The media attention and subsequent scientific backlash engendered by the claim, announced by spokespeople for the Encyclopedia of DNA Elements project, that 80% of the human genome has a “biochemical function” highlights the need for a clearer understanding of function concepts in biology. This article provides an overview of two major function concepts that have been developed in the philosophy of science – the “causal role” concept and the “selected effects” concept – and their relevance to ENCODE. Unlike some previous (...) critiques, the ENCODE project is not considered problematic because it employed a causal role definition of function, but because of how this concept was misused. In addition, several unique challenges that arise when dealing with transposable elements, but which were ignored by ENCODE, are highlighted. These include issues surrounding TE-level versus organism-level selection, the origins versus the persistence of elements, and accidental versus functional organism-level benefits. Finally, some key questions are presented that should be addressed in any studies aiming to ascribe functions to major portions of large eukaryotic genomes, the majority of which is made up of transposable elements. (shrink)

Considerable variation exists not only in the kinds of transposable elements (TEs) occurring within the genomes of different species, but also in their abundance and distribution. Noting a similarity to the assortment of organisms among ecosystems, some researchers have called for an ecological approach to the study of transposon dynamics. However, there are several ways to adopt such an approach, and it is sometimes unclear what an ecological perspective will add to the existing co-evolutionary framework for explaining transposon-host interactions. This (...) review aims to clarify the conceptual foundations of transposon ecology in order to evaluate its explanatory prospects. We begin by identifying three unanswered questions regarding the abundance and distribution of TEs that potentially call for an ecological explanation. We then offer an operational distinction between evolutionary and ecological approaches to these questions. By determining the amount of variance in transposon abundance and distribution that is explained by ecological and evolutionary factors, respectively, it is possible empirically to assess the prospects for each of these explanatory frameworks. To illustrate how this methodology applies to a concrete example, we analyzed whole-genome data for one set of distantly related mammals and another more closely related group of arthropods. Our expectation was that ecological factors are most informative for explaining differences among individual TE lineages, rather than TE families, and for explaining their distribution among closely related as opposed to distantly related host genomes. We found that, in these data sets, ecological factors do in fact explain most of the variation in TE abundance and distribution among TE lineages across less distantly related host organisms. Evolutionary factors were not significant at these levels. However, the explanatory roles of evolution and ecology become inverted at the level of TE families or among more distantly related genomes. Not only does this example demonstrate the utility of our distinction between ecological and evolutionary perspectives, it further suggests an appropriate explanatory domain for the burgeoning discipline of transposon ecology. The fact that ecological processes appear to be impacting TE lineages over relatively short time scales further raises the possibility that transposons might serve as useful model systems for testing more general hypotheses in ecology. (shrink)

Are learning processes selection processes? This paper takes a slightly modified version of the account of selection presented in Hull et al. (Behav Brain Sci 24:511–527, 2001) and asks whether it applies to learning processes. The answer is that although some learning processes are selectional, many are not. This has consequences for teleological theories of mental content. According to these theories, mental states have content in virtue of having proper functions, and they have proper functions in virtue of being the (...) products of selection processes. For some mental states, it is plausible that the relevant selection process is natural selection, but there are many for which it is not plausible. One response to this (due to David Papineau) is to suggest that the learning processes by which we acquire non-innate mental states are selection processes and can therefore confer proper functions on mental states. This paper considers two ways in which this response could be elaborated, and argues that neither of them succeed: the teleosemanticist cannot rely on the claim that learning processes are selection processes in order to justify the attribution of proper functions to beliefs. (shrink)

This paper examines a specific kind of part-whole relations that exist in the molecular genetic domain. The central question is under which conditions a particular molecule, such as a DNA sequence, is a biological part of the human genome. I address this question by analyzing how biologists in fact partition the human genome into parts. This paper thus presents a case study in the metaphysics of biological practice. I develop a metaphysical account of genomic parthood by analyzing the investigative and (...) reasoning practices in the ENCODE (ENCyclopedia Of DNA Elements) project. My account reveals two conditions that determine whether a molecule is a part of the human genome (i.e., a genomic part). First, genomic parts must possess a causal role function in the genome as a whole, that is, their functions must contribute to the genome directing the overall functioning of the cell. Second, genomic parts must have a specific chemical structure and be actual segments of the DNA sequence of the genome. (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)

