Marie I. Kaiser

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.

In this paper I argue that it is finally time to move beyond the Nagelian framework and to break new ground in thinking about epistemic reduction in biology. I will do so, not by simply repeating all the old objections that have been raised against Ernest Nagel’s classical model of theory reduction. Rather, I grant that a proponent of Nagel’s approach can handle several of these problems but that, nevertheless, Nagel’s general way of thinking about epistemic reduction in terms of theories and their logical relations is entirely inadequate with respect to what is going on in actual biological research practice.

Biology and history are often viewed as closely related disciplines, with biology informed by history, especially in its task of charting our evolutionary past. Maximizing the opportunities for cross-fertilization in these two fields requires an accurate reckoning of their commonalities and differences-precisely what this volume sets out to achieve. Specially commissioned essays by a team of recognized international researchers cover the full panoply of topics in these fields and include notable contributions on the correlativity of evolutionary and historical explanations, applying to history the latest causal-mechanical approach in the philosophy of biology, and the question of generalized laws that might pertain across the two subjects. The collection opens with a vital interrogation of general issues on explanation that apart from potentially fruitful areas of interaction (could the etiology of the causal-mechanical perspective in biology account for the historical trajectory of the Roman Empire?) this volume also seeks to chart relative certainties distinguishing explanations in biology and history. It also assesses techniques such as the use of probabilities in biological reconstruction, deployed to overcome the inevitable gaps in physical evidence on early evolution. Methodologies such as causal graphs and semantic explanation receive in-depth analysis. Contributions from a host of prominent and widely read philosophers ensure that this new volume has the stature of a major addition to the literature.

Evo-devo is a multidisciplinary field that investigates the interplay between evolutionary and developmental processes and brings together different kinds of explanatory strategies. This chapter examines the structure of paradigmatic explanations in evo-devo (e.g., the explanation of the origin of an evolutionary novelty) and raises philosophical questions about explanation in evo-devo. Much research in evo-devo is concerned with studying the developmental mechanisms that constrain and facilitate phenotypic evolution, which suggests that a distinctive feature of evo-devo is that it constructs mechanistic explanations. In this chapter, I discuss three major challenges for thinking about evo-devo as providing mechanistic explanations. First, an explanation of an evolutionary novelty consists of several mechanistic explanations, rather than being a single one. Second, developmental mechanisms are ontogenetically and phylogenetically dynamic and thus difficult to individuate. Third, an explanation of an evolutionary novelty also has a non-mechanistic, historical part. Finally, I discuss whether evo-devo’s emphasis on mechanistic explanation promotes explanatory integration or results in a reductionist view of evolution.

According to Richard Swinburne, the principle of simplicity is of great importance to theory choice scenarios and theoretical changes in the sciences. In particular, he holds that the theory choice criterion of fit with background evidence can be reduced to the criteria of simplicity and of yielding the data. We will, however, rebut this reduction thesis and show that three central aspects of theoretical change (confirming power of empirical data, reliability of experimental methods, and truth of new theoretical proposals) cannot be adequately reconstructed if simplicity is regarded as a key criterion of theory choice.

Back cover: This book develops a philosophical account that reveals the major characteristics that make an explanation in the life sciences reductive and distinguish them from non-reductive explanations. Understanding what reductive explanations are enables one to assess the conditions under which reductive explanations are adequate and thus enhances debates about explanatory reductionism. The account of reductive explanation presented in this book has three major characteristics. First, it emerges from a critical reconstruction of the explanatory practice of the life sciences itself. Second, the account is monistic since it specifies one set of criteria that apply to explanations in the life sciences in general. Finally, the account is ontic in that it traces the reductivity of an explanation back to certain relations that exist between objects in the world (such as part-whole relations and level relations), rather than to the logical relations between sentences. Beginning with a disclosure of the meta-philosophical assumptions that underlie the author’s analysis of reductive explanation, the book leads into the debate about reduction(ism) in the philosophy of biology and continues with a discussion on the two perspectives on explanatory reduction that have been proposed in the philosophy of biology so far. The author scrutinizes how the issue of reduction becomes entangled with explanation and analyzes two concepts, the concept of a biological part and the concept of a level of organization. The results of these five chapters constitute the ground on which the author bases her final chapter, developing her ontic account of reductive explanation.

