This chapter presents a displacement of the organism as a privileged level of analysis in evolutionary biology. It is concerned with the ontology of biology systems, with particular reference to hierarchical organization. It argues that the concept of a rank-free hierarchy can be transposed to the major transitions hierarchy, with interesting consequences. This chapter shows that the idea of rank freedom makes good sense of a number of facets of the recent discussion of evolutionary transitions and multilevel selection. It (...) suggests that the idea of rank freedom is already at work, implicitly, in much theorizing about evolutionary transitions and/or multilevel selection. (shrink)

Systems biology has provided new resources for discovering and reasoning about mechanisms. In addition to generating databases of large bodies of data, systems biologists have introduced platforms such as Cytoscape to represent protein–protein interactions, gene interactions, and other data in networks. Networks are inherently flat structures. One can identify clusters of highly connected nodes, but network representations do not represent these clusters as at a higher level than their constituents. Mechanisms, however, are hierarchically organized: they can be decomposed into their (...) parts and their activities can be decomposed into component operations. A potent bridge between flat networks and hierarchical mechanisms is provided by biological ontologies, both those curated by hand such as Gene Ontology and those extracted directly from databases such as Network Extracted Ontology. I examine several examples in which by applying ontologies to networks, systems biologists generate new hypotheses about mechanisms and characterize these novel strategies for developing mechanistic explanations. (shrink)

Metagenomics is an emerging microbial systems science that is based on the large-scale analysis of the DNA of microbial communities in their natural environments. Studies of metagenomes are revealing the vast scope of biodiversity in a wide range of environments, as well as new functional capacities of individual cells and communities, and the complex evolutionary relationships between them. Our examination of this science focuses on the ontological implications of these studies of metagenomes and metaorganisms, and what they mean for common (...) sense and philosophical understandings of multicellularity, individuality and organism. We show how metagenomics requires us to think in different ways about what human beings are and what their relation to the microbial world is. Metagenomics could also transform the way in which evolutionary processes are understood, with the most basic relationship between cells from both similar and different organisms being far more cooperative and less antagonistic than is widely assumed. In addition to raising fundamental questions about biological ontology, metagenomics generates possibilities for powerful technologies addressed to issues of climate, health and conservation. We conclude with reflections about process-oriented versus entity-oriented analysis in light of current trends towards systems approaches. (shrink)

I argue for the usefulness of the evolutionary kind of biological individual.

This is an extended review of John Dupré's _Processes of Life_, a collection of essays. It clarifies Dupré's concepts of reductionism and anti-reductionism, and critically examines his associated discussions of downward causation, and both the context sensitivity and multiple realization of categories. It reviews his naturalistic monism, and critically distinguishes between his realism about categories and constructivism about classification. Challenges to his process ontology are presented, as are arguments for his pluralism about scientific categories. None of his main conclusions (...) are rejected; rather it is main arguments for them that are the focus. (shrink)

Biomedical research is increasingly a matter of the navigation through large computerized information resources deriving from functional genomics or from the biochemistry of disease pathways. To make such navigation possible, controlled vocabularies are needed in terms of which data from different sources can be unified. One of the most influential developments in this regard is the so-called Gene Ontology, which consists of controlled vocabularies of terms used by biologists to describe cellular constituents, biological processes and molecular functions, organized (...) into hierarchies via the relation of class subsumption. Here we seek to provide a rigorous account of the logic of classification that underlies GO and similar biomedical ontologies. Drawing on Aristotle, we develop a system of axioms and definitions for the treatment of biological classes and instances. (shrink)

A longstanding philosophical premise perceives simplicity as a desirable attribute of scientific theories. One of several raised justifications for this notion is that simple theories are more likely to indicate the true makeup of natural systems. Qualitatively parsimonious hypotheses and theories keep to a minimum the number of different postulated entities within a system. Formulation of such ontologically simple working hypotheses proved to be useful in the experimental probing of narrowly defined bio systems. It is less certain, however, whether qualitatively (...) parsimonious theories are effective indicators of the true nature of complex biological systems. This paper assesses the success of ontologically simple theories in envisaging the makeup of three complex systems in bacteriology, immunology, and molecular biology. Evidence shows that parsimonious theories completely misconstrued the actual ontologically complex constitutions of the three examined systems. Since evolution and selective pressures typically produce ontologically intricate rather than simple bio systems, qualitatively parsimonious theories are mostly inapt indicators of the true nature of complex biological systems. (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data (...) visualization’, ‘statistical data analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

