Catherine Elizabeth Kendig

Discussions over whether these natural kinds exist, what is the nature of their existence, and whether natural kinds are themselves natural kinds aim to not only characterize the kinds of things that exist in the world, but also what can knowledge of these categories provide. Although philosophically critical, much of the past discussions of natural kinds have often answered these questions in a way that is unresponsive to, or has actively avoided, discussions of the empirical use of natural kinds and what I dub “activities of natural kinding” and “natural kinding practices”. The natural kinds of a particular discipline are those entities, events, mechanisms, processes, relationships, and concepts that delimit investigation within it—but we might reasonably ask: How are these natural kinds discovered?, How are they made?, Are they revisable?, and Where do they come from? A turn to natural kinding practices reveals a new set of questions open for investigation: How do natural kinds explain through practice?, What are natural kinding practices and classifications and why should we care?, What is the nature of natural kinds viewed as a set of activities?, and How do practice approaches to natural kinds shape and reconfigure scientific disciplines? Natural kinds have traditionally been discussed in terms of how they classify the contents of the world. The metaphysical project has been one which identifies essences, laws, sameness relations, fundamental properties, and clusters of family resemblances and how these map out the ontological space of the world. But actually how this is done has been less important in the discussion than the resultant categories that are produced. I aim to rectify these omissions and suggest a new metaphysical project investigating kinds in practice.

“Proof of concept” is a phrase frequently used in descriptions of research sought in program announcements, in experimental studies, and in the marketing of new technologies. It is often coupled with either a short definition or none at all, its meaning assumed to be fully understood. This is problematic. As a phrase with potential implications for research and technology, its assumed meaning requires some analysis to avoid it becoming a descriptive category that refers to all things scientifically exciting. I provide a short analysis of proof of concept research and offer an example of it within synthetic biology. I suggest that not only are there activities that circumscribe new epistemological categories but there are also associated normative ethical categories or principles linked to the research. I examine these and provide an outline for an alternative ethical account to describe these activities that I refer to as “extended agency ethics”. This view is used to explain how the type of research described as proof of concept also provides an attendant proof of principle that is the result of decision-making that extends across practitioners, their tools, techniques, and the problem solving activities of other research groups.

Homology has been one of, if not the most, fecund concepts which has been used towards the understanding of the genomes of the model organisms. The evidence for this claim can be supported best with an examination of current research in comparative genomics. In comparative genomics, the information of genes or segments of the genome, and their location and sequence, are used to search for genes similar to them, known as 'homologues'. Homologues can be either within that same organism (paralogues), or among different species (orthologues). The importance in finding homologous genes within organisms or across species is that these similarities indicate the possibility of ascribing functions, mechanisms or structures which are required by a variety of species which present the same homology. The interest in structures and functions of genes and proteins common to multiple species is one of the main foci of comparative genomics. Because of this, research into the conservation of genes has been the basis of comparison with regards to homologous genes among diverse organisms. Different causal processes are involved in genetic pathways and mechanisms. Explanations of these depend upon which pathway, structure or mechanism is picked out. Each process has a different causal network to which different explanations refer. What comparative genomics explains are the different causal mechanisms which occur in processes such as differentiation, protein synthesis, and gene regulation. How these processes interact within the organism can only be understood when compared with organisms which possess homologous genes, gene sequences, similar developmental mechanisms, or those whose mechanisms for gene regulation are similar. Explanations which result from comparative genomics contribute to a more comprehensive understanding of both the complex structures and the diverse functions within the genomes of different organisms. There are two related problems which have plagued attempts to define the concept of homology. The first problem arises in clarifying what kind of similarity is involved in a homological comparison. A second problem occurs if more than one concept of homology is needed to pick out the kinds of similarity in different contexts of homological comparison. Homology is usually understood as picking out what counts as 'the same' between two or more organisms. Many of the attempts which have been made to define the concept of homology focus on which criteria are used to restrict the kinds of similarity which exist between two or more organisms or parts being compared. These are criteria which can be used reliably to infer shared ancestry. However, there have been many different attempts to define similarity which have produced a profusion of homology concepts. This profusion has led both to the conflation of what counts as 'the same' in different contexts and has also muddled the relations of comparison which various concepts use to identify homologues.

