In the context of scientists' reflections on genomics, we examine some fundamental issues in the emerging postgenomic discipline of systems biology. Systems biology is best understood as consisting of two streams. One, which we shall call ‘pragmatic systems biology’, emphasises large‐scale molecular interactions; the other, which we shall refer to as ‘systems‐theoretic biology’, emphasises system principles. Both are committed to mathematical modelling, and both lack a clear account of what biological systems are. We discuss the underlying issues in identifying systems (...) and how causality operates at different levels of organisation. We suggest that resolving such basic problems is a key task for successful systems biology, and that philosophers could contribute to its realisation. We conclude with an argument for more sociologically informed collaboration between scientists and philosophers. BioEssays 27:1270–1276, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

Microbes and microbiology are seldom encountered in philosophical accounts of the life sciences. Although microbiology is a well-established science and microbes the basis of life on this planet, neither the organisms nor the science have been seen as philosophically significant. This book will change that. It fills a major gap in the philosophy of biology by examining central philosophical issues in microbiology. Topics are drawn from evolutionary microbiology, microbial ecology, and microbial classification. These discussions are aimed at philosophers and scientists (...) who wish to gain insight into the basic philosophical issues of microbiology. (shrink)

The discovery and ongoing investigation of microRNAs suggest important conceptual and methodological lessons for philosophers and historians of biology. This paper provides an account of miRNA research and the shift from viewing these tiny regulatory entities as minor curiosities to seeing them as major players in the post-transcriptional regulation of genes. Conceptually, the study of miRNAs is part of a broader change in understandings of genetic regulation, in which simple switch-like mechanisms were reinterpreted as aspects of complex cellular and genome-wide (...) processes. Among them are the activities of small RNAs, previously regarded as non-functional. Methodologically, the miRNA story suggests new ways of characterizing biological research that should prove helpful to philosophers of science who seek to develop more pluralistic, pragmatic models of scientific inquiry. miRNA research displays iterative movements between multiple modes of investigation that include not only the proposal and testing of hypotheses but also exploratory, technology-oriented and question-driven modes of research. As an exemplary story of scientific discovery and development, the miRNA case illustrates transitions from genetics to genomics and systems biology, and it shows how diverse configurations of research practice are related to major scientific advances. (shrink)

Reproduction is central to biology and evolution. Standard concepts of reproduction are drawn from animals. Nonstandard examples of reproduction can be found in unicellular eukaryotes that distribute their reproductive strategies across multiple generations, and in mutualistic systems that combine different modes of reproduction across multiple lineages. Examining multigenerational and multilineal reproducers and how they align fitness has implications for conceptualizing units of evolution.

Multilevel research strategies characterize contemporary molecular inquiry into biological systems. We outline conceptual, methodological, and explanatory dimensions of these multilevel strategies in microbial ecology, systems biology, protein research, and developmental biology. This review of emerging lines of inquiry in these fields suggests that multilevel research in molecular life sciences has significant implications for philosophical understandings of explanation, modeling, and representation.

Synthetic biology is an increasingly high-profile area of research that can be understood as encompassing three broad approaches towards the synthesis of living systems: DNA-based device construction, genome-driven cell engineering and protocell creation. Each approach is characterized by different aims, methods and constructs, in addition to a range of positions on intellectual property and regulatory regimes. We identify subtle but important differences between the schools in relation to their treatments of genetic determinism, cellular context and complexity. These distinctions tie into (...) two broader issues that define synthetic biology: the relationships between biology and engineering, and between synthesis and analysis. These themes also illuminate synthetic biology's connections to genetic and other forms of biological engineering, as well as to systems biology. We suggest that all these knowledge-making distinctions in synthetic biology raise fundamental questions about the nature of biological investigation and its relationship to the construction of biological components and systems. (shrink)

Obesity is the focus of multiple lines of inquiry that have -- together and separately -- produced many deep insights into the physiology of weight gain and maintenance. We examine three such streams of research and show how they are oriented to obesity intervention through multilevel integrated approaches. The first research programme is concerned with the genetics and biochemistry of fat production, and it links metabolism, physiology, endocrinology and neurochemistry. The second account of obesity is developmental and draws together epigenetic (...) and environmental explanations that can be embedded in an evolutionary framework. The third line of research focuses on the role of gut microbes in the production of obesity, and how microbial activities interact with host genetics, development and metabolism. These interwoven explanatory strategies are driven by an orientation to intervention, both for experimental and therapeutic outcomes. We connect the integrative and intervention-oriented aspects of obesity research through a discussion of translation, broadening the concept to capture the dynamic, iterative processes of scientific practice and therapy development. This system-oriented analysis of obesity research expands the philosophical scrutiny of contemporary developments in the biosciences and biomedicine, and has the potential to enrich philosophy of science and medicine. (shrink)