The etiological approach to ‘proper functions’ in biology can be strengthened by relating it to Robert Cummins' general treatment of function ascription. The proper functions of a biological trait are the functions it is assigned in a Cummins-style functional explanation of the fitness of ancestors. These functions figure in selective explanations of the trait. It is also argued that some recent etiological theories include inaccurate accounts of selective explanation in biology. Finally, a generalization of the notion of selective explanation allows (...) an analysis of the proper functions of human artifacts. (shrink)

Biological functions are dispositions or effects a trait has which explain the recent maintenance of the trait under natural selection. This is the "modern history" approach to functions. The approach is historical because to ascribe a function is to make a claim about the past, but the relevant past is the recent past; modern history rather than ancient.

The biological functions debate is a perennial topic in the philosophy of science. In the first full-length account of the nature and importance of biological functions for many years, Justin Garson presents an innovative new theory, the 'generalized selected effects theory of function', which seamlessly integrates evolutionary and developmental perspectives on biological functions. He develops the implications of the theory for contemporary debates in the philosophy of mind, the philosophy of medicine and psychiatry, the philosophy of biology, and biology itself, (...) addressing issues ranging from the nature of mental representation to our understanding of the function of the human genome. Clear, jargon-free, and engagingly written, with accessible examples and explanatory diagrams to illustrate the discussion, his book will be highly valuable for readers across philosophical and scientific disciplines. (shrink)

Despite the voluminous literature on biological functions produced over the last 40 years, few philosophers have studied the concept of function as it is used in neuroscience. Recently, Craver (forthcoming; also see Craver 2001) defended the causal role theory against the selected effects theory as the most appropriate theory of function for neuroscience. The following argues that though neuroscientists do study causal role functions, the scope of that theory is not as universal as claimed. Despite the strong prima facie superiority (...) of the causal role theory, the selected effects theory (when properly developed) can handle many cases from neuroscience with equal facility. It argues this by presenting a new theory of function that generalizes the notion of a ‘selection process’ to include processes such as neural selection, antibody selection, and some forms of learning—that is, to include structures that have been differentially retained as well as those that have been differentially reproduced. This view, called the generalized selected effects theory of function, will be defended from criticism and distinguished from similar views in the literature. (shrink)

At the beginning of the twentieth century, the French philosopher of science Edmond Goblot wrote three prescient papers on function and teleology. He advanced the remarkable thesis that functions are, as a matter of conceptual analysis, selected effects. He also argued that “selection” must be understood broadly to include both evolutionary natural selection and intelligent design. Here, I do three things. First, I give an overview of Goblot’s thought. Second, I identify his core thesis about function. Third, I argue that, (...) despite its ingenuity, Goblot’s expansive construal of function cannot be right. Still, Goblot deserves long-overdue credit for his work. (shrink)

I present and defend the generalized selected effects theory (GSE) of function. According to GSE, the function of a trait consists in the activity that contributed to its bearer’s differential reproduction, or differential retention, within a population. Unlike the traditional selected effects (SE) theory, it does not require that the functional trait helped its bearer reproduce; differential retention is enough. Although the core theory has been presented previously, I go significantly beyond those presentations by providing a new argument for GSE (...) and defending it from a recent objection. I also sketch its implications for teleosemantics and philosophy of medicine. (shrink)