An ontology is a domain of knowledge structured through formal rules so that it can be interpreted and used by computers. Ontologies are becoming increasingly important in bioinformatics because they can be linked to the information in databases and their knowledge then used to query the databases. Typical examples in current use are the Gene Ontology, which incorporates much of our knowledge about gene products, and ontologies of developmental anatomy, which, for example, facilitate tissue‐based queries to gene expression (...) databases both textually and spatially. This article considers the production, formulation and types of bio‐ontologies together with the reasons why they are so useful. © BioEssays 25:501–506, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

In this paper I explore how the discussion about the existence of laws in biology, more specifically laws about species taxa, bears on the issue of whether species are kinds or individuals. One of the main arguments offered in favor of the view that species are individuals is that it explains the lack of laws about species taxa, since laws cannot refer to individuals. My aim in this paper is to question the premise that there are no laws about species (...) axa and consequently to show that the proposed argument fails. I will argue that even if there are no strict scientific laws about species taxa, still, scientifically interesting, law-like generalizations are made which are used for explaining phenomena and predicting properties of species members. The existence of these law-like generalizations, in turn, suggests that species are, at least prima facie, best conceived of as kinds. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. (...) This paper summarises ENVO’s motivation, content, structure, adoption, and governance approach. (shrink)

Biology lacks a central organism concept that unambiguously marks the distinction between organism and non-organism because the most important questions about organisms do not depend on this concept. I argue that the two main ways to discover useful biological generalizations about multicellular organization--the study of homology within multicellular lineages and of convergent evolution across lineages in which multicellularity has been independently established--do not require what would have to be a stipulative sharpening of an organism concept.

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to (...) be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (shrink)

This paper investigates which of the variouslegal notions proposed for human DNA is themost appropriate from an ontological viewpoint – unique legal status, private property, commonproperty, person, or information. The focus is onthe difficulties that private property, commonproperty and person present. By usingHarré''s notion of ``file-self'''' we arguethat, ontologically, the most appropriate legalnotion to be applied is information. This hasconsequences for storage, control and use ofgenetic information as well as identifiablehuman body material.

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community (...) critique and to describe a number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

This article is concerned with two interrelated questions: what, if anything, distinguishes synthetic from natural organisms, and to what extent, if any, creating the former is of moral significance. These are ontological and ethical questions, respectively. As the title indicates, I address both from a broadly neo-Aristotelian perspective, i.e. a teleological philosophy of life and virtue ethics. For brevity’s sake, I shall not argue for either philosophical position at length, but instead hope to demonstrate their legitimacy through their explanatory power. (...) I firstly argue that synthetic organisms differ in kind from natural organisms and machines, and differ only by degree from genetically modified organisms. I then suggest that this is nevertheless sufficient to give us specific ethical reservations about synthetic biology: namely, that more than any other widely used biotechnology, it is characterised by a drive to mastery that stands opposed to due appreciation of the giftedness of life. (shrink)

Although synthetic biology is a promising discipline, it also raises serious ethical questions that must be addressed in order to prevent unwanted consequences and to ensure that its progress leads toward the good of all. Questions arise about the role of this discipline in a possible redefinition of the concept of life and its creation. With regard to the products of synthetic biology, the moral status that they should be given as well as the ethically correct way to behave towards (...) them are not clear. Moreover, risks that could result from a misuse of this technology or from an accidental release of synthetic organisms into the environment cannot be ignored; concerns about biosecurity and biosafety appear. Here we discuss these and other questions from a personalist ontological framework, which defends human life as an essential value and proposes a set of principles to ensure the safeguarding of this and other values that are based on it. (shrink)

Stamos squarely confronts the problem of determining what a biological species is, whether species are real, and the nature of their reality. He critically considers the evolution of the major contemporary views of species and also offers his own solution to the species problem.

Stamos squarely confronts the problem of determining what a biological species is, whether species are real, and the nature of their reality. He critically considers the evolution of the major contemporary views of species and also offers his own solution to the species problem.

