The identity of a natural kind can be construed in terms of its causal profile. This conception is more appropriate to science than two alternatives. The identity of a natural kind is not determined by one causal role because one natural kind can have many causal roles and several functions and because some functions are shared by different kinds. Furthermore, the microstructuralist thesis is wrong: The identity of certain natural kinds is not determined by their microstructure. It is true that (...) if A and B have the same microstructural composition then a sample of a chemical substance A is of the same chemical substance as a sample of B. However, the reverse does not hold. It is not the case that if a sample of a chemical substance A is of the same chemical substance as a sample of B then A and B have the same microstructural composition. This is because a macroscopic NK can be “multiconstituted” by different microstructures. (shrink)

Recent discussions of emergence in physics have focussed on the use of limiting relations, and often particularly on singular or asymptotic limits. We discuss a putative example of emergence that does not fit into this narrative: the case of phonons. These quasi-particles have some claim to be emergent, not least because the way in which they relate to the underlying crystal is almost precisely analogous to the way in which quantum particles relate to the underlying quantum field theory. But there (...) is no need to take a limit when moving from a crystal lattice based description to the phonon description. Not only does this demonstrate that we can have emergence without limits, but also provides a way of understanding cases that do involve limits. (shrink)

The present paper discusses different approaches to metaphysics and defends a specific, non-deflationary approach that nevertheless qualifies as scientifically-grounded and, consequently, as acceptable from the naturalistic viewpoint. By critically assessing some recent work on science and metaphysics, we argue that such a sophisticated form of naturalism, which preserves the autonomy of metaphysics as an a priori enterprise yet pays due attention to the indications coming from our best science, is not only workable but recommended.

Robustness is often presented as a guideline for distinguishing the true or real from mere appearances or artifacts. Most of recent discussions of robustness have focused on the kind of derivational robustness analysis introduced by Levins, while the related but distinct idea of robustness as multiple accessibility, defended by Wimsatt, has received less attention. In this paper, I argue that the latter kind of robustness, when properly understood, can provide justification for ontological commitments. The idea is that we are justified (...) in believing that things studied by science are real insofar as we have robust evidence for them. I develop and analyze this idea in detail, and based on concrete examples show that it plays an important role in science. Finally, I demonstrate how robustness can be used to clarify the debate on scientific realism and to formulate new arguments. (shrink)

In its last round of publications in September 2012, the Encyclopedia Of DNA Elements (ENCODE) assigned a biochemical function to most of the human genome, which was taken up by the media as meaning the end of ‘Junk DNA’. This provoked a heated reaction from evolutionary biologists, who among other things claimed that ENCODE adopted a wrong and much too inclusive notion of function, making its dismissal of junk DNA merely rhetorical. We argue that this criticism rests on misunderstandings concerning (...) the nature of the ENCODE project, the relevant notion of function and the claim that most of our genome is junk. We argue that evolutionary accounts of function presuppose functions as ‘causal roles’, and that selection is but a useful proxy for relevant functions, which might well be unsuitable to biomedical research. Taking a closer look at the discovery process in which ENCODE participates, we argue that ENCODE’s strategy of biochemical signatures successfully identified activities of DNA elements with an eye towards causal roles of interest to biomedical research. We argue that ENCODE’s controversial claim of functionality should be interpreted as saying that 80 % of the genome is engaging in relevant biochemical activities and is very likely to have a causal role in phenomena deemed relevant to biomedical research. Finally, we discuss ambiguities in the meaning of junk DNA and in one of the main arguments raised for its prevalence, and we evaluate the impact of ENCODE’s results on the claim that most of our genome is junk. (shrink)

one takes to be the most salient, any pair could be judged more similar to each other than to the third. Goodman uses this second problem to showthat there can be no context-free similarity metric, either in the trivial case or in a scientifically ...