This book is a critical survey of and guidebook to the literature on biological functions. It ties in with current debates and developments, and at the same time, it looks back on the state of discourse in naturalized teleology prior to the 1970s. It also presents three significant new proposals. First, it describes the generalized selected effects theory, which is one version of the selected effects theory, maintaining that the function of a trait consists in the activity that led to (...) its differential persistence or reproduction in a population, and not merely its differential reproduction. Secondly, it advances “within-discipline pluralism” (as opposed to between-discipline pluralism) a new form of function pluralism, which emphasizes the coexistence of function concepts within diverse biological sub-disciplines. Lastly, it provides a critical assessment of recent alternatives to the selected effects theory of function, namely, the weak etiological theory and the systems-theoretic theory. The book argues that, to the extent that functions purport to offer causal explanations for the existence of a trait, there are no viable alternatives to the selected effects view. -/- The debate about biological functions is still as relevant and important to biology and philosophy as it ever was. Recent controversies surrounding the ENCODE Project Consortium in genetics, the nature of psychiatric classification, and the value of ecological restoration, all point to the continuing relevance to biology of philosophical discussion about the nature of functions. In philosophy, ongoing debates about the nature of biological information, intentionality, health and disease, mechanism, and even biological trait classification, are closely related to debates about biological functions. (shrink)

The book presents a new way of understanding Darwinism and evolution by natural selection, combining work in biology, philosophy, and other fields.

In this paper I defend an etiological theory of biological functions (according to which the proper function of a trait is the effect for which it was selected by natural selection) against three objections which have been influential. I argue, contrary to Millikan, that it is wrong to base our defense of the theory on a rejection of conceptual analysis, for conceptual analysis does have an important role in philosophy of science. I also argue that biology requires a normative notion (...) of a "proper function", and that a normative notion is not ahistorical. (shrink)

Natural selection comes in degrees. Some biological traits are subjected to stronger selective force than others, selection on particular traits waxes and wanes over time, and some groups can only undergo an attenuated kind of selective process. This has downstream consequences for any notions that are standardly treated as binary but depend on natural selection. For instance, the proper function of a biological structure can be defined as what caused that structure to be retained by natural selection in the past. (...) We usually think of proper functions in binary terms: storing bile is a function of the gall bladder, but making stones is not. However, if functions arise through natural selection, and natural selection comes in degrees, then a binary approach to proper functions is in tension with the biological facts. In order to resolve this tension, we need to revise our standard accounts of proper function. In particular, we may have to seriously consider the possibility that functions themselves come in degrees, in spite of the ramifications this will have for the way we speak about functions and related concepts such as dysfunction, disease, and teleosemantic content. (shrink)

We introduce a new type of pluralism about biological function that, in contrast to existing, demonstrates a practical integration among the term’s different meanings. In particular, we show how to generalize Sandra Mitchell’s notion of integrative pluralism to circumstances where multiple epistemic tools of the same type are jointly necessary to solve scientific problems. We argue that the multiple definitions of biological function operate jointly in this way based on how biologists explain the evolution of protein function. To clarify how (...) our account relates to existing views, we introduce a general typology for monist and pluralist accounts along with standardized criteria for judging which is best supported by evidence. (shrink)

Herman Cappelen investigates how language and other representational devices can go wrong, and how to fix them. We use language to understand and talk about the world, but what if our language has deficiencies that prevent it from playing that role? How can we revise our concepts, and what are the limits on revision?

1. IntroductionIn What Biological Functions Are and Why They Matter, Justin Garson offers a novel theory of biological functions, the generalized selected effects (GSE) theory.1 He presents the theory in a clear and comprehensive way, defends it against various objections and applies it to different areas of philosophy, including the philosophy of psychiatry, the debate about mechanisms and the debate about teleosemantic theories of mental content.2Like other proponents of the aetiological approach to functions, Garson maintains that a trait’s biological functions (...) are grounded in its selectional history. However, his GSE theory differs from standard versions of the aetiological approach – so-called selected effects (SE) theories – in a crucial respect: while SE theories assume that all biological functions must ultimately be grounded in phylogenetic processes of natural selection or other (closely analogous) processes of differential reproduction (Millikan 1984: 15–82, Neander 1991, Godfrey-Smith 1994), the GSE theory allows that functions may also be grounded in processes of differential retention (see §2 for details). Garson forcefully argues that this broader account is theoretically well-motivated and has significant advantages over standard SE accounts when it comes to accommodating certain important classes of ontogenetically determined functions. (shrink)