Ernst Mayr’s influence on philosophy of biology has given the field a particular perspective on evolution, phylogeny and life in general. Using debates about the tree of life as a guide, I show how Mayrian evolutionary biology excludes numerous forms of life and many important evolutionary processes. Hybridization and lateral gene transfer are two of these processes, and they occur frequently, with important outcomes in all domains of life. Eukaryotes appear to have a more tree-like history because successful lateral events (...) tend to occur among more closely related species, or at a lower frequency, than in prokaryotes, but this is a difference of degree rather than kind. Although the tree of life is especially problematic as a representation of the evolutionary history of prokaryotes, it can function more generally as an illustration of the limitations of a standard evolutionary perspective. Moreover, for philosophers, questions about the tree of life can be applied to the Mayrian inheritance in philosophy of biology. These questions make clear that the dichotomy of life Mayr suggested is based on too narrow a perspective. An alternative to this dichotomy is a multidimensional continuum in which different strategies of genetic exchange bestow greater adaptiveness and evolvability on prokaryotes and eukaryotes. (shrink)

Ecology is usually described as the study of organisms interacting with one another and their environments. From this view of ecology, viruses – not usually considered to be organisms – would merely be part of the environment. Since the late 1980s, however, a growing stream of micrographic, experimental, molecular, and model-based (theoretical) research has been investigating how and why viruses should be understood as ecological actors of the most important sort. Viruses, especially phage, have been revealed as participants in the (...) planet's most crucial food webs, even though viruses technically consume nothing (they do not metabolize by themselves). Even more impressively, viruses have been identified as regulators of planetary biogeochemistry, in which they control cycles such as carbon, nitrogen and phosphorus – cycles on which all life depends. Although much biogeochemical research black-boxes the entities filling functional roles, it is useful to focus a little more closely to understand how viruses can be held responsible for the global processes of life. This paper will give a brief overview of the history of virus ecology and tease out the implications of large-scale ecological modelling with viruses. This analysis suggests that viruses should be conceptualized as ecological actors that are at least comparable and possibly equal to organismal actors. Ecological agency can therefore be distinguished from standard interpretations of biological agency. (shrink)

. Early microbiome research found numerous associations between microbial community patterns and host physiological states. These findings hinted at community-level explanations. “Top-down” experiments, working with whole communities, strengthened these explanatory expectations. Now, “bottom-up” mechanism-seeking approaches are dissecting communities to focus on specific microbes carrying out particular biochemical activities. To understand the interplay between methodological and explanatory scales, we examine claims of “dysbiosis,” when host illness is proposed as the consequence of a community state. Our analysis concludes with general observations about (...) how methodologies relate to explanations, and the implications for microbiome research. (shrink)

In this paper, I aim to clarify the role of ‘wonder’ in education. Most of us who work in education want to provide valuable experiences for our students, and we want them to be driven by intrinsic values such as truth and recognition of the dignity of human existence. However, whilst I echo many of the sentiments espoused by advocates of the utility and ethical significance of wonder, I contend that some recent developments—and in particular, Schinkel’s argument that ‘deep’ (‘contemplative’ (...) or ‘cosmic’) wonder has a ‘fundamental’ role in education—are misconceived. This is, I argue, because any concept deployable within educational spaces (whether formal or informal) must pay due regard to the conceptual constraints of the concept of ‘education’; that is, attention must be paid to the role of ‘learning’. Schinkel’s proposals are, I suggest, vulnerable to a critique of sentimentalism and excessive romanticism. As such, they offer little in terms of practical import for educators. As I will propose, if we are to take ‘wonder’ seriously in educational contexts, we must pay attention to the purpose of wonder as an epistemic emotion; namely, aiming for knowledge and understanding, and getting there requires sensitivity to practical know-how and conceptual competence. (shrink)