Although synthetic biology is a promising discipline, it also raises serious ethical questions that must be addressed in order to prevent unwanted consequences and to ensure that its progress leads toward the good of all. Questions arise about the role of this discipline in a possible redefinition of the concept of life and its creation. With regard to the products of synthetic biology, the moral status that they should be given as well as the ethically correct way to behave towards (...) them are not clear. Moreover, risks that could result from a misuse of this technology or from an accidental release of synthetic organisms into the environment cannot be ignored; concerns about biosecurity and biosafety appear. Here we discuss these and other questions from a personalist ontological framework, which defends human life as an essential value and proposes a set of principles to ensure the safeguarding of this and other values that are based on it. (shrink)

The phenomenological starting point of this paper is the world of the bioethical subject, the person engaged in moral deliberation about practices of intervention on living bodies. This paper develops a perspective informed by the hermeneutic tradition in phenomenology, approaching bioethical thinking as situated within specific contexts of meaning and conceptuality, frameworks through which the phenomena of the world are interpreted and made sense of by the reasoning subject. It focuses on one dimension of the hermeneutic world of contemporary bioethics, (...) that of the relation between bioethics and biological science. This paper shows how taking a phenomenological-hermeneutic perspective can highlight an important but often overlooked way in which biology helps to structure spaces of bioethical sense-making, with substantive consequences for moral judgement. Bioscientific discourse provides us with interpretive resources for making sense of the living world around us and within us. Different interpretive resources reflect different assumptions about the ontology of living beings, humans included. Since, as is argued here, judgements about moral significance in bioethics can depend upon suppositions about the ontology of life, the way that scientific discourse interpretively constitutes the phenomena of life as intentional objects can thereby channel moral thinking in particular ways. The central thesis of this paper is that critical engagement with this ‘hermeneutics of biology’ is vital for contemporary bioethics. To illustrate, the paper explores the hermeneutic constitution of the genome and its relationship to issues of human identity in the context of genetic technology. Alternative interpretations of the genome—as ‘programme’ or as ‘developmental resource’—differently shape bioethical reasoning in this context. Choices of description in bioscience are in this way partly ethical questions, questions about how we ought to comport ourselves towards each other and the living world beyond. (shrink)

Biology lacks a central organism concept that unambiguously marks the distinction between organism and non-organism because the most important questions about organisms do not depend on this concept. I argue that the two main ways to discover useful biological generalizations about multicellular organization—the study of homology within multicellular lineages and of convergent evolution across lineages in which multicellularity has been independently established—do not require what would have to be a stipulative sharpening of an organism concept.

In recent years, postgenomic research, and the fields of epigenetics and microbiome science in particular, have described novel ways in which social processes of racialization can become embodied and result in physiological and health-related racial difference. This new conception of biosocial race has important implications for philosophical debates on the ontology of race. We argue that postgenomic research on race exhibits two key biases in the way that racial schemas are deployed. Firstly, although the ‘new biosocial race’ has been (...) characterized as social race entering into biological processes, it is only particular aspects of social race that are taken to cross the biosocial boundary, resulting in a distorted view of the social component of biosocial race. Secondly, racial categories are assumed to be stable across time and space. This assumption is epistemically limiting, as well as indicating a reliance on a fixed racial ontology. However, the causal pathways for the embodiment of social race, and the different possible modes of embodiment, that postgenomic science is uncovering themselves present a challenge for fixed or static racial ontologies. Given these tensions, we argue that the emerging picture of a shifting landscape of entanglement between the social and the biological requires us to increase the complexity of our ontologies of race, or even embrace a deflationary metaphysics of race. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for (...) the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (shrink)

ABSTRACT:Novel biotechnologies produce new person-related biological entities, such as cell lines, organoids, and synthetic organisms, that tend to disrupt existing concepts, taxonomies, modes of evidence production, as well as moral norms and values. This raises the question of how we can manage these new person-related biological entities. This article identifies and analyzes key conceptual, ontological, epistemological, and ethical aspects of such entities in order to suggest how to make, manage, and regulate them. It argues that in order to (...) avoid conceptual vagueness and taxonomic confusion, it is important to clarify how person-related biological entities relate to existing concepts and to make new concepts where necessary. Ontologically, we need to determine the thing- and person-likeness of such entities. Epistemically, we must provide measures to verify the characteristics of person-related biological entities and to provide high-quality knowledge of their implications (outcomes). And ethically, we must clarify the moral status, rights, and responsibility for and of the entities, and how they will change our norms and values. Addressing these issues up front may improve our making and managing of person-related biological entities. (shrink)

