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How should theorists understand the living system type, especially given all the rapid, technical and intellectual advancements that biology has made? This central question for theoretical biologists is difficult to answer in part due to the heterogeneity of contemporary biological understanding. Another part of the difficulty is in circumscribing the domain of the explanandum at a sufficient level of abstraction. In this doctoral dissertation, I hypothesise that there are at least three broad and recurring patterns, corresponding to three different ways of explaining the uniqueness of the living system type. I call this the three faces of living systems, and this comprises understanding their organisation, their individuality, and their subjectivity (sensu lato). Determining the phenomenal and epistemic structure between the three faces is a problem that is critical to formulating a theoretical understanding of living systems. My principal aim is to assess the extent of dependence and connection between the three faces. I do this by exploring and analysing a set of theorists as case studies. The case studies include the work of Humberto Maturana and Francisco Varela, Thomas Pradeu, and Peter Godfrey-Smith. To analyse the epistemic relationships between the three faces, I harness Angela Potochnik's coordinate theory about the structure of science, whilst developing a concept of patchwork theorising from the work of Karl Popper and Pradeu. With these epistemological resources, I design a method to assess the extent of epistemic interdependency between the three faces, according to the coordination of patchwork theorising. I survey and find that there are a substantially wide range of cross-disciplinary research contexts, wherein conjectures about the organisation, individuality and subjectivity of living systems are explicitly and implicitly formed. This supports the initial hypothesis. I also conduct an extensive analysis of my cases and find a range of different instances of non-trivial epistemic interdependence between them. From these findings I formulate the argument that all three faces have some form of interdependence, mutually affecting how each facet should be understood. I call this the entanglement conjecture, and it is my contribution to the philosophical and biological discourse concerning a living systems theory. Previous research on either the organisation, individuality, or subjectivity of living systems has overemphasised the explanatory autonomy of each, and it has appeared as though the heterogeneity of biological understanding reinforces a picture of epistemic independence. This has resulted in skepticism towards the formulation of living systems theory, especially with respect to the abstraction of a general type. From the findings of my analyses, I argue that there are several instances of (non-trivial) epistemic entanglement, despite the explanatory autonomy. The thesis therefore provides an intellectual scaffold for the pursuit of a living systems theory.

A cognitive system is a set of processes responsible for intelligent behaviour. This thesis is an attempt to answer the question: how can cognitive systems be demarcated; that is, what criterion can be used to decide where to draw the boundary of the system? This question is important because it is one way of couching the hypothesis of extended cognition - is it possible for cognitive systems to transcend the boundary of the brain or body of an organism? Such a criterion can be supplied by what is called in the literature a 'mark of the cognitive'. The main task of this thesis is to develop a general mark of the cognitive. The starting point is that a system responsible for intelligent behaviour is a coordinated coalition of processes. This account proposes a set of functional conditions for coordination. These conditions can then be used as a sufficient condition for membership of a cognitive system. In certain circumstances, they assert that a given process plays a coordination role in the system and is therefore part of the system. The controversy in the extended cognition debate surrounds positive claims of systemhood concerning 'external' processes so a sufficient condition will help settle some of these debates. I argue that a Coordinated Systems Approach like this will help to move the extended cognition debate forward from its current impasse. Moreover, the application of the approach to social systems and stygmergic systems - systems where current processes are coordinated partly by the trace of previous action - promises new directions for research.

This thesis explores the relation between the normative structures brought to bear on the evaluation of life and the way in which the coming-into-being of living organisms is fundamentally understood. It provides a new analysis and critique of the standard concept of ‘flourishing’ in neo-Aristotelian meta-ethics, by uncovering the underlying interpretation of organismic becoming on which it relies, and showing how the turn to a ‘constructivist’ conception of development in contemporary biological theory both disrupts this underlying metaphysics, and provides resources for re-thinking flourishing on a fundamentally different basis. The central claim is that we should turn from a view in which life is given a form to fulfil, and becoming is the process of its fulfilment, to one in which living is the process of creating a way in the world, as life goes along.

This thesis addresses key issues of scientific realism in the philosophy of biology and chemistry through investigation of an underexplored research domain: olfaction theory, or the science of smell. It also provides the first systematic overview of the development of olfactory practices and research into the molecular basis of odours across the 19th and 20th century. Historical and contemporary explanations and modelling techniques for understanding the material basis of odours are analysed with a specific focus on the entrenchment of technological process, research tradition and the definitions of materiality for understanding scientific advancement. The thesis seeks to make sense of the explanatory and problem solving strategies, different ways of reasoning and the construction of facts by drawing attention to the role and application of scientific representations in olfactory practices. Scientific representations such as models, classifications, maps, diagrams, lists etc. serve a variety of purposes that range from the stipulation of relevant properties and correlations of the research materials and the systematic formation of research questions, to the design of experiments that explore or test particular hypotheses. By examining a variety of modelling strategies in olfactory research, I elaborate on how I understand the relation between representations and the world and why this relation requires a pluralist perspective on scientific models, methods and practices. Through this work I will show how a plurality of representations does not pose a problem for realism about scientific entities and their theoretical contexts but, on the contrary, that this plurality serves as the most reliable grounding for a realistic interpretation of scientific representations of the world and the entities it contains. The thesis concludes that scientific judgement has to be understood through its disciplinary trajectory, and that scientific pluralism is a direct consequence of the historicity of scientific development.