This book is the fruit of a critical inquiry into the nature and scope of Marcel's philosophie achievement. As such, it is concerned less with affixing the appropriate label (personalist or existentialist) to Marcel's thought -and with it making it stick - than with discovering the precise impulse and tenor ofhis philosophy. In the process ofthat more general inquiry, the writer found being forced upon hirn a central concept as integrating focus of Marcel's philosophie investigations. This eoneept was that of (...) the person. Gradually it emerged as a concept not only of prime importance for understanding the underlying harmony that pervades Marcel's professedly unsystematic researches, but equally as one of profound significanee for any philosophy that pretends adequately to aecount for human experienee. Furthermore, it seemed that the eoneept derived much ofthat significance from its acceptance precisely in the context of Marcel's thought. This feature ofMareel's philosophie writings alone is warrant enough for overeoming any initial embarrassment aroused in Anglo-Saxon breasts by his style. For, to speak candidly, that style is of a generation and a climate whose tastes little aecord with palates trained to a greater astringeney. Nor will Marcel's evident and unashamed coneern with life and its problems necessarily evoke a warm response in minds aceustomed to operate in an atmosphere of stricter and more aeademic reserve. (shrink)

Since the 1940s, microbiologists, biochemists and population geneticists have experimented with the genetic mechanisms of microorganisms in order to investigate evolutionary processes. These evolutionary studies of bacteria and other microorganisms gained some recognition from the standard-bearers of the modern synthesis of evolutionary biology, especially Theodosius Dobzhansky and Ledyard Stebbins. A further period of post-synthesis bacterial evolutionary research occurred between the 1950s and 1980s. These experimental analyses focused on the evolution of population and genetic structure, the adaptive gain of new functions, (...) and the evolutionary consequences of competition dynamics. This large body of research aimed to make evolutionary theory testable and predictive, by giving it mechanistic underpinnings. Although evolutionary microbiologists promoted bacterial experiments as methodologically advantageous and a source of general insight into evolution, they also acknowledged the biological differences of bacteria. My historical overview concludes with reflections on what bacterial evolutionary research achieved in this period, and its implications for the still-developing modern synthesis. (shrink)

Although the cell is commonly addressed as the unit of life, historians and philosophers have devoted relatively little attention to this concept in comparison to other fundamental concepts of biology such as the gene or species. As a partial remedy to this neglect, we introduce the cell as a major point of connection between various disciplinary approaches, epistemic strategies, technological vectors and overarching biological processes such as metabolism, growth, reproduction and evolution. We suggest that the role of the cell as (...) a nexus forms the basis for a new philosophical and historical appreciation of cell biology. This perspective focuses less on the cell as a well-defined, stable object and places more emphasis on its role as a mediator of fundamental biological processes. (shrink)

Systems biology is the rapidly growing and heavily funded successor science to genomics. Its mission is to integrate extensive bodies of molecular data into a detailed mathematical understanding of all life processes, with an ultimate view to their prediction and control. Despite its high profile and widespread practice, there has so far been almost no bioethical attention paid to systems biology and its potential social consequences. We outline some of systems biology's most important socioethical issues by contrasting the concept of (...) systems as dynamic processes against the common static interpretation of genomes. New issues arise around systems biology's capacities for in silico testing, changing cultural understandings of life, synthetic biology, and commercialization. We advocate an interdisciplinary and interactive approach that integrates social and philosophical analysis and engages closely with the science. Overall, we argue that systems biology socioethics could stimulate new ways of thinking about socioethical studies of life sciences. (shrink)

The papers published here were given at the second biennial conference of the Hegel Society of America, held at the University of Notre Dame, November 9-11, 1972. They appear in an order which reflects roughly two headings: (1) Hegel's conception of the history of philosophy in general, and (2) his relation to individual thinkers both before and after him. Given the importance of the history of philosophy for Hegel, and the far-reaching impact of his thought upon subsequent philosophy, it becomes (...) immediately apparent that we have here only a beginning. At the conference, cries went up "Why not Hegel and Aristotle, Aquinas, HusserI and Hart mann?" Indeed, why not? The answer, of course, might be given by Hegel himself : if we wish to accomplish anything, we have to limit ourselves. We trust that future conferences and scholarship will bring to light these relationships and the many more which testify to Hegel's profound presence in the mainstream of past and present thought. It is furthermore no accident that the renaissance of Hegelian studies has brought with it a rebirth of the history of philosophy as something relevant to our own problems. For Hegel, the object of philosophy is alone the truth, the history of philosophy is philosophy itself, and this truth which it gives us cannot be what has passed away. (shrink)

