The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking account (...) of certain organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO’s consistency and coherence and thus its future applicability in the automated processing of biological data. (shrink)

The rapid development of CRISPR-based gene editing has been accompanied by a polarized governance debate about the status of CRISPR-edited crops as genetically modified organisms. This article argues that the polarization around the governance of gene editing partly reflects a failure of public engagement with the current state of research in genomics and postgenomics. CRISPR-based gene-editing technology has become embedded in a narrow narrative about the ease and precision of the technique that presents the gene as (...) a stable object under technological control. By tracing the considerably destabilized scientific understanding of the gene in genomics and postgenomics, this article highlights that this publicly mediated ontology strategically avoids positioning the “ease of CRISPR-based editing” in the wider context of the “complexity of the gene.” While this strategic narrowness of CRISPR narratives aims to create public support for gene-editing technologies, we argue that it stands in the way of socially desirable anticipatory governance and open public dialogue about societal promises and the unintended consequences of gene editing. In addressing the polarization surrounding CRISPR-based editing technology, the article emphasizes the need for engagement with the complex state of postgenomic science that avoids strategic simplifications of the scientific literature in promoting or opposing the commercial use of the gene-editing technology. (shrink)

The condition of explicit theoretically discursive cognitive performance, as it culminates in scientific activity, is, I claim, the life world. I contrast life world and scientific world and argue that the latter arises from the first and that contrary to the prevailing views the scientific world (actually, worlds, since the classical world is substantially different from the quantum world) finds its completion in the life world and not the other way around. In other words: the closure we used to search (...) in a complete and comprehensive scientific description of all aspects of experience by referring it back to underlying atoms, genes and other scientific objects and the covering laws ruling them, should be sought in a reintegrating and occasionally dissolving of the abstract scientific model in the self-organizational fluidity and superposition-like indeterminateness and non-locality of the life world: “We have to acknowledge the indeterminate as a positive phenomenon” (Merleau-Ponty in his The Phenomenology of Perception). (shrink)

Formal principles governing best practices in classification and definition have for too long been neglected in the construction of biomedical ontologies, in ways which have important negative consequences for data integration and ontology alignment. We argue that the use of such principles in ontology construction can serve as a valuable tool in error-detection and also in supporting reliable manual curation. We argue also that such principles are a prerequisite for the successful application of advanced data integration techniques such (...) as ontology-based multi-database querying, automated ontology alignment and ontology-based text-mining. These theses are illustrated by means of a case study of the Gene Ontology, a project of increasing importance within the field of biomedical data integration. (shrink)

