Calculating life? Duelling discourses in interdisciplinary systems biology

A high profile context in which physics and biology meet today is in the new field of systems biology. Systems biology is a fascinating subject for sociological investigation because the demands of interdisciplinary collaboration have brought epistemological issues and debates front and centre in discussions amongst systems biologists in conference settings, in publications, and in laboratory coffee rooms. One could argue that systems biologists are conducting their own philosophy of science. This paper explores the epistemic aspirations of the field by drawing on interviews with scientists working in systems biology, attendance at systems biology conferences and workshops, and visits to systems biology laboratories. It examines the discourses of systems biologists, looking at how they position their work in relation to previous types of biological inquiry, particularly molecular biology. For example, they raise the issue of reductionism to distinguish systems biology from molecular biology. This comparison with molecular biology leads to discussions about the goals and aspirations of systems biology, including epistemic commitments to quantification, rigor and predictability. Some systems biologists aspire to make biology more similar to physics and engineering by making living systems calculable, modelable and ultimately predictable-a research programme that is perhaps taken to its most extreme form in systems biology's sister discipline: synthetic biology. Other systems biologists, however, do not think that the standards of the physical sciences are the standards by which we should measure the achievements of systems biology, and doubt whether such standards will ever be applicable to 'dirty, unruly living systems'. This paper explores these epistemic tensions and reflects on their sociological dimensions and their consequences for future work in the life sciences.     

Two sides of the same coin? The (techno)epistemic cultures of systems and synthetic biology

Systems and synthetic biology both emerged around the turn of this century as labels for new research approaches. Although their disciplinary status as well as their relation to each other is rarely discussed in depth, now and again the idea is invoked that both approaches represent ‘two sides of the same coin’. The following paper focuses on this general notion and compares it with empirical findings concerning the epistemic cultures prevalent in the two contexts. Drawing on interviews with researchers from both fields, on participatory observation in conferences and courses and on documentary analysis, this paper delineates differences and similarities, incompatibilities and blurred boundaries. By reconstructing systems and synthetic biology’s epistemic cultures, this paper argues that they represent two ‘communities of vision’, encompassing heterogeneous practices. Understanding the relation of the respective visions of understanding nature and engineering life is seen as indispensible for the characterisation of (techno)science in more general terms. Depending on the conceptualisation of understanding and construction (or: science and engineering), related practices such as in silico modelling for enhancing understanding or enabling engineering can either be seen as incommensurable or ‘two sides of one coin’.     

Faith-based perspectives on the use of chimeric organisms for medical research

Efforts to advance our understanding of neurodegenerative diseases involve the creation chimeric organisms from human neural stem cells and primate embryos—known as prenatal chimeras. The existence of potential mentally complex beings with human and non-human neural apparatus raises fundamental questions as to the ethical permissibility of chimeric research and the moral status of the creatures it creates. Even as bioethicists find fewer reasons to be troubled by most types of chimeric organisms, social attitudes towards the non-human world are often influenced by religious beliefs. In this paper scholars representing eight major religious traditions provide a brief commentary on a hypothetical case concerning the development and use of prenatal human–animal chimeric primates in medical research. These commentaries reflect the plurality and complexity within and between religious discourses of our relationships with other species. Views on the moral status and permissibility of research on neural human animal chimeras vary. The authors provide an introduction to those who seek a better understanding of how faith-based perspectives might enter into biomedical ethics and public discourse towards forms of biomedical research that involves chimeric organisms.     

Introducing experimental design by evaluating efficacy of herbal remedies (Do herbal remedies really work?)