Recent discoveries of geographical patterns in microbial distribution are undermining microbiology’s exclusively ecological explanations of biogeography and their fundamental assumption that ‘everything is everywhere: but the environment selects’. This statement was generally promulgated by Dutch microbiologist Martinus Wilhelm Beijerinck early in the twentieth century and specifically articulated in 1934 by his compatriot, Lourens G. M. Baas Becking. The persistence of this precept throughout twentieth-century microbiology raises a number of issues in relation to its formulation and widespread acceptance. This paper will (...) trace the conceptual history of Beijerinck’s claim that ‘everything is everywhere’ in relation to a more general account of its theoretical, experimental and institutional context. His principle also needs to be situated in relationship to plant and animal biogeography, which, this paper will argue, forms a continuum of thought with microbial biogeography. Finally, a brief overview of the contemporary microbiological research challenging ‘everything is everywhere’ reveals that philosophical issues from Beijerinck’s era of microbiology still provoke intense discussion in twenty-first century investigations of microbial biogeography. (shrink)

The types of cetacean cultural behavior patterns described (primarily food-related and communication-related) reflect a very different research focus than that found in primatology, where dietary variation and food processing is emphasized and other potentially patterns have (until recently) been relatively neglected. The lack of behavioral research in all but a few cetacean species is also notable, as it mirrors a bias in primatology towards only a few genera.

We address three fundamental questions: What does it mean for an entity to be living? What is the role of inter-organismic collaboration in evolution? What is a biological individual? Our central argument is that life arises when lineage-forming entities collaborate in metabolism. By conceiving of metabolism as a collaborative process performed by functional wholes, which are associations of a variety of lineage-forming entities, we avoid the standard tension between reproduction and metabolism in discussions of life – a tension particularly evident (...) in discussions of whether viruses are alive. Our perspective assumes no sharp distinction between life and non-life, and does not equate life exclusively with cellular or organismal status. We reach this conclusion through an analysis of the capabilities of a spectrum of biological entities, in which we include the pivotal case of viruses as well as prions, plasmids, organelles, intracellular and extracellular symbionts, unicellular and multicellular life-forms. The usual criterion for classifying many of the entities of our continuum as non-living is autonomy. This emphasis on autonomy is problematic, however, because even paradigmatic biological individuals, such as large animals, are dependent on symbiotic associations with many other organisms. These composite individuals constitute the metabolic wholes on which selection acts. Finally, our account treats cooperation and competition not as polar opposites but as points on a continuum of collaboration. We suggest that competitive relations are a transitional state, with multi-lineage metabolic wholes eventually outcompeting selfish competitors, and that this process sometimes leads to the emergence of new types or levels of wholes. Our view of life as a continuum of variably structured collaborative systems leaves open the possibility that a variety of forms of organized matter – from chemical systems to ecosystems – might be usefully understood as living entities. (shrink)

Fines and monetary damages account for the majority of legal sanctions across the whole spectrum of legal governance. Money is, in key respects, the primary tool law has to achieve compliance. Yet money has largely been ignored by social analyses of law, and especially by social theory. _The Currency of Justice_ examines the differing rationalities, aims and assumptions built into money’s deployment in diverse legal fields and sanctions. This raises major questions about the extent to which money appears as an (...) abstract universal or whether it takes on more particular meanings when deployed in various areas of law. Indeed, money may be unique in that it can take on the meanings of punishment, compensation, denunciation or regulation. _The Currency of Justice_ examines the implications of the ‘monetization of justice’ as life is increasingly regulated through this single medium. Money not only links diverse domains of law; it also links legal sanctions to other monetary techniques which govern everyday life. Like these, the concern with monetary sanctions is not who pays, but that money is paid. Money is perhaps the only form of legal sanction where the burden need not be borne by the wrongdoer. In this respect, this book explores the view that contemporary governance is less concerned with disciplining individuals and more concerned with regulating distributions and flows of behaviours and the harms and costs linked with these. (shrink)

Own Yourself is "hands-on" course in ethics and morality. Its goal is to assist students to come to know who they genuinely are and who they want to become as they move into adulthood.