This is one of two papers about emergence, reduction and supervenience. It expounds these notions and analyses the general relations between them. The companion paper analyses the situation in physics, especially limiting relations between physical theories. I shall take emergence as behaviour that is novel and robust relative to some comparison class. I shall take reduction as deduction using appropriate auxiliary definitions. And I shall take supervenience as a weakening of reduction, viz. to allow infinitely long definitions. The overall claim (...) of this paper will be that emergence is logically independent both of reduction and of supervenience. In particular, one can have emergence with reduction, as well as without it; and emergence without supervenience, as well as with it. Of the subsidiary claims, the four main ones are: : I defend the traditional Nagelian conception of reduction ; : I deny that the multiple realizability argument causes trouble for reductions, or ``reductionism'' ; : I stress the collapse of supervenience into deduction via Beth's theorem ; : I adapt some examples already in the literature to show supervenience without emergence and vice versa. (shrink)

Recent work on gene concepts has been influenced by recognition of the extent to which RNA transcripts from a given DNA sequence yield different products in different cellular environments. These transcripts are altered in many ways and yield many products based, somehow, on the sequence of nucleotides in the DNA. I focus on alternative splicing of RNA transcripts (which often yields distinct proteins from the same raw transcript) and on 'gene sharing', in which a single gene produces distinct proteins with (...) the exact same amino acid sequence. These are instances of molecular pleiotropy, in which distinct molecules are derived from a single putative gene. In such cases the cellular and external environments play major roles in determining which protein is produced. Where there is molecular pleiotropy, alternative gene concepts are naturally deployed; molecular epigenesis (revision of sequence-based information by altering molecular conformations or by action of non-informational molecules) plays a major role in orderly development. These results show that gene concepts in molecular biology do, and should, have both structural and functional components. They also show the need for a plurality of gene concepts and reveal fundamental difficulties in stabilizing gene concepts solely by reference to nucleotide sequence. (shrink)

Motivated by the seeming structure of the sciences, metaphysical emergence combines broadly synchronic dependence coupled with some degree of ontological and causal autonomy. Reflecting the diverse, frequently incompatible interpretations of the notions of dependence and autonomy, however, accounts of emergence diverge into a bewildering variety. Here I argue that much of this apparent diversity is superficial. I first argue, by attention to the problem of higher-level causation, that two and only two strategies for addressing this problem accommodate the genuine emergence (...) of special science entities. These strategies in turn suggest two distinct schema for metaphysical emergence---'Weak' and 'Strong' emergence, respectively. Each schema imposes a condition on the powers of entities taken to be emergent: Strong emergence requires that higher-level features have more token powers than their dependence base features, whereas Weak emergence requires that higher-level features have a proper subset of the token powers of their dependence base features. Importantly, the notion of “power” at issue here is metaphysically neutral, primarily reflecting commitment just to the plausible thesis that what causes an entity may bring about are associated with how the entity is---that is, with its features. (shrink)

Definitions of the term gene typically superimpose molecular genetics onto Mendelism. What emerges are persistent attempts to regard the gene as a unit of structure and/or function, language that creates multiple meanings for the term and fails to acknowledge the diversity of gene architecture. I argue that coherence at the molecular level requires abandonment of the classical unit concept and recognition that a gene is constructed from an assemblage of domains. Hence, a domain set (1) conforms more closely to empirical (...) evidence for genetic organization of DNA regions capable of transcription and (2) has ontological properties lacking in the traditional unit definition. (shrink)

We outline three very different concepts of the gene—instrumental, nominal, and postgenomic. The instrumental gene has a critical role in the construction and interpretation of experiments in which the relationship between genotype and phenotype is explored via hybridization between organisms or directly between nucleic acid molecules. It also plays an important theoretical role in the foundations of disciplines such as quantitative genetics and population genetics. The nominal gene is a critical practical tool, allowing stable communication between bioscientists in a wide (...) range of fields grounded in well-defined sequences of nucleotides, but this concept does not embody major theoretical insights into genome structure or function. The post-genomic gene embodies the continuing project of understanding how genome structure supports genome function, but with a deflationary picture of the gene as a structural unit. This final concept of the gene poses a significant challenge to conventional assumptions about the relationship between genome structure and function, and between genotype and phenotype. (shrink)

Several modern accounts of explanation acknowledge the importance of abstraction and idealization for our explanatory practice. However, once we allow a role for abstraction, questions remain. I ask whether the relation between explanations at different theoretical levels should be thought of wholly in terms of abstraction, and argue that changes of the quantities in terms of which we describe a system can lead to novel explanations that are not merely abstractions of some more detailed picture. I use the example of (...) phase transitions as described by statistical mechanics and thermodynamics to illustrate this, and to demonstrate some details of the relationship between abstraction, idealization, and novel explanation. (shrink)