This edited volume of 13 new essays aims to turn past discussions of natural kinds on their head. Instead of presenting a metaphysical view of kinds based largely on an unempirical vantage point, it pursues questions of kindedness which take the use of kinds and activities of kinding in practice as significant in the articulation of them as kinds. The book brings philosophical study of current and historical episodes and case studies from various scientific disciplines to bear on natural kinds as traditionally conceived of within metaphysics. Focusing on these practices reveals the different knowledge-producing activities of kinding and processes involved in natural kind use, generation, and discovery. -/- Specialists in their field, the esteemed group of contributors use diverse empirically responsive approaches to explore the nature of kindhood. This groundbreaking volume presents detailed case studies that exemplify kinding in use. Newly written for this volume, each chapter engages with the activities of kinding across a variety of disciplines. Chapter topics include the nature of kinds, kindhood, kinding, and kind-making in linguistics, chemical classification, neuroscience, gene and protein classification, colour theory in applied mathematics, homology in comparative biology, sex and gender identity theory, memory research, race, extended cognition, symbolic algebra, cartography, and geographic information science. -/- The volume seeks to open up an as-yet unexplored area within the emerging field of philosophy of science in practice, and constitutes a valuable addition to the disciplines of philosophy and history of science, technology, engineering, and mathematics. -/- Contributions from a diverse group of established and junior scholars in the fields of Philosophy and History and Philosophy of Science including Hasok Chang, Jordi Cat, Sally Haslanger, Joyce C. Havstad, Catherine Kendig, Bernhard Nickel, Josipa Petrunic, Samuli Pöyhönen, Thomas A. C. Reydon, Quayshawn Spencer, Jackie Sullivan, Michael Wheeler, and Rasmus Grønfeldt Winther

Homology is a natural kind concept, but one that has been notoriously elusive to pin down. There has been sustained debate over the nature of correspondence and the units of comparison. But this continued debate over its meaning has focused on defining homology rather than on its use in practice. The aim of this chapter is to concentrate on the practices of homologizing. I define “homologizing” to be a concept-in-use. Practices of homologizing are kinds of rule following, the satisfaction of which demarcates a category—that of being a homologue. Identifying, explaining, discovering, and understanding are exchanges that connect practice to concept through the performance of a rule by practitioners. These practices are constitutive of natural kinding activities. If homologizing is a kind of kinding, consideration of these practices of discovery, tracking, and identification not only clarifies the meaning, use, and progression of the concept of homology, but provides further understanding of the processes and progression of natural kinds and kinding practices in general.

Synthetic biology is a field of research that concentrates on the design, construction, and modification of new biomolecular parts and metabolic pathways using engineering techniques and computational models. By employing knowledge of operational pathways from engineering and mathematics such as circuits, oscillators, and digital logic gates, it uses these to understand, model, rewire, and reprogram biological networks and modules. Standard biological parts with known functions are catalogued in a number of registries (e.g. Massachusetts Institute of Technology Registry of Standard Biological Parts). Biological parts can then be selected from the catalogue and assembled in a variety of combinations to construct a system or pathway in a microbe. Through the innovative re-engineering of biological circuits and the optimization of certain metabolic pathways, biological modules can be designed to reprogram organisms to produce products or behaviors. Synthetic biology is what is known as a “platform technology”. That is, it generates highly transferrable theoretical models, engineering principles, and know-how that can be applied to create potential products in a wide variety of industries. Proponents suggest that applications of synthetic biology may be able to provide scientific and engineered solutions to a multitude of worldwide problems from health to energy. Synthetic biology research has already been successful in constructing microbial products which promise to offer cheaper pharmaceuticals such as the antimalarial synthetic drug artemisinin, engineered microbes capable of cleaning up oil spills, and the engineering of biosensors that can detect the presence of high concentrations of arsenic in drinking water. One of the potential benefits of synthetic biology research is in its application to biofuel production. It is this application which is the focus of this entry. The term “biofuel” has referred generally to all liquid fuels that are sourced from plant or plant byproducts and are used for energy necessary for transportation vehicles (Thompson 2012). Biofuels that are produced using synthetic biological techniques re-engineer microbes into biofuel factories are a subset of these.