As China has celebrated its economic boom over the past decades, scientific research within the R&D sector of industry has become an active arena for Science and Technology Studies (STS) in understanding how science contributes to social change in China. Two themes are central in this sociological work: the study of secular change in China, in particular, change in its biotech industries exemplified by work in the BGI (formerly known as Beijing Genomics Institute); the investigation of interdisciplinarity in that context. This research sheds new light on explanatory practice in interdisciplinary research (IDR) strategy as patterns of interaction in the social process of scientific knowledge production, and its contribution also includes bridging the sociology of scientific knowledge production and research policy studies. In this thesis, I examine a number of topics at three interrelated levels of analysis. First, it explores the theoretical development of the academic discipline and the notion of interdisciplinarity, with a focus on the balance of normative and descriptive approaches in understanding their social functionality as embodied by what I name as Paradiscipline (the initial stage of IDR project). The second level investigates closely how IDR patterns emerge and evolve in the sequencing-based industrial R&D practice in the case of the BGI. Social, cultural, and institutional factors directing and conditioning collective actions by status groups within interaction network are carefully weighed against the context that scientific expertise speak to power in China's social setting. The last level is dedicated to yield more pervasive implications including the organizational structure of interaction and modelling of scientific research, via comparative analysis of traditional S&T management and governing 'Big Science'. It further addresses the issues around on-site governance of China's biotechnology industry R&D, at both management practice and policy making levels, on the basis of social embedment.

This is a philosophical enquiry into scientific research that studies the causes of behaviour, principally human, using the findings, techniques or tools of genomic science. The objectives, concepts and methods of eight selected disciplines are analysed: biomolecular archaeology, evolutionary biomechanics, molecular neurobiology, Down syndrome research, human behavioural ecology, behavioural genetics, human evolutionary genetics and human developmental genetics. Nine semi-structured interviews were conducted with leading researchers in these fields. The results are analysed in terms of a set of fourteen criteria, chosen to illustrate diversity in the conceptual approaches of the researchers concerned. Some of these, for example, put the accent in their work on phylogeny rather than ontogeny. Some study the action of nuclear genes; some concentrate on mitochondrial DNA. The results are also plotted in a Criterion Matrix. The researchers spoke as individuals, not as representatives of their discipline. In parallel, sources in the literature as well as the interviews were used to generate a Genomic Workbench Analysis Model, identifying the different regions of the human and other genomes used by different disciplines in their research. The process of enquiry is presented as a conceptual mapping of the putative field of behavioural genomics. The two principal tools of the method – the Criterion Matrix and the Genomic Workbench Analysis Model – convey a picture of rich and complex diversity among the target disciplines. It is concluded that this diversity is inconsistent with a two-clusters model such as might have been suggested in the past by a polarisation of the nature-nurture debate along a single axis. Other conclusions of the conceptual mapping study are presented. A suggestion is made for the future development of a field of behavioural environomics.

In this thesis I examine a number of topics that bear on explanation and understanding in molecular and cell biology, in order to shed new light on explanatory practice in those areas and to find novel angles from which to approach relevant philosophical debates. The topics I look at include mechanism, emergence, cellular complexity, and the informational role of the genome. I develop a perspective that stresses the intimacy of the relations between ontology and epistemology. Whether a phenomenon looks mechanistic, or complex, or indeed emergent, is largely an epistemic matter, yet has an objective basis in features of the world. After reviewing several concepts of mechanism I consider the influential recent account of Machamer, Darden and Craver (MDC). That account makes interesting proposals concerning the relationship between mechanistic explanation and intelligibility, which are consistent with the results of the investigation I undertake into the science surrounding protein folding. In relation to a number of other issues pertaining to biological systems I conclude that the MDC account is insufficiently nuanced, however, leading me to outline an alternative approach to mechanism. This emphasizes the importance of structure—function relations and addresses issues raised by reflection on the nature of cellular complexity. These include the distinction between structure and process and the different possible bases on which system organization may be maintained. The account I give of emergence construes the phenomenon in terms of psychological deficit: phenomena are emergent when we lack the capacity to trace through and model their causal structures using our cognitive schemas. I conclude by developing these ideas into a preliminary and partial account of explanation and understanding. This aspires to cover the significant fraction of work in molecular and cell biology that correlates biological structures, processes and functions by visualizing phenomena and making them imaginable.

Genetic sex -the apparent fundamental biological cause of the two male and female human varieties- is a 20th century construct. Looking down the microscope, the stained chromosomes are concrete countable entities and lend themselves easily to genetic determinism. As the chromosome composition of a person is generally fixed at the time of conception, when a Y- or X-bearing sperm is united with the X-bearing egg, a person’s genetic sex is taken as permanent and unchanging throughout their life. Drawing upon gender theory as well as science and technology studies this thesis explores how our particular construction of the concept of ‘genetic sex’ relies on four features of biological sex (binary, fixed, spanning nature, and found throughout the body) and in addition proposes one unique feature, inheritance. The empirical research is based on an analysis of popular science books as well as two case studies of how genes relate to sex determination and development. The analysis of the metaphors used in these books and journal articles reveals how now, with genomic efforts to explore gene expression profiles, there is a shift away from seeing genes as having ‘responsibilities’ for determining phenotypes towards seeing them play a role along with other genes in genetic cascades where other factors such as timing can be incorporated. The analysis of genomic features such as imprinting and X-chromosome inactivation also provide evidence that such a change should be recognised. Rather than seeing sex in terms of fixed and static differences and similarities, current research offers new ways of conceptualising similarities and differences as dynamic and responsive to environment. This supports wider understandings of ‘biology’ as relying on the interactions between genetic processes, cellular environment, and tissue environment – in which the social physicality of bodies is important in forming and maintaining a person’s biology and genetic processes. Yet as the historical analysis of the shift between the one sex to two sex model indicates, it remains to be seen whether the social sphere will respond by incorporating this new evidence into the tacit, everyday understandings of sex or seek to maintain the binary and fixed relationship(s) between men and women by governing them as males and females.