Evolutionary systems biology is an emerging hybrid approach that integrates methods, models, and data from evolutionary and systems biology. Drawing on themes that arose at a cross-disciplinary meeting on ESB in 2013, we discuss in detail some of the explanatory friction that arises in the interaction between evolutionary and systems biology. These tensions appear because of different modeling approaches, diverse explanatory aims and strategies, and divergent views about the scope of the evolutionary synthesis. We locate these discussions in the context (...) of long-running philosophical deliberations on explanation, modeling, and theoretical synthesis. We show how many of the issues central to ESB’s progress can be understood as general philosophical problems. The benefits of addressing these philosophical issues feed back into philosophy too, because ESB provides excellent examples of scientific practice for the development of philosophy of science and philosophy of biology. (shrink)

Evolutionary systems biology (ESB) is a rapidly growing integrative approach that has the core aim of generating mechanistic and evolutionary understanding of genotype‐phenotype relationships at multiple levels. ESB's more specific objectives include extending knowledge gained from model organisms to non‐model organisms, predicting the effects of mutations, and defining the core network structures and dynamics that have evolved to cause particular intracellular and intercellular responses. By combining mathematical, molecular, and cellular approaches to evolution, ESB adds new insights and methods to the (...) modern evolutionary synthesis, and offers ways in which to enhance its explanatory and predictive capacities. This combination of prediction and explanation marks ESB out as a research manifesto that goes further than its two contributing fields. Here, we summarize ESB via an analysis of characteristic research examples and exploratory questions, while also making a case for why these integrative efforts are worth pursuing. (shrink)

In a pioneering book, Philosophy of Microbiology, Maureen O’Malley argues for the philosophical importance of microbes through an examination of their impact on ecosystems, evolution, biological classification, collaborative behavior, and multicellular organisms. She identifies many understudied conceptual issues in the study of microbes. If philosophers follow her lead, the philosophy of biology will be expanded and enriched.

Reports of ethical lapses in the business world have been numerous and widespread. Ethical awareness in business education has received a great deal of attention because of the number and severity of business scandals. Given Sarbanes-Oxley legislation and recent Association to Advance Collegiate Schools of Business International’s (AACSBI) recommendations, this study examined respective websites of Securities and Exchange Commission (SEC) regulated public companies and AACSBI-accredited business schools for ethical policy statement content. The analysis was accomplished by classifying ethical expressions into (...) a framework consisting of the attributes of thematic content and focus/themes partially based on the 2004 research of Gaumnitz and Lere. Findings indicate that public companies have been diligent in presenting website ethical content that closely follows authoritative recommendations. Business schools appear not to have prioritized such disclosure to the extent done so by public companies. Although there was improvement between two samples taken in 2005 and 2007, this study provides evidence that many accredited business schools have little or no disclosed ethical expectations in their mission, vision, goals, or other similar types of statements on their websites. Additional findings provide several opportunities for future research. (shrink)

Purpose. The dynamics and pace of social and economic transformations that are characteristic of modern society, lead to an increase in tension and the destruction of habitual stereotypes – ideals, values, norms, patterns of behaviour that unite people. These moments encourage us to rethink the understanding of "security" essence, in particular, psychological, which emphasizes the urgency of its study in the philosophical and sociocultural coordinates. Theoretical basis of the research is based on the philosophical methodology of K. Jaspers, E. Fromm (...) and the A. Maslow’s psychological approach to understanding of a person. Originality. Psychological security is considered at different levels: first and foremost, society is a characteristic of social security, that is an analysis of how today’s social technologies, social changes affect the quality of life of the country’s population; secondly, the social environment – the family, the immediate environment, reference groups, training teams; thirdly, a person is an experience of his own security-insecurity, when it is possible to talk about the manifestations of psychological violence, when certain behavioral acts contribute to the violation of the security of the other or to self-destruction. It is found out that the knowledge of psychological security is closely connected with the socio-historical conditions of being, with the level of development of material and spiritual culture, with the interests and values prevailing in society, which determines its ontological, epistemological and axiological features. The presented issue is considered in the correlation of psychological security with types of scientific rationality – classical, nonclassical and post-nonclassical approaches, within the framework of which various perspectives, aspects, forms and types of psychological security are studied. Conclusions. The concept of security requires a systematic description of its manifestations, types, levels, concepts: security as the absence of dangers ; security as a certain activity to ensure or to prevent any threats or dangers ; security as a conscious necessity, the value of the individual. The study systematizes various ideas about psychological security in accordance with the logic of scientific knowledge: in the mainstream of classical, non-classical and post-nonclassical approaches. (shrink)

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. BioEssays 30:57–65, 2008. © 2007 Wiley Periodicals, Inc. (shrink)

The Past Masters Søren Kierkegaard : Samlede Vårker database is based on the third edition of Kierkegaard's complete works in Danish, and has been edited by Professor Alistair McKinnon of McGill University.

