Integration in biology: Philosophical perspectives on the dynamics of interdisciplinarity

Epistemology of synthetic biology: a new theoretical framework based on its potential objects and objectives

Synthetic biology is a new research field which attempts to understand, modify, and create new biological entities by adopting a modular and systemic conception of the living organisms. The development of synthetic biology has generated a pluralism of different approaches, bringing together a set of heterogeneous practices and conceptualizations from various disciplines, which can lead to confusion within the synthetic biology community as well as with other biological disciplines. I present in this manuscript an epistemological analysis of synthetic biology in order to better define this new discipline in terms of objects of study and specific objectives. First, I present and analyze the principal research projects developed at the foundation of synthetic biology, in order to establish an overview of the practices in this new emerging discipline. Then, I analyze an important scientometric study on synthetic biology to complete this overview. Afterwards, considering this analysis, I suggest a three-level classification of the object of study for synthetic biology (which are different kinds of living entities that can be built in the laboratory), based on three successive criteria: structural hierarchy, structural origin, functional origin. Finally, I propose three successively linked objectives in which synthetic biology can contribute (where the achievement of one objective led to the development of the other): interdisciplinarity collaboration (between natural, artificial, and theoretical sciences), knowledge of natural living entities (past, present, future, and alternative), pragmatic definition of the concept of "living" (that can be used by biologists in different contexts). Considering this new theoretical framework, based on its potential objects and objectives, I take the position that synthetic biology has not only the potential to develop its own new approach (which includes methods, objects, and objectives), distinct from other subdisciplines in biology, but also the ability to develop new knowledge on living entities.

The agential perspective: Countermapping the modern synthesis

We compare and contrast two theoretical perspectives on adaptive evolution-the orthodox Modern Synthesis perspective, and the nascent Agential Perspective. To do so, we develop the idea from Rasmus Grønfeldt Winther of a 'countermap', as a means for comparing the respective ontologies of different scientific perspectives. We conclude that the modern Synthesis perspective achieves an impressively comprehensive view of a universal set of dynamical properties of populations, but at the considerable cost of radically distorting the nature of the biological processes that contribute to evolution. For its part, the Agential Perspective offers the prospect of representing the biological processes of evolution with much greater fidelity, but at the expense of generality. Trade-offs of this sort are endemic to science, and inevitable. Recognizing them helps us to avoid the pitfalls of 'illicit reification', i.e. the mistake of interpreting a feature of a scientific perspective as a feature of the non-perspectival world. We argue that much of the traditional Modern Synthesis representation of the biology of evolution commits this illicit reification.

Mechanistic inquiry and scientific pursuit: The case of visual processing

Why is it rational for scientists to pursue multiple models of a phenomenon at the same time? The literatures on mechanistic inquiry and scientific pursuit each develop answers to a version of this question which is rarely discussed by the other. The mechanistic literature suggests that scientists pursue different complementary models because each model provides detailed insights into different aspects of the phenomenon under investigation. The pursuit literature suggests that scientists pursue competing models because alternative models promise to solve outstanding empirical and conceptual problems. Looking into research on visual processing as a case study, we suggest an integrated account of why it is rational for scientists to pursue both complementary and competing models of the same mechanism in scientific practice.

Non-Lethal Sampling Supports Integrative Movement Research in Freshwater Fish

Freshwater ecosystems and fishes are enormous resources for human uses and biodiversity worldwide. However, anthropogenic climate change and factors such as dams and environmental contaminants threaten these freshwater systems. One way that researchers can address conservation issues in freshwater fishes is via integrative non-lethal movement research. We review different methods for studying movement, such as with acoustic telemetry. Methods for connecting movement and physiology are then reviewed, by using non-lethal tissue biopsies to assay environmental contaminants, isotope composition, protein metabolism, and gene expression. Methods for connecting movement and genetics are reviewed as well, such as by using population genetics or quantitative genetics and genome-wide association studies. We present further considerations for collecting molecular data, the ethical foundations of non-lethal sampling, integrative approaches to research, and management decisions. Ultimately, we argue that non-lethal sampling is effective for conducting integrative, movement-oriented research in freshwater fishes. This research has the potential for addressing critical issues in freshwater systems in the future.

Evaluating integration in collaborative cross-disciplinary FDA new drug reviews using an input-process-output model

BACKGROUND/OBJECTIVES

The US Food and Drug Administration (FDA) is responsible for assessing safety (risks) and effectiveness (benefits) of new drug products using the data provided in a Sponsor's new drug product marketing application before they can be marketed. The FDA forms cross-disciplinary review teams to conduct these assessments. Recently, the FDA began implementing more interdisciplinary approaches to its assessments, reducing redundancy in review processes and documentation by increasing team integration around review issues.

METHODS

Through a phenomenological descriptive comparative case study, the impact of FDA's new interdisciplinary approach on review team integration was compared with its traditional multidisciplinary review approach.

RESULTS

We identified collaborative integration occurring in one FDA review team using the new interdisciplinary review and another team using the traditional review and then modeled and analyzed the collaborative, cross-disciplinary integration in each case using an input-process-output (IPO) model drawn from the Science-of-Team-Science (SciTS).