Philosophical interest in the biological concept of function stems largely from concerns about its teleological associations. Assigning something a function seems akin to assigning it a purpose, and discussion of the purpose of items has long been off-limits to science. Analytic philosophers have attempted to defend ‘function’ by showing that claims about functions do not involve any reference to a problematic notion of purpose. To do this, philosophers offer short lists of necessary and sufficient conditions for the application of the (...) concept—where the conditions involve only acceptable physical or biological notions—and claim that the set of conditions captures the import of function statements. (shrink)

This book dares to challenge natural selection--not in the name of religion but in the name of good science. Most scientists are so terrified of religious attacks on the theory of evolution that it is never examined critically. There are significant scientific and philosophical problems with the theory of natural selection. Darwin claimed the factors that determine the course of evolution are very largely environmental. Empirical results in biology are increasingly calling this thesis into question. The authors show that Darwinism (...) is committed to inferring, from the premise that a kind of creature with a certain trait was selected, the conclusion that that kind of creature was selected for having that trait. Though such inferences are fallacious, they are nevertheless unavoidable within the Darwinist framework. Ultimately, Jerry Fodor and Massimo Piattelli-Palmarini level a devastating critique against Darwinist orthodoxy and suggest new ways of thinking about evolution.--From publisher description. (shrink)

Biologists studying ecology and evolution use the term “population” in many different ways. Yet little philosophical analysis of the concept has been done, either by biologists or philosophers, in contrast to the voluminous literature on the concept of “species.” This is in spite of the fact that “population” is arguably a far more central concept in ecological and evolutionary studies than “species” is. The fact that such a central concept has been employed in so many different ways is potentially problematic (...) for the reason that inconsistent usages (especially when the usage has not been made explicit) might lead to false controversies in which disputants are simply talking past one another. However, the inconsistent usages are not the only, or even the most important reason to examine the concept. If any set of organisms is legitimately called a “population,” selection and drift processes become purely arbitrary, too. Moreover, key ecological variables, such as abundance and distribution, depend on a nonarbitrary way of identifying populations. I sketch the beginnings of a population concept, drawing inspiration from the Ghiselin-Hull individuality thesis, and show why some alternative approaches are nonstarters. (shrink)

A promising recent development in molecular biology involves viewing the genome as a miniecosystem, where genetic elements are compared to organisms and the surrounding cellular and genomic structures are regarded as the local environment. Here we critically evaluate the prospects of Ecological Neutral Theory, a popular model in ecology, as it applies at the genomic level. This assessment requires an overview of the controversy surrounding neutral models in community ecology. In particular, we discuss the limitations of using ENT both as (...) an explanation of community dynamics and as a null hypothesis. We then analyze a case study in which ENT has been applied to genomic data. Our central finding is that genetic elements do not conform to the requirements of ENT once its assumptions and limitations are made explicit. We further compare this genome-level application of ENT to two other, more familiar approaches in genomics that rely on neutral mechanisms: Kimura’s Molecular Neutral Theory and Lynch’s Mutational Hazard Model. Interestingly, this comparison reveals that there are two distinct concepts of neutrality associated with these models which we dub ‘fitness-neutrality’ and ‘competitive neutrality’. This distinction helps to clarify the various roles for neutral models in genomics, for example, in explaining the evolution of genome size. (shrink)

This paper presents an account of the biological populations that can undergo paradigmatic natural selection. I argue for, and develop Peter Godfrey-Smith’s claim that reproductive competition is a core attribute of such populations. However, as Godfrey-Smith notes, it is not the only important attribute. I suggest what the missing element is, co-opting elements of Alan Templeton’s notion of exchangeability. The final framework is then compared to two recent discussions regarding biological populations proposed by Roberta Millstein and Jacob Stegenga.

This paper aims to illustrate one of the primary goals of the philosophy of biology⎯namely, the examination of central concepts in biological theory and practice⎯through an analysis of the concepts of population and metapopulation in evolutionary biology and ecology. I will first provide a brief background for my analysis, followed by a characterization of my proposed concepts: the causal interactionist concepts of population and metapopulation. I will then illustrate how the concepts apply to six cases that differ in their population (...) structure; this analysis will also serve to flesh out and defend the concepts a bit more. Finally, I will respond to some possible questions that my analysis may have raised and then conclude briefly. (shrink)