This paper is based upon experiments developed as part of a Directed Research course designed to provide undergraduate biology students experience in the principles and processes of the scientific method used in biological research. The project involved the evaluation of herbal remedies used in many parts of the world in the treatment of diseases producing diarrhea as a major symptom. Methods used for testing the efficacy of these remedies vary greatly, and this provides an opportunity for inquiry in the classroom. The nematode Caenorhabditis elegans is used as the test organism. Survival of this worm is easily determined by assessing motility using a dissection microscope. The influence of two solvents commonly used for testing these treatments, M9 salt solution and purified water, on survival of worms is examined. The results were important to a graduate project evaluating the influence of these solvents on bioassay sensitivity testing partially purified extracts of the West African plant, Anogeissus leiocarpus, used for treatment of diarrhea. Directed research projects allow undergraduate biology students to become engaged in science and develop a deeper understanding of science process skills. The experiments can be extended to examine other variables as directed research projects or modified to use as experimental case examples as part of a laboratory exercise.     

Convenience experimentation

Systems biology aims at explaining life processes by means of detailed models of molecular networks, mainly on the whole-cell scale. The whole cell perspective distinguishes the new field of systems biology from earlier approaches within molecular cell biology. The shift was made possible by the high throughput methods that were developed for gathering 'omic' (genomic, proteomic, etc.) data. These new techniques are made commercially available as semi-automatic analytic equipment, ready-made analytic kits and probe arrays. There is a whole industry of supplies for what may be called convenience experimentation. My paper inquires some epistemic consequences of strong reliance on convenience experimentation in systems biology. In times when experimentation was automated to a lesser degree, modeling and in part even experimentation could be understood fairly well as either being driven by hypotheses, and thus proceed by the testing of hypothesis, or as being performed in an exploratory mode, intended to sharpen concepts or initially vague phenomena. In systems biology, the situation is dramatically different. Data collection became so easy (though not cheap) that experimentation is, to a high degree, driven by convenience equipment, and model building is driven by the vast amount of data that is produced by convenience experimentation. This results in a shift in the mode of science. The paper shows that convenience driven science is not primarily hypothesis-testing, nor is it in an exploratory mode. It rather proceeds in a gathering mode. This shift demands another shift in the mode of evaluation, which now becomes an exploratory endeavor, in response to the superabundance of gathered data.     

Biofilms: the matrix revisited

Microbes often construct and live within surface-associated multicellular communities known as biofilms. The precise structure, chemistry and physiology of the biofilm all vary with the nature of its resident microbes and local environment. However, an important commonality among biofilms is that their structural integrity critically depends upon an extracellular matrix produced by their constituent cells. Extracellular matrices might be as diverse as biofilms, and they contribute significantly to the organization of the community. This review discusses recent advances in our understanding of the extracellular matrix and its role in biofilm biology.     

Equine Gatekeepers,Animal Narratives and Foxhunting Landscapes

Firstly, this paper analyzes the dynamic between horse, rider, and landscape in foxhunting culture. Secondly, it considers nonhuman animals as active elements within the research process. The methodology principally involved extensive, in-depth participation as a rider within mounted foxhound packs, as I originally participated as a rider/ethnographer in order to understand the nexus between foxhunting culture and the landscape. However, the equine focus in my research emerged unexpectedly as my fieldwork drew me into a collaboration with an unanticipated character in this network; the “made hunter,” a horse seasoned for hunting. These animals acted as my equine gatekeepers literally incorporating me into this hunting world. I relied on and respected their experience and capabilities as novice and experienced foxhunters have done for centuries. This paper presents an analysis of the quadripartite synthesis of foxhunting culture, rider, horse, and landscape and involves a corporeal and sensory exploration of the human/nonhuman inter-Hunt dynamic that defines foxhunting. Hunting cultures rely upon the capabilities of animals and have developed an ability to translate animal narratives and semiotics. Thus, they provide us with a platform for developing the multi-species perspective in social science. This paper calls for an ethnographic approach which draws upon these epistemic systems and incorporates the superhuman abilities of animals into our understanding of our relationship with space. Animals, I argue, offer more than potential subjects to study. By incorporating their knowledge, experiences, and perspectives, and by translating their engagements with the world, we have the potential to augment our perception of our shared environment.     