There are a bewildering variety of ways the terms "realism" and "anti-realism" have been used in philosophy and furthermore the different uses of these terms are only loosely connected with one another. Rather than give a piecemeal map of this very diverse landscape, the authors focus on what they see as the core concept: realism about a particular domain is the view that there are facts or entities distinctive of that domain, and their existence and nature is in some important (...) sense objective and mind-independent. The authors carefully set out and explain the different realist and anti-realist positions and arguments that occur in five key domains: science, ethics, mathematics, modality and fictional objects. For each area the authors examine the various styles of argument in support of and against realism and anti-realism, show how these different positions and arguments arise in very different domains, evaluate their success within these fields, and draw general conclusions about these assorted strategies. Error theory, fictionalism, non-cognitivism, relativism and response-dependence are taken as the most important positions in opposition to the realist and these are explored in depth. Suitable for advanced level undergraduates, the book offers readers a clear introduction to a subject central to much contemporary work in metaphysics, epistemology and philosophy of language. (shrink)

Inter-level mechanistic explanations in the sciences have long been a focus of philosophical interest, but attention has recently turned to the compositional character of these explanations which work by explaining higher level entities, whether processes, individuals or properties, using the lower level entities they take to compose them. However, we still have no theoretical account of the constitution or parthood relations between individuals deployed in such explanations, nor any accounts of multiple constitution. My primary focus in this paper is to (...) outline a positive account of the constitution/part-whole relations between individuals posited in inter-level mechanistic explanations that takes constituents in the sciences to be ‘working parts’. Using this account, I then go on to illuminate the nature, and varieties, of multiple constitution that we find in the sciences and provide a starting theoretical framework for multiple constitution as well. (shrink)

Multiple realization has traditionally been characterized as a thesis about the relation between kinds posited by the taxonomic systems of different sciences. In this paper, I argue that there are good reasons to move beyond this framing. I begin by showing how the traditional framing is tied to positivist models of explanation and reduction and proceed to develop an alternate framing that operates instead within causal explanatory frameworks. I draw connections between this account and the notion of functional robustness in (...) biology and neuroscience. I then examine two cases from systems neuroscience that substantiate my account and show how traditional debates fail to track important features of these cases. (shrink)

In the past century, nearly all of the biological sciences have been directly affected by discoveries and developments in genetics, a fast-evolving subject with important theoretical dimensions. In this rich and accessible book, Paul Griffiths and Karola Stotz show how the concept of the gene has evolved and diversified across the many fields that make up modern biology. By examining the molecular biology of the 'environment', they situate genetics in the developmental biology of whole organisms, and reveal how the molecular (...) biosciences have undermined the nature/nurture distinction. Their discussion gives full weight to the revolutionary impacts of molecular biology, while rejecting 'genocentrism' and 'reductionism', and brings the topic right up to date with the philosophical implications of the most recent developments in genetics. Their book will be invaluable for those studying the philosophy of biology, genetics and other life sciences. (shrink)

In this article I consider the challenges for exporting causal knowledge raised by complex biological systems. In particular, James Woodward’s interventionist approach to causality identified three types of stability in causal explanation: invariance, modularity, and insensitivity. I consider an example of robust degeneracy in genetic regulatory networks and knockout experimental practice to pose methodological and conceptual questions for our understanding of causal explanation in biology. †To contact the author, please write to: Department of History and Philosophy of Science, University of (...) Pittsburgh, 1017 Cathedral of Learning, Pittsburgh, PA 15260; e‐mail: [email protected]. (shrink)

Analysis of two key ways of characterizing genes—as causes of phenotypic effects and as genomic DNA sequences—has yielded widespread pessimism that they can be united in a coherent gene concept. This raises important questions about the epistemology of genomic research: If analysis of a genome sequence cannot yield information about genes defined both in terms of their products and their DNA sequence, then what could we learn from it? I investigate basic tools of genomic analysis, argue that they do not (...) reflect the application of either gene concept, and clarify how we learn from genomic research. (shrink)