Leuridan (2011) questions whether mechanisms can really replace laws at the heart of our thinking about science. In doing so, he enters a long-standing discussion about the relationship between the mech-anistic structures evident in the theories of contemporary biology and the laws of nature privileged especially in traditional empiricist traditions of the philosophy of science (see e.g. Wimsatt 1974; Bechtel and Abrahamsen 2005; Bogen 2005; Darden 2006; Glennan 1996; MDC 2000; Schaffner 1993; Tabery 2003; Weber 2005). In our view, Leuridan misconstrues this discussion. His weak positive claim that mechanistic sciences appeal to generalizations is true but uninteresting. His stronger claim, that all causal claims require laws, is unsupported by his arguments. Though we proceed by criticizing Leuridan’s arguments, our greater purpose is to embellish his arguments in order to show how thinking about mechanisms enriches and transforms old philosophical debates about laws in biology and provides new insights into how generalizations afford prediction, explanation and control.

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.

The observable/unobservable distinction, realistically construed, is a feature which lies at the very heart of van Fraassen’s constructive empiricism. The aim of this paper is to approach it by taking a close look at van Fraassen’s concept of observation. We will argue that if van Fraassen’s most recent writings about “literate experience”, especially his remarks on the status of observation reports and his general a-metaphysical stance, are taken into account, his realistic interpretation of the observable/unobservable distinction paves the road for inconsistency. In particular, we will show that a dilemma emerges to the effect that van Fraassen is forced to accept skeptical consequences blatantly at odds with constructive empiricism and its restatement of the aim of science. We will finally suggest that the only way out for van Fraassen involves giving up his realistic construal of observability and thus taking sides with constructivism.

We take the potentialities that are studied in the biological sciences (e.g., totipotency) to be an important subtype of biological dispositions. The goal of this paper is twofold: first, we want to provide a detailed understanding of what biological dispositions are. We claim that two features are essential for dispositions in biology: the importance of the manifestation process and the diversity of conditions that need to be satisfied for the disposition to be manifest. Second, we demonstrate that the concept of a disposition (or potentiality) is a very useful tool for the analysis of the explanatory practice in the biological sciences. On the one hand it allows an in-depth analysis of the nature and diversity of the conditions under which biological systems display specific behaviors. On the other hand the concept of a disposition may serve a unificatory role in the philosophy of the natural sciences since it captures not only the explanatory practice of biology, but of all natural sciences. Towards the end we will briefly come back to the notion of a potentiality in biology.

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.

In this paper, we discuss some problems and prospects of interdisciplinary encounters by focusing on philosophy of science as a case study. After introducing the case, we give an overview about the various ways in which philosophy of science can be interdisciplinary in Section 2. In Section 3, we name some general problems concerning the possible points of interaction between philosophy of science and the sciences studied. In Section 4 we compare the advantages and risks of interdisciplinarity for individual researchers and institutions. In Section 5, we discuss interdisciplinary PhD programs, in particular concerning two main problems: increased workload and the quality of supervision. In the final Section 6, we look at interdisciplinary careers beyond the PhD.

What is the level of organization on which natural selection operates? Are genes, organisms or groups the entities that are selected in adaptive evolutionary processes? This book discusses recent pluralistic solutions to the problem of the units of selection. After introducing central concepts and ideas from evolutionary biology, this book constructs a novel map of the philosophical debate and locates gene selectionism, multilevel selection theory, and description pluralism on the map. The book closes with a critical discussion of different versions of description pluralism and assesses their ability to solve the units of selection problem.

This paper examines the adequacy of causal graph theory as a tool for modeling biological phenomena and formalizing biological explanations. I point out that the causal graph approach reaches it limits when it comes to modeling biological phenomena that involve complex spatial and structural relations. Using a case study from molecular biology, DNA-binding and -recognition of proteins, I argue that causal graph models fail to adequately represent and explain causal phenomena in this field. The inadequacy of these models is due to their failure to include relevant spatial and structural information in a way that does not render the model non-explanatory, unmanageable, or inconsistent with basic assumptions of causal graph theory.