While it is acknowledged that there is a need for more qualitative research on suicide, it is also clear that the ethics of undertaking such research need to be addressed. This article uses the case study of the authors’ experience of gaining ethics approval for a research project that asks people what it is like to feel suicidal to (a) analyse the limits of confidentiality and anonymity and (b) consider the ways in which the process of ethics review can shape (...) and constrain suicide research. This leads to a discussion of the ways in which ethics committees assess and monitor qualitative research more generally and some preliminary suggestions for how this might be improved. (shrink)

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)

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)

Open peer commentary on the article “Exploration of the Functional Properties of Interaction: Computer Models and Pointers for Theory” by Etienne B. Roesch, Matthew Spencer, Slawomir J. Nasuto, Thomas Tanay & J. Mark Bishop. Upshot: We support Roesch and his co-authors’ theoretical stance on constructivist artificial agents, and wish to enrich their “exploration of the functional properties of interaction” with complementary results. By revisiting their experiments with an agent that we developed previously, we explore two issues that they deliberately left (...) aside: autonomous intentionality and dynamic reutilization of knowledge by the agent. Our results reveal an alternative pathway to constructivism that addresses the central question of intentionality in a single agent from the very beginning of its design, suggesting that the property of distributed processing proposed by Roesch et al. is not essential to constructivism. (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)

The model of major transitions in evolution devised by Maynard Smith and Szathmáry has exerted tremendous influence over evolutionary theorists. Although MTE has been criticized for inconsistently combining different types of event, its ongoing appeal lies in depicting hierarchical increases in complexity by means of evolutionary transitions in individuality. In this paper, we consider the implications of major evolutionary events overlooked by MTE and its ETI-oriented successors, specifically the biological oxygenation of Earth, and the acquisitions of mitochondria and plastids. By (...) reflecting on these missed events, we reveal a central philosophical disagreement over the explanatory goals of major transitions theory that has yet to be made explicit in the literature. We go on to argue that this philosophical disagreement is only reinforced by Szathmáry’s recent revisions of MTE in the form of MTE 2.0. This finding motivates us to propose an alternative explanatory strategy: specifically, an interactionist metabolic perspective on major transitions. A metabolic framework not only avoids many of the criticisms that beset classic and revised MTE models, but also accommodates missing events and provides crucial explanatory components for standard major transitions. Although we do not provide a full-blown alternative theory and do not claim to achieve unity, we explain why foregrounding metabolism is crucial for any attempt to capture the major turning points in evolution, and why it does not lead to unmanageable pluralism. (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)

Thomas Kuhn had little to say about scientific change in biological science, and biologists are ambivalent about how applicable his framework is for their disciplines. We apply Kuhn’s account of paradigm change to evolutionary microbiology, where key Darwinian tenets are being challenged by two decades of findings from molecular phylogenetics. The chief culprit is lateral gene transfer, which undermines the role of vertical descent and the representation of evolutionary history as a tree of life. To assess Kuhn’s relevance to this (...) controversy, we add a social analysis of the scientists involved to the historical and philosophical debates. We conclude that while Kuhn’s account may capture aspects of the pattern of an episode of scientific change, he has little to say about how the process of generating new understandings is occurring in evolutionary microbiology. Once Kuhn’s application is limited to that of an initial investigative probe into how scientific problem-solving occurs, his disciplinary scope becomes broader. (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)

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)

Literature on consumer ethics tends to focus on issues within the public sphere, such as the environment, and treats other drivers of consumption decisions, such as family, as non-moral concerns. Consequently, an attitude–behaviour gap is viewed as a straightforward failure by consumers to act ethically. We argue that this is based upon a view of consumer behaviour as linear and unproblematic, and an approach to moral reasoning, arising from a stereotypically masculine understanding of morality, which foregrounds abstract principles. By demonstrating (...) the importance of context to consumption decisions and articulating the impact of caring relationships, we highlight how such decisions are both complex and situated. This is particularly evident for decisions involving the needs of others, as occurs in family life. We argue that the incorporation of care ethics provides both theoretical insights and a more complete account of consumer ethics. This is explored empirically through an investigation of the ethical dilemmas arising from consumption decisions made by mothers of young children. Such decisions juxtapose an ethical consumption orientation with care for one’s child. Therefore, what has been previously considered a failure to act ethically may in fact be the outcome of complex decision making, which involves competing ethical considerations. We discuss the implications of our findings for theory and practice and how this approach to consumer ethics could be applied more widely. (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)

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)

Weaving together a social history of the American beef industry withher ownaccount of growing up in the shadow of her grandfather’s cattle business, Halley juxtaposes the two worlds and creates a link between the meat industry and her own experience of the formation of gender and sexuality through family violence.

Philosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy (...) of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations. (shrink)

The results of two experiments provide the first direct demonstration that subjects can process a word lexically despite concurrently being engaged in decoding a task cue telling them which of two tasks to perform. These results, taken together with others, point to qualitative differences between the mind‘s ability to engage in lexical versus sublexical processing during the time they are engaged with other tasks. The emerging picture is one in which some form of resource plays little role during lexical processing (...) whereas the need for some form of resource during sublexical processing serves to bottleneck performance. (shrink)

We present an experimental test of the validity of the Pauli Exclusion Principle for electrons based on the concept put forward a few years ago by Ramberg and Snow. In this experiment we perform a very accurate search of X-rays from the Pauli-forbidden atomic transitions of electrons in the already filled 1S shells of copper atoms. Although the experiment has a simple structure, it poses deep conceptual and interpretational problems. Here we describe the experimental method and recent experimental results, which (...) we interpret as an upper limit for the probability to violate the Pauli Exclusion Principle. We present also future plans to upgrade the experimental apparatus using Silicon Drift Detectors. (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)

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)