Molecular evolution: concepts and the origin of disciplines

This paper focuses on the consolidation of Molecular Evolution, a field originating in the 1960s at the interface of molecular biology, biochemistry, evolutionary biology, biophysics and studies on the origin of life and exobiology. The claim is made that Molecular Evolution became a discipline by integrating different sorts of scientific traditions: experimental, theoretical and comparative. The author critically incorporates Timothy Lenoir’s treatment of disciplines (1997), as well as ideas developed by Stephen Toulmin (1962) on the same subject. On their account disciplines are spaces where the social and epistemic dimensions of science are deeply and complexly interwoven. However, a more detailed account of discipline formation and the dynamics of an emerging disciplinary field is lacking in their analysis. The present essay suggests focusing on the role of scientific concepts in the double configuration of disciplines: the social/political and the epistemic order. In the case of Molecular Evolution the concepts of molecular clock and informational molecules played a central role, both in differentiating molecular from classical evolutionists, and in promoting communication between the different sorts of traditions integrated in Molecular Evolution. The paper finishes with a reflection on the historicity of disciplines, and the historicity of our concepts of disciplines.     

The ecology of Ebola virus

Since Ebola virus was first identified more than 30 years ago, tremendous progress has been made in understanding the molecular biology and pathogenesis of this virus. However, the means by which Ebola virus is maintained and transmitted in nature remains unclear despite dedicated efforts to answer these questions. Recent work has provided new evidence that fruit bats might have a role as a reservoir species, but it is not clear whether other species are also involved or how transmission to humans or apes takes place. Two opposing hypotheses for Ebola emergence have surfaced; one of long-term local persistence in a cryptic and infrequently contacted reservoir, versus another of a more recent introduction of the virus and directional spread through susceptible populations. Nevertheless, with the increasing frequency of human filovirus outbreaks and the tremendous impact of infection on the already threatened great ape populations, there is an urgent need to better understand the ecology of Ebola virus in nature.     

Ecological gradients as a framework for analysis of land-use change in East Africa

This paper discusses the ecological gradient as an organizing framework to assist understanding the complex interactions between societal and ecological processes underlying land-use change in East Africa. Detailed case studies on the gradients of the slopes of Mt Kilimanjaro, Kenya show how land-use change is responsive to the dynamics of both local and external driving forces. The study has shown that the distinct ecological conditions at the extremities of gradients are associated with specific land uses which may be different within livelihood systems such as for wet and dry season grazing. Access to water for cultivation, domestic use, livestock and wildlife is critical in determining the nature and distribution of livelihood systems. Land-use systems interact across the different ecological zones of the gradients characterized by vigorous spatial, cultural and economic interactions. Sometime conflicts occur between or within land-use/livelihood systems. There is strong evidence that the areas of higher economic potential remain advantaged compared with areas lower on the gradient. The ecological characteristics have been found to influence human activities and distribution. Interactions between societies are important in terms of trade, social relations and access to resources.     

Foucault in the Bush. The Social Life of Post-Structuralist Theory in East Berlin's Prenzlauer Berg

This essay seeks to make critical theory an object of ethnographic con-textualization and inquiry through an exploration of the social life of post-structuralist theory in 1980s East Berlin. The 'Prenzlauer Berg Scene' of artists and writers utilized post-structuralism as a distinctive register for defining their social identity and as an analytical and interpretive paradigm for articulating their alienation from the state-crafted language of GDR public culture. The essay discusses how the subversive practice of post-structuralism in the Prenzlauer Berg came at the price of linguistic exclusion and political withdrawal from mainstream GDR society. In conclusion, it is argued that the Prenzlauer Berg case emblematizes the difficulty of politicizing expert theoretical registers since these registers' objective critical 'power' relies upon structures of epistemic inequity that cultivate distinctions between critical experts and naïve practitioners.     

