The identity and the existence of genes has been challenged by postgenomic discoveries. Specifically, the consideration of molecular and cellular phenomena in which genes are embedded has proved relevant for their understanding. In response to these challenges, I will argue that the complexity of genetic phenomena supports the weak emergence of genes from the DNA. In Section 2, I will expose what genes are taken to be in the postgenomic world. In Section 3, I will present the relevant account of (...) emergence. I consider weak emergence as in Franklin and Knox, for which a phenomenon is emergent when it displays novelty and robustness. In Section 4, I will argue that genes are weakly emergent since they are novel, improving explanations, and robust in respect to some perturbations. Then, I will conclude in Section 5 that genes’ emergence is a way to allow genes’ flexibility and context dependency, without compromising their existence. (shrink)

Asking whether the sexes are natural kinds amounts to asking whether the categories, female and male, identify real divisions in nature, like the distinctions between biological species, or whether they mark merely artificial or arbitrary distinctions. The distinction between females and males in the animal kingdom is based on the relative size of the gametes they produce, with females producing larger gametes (ova) and males producing smaller gametes (sperm). This chapter argues that the properties of producing relatively large and small (...) gametes are causally correlated with a range of other properties in a wide variety of organisms, and this is what makes females and males natural kinds in the animal kingdom. The chapter concludes with a discussion of the relationship between sex and gender: while the difference between the sexes is biologically grounded, the difference between genders is socially based. Since gender depends in part on the perception of sex, whether or not gender is real or not does not depend on whether sex is, since social reality is constituted in part by our perceptions. The claim that sexes are natural kinds in the animal kingdom does not imply that the biological differences among female and male humans do and should have social consequences. (shrink)

Covering some of science's most divisive topics, such as philosophical issues in genetics and evolution, the philosophy of biology also encompasses more traditional philosophical questions, such as free will, essentialism, and nature vs nurture. Here, Samir Okasha outlines the core issues with which contemporary philosophy of biology is engaged.

There have been many attempts to determine what makes a natural kind real, chief among them is the criterion according to which natural kinds must be mind-independent. But it is difficult to specify this criterion: many supposed natural kinds have an element of mind-dependence. I will argue that the mind-independence criterion is nevertheless a good one, if correctly understood: the mind-independence criterion concerns the unification principles for natural kinds. Unification principles determine how natural kinds unify their properties, and only those (...) natural kinds that have a mind-independent unification principle should be considered real. (shrink)

Talk of different types of cells is commonplace in the biological sciences. We know a great deal, for example, about human muscle cells by studying the same type of cells in mice. Information about cell type is apparently largely projectible across species boundaries. But what defines cell type? Do cells come pre-packaged into different natural kinds? Philosophical attention to these questions has been extremely limited [see e.g., Wilson (Species: New Interdisciplinary Essays, pp 187–207, 1999; Genes and the Agents of Life, (...) 2005; Wilson et al. Philos Top 35(1/2):189–215, 2007)]. On the face of it, the problems we face in individuating cellular kinds resemble those biologists and philosophers of biology encountered in thinking about species: there are apparently many different (and interconnected) bases on which we might legitimately classify cells. We could, for example, focus on their developmental history (a sort of analogue to a species’ evolutionary history); or we might divide on the basis of certain structural features, functional role, location within larger systems, and so on. In this paper, I sketch an approach to cellular kinds inspired by Boyd’s Homeostatic Property Cluster Theory, applying some lessons from this application back to general questions about the nature of natural kinds. (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)

When we ask what natural kinds are, there are two different things we might have in mind. The first, which I’ll call the taxonomy question, is what distinguishes a category which is a natural kind from an arbitrary class. The second, which I’ll call the ontology question, is what manner of stuff there is that realizes the category. Many philosophers have systematically conflated the two questions. The confusion is exhibited both by essentialists and by philosophers who pose their accounts in (...) terms of similarity. It also leads to misreading philosophers who do make the distinction. Distinguishing the questions allows for a more subtle understanding of both natural kinds and their underlying metaphysics. (shrink)

The accepted narrative treats John Stuart Mill’s Kinds as the historical prototype for our natural kinds, but Mill actually employs two separate notions: Kinds and natural groups. Considering these, along with the accounts of Mill’s nineteenth-century interlocutors, forces us to recognize two distinct questions. First, what marks a natural kind as worthy of inclusion in taxonomy? Second, what exists in the world that makes a category meet that criterion? Mill’s two notions offer separate answers to the two questions: natural groups (...) for taxonomy and Kinds for ontology. This distinction is ignored in many contemporary debates about natural kinds and is obscured by the standard narrative that treats our natural kinds just as a development of Mill’s Kinds. (shrink)

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)