In the contemporary life sciences more and more researchers emphasize the “limits of reductionism” (e.g. Ahn et al. 2006a, 709; Mazzocchi 2008, 10) or they call for a move “beyond reductionism” (Gallagher/Appenzeller 1999, 79). However, it is far from clear what exactly they argue for and what the envisioned limits of reductionism are. In this paper I claim that the current discussions about reductionism in the life sciences, which focus on methodological and explanatory issues, leave the concepts of a reductive method and a reductive explanation too unspecified. In order to fill this gap and to clarify what the limits of reductionism are I identify three reductive methods that are crucial in the current practice of the life sciences: decomposition, focusing on internal factors, and studying parts in isolation. Furthermore, I argue that reductive explanations in the life sciences exhibit three characteristics: first, they refer only to factors at a lower level than the phenomenon at issue, second, they focus on internal factors and thus ignore or simplify the environment of a system, and, third, they cite only the parts of a system in isolation.

What are the conditions under which one biological object is a part of another biological object? This paper answers this question by developing a general, systematic account of biological parthood. I specify two criteria for biological parthood. Substantial Spatial Inclusionrequires biological parts to be spatially located inside or in the region that the natural boundary of t he biological whole occupies. Compositional Relevance captures the fact that a biological part engages in a biological process that must make a necessary contribution to a condition that is minimally sufficient to one or more of the characteristic behaviors of the biological whole. Instead of emphasizing the diversity of part-whole relations in the biological world, this paper asks what biological part-whole relations have in common and what constrains their existence, in general. After presenting the two criteria for biological parthood I discuss in how far my account can cope with hard cases (e.g., redundant parts) and I reveal the merits and limits of monism.

In his recent article Philosophy Inside Out, Philip Kitcher presents a metaphilosophical outlook that aims at nothing less than a renewal of philosophy. His idea is to draw philosophers’ attention away from “timeless questions” in the so-called “core areas” of philosophy. Instead, philosophers should address questions that matter to human lives. The aim of this paper is twofold: first, to reconstruct Kitcher’s view of how philosophy should be renewed; second, to point out some difficulties relating to his position. These difficulties concern the integration of his naturalism into the pragmatic vision of philosophy, the role of putative philosophical experts, and the ideal status of the program of well-ordered inquiry.

Convincing disputes about explanatory reductionism in the philosophy of biology require a clear and precise understanding of what a reductive explanation in biology is. The central aim of this book is to provide such an account by revealing the features that determine the reductive character of a biological explanation. Chapters I-IV provide the ground, on which I can then, in Chapter V, develop my own account of explanatory reduction in biology: Chapter I reveals the meta-philosophical assumptions that underlie my analysis of reduction, Chapter II introduces the previous debate about reduction in the philosophy of biology by pointing out the most crucial lessons one should learn from this debate, Chapter III critically discusses the two perspectives on explanatory reduction that have been proposed in the philosophy of biology so far, and Chapter IV clarifies in what ways the issue of reduction is entangled with the issue of explanation. In Chapter V I present my own account of explanatory reduction. My main claim is that reductive explanations in the biological sciences possess three main characteristics: they explain the behavior of a biological system S, first, exclusively in terms of factors that are located on a lower level of organization than S, second, by focusing on factors that are internal to S , and third, by describing the genuine parts of S only as “parts in isolation”. This account is ontic because it traces the reductivity of an explanation back to certain relations that exist in the world.

Charles Darwin hat eindrucksvoll gezeigt, dass der Mensch ebenso wie alle anderen Lebewesen ein Produkt der biologischen Evolution ist. Die sich an Darwin anschließende Forschung hat außerdem plausibel gemacht, dass sich nicht nur viele der körperlichen Merkmale des Menschen, sondern auch (zumindest einige) seiner Verhaltensdispositionen in adaptiven Selektionsprozessen herausgebildet haben. Die Vorstellung, dass auch die menschliche Moralität evolutionär bedingt ist, scheint daher auf den ersten Blick ganz überzeugend. Schließlich hat die Evolutionstheorie in den vergangenen Jahrzehnten in vielen Bereichen (auch außerhalb der Biologie) ihre weitreichende Bedeutung unter Beweis gestellt. Warum sollte, so könnte man beispielsweise fragen, gerade die Fähigkeit des Menschen, moralische Normen aufzustellen und gemäß ihnen zu handeln, nicht evolutionär erklärt werden können? Und warum sollte eine solche evolutionäre Erklärung der menschlichen Moralität irrelevant für die Rechtfertigung moralischer Normen sein? Warum sollte die Ethik eine Bastion der Philosophen bleiben, für die evolutionsbiologische Forschungsergebnisse über den Menschen und seine nächsten Verwandten keinerlei Relevanz besitzen?