has been a microstructuralist one. To be a microstructuralist about chemical kinds is to think that membership in said kinds is conferred by microstructural properties. Recently, the received microstructuralist view has been elaborated and defended, but it has also been attacked on the basis of complexities, both chemical and ontological. Here, I look at which complexities really challenge the microstructuralist view; at how the view itself might be made more complicated (...) in order to accommodate such challenges; and finally, at what this increasingly complicated picture implies for our standard assessment of chemical kindhood—primarily, for the widespread assumption that chemical kinds in general are more neat and tidy than those messy biological ones. _1_ The Received View _2_ A Taxonomy of Chemical Kinds _3_ Atomic Number _4_ H2O, H3O+, OH−, and More _5_ Complicating the Microstructuralist Picture _6_ Concrete and Other Mixtures _7_ Macromolecules, Especially Proteins _8_ Abandoning Sameness of Elemental Composition _9_ Not So Different after All. (shrink)

This paper considers two recent arguments that structure should not be regarded as the fundamental individuating property of proteins. By clarifying both what it might mean for certain properties to play a fundamental role in a classification scheme and the extent to which structure plays such a role in protein classification, I argue that both arguments are unsound. Because of its robustness, its importance in laboratory practice, and its explanatory centrality, primary structure should be regarded as the fundamental distinguishing characteristic (...) of protein taxonomy. (shrink)

The paper argues for a pragmatic account of genetic explanation. This is to say that when a disease or other trait is termed genetic, the reasons for singling out genes as causes over other, also necessary, genetic and nongenetic conditions are not wholly theoretical but include pragmatic dimensions. Whether the explanation is the presence of a trait in an individual or differences in a trait among individuals, genetic explanations are context-dependent in three ways: they are relative to a causal background (...) of genetic and nongenetic factors; they are relative to a population; and they are relative to the present state of knowledge. Criteria like causal priority, nonstandardness, and causal efficacy that purport to distinguish objectively between genetic causes and nongenetic conditions either incorporate pragmatic elements or fail for other reasons. When the pragmatic dimensions of genetic explanations are recognized, we come to understand the current phenomenon of geneticization to be a reflection of increased technological capacities to manipulate genes in the laboratory, and potentially the clinic, rather than theoretical progress in understanding how diseases and other traits arise. This calls into question the value of the search for theoretical definitions of designations like genetic disease or genetic susceptibility as directives for action. (shrink)

Biochemical kinds such as proteins pose interesting problems for philosophers of science, as they can be studied from the points of view of both biology and chemistry. The relationship between the biological functions of biochemical kinds and the microstructures that they are related to is the key question. This leads us to a more general discussion about ontological reductionism, microstructuralism, and multiple realization at the biology-chemistry interface. On the face of it, biochemical kinds seem to pose a challenge for ontological (...) reductionism and hence motivate a dual theory of chemical and biological kinds, a type of pluralism about natural kinds. But it will be argued that the challenge, which is based on multiple realization, can be addressed. The upshot is that there are reasonable prospects for ontological reductionism about biochemical kinds, which corroborates natural kind monism. (shrink)

In this book Ron Amundson examines two hundred years of scientific views on the evolution-development relationship from the perspective of evolutionary developmental biology. This perspective challenges several popular views about the history of evolutionary thought by claiming that many earlier authors had made history come out right for the Evolutionary Synthesis. The book starts with a revised history of nineteenth-century evolutionary thought. It then investigates how development became irrelevant with the Evolutionary Synthesis. It concludes with an examination of the contrasts (...) that persist between mainstream evolutionary theory and evo-devo. This book will appeal to students and professionals in the philosophy and history of science, and biology. (shrink)

An analysis of two heuristic strategies for the development of mechanistic models, illustrated with historical examples from the life sciences. In Discovering Complexity, William Bechtel and Robert Richardson examine two heuristics that guided the development of mechanistic models in the life sciences: decomposition and localization. Drawing on historical cases from disciplines including cell biology, cognitive neuroscience, and genetics, they identify a number of "choice points" that life scientists confront in developing mechanistic explanations and show how different choices result in divergent (...) explanatory models. Describing decomposition as the attempt to differentiate functional and structural components of a system and localization as the assignment of responsibility for specific functions to specific structures, Bechtel and Richardson examine the usefulness of these heuristics as well as their fallibility—the sometimes false assumption underlying them that nature is significantly decomposable and hierarchically organized. When Discovering Complexity was originally published in 1993, few philosophers of science perceived the centrality of seeking mechanisms to explain phenomena in biology, relying instead on the model of nomological explanation advanced by the logical positivists (a model Bechtel and Richardson found to be utterly inapplicable to the examples from the life sciences in their study). Since then, mechanism and mechanistic explanation have become widely discussed. In a substantive new introduction to this MIT Press edition of their book, Bechtel and Richardson examine both philosophical and scientific developments in research on mechanistic models since 1993. (shrink)