Ostracism as a social and biological phenomenon: An introduction

Ostracism refers to the general process of rejection and exclusion, observed in human groups and in many other species. It occurs as “shunning” in small homogenous groups like the Amish or as rejection among children. Ostracism in various forms is also deeply embedded in our own legal tradition, and is used in the formal and informal legal procedures of other cultures, used to maintain order, to punish deviance, and to increase social cohesion. Hence, it is plausible to hypothesize that human ostracism may have physiological substrates or biological functions in addition to cultural, moral, and legal dimensions. Biological research shows that human emotions (anger, fear, reassurance, self-confidence) involve responses of the limbic system as well as ideas or thoughts in the cerebral cortex and that human behavior continually integrates biological and cultural factors. The legal system expresses and channels human behavior. For this reason laws should be more effective if their functions complement (rather than ignore) the function of the behavior being regulated. To look at law as it affects human behavior in the light of the life sciences does not imply the intention of finding a universally valid “natural law,” akin to theological or ideological doctrine. On the contrary, we find that humans can form radically different social systems due to the plasticity of their behavior. However, an interdisciplinary analysis of ostracism as a common area of behavior, combining biology, law, and the social sciences can produce insights that none of these fields alone can provide. Such an approach should increase our understanding of human nature and the functions of law.     

Basic science through engineering? Synthetic modeling and the idea of biology-inspired engineering

Synthetic biology is often understood in terms of the pursuit for well-characterized biological parts to create synthetic wholes. Accordingly, it has typically been conceived of as an engineering dominated and application oriented field. We argue that the relationship of synthetic biology to engineering is far more nuanced than that and involves a sophisticated epistemic dimension, as shown by the recent practice of synthetic modeling. Synthetic models are engineered genetic networks that are implanted in a natural cell environment. Their construction is typically combined with experiments on model organisms as well as mathematical modeling and simulation. What is especially interesting about this combinational modeling practice is that, apart from greater integration between these different epistemic activities, it has also led to the questioning of some central assumptions and notions on which synthetic biology is based. As a result synthetic biology is in the process of becoming more “biology inspired.”     

Social responsibility in human genetics – a survey

The potential for molecular biological manipulation of human beings is a challenge to the social responsibility of human geneticists. The concept of individual healthcare is compromised by a reductionist approach to human biology which defines health solely in terms of genetics. The ability of professionals working in the fields of molecular biology and human genetics to understand the wider social context of their work and the effects it may have on individual health is rarely discussed. This is a report of a survey of social attitudes and awareness carried out among molecular biologists and human geneticists in Germany. The results reveal differences in the understanding of health and these perceptions are shown to depend on the age and gender of the professionals involved.     

Hierarchy Theory of Evolution and the Extended Evolutionary Synthesis: Some Epistemic Bridges,Some Conceptual Rifts

Contemporary evolutionary biology comprises a plural landscape of multiple co-existent conceptual frameworks and strenuous voices that disagree on the nature and scope of evolutionary theory. Since the mid-eighties, some of these conceptual frameworks have denounced the ontologies of the Modern Synthesis and of the updated Standard Theory of Evolution as unfinished or even flawed. In this paper, we analyze and compare two of those conceptual frameworks, namely Niles Eldredge’s Hierarchy Theory of Evolution (with its extended ontology of evolutionary entities) and the Extended Evolutionary Synthesis (with its proposal of an extended ontology of evolutionary processes), in an attempt to map some epistemic bridges (e.g. compatible views of causation; niche construction) and some conceptual rifts (e.g. extra-genetic inheritance; different perspectives on macroevolution; contrasting standpoints held in the “externalism–internalism” debate) that exist between them. This paper seeks to encourage theoretical, philosophical and historiographical discussions about pluralism or the possible unification of contemporary evolutionary biology.     