The ‘Tree of Life’ is intended to represent the pattern of evolutionary processes that result in bifurcating species lineages. Often justified in reference to Darwin’s discussions of trees, the Tree of Life has run up against numerous challenges especially in regard to prokaryote evolution. This special issue examines scientific, historical and philosophical aspects of debates about the Tree of Life, with the aim of turning these criticisms towards a reconstruction of prokaryote phylogeny and even some aspects of the standard evolutionary (...) understanding of eukaryotes. These discussions have arisen out of a multidisciplinary collaboration of people with an interest in the Tree of Life, and we suggest that this sort of focused engagement enables a practical understanding of the relationships between biology, philosophy and history. (shrink)

From 1897 through about 1912, film producers would shoot their footage and then make a contact print of the entire film on a roll of photographic paper. Mailed to the Library of Congress, these rolls of paper established copyright. The films document a very busy world indeed. They show people thronging streets, working, shopping; they show crowds shuffling through gates at Ellis Island or welcoming returning war heroes. More than just documentary, the films include satire ad commentary on the nature (...) of life at the turn of the last century. In these early films, which almost never run much longer than two or three minutes, the camera almost never moves—no zooms, pans, or fast cuts or clever editing. But the screens are never still, full of action and movement. They document great disasters and everyday events, the dynamic world of the turn of the last century. These very early films played almost entirely to a working class audience. Indeed, when middle class observers began noticing this new phenomenon, the “movies,” sweeping working class neighborhoods they saw it as both fast paced, as a “get thrills quick” medium that played magical games with time and space, and also as a dangerous soporific. They show a busy world, but they show confusion about what “busy” means. (shrink)

In this first systematic reconstruction of the concept of human flourishing, Eri Mountbatten-O'Malley addresses the central problems with the treatment of the concept in psychology, education, policy and science. He develops a sophisticated methodology of conceptual analysis and makes the case for paying closer attention to complex human contexts, purposes and uses. Re-humanizing current research on the concept that is technicalized and detached from ordinary uses, this volume takes the 'human' in conceptions of human flourishing seriously.

Must readers intend to process a word to activate various levels of representation, or is such processing simply triggered by the presentation of a word ? This issue was addressed via the use of Besner and Care’s Task Set paradigm. On each trial a cue, which indicated which of two tasks to perform appeared either before the target, or at the same time as the target. If subjects can process the target while preparing a task set, then the effect of (...) a manipulated psycholinguistic factor should be absorbed into the time taken to process the cue. Despite robust main effects of SOA and word frequency there was no interaction between these factors when the task was to read aloud. This result implies that target processing is delayed until the subject knows what task to perform, and therefore that intention plays an important role when reading words aloud. (shrink)

Synthetic biology is an umbrella term that covers a range of aims, approaches, and techniques. They are all brought together by common practices of analogizing, synthesizing, mechanicizing, and kludging. With a focus on kludging as the connection point between biology, engineering, and evolution, I show how synthetic biology’s successes depend on custom-built kludges and a creative, “make-it-work” attitude to the construction of biological systems. Such practices do not fit neatly, however, into synthetic biology’s celebration of rational design. Nor do they (...) straightforwardly embody Richard Feynman’s “last blackboard” statement that without creating something it cannot be understood. Reflecting further on the relationship between synthetic construction and knowledge making gives philosophy of science new avenues of insight into scientific practice. (shrink)

Much is being written these days about integration, its desirability and even its necessity when complex research problems are to be addressed. Seldom, however, do we hear much about the failure of such efforts. Because integration is an ongoing activity rather than a final achievement, and because today’s literature about integration consists mostly of manifesto statements rather than precise descriptions, an examination of unsuccessful integration could be illuminating to understand better how it works. This paper will examine the case of (...) prokaryote phylogeny and its apparent failure to achieve integration within broader tree-of-life accounts of evolutionary history. Despite the fact that integrated databases exist of molecules pertinent to the phylogenetic reconstruction of all lineages of life, and even though the same methods can be used to construct phylogenies wherever the organisms fall on the tree of life, prokaryote phylogeny remains at best only partly integrated within tree-of-life efforts. I will examine why integration does not occur, compare it with integrative practices in animal and other eukaryote phylogeny, and reflect on whether there might be different expectations of what integration should achieve. Finally, I will draw some general conclusions about integration and its function as a ‘meta-heuristic’ in the normative commitments guiding scientific practice. (shrink)