In this paper I offer a unified causal account of natural kinds. Using as a starting point the widely held view that natural kind terms or predicates are projectible, I argue that the ontological bases of their projectibility are the causal properties and relations associated with the natural kinds themselves. Natural kinds are not just concatenations of properties but ordered hierarchies of properties, whose instances are related to one another as causes and effects in recurrent causal processes. The resulting account (...) of natural kinds as clusters of core causal properties that give rise to clusters of derivative properties enables us to distinguish genuine natural kinds from non-natural kinds. For instance, it enables us to say why some of the purely conventional categories derived from the social domain do not correspond to natural kinds, though other social categories may. (shrink)

There are many ways of construing the claim that some categories are more “natural" than others. One can ask whether a system of categories is innate or acquired by learning, whether it pertains to a natural phenomenon or to a social institution, whether it is lexicalized in natural language or requires a compound linguistic expression. This renders suspect any univocal answer to this question in any particular case. Yet another question one can ask, which some authors take to have a (...) bearing on the issue of the naturalness of categories, is whether a system of categories constitutes a unique way of organizing a particular set of entities or phenomena, or whether there are other legitimate classification schemes that can coexist with it. Another way of putting this is by asking whether systems of categories can cut across one another, and if so, under what circumstances. Some philosophers have claimed that crosscutting systems of categories cannot exist as genuine natural kinds. This paper examines that claim and puts forward some counterexamples, concluding that this notion of natural kind is not in tune with scientific classification and ought to be rejected in favor of an alternative. (shrink)

This paper examines the phenomenon of ‘interactive kinds’ first identified by Ian Hacking. An interactive kind is one that is created or significantly modified once a concept of it has been formulated and acted upon in certain ways. Interactive kinds may also ‘loop back’ to influence our concepts and classifications. According to Hacking, interactive kinds are found exclusively in the human domain. After providing a general account of interactive kinds and outlining their philosophical significance, I argue that they are not (...) confined to the human realm, but that they can also occur elsewhere. Hence, I conclude by arguing that interactive kinds pose a challenge to scientific realism about kinds by making it difficult to make a distinction between real and non-real kinds. (shrink)

Kinds that share historical properties are dubbed “historical kinds” or “etiological kinds,” and they have some distinctive features. I will try to characterize etiological kinds in general terms and briefly survey some previous philosophical discussions of these kinds. Then I will take a closer look at a few case studies involving different types of etiological kinds. Finally, I will try to understand the rationale for classifying on the basis of etiology, putting forward reasons for classifying phenomena on the basis of (...) diachronic features, thereby making a provisional case for considering at least some etiological kinds to be natural kinds. (shrink)

This paper discusses a philosophical issue in taxonomy. At least one philosopher has suggested thc taxonomic principle that scientific kinds are disjoint. An opposing position is dcfcndcd here by marshalling examples of nondisjoint categories which belong to different, cocxisting classification schcmcs. This dcnial of thc disjoinmcss principle can bc recast as thc claim that scientific classification is "int<-:rcst—rclativc". But why would anyone have held that scientific categories arc disjoint in the first place'? It is argued that this assumption is nccdcd (...) in one attempt t0 dcrivc csscntialism. This shows why the csscntialist and intc-:rcst—r<-zlativc approaches to classification arc in conflict. (shrink)

There is a perennial philosophical dream of a certain natural order for the natural kinds. The name of this dream is ‘the hierarchy requirement’. According to this postulate, proper natural kinds form a taxonomy which is both unique and traditional. Here I demonstrate that complex scientific objects exist: objects which generate different systems of scientific classification, produce myriad legitimate alternatives amongst the nonetheless still natural kinds, and make the hierarchical dream impossible to realize, except at absurdly great cost. Philosophical hopes (...) for a certain order in nature cannot be fulfilled. Natural kinds crosscut one another, ubiquitously so, and this crosscutting spells the end of the hierarchical dream. (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)

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)

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)

The notion of 'natural kinds' has been central to contemporary discussions of metaphysics and philosophy of science. Although explicitly articulated by nineteenth-century philosophers like Mill, Whewell and Venn, it has a much older history dating back to Plato and Aristotle. In recent years, essentialism has been the dominant account of natural kinds among philosophers, but the essentialist view has encountered resistance, especially among naturalist metaphysicians and philosophers of science. Informed by detailed examination of classification in the natural and social sciences, (...) this book argues against essentialism and for a naturalist account of natural kinds. By looking at case studies drawn from diverse scientific disciplines, from fluid mechanics to virology and polymer science to psychiatry, the author argues that natural kinds are nodes in causal networks. On the basis of this account, he maintains that there can be natural kinds in the social sciences as well as the natural sciences. (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)