The French philosopher Renaud Barbaras remarked that late in Maurice Merleau-Ponty’s career, “The phenomenology of perception fulfills itself as a philosophy of expression.” In _Tracing Expression in Merleau-Ponty: Aesthetics, Philosophy of Biology, and Ontology, _Véronique M. Fóti_ _addresses the guiding yet neglected theme of expression in Merleau-Ponty’s thought. She traces Merleau-Ponty’s ideas about how individuals express creative or artistic impulses through his three essays on aesthetics, his engagement with animality and the “new biology” in the second of his lecture (...) courses on nature of 1957–58, and in his late ontology, articulated in 1964 in the fragmentary text of _Le visible et l’invisible _. With the exception of a discussion of Merleau-Ponty’s 1945 essay “Cezanne’s Doubt,” Fóti engages with Merleau-Ponty’s late and final thought, with close attention to both his scientific and philosophical interlocutors, especially the continental rationalists. Expression shows itself, in Merleau-Ponty’s thought, to be primordial, and this innate and fundamental nature of expression has implications for his understanding of artistic creation, science, and philosophy. (shrink)

Well prior to the invention of the term ‘biology’ in the early 1800s by Lamarck and Treviranus (and lesser-known figures in the decades prior), and also prior to the appearance of terms such as ‘organism’ under the pen of Leibniz and Stahl in the early 1700s, the question of ‘Life’, that is, the status of living organisms within the broader physico-mechanical universe, agitated different corners of the European intellectual scene. From modern Epicureanism to medical Newtonianism, from Stahlian animism to the (...) discourse on the ‘animal economy’ in vitalist medicine, models of living being were constructed in opposition to ‘merely anatomical’, structural, mechanical models. It is therefore striking that the classic narratives of the Scientific Revolution conspicuously avoid any consideration of what status to grant living beings in a newly physicalized universe (I discuss this in Wolfe 2011, 2019 chapt. 1). Neither Harvey, nor Boyle, nor Locke (to name some likely candidates, the latter having studied with Willis and collaborated with Sydenham) ever ask what makes organisms unique, or conversely, what does not. In this chapter I seek to establish how something we might call ‘the knowledge of Life’, to use an expression of Georges Canguilhem’s, emerged as part of early modernity without being part of the mainstream history of life science. This leads to the question, can one can correlate early modern “knowledge of life” with the emergence of a science called ‘biology’? (see Zammito 2018, Wolfe 2019, Bognon-Küss and Wolfe eds. 2019). It was once fashionable to speak of, e.g. ‘precursors of Darwin’, and then Canguilhem and Foucault famously did away with the category of precursor. But how then do we account for the phase that precedes the constitution of a science? With the case of biology, how do we account for the increasing fascination with the ontology of Life during the decades prior to the ‘naming of biology’, as McLaughlin has called it, at the end of the eighteenth century? This increased focus on Life and the ontology of Life sits awkwardly, both with mainstream narratives of the Scientific Revolution and of the history of biology. In seeking to address this increased focus (in which vitalism plays a role but was by no means the only conceptual actor: Wolfe 2020), I critically examine Foucault’s notorious claim (Foucault 1966) that there was no such thing as ‘Life’ in the eighteenth century and thus no such thing as biology. (shrink)

Although contemporary metaphysics has recently undergone a neo-Aristotelian revival wherein dispositions, or capacities are now commonplace in empirically grounded ontologies, being routinely utilised in theories of causality and modality, a central Aristotelian concept has yet to be given serious attention – the doctrine of hylomorphism. The reason for this is clear: while the Aristotelian ontological distinction between actuality and potentiality has proven to be a fruitful conceptual framework with which to model the operation of the natural world, the distinction between (...) form and matter has yet to similarly earn its keep. In this chapter, I offer a first step toward showing that the hylomorphic framework is up to that task. To do so, I return to the birthplace of that doctrine - the biological realm. Utilising recent advances in developmental biology, I argue that the hylomorphic framework is an empirically adequate and conceptually rich explanatory schema with which to model the nature of organisms. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the (...) Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as (...) adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

The viability of enactivist philosophy in providing descriptions of biological phenomena across the phylogenetic spectrum relies in large part on the scalability of its central concepts, i.e. whether they remain operative at varying levels of biological complexity. In this paper, I will examine the possibility of scaling two deeply intertwined concepts: cognition and surrounding world. Contra some indications from Varela and others, I will argue that the concept of embodied cognition can be scaled down below the level of (...) the organism. I will draw upon the “cognitive biology” espoused by Kováč and Monod’s studies of protein behaviour to make this case. The downscaling of embodied cognition below the level of the organism has ramifications for how we understand the concept of surrounding world. Reconfiguring the relation between these two central bioenactive concepts has further consequences for what ontological commitments bioenactive thinking leads to, and what paths of investigation it points us toward. (shrink)