CONCLUSION

This study provides a systematic method for understanding and visualizing integration in each type of review previously and presently used at FDA and illustrates how the new interdisciplinary approach can ensure more integration than more traditional approaches previously used. In addition, our study suggests that an IPO model of integration can characterize how effectively FDA review teams are integrating around issues and assist in the evaluation of differences in integration between FDA's new interdisciplinary review and the existing multidisciplinary approach. The approach used here is a new application of SciTS scholarship in a unique sector, and it also serves as an example for measuring review team effectiveness.

Best behaviour: A proposal for a non-binary conceptualization of behaviour in biology

Behaviour is a widespread object of research in biology, yet it is often left undefined, and the variety of existing definitions have not led to a consensus. We argue that the fundamental problem in defining behaviour has been the assumption that the concept must be categorical: either a phenomenon is a behaviour or it is not. We propose instead that 'behaviour' is best understood as a spectrum concept. We have identified three major characteristics of phenomena which, we argue, fuel the intuitions of biologists regarding the classification of cases as behaviour. All are related to the mechanistic explanations put forth to account for the phenomena, and are (i) the complexity of the mechanism, (ii) the stability of the constitutive entities, and (iii) the quantity and significance of the inputs to the underlying mechanism. We illustrate this new conceptualisation through a three-dimensional behaviour-space which highlights the apparently different conceptualizations of behaviour attributed to humans, animals and plants, showing that they, in fact, all partake of a unified, malleable understanding of a single concept.

Making the Most of Trait-Based Approaches for Microbial Ecology

There is an increasing interest in applying trait-based approaches to microbial ecology, but the question of how and why to do it is still lagging behind. By anchoring our discussion of these questions in a framework derived from epistemology, we broaden the scope of trait-based approaches to microbial ecology from one oriented mostly around explanation towards one inclusive of the predictive and integrative potential of these approaches. We use case studies from macro-organismal ecology to concretely show how these goals for knowledge development can be fulfilled and propose clear directions, adapted to the biological reality of microbes, to make the most of recent advancements in the measurement of microbial phenotypes and traits.

Evaluating evidential pluralism in epidemiology: mechanistic evidence in exposome research

In current philosophical discussions on evidence in the medical sciences, epidemiology has been used to exemplify a specific version of evidential pluralism. According to this view, known as the Russo-Williamson Thesis, evidence of both difference-making and mechanisms is produced to make causal claims in the health sciences. In this paper, I present an analysis of data and evidence in epidemiological practice, with a special focus on research on the exposome, and I cast doubt on the extent to which evidential pluralism holds in this case. I start by focusing on the claim that molecular data allows for the production of mechanistic evidence. On the basis of a close look at the ways in which molecular data is used in exposome research, I caution against interpretations in terms of mechanistic evidence. Secondly, I expand my critical remarks on the thesis by addressing the conditions under which data is categorised as evidence in exposome research. I argue that these show that the classification of a dataset as a type of evidence is dependent on the ways in which the data is used. This is in contrast with the approach of evidential pluralism, where evidence is classified in different types on the basis of its intrinsic properties. Finally, I come back to what I consider the core of the thesis and suggest that the epidemiological research analysed in the paper indicates different interpretations of evidential pluralism and its applicability in the health sciences.

Repertoires: A post-Kuhnian perspective on scientific change and collaborative research

We propose a framework to describe, analyze, and explain the conditions under which scientific communities organize themselves to do research, particularly within large-scale, multidisciplinary projects. The framework centers on the notion of a research repertoire, which encompasses well-aligned assemblages of the skills, behaviors, and material, social, and epistemic components that a group may use to practice certain kinds of science, and whose enactment affects the methods and results of research. This account provides an alternative to the idea of Kuhnian paradigms for understanding scientific change in the following ways: (1) it does not frame change as primarily generated and shaped by theoretical developments, but rather takes account of administrative, material, technological, and institutional innovations that contribute to change and explicitly questions whether and how such innovations accompany, underpin, and/or undercut theoretical shifts; (2) it thus allows for tracking of the organization, continuity, and coherence in research practices which Kuhn characterized as 'normal science' without relying on the occurrence of paradigmatic shifts and revolutions to be able to identify relevant components; and (3) it requires particular attention be paid to the performative aspects of science, whose study Kuhn pioneered but which he did not extensively conceptualize. We provide a detailed characterization of repertoires and discuss their relationship with communities, disciplines, and other forms of collaborative activities within science, building on an analysis of historical episodes and contemporary developments in the life sciences, as well as cases drawn from social and historical studies of physics, psychology, and medicine.

On the nature of cross-disciplinary integration: A philosophical framework

Meeting grand challenges requires responses that constructively combine multiple forms of expertise, both academic and non-academic; that is, it requires cross-disciplinary integration. But just what is cross-disciplinary integration? In this paper, we supply a preliminary answer by reviewing prominent accounts of cross-disciplinary integration from two literatures that are rarely brought together: cross-disciplinarity and philosophy of biology. Reflecting on similarities and differences in these accounts, we develop a framework that integrates their insights-integration as a generic combination process the details of which are determined by the specific contexts in which particular integrations occur. One such context is cross-disciplinary research, which yields cross-disciplinary integration. We close by reflecting on the potential applicability of this framework to research efforts aimed at meeting grand challenges.