Academic and molecular matrices: a study of the transformations of connective tissue research at the University of Manchester (1947-1996)

This paper explores the different identities adopted by connective tissue research at the University of Manchester during the second half of the 20th century. By looking at the long-term redefinition of a research programme, it sheds new light on the interactions between different and conflicting levels in the study of biomedicine, such as the local and the global, or the medical and the biological. It also addresses the gap in the literature between the first biomedical complexes after World War II and the emergence of biotechnology. Connective tissue research in Manchester emerged as a field focused on new treatments for rheumatic diseases. During the 1950s and 60s, it absorbed a number of laboratory techniques from biology, namely cell culture and electron microscopy. The transformations in scientific policy during the late 70s and the migration of Manchester researchers to the US led them to adopt recombinant DNA methods, which were borrowed from human genetics. This resulted in the emergence of cell matrix biology, a new field which had one of its reference centres in Manchester. The Manchester story shows the potential of detailed and chronologically wide local studies of patterns of work to understand the mechanisms by which new biomedical tools and institutions interact with long-standing problems and existing affiliations.     

Before and below 'theory of mind': embodied simulation and the neural correlates of social cognition

The automatic translation of folk psychology into newly formed brain modules specifically dedicated to mind-reading and other social cognitive abilities should be carefully scrutinized. Searching for the brain location of intentions, beliefs and desires-as such-might not be the best epistemic strategy to disclose what social cognition really is. The results of neurocognitive research suggest that in the brain of primates, mirror neurons, and more generally the premotor system, play a major role in several aspects of social cognition, from action and intention understanding to language processing. This evidence is presented and discussed within the theoretical frame of an embodied simulation account of social cognition. Embodied simulation and the mirror neuron system underpinning it provide the means to share communicative intentions, meaning and reference, thus granting the parity requirements of social communication.     

Epistemic values in the Burgess Shale debate

Focusing primarily on papers and books discussing the evolutionary and systematic interpretation of the Cambrian animal fossils from the Burgess Shale fauna, this paper explores the role of epistemic values in the context of a discipline (paleontology) striving to establish scientific authority within a larger domain of epistemic problems and issues (evolutionary biology). The focal point of this analysis is the repeated claims by paleontologists that the study of fossils gives their discipline a unique ‘historical dimension’ that makes it possible for them to unravel important aspects of evolution invisible to scientists who study the extant biosphere. The first part of the paper explores the shifting of emphasis in the writings of paleontologists between two strategies that employ opposing views on the classical positivist and physicalist ideal of science. The second part analyzes paleontologists’ claims of privileged access to life’s historical dimension in a situation where a theoretical upheaval occurring independent of the epistemical problem at hand completely shifts the standards for evaluating the legitimacy of various knowledge claims. Though the various strategies employed in defending the privileged historical perspective of paleontology have been disparate and, to an extent contradictory, each impinges on the acceptance of a specific epistemic ideal or set of values and success or failure of each depends on the compatibility of this ideal with the surrounding community of scientists.     

Measuring Neural and Behavioral Activity During Ongoing Computerized Social Interactions: An Examination of Event-Related Brain Potentials

Social exclusion is a complex social phenomenon with powerful negative consequences. Given the impact of social exclusion on mental and emotional health, an understanding of how perceptions of social exclusion develop over the course of a social interaction is important for advancing treatments aimed at lessening the harmful costs of being excluded. To date, most scientific examinations of social exclusion have looked at exclusion after a social interaction has been completed. While this has been very helpful in developing an understanding of what happens to a person following exclusion, it has not helped to clarify the moment-to-moment dynamics of the process of social exclusion. Accordingly, the current protocol was developed to obtain an improved understanding of social exclusion by examining the patterns of event-related brain activation that are present during social interactions. This protocol allows greater precision and sensitivity in detailing the social processes that lead people to feel as though they have been excluded from a social interaction. Importantly, the current protocol can be adapted to include research projects that vary the nature of exclusionary social interactions by altering how frequently participants are included, how long the periods of exclusion will last in each interaction, and when exclusion will take place during the social interactions. Further, the current protocol can be used to examine variables and constructs beyond those related to social exclusion. This capability to address a variety of applications across psychology by obtaining both neural and behavioral data during ongoing social interactions suggests the present protocol could be at the core of a developing area of scientific inquiry related to social interactions.