“Evolvability,” writes Evelyn Fox Keller, “refers to the capacity to generate any kind of heritable phenotypic variation upon which selection can act” . Whether one considers genes or organisms, the potential to adapt and evolve, to respond flexibly to a changing environment, is now recognized by many biologists as itself a trait actively favored by natural selection. Keller correctly presents this idea as an antidote to an old notion of genetic stability. She seems not to appreciate how well it applies (...) to her own subject.The Century of the Gene is Keller's latest collection of linked essays, six tidy, intelligent shovelfuls from her ongoing effort to undermine the claims of mainstream molecular biology and to substitute from the scientific margins an alternative interpretation. This project stems from her philosophical biography of the geneticist Barbara McClintock, published in 1983. In her Nobel speech, also from 1983, McClintock wrote of the genome as a dynamic “sensitive organ of the cell,” responsive, flexible, and interacting with the environment. For half a century, McClintock had railed at biologists that genes must be studied not as autonomous, independently acting units but rather as parts of an exquisite whole, acting in concert. Keller celebrated this in McClintock's work, though many have read Keller as applying to this view of nature a gloss of feminism that McClintock rejected. More recently, among other projects, Keller has criticized the “master molecule” concept in biology, examined the use of metaphor in science, and celebrated Christiane Nüsslein‐Vollhard's studies in developmental biology. Through it all, she maintains a fascination with gender and with language as shapers of scientific thought.Here Keller explores what she sees as the divergent histories of studies of genes and use of the term “gene.” While scientists continue to talk of genes much as they have done for a century now—as stable, discrete units directing the activities of the cell and the development of the organism—the molecular biology of the last forty years has seen a breaking down of the boundaries of the gene, physically, chemically, and physiologically. Keller begins by attacking the notion of genetic stability—whence the introductory quotation about evolvability. Next she explores the idea of genetic regulation, the fact that genes do not make anything, nor do they literally control anything. The molecular biologist's version of the chicken‐and‐egg problem is: Which comes first—proteins or genes? Proteins read the DNA that provides the instructions to make more proteins. Keller argues for chickens.The most important idea in the book is Keller's distinction between a developmental program and a genetic program. The former is a sequence of ontological steps in the life of an organism; it does not presuppose that all steps in the program are encoded in genes or that all steps are determined prior to the beginning of development. Developmental programs may be derived empirically, independently of genetic analysis. In contrast, the genetic program is a more recent idea that does locate the program instructions in the nucleus in the fertilized egg. For Keller, genetic programs carry implications of determinism, a restriction of vision in our attempts to understand nature.The term “gene,” Keller concludes, has outlived its utility. Molecular biologists no longer work with anything so discrete as genes. Their own data, she argues, show that genes and genomes are flexible, modular, and interactive. Keller wishes for, but does not offer, a new term or set of terms that would better reflect current understanding of genetics and development.If biologists have shown that the gene concept is outmoded, why don't they know it? Keller's answer is that the biologists have not yet recognized the implications of their own results; their language lags behind their knowledge. Eventually, she believes, either they will drop the term “gene” or biology must suffocate in its shell. Yet the changes she describes have been under way for decades and biology shows no signs of slowing. Keller recognizes this, and in the conclusion she briefly acknowledges the obvious solution to the conundrum: that biology continues to grow because of, not despite, this linguistic flexibility. This important idea deserves fuller treatment.As with the gene in nature, so with the word “gene” in the scientific lexicon: its very evolvability is selected for, a crucial trait that ensures its survival. (shrink)

Gene drives are potentially ontologically and morally disruptive technologies. The potential to shape evolutionary processes and to eradicate (e.g. malaria-transmitting or invasive) populations raises ontological questions about evolution, nature, and wilderness. The transformative promises and perils of gene drives also raise pressing ethical and political concerns. The aim of this article is to arrive at a better understanding of the gene drive debate by analysing how ontological and moral assumptions are coproduced in this debate. Combining philosophical analysis (...) with a critical reading of the gene drive literature and an ethnographic study of two leading research groups, the article explores the hypothesis that the development of and debate about gene drives are characterized by a particular intervention-oriented mode of coproduction. Based on the results of this exploration, we highlight the need for a broadening of the perspective on gene drives in which empirical, moral, and ontological concerns are addressed explicitly in their interplay rather than in (disciplinary) isolation from each other. (shrink)

This paper argues that Monologion and Proslogion though distinguishable are not really separable. They are distinct as "the way in" and "the way when one is in" but "the way in" reveals itself as a discovery of already being in; thus these ways are distinct in act, but not in being. Monologion moves from imaginary ignorance to real reverence, while Proslogion begins within reverence to achieve understanding.

Although Burt provides a valuable critique of the scientific value of integrating genetic data into social science research, she reinforces rather than disrupts the age-old horserace between genetic effects and environmental effects. We must move past this false dichotomy to create a new ontology that recognizes the ways in which genetic and environmental processes are inextricably intertwined.

The aim of this paper is to explore in the light of recent scientific discoveries, coupled with a return to biblical orthodoxy, the question of the Fall, and the apparent intergenerational conditions of original sin. This is the human condition – East of Eden. Invoking Darwin's theory of evolution through natural selection from random mutation as a means of repudiating the existence of original sin can no longer be sustained, scientifically; the biology of horizontal gene transfer, transgenerational epigenetics, accelerated (...) evolution and biological plasticity has rendered Darwinism grounded in a Naturalistic methodology an inadequate explanation. If humanity is ‘born this way’ – mired in sin – have we condemned ourselves and our children to this status? How does this affect the relationship between biology and free will, between a form of predestination and decision-making? Therefore, this paper is towards an understanding of the ontology of the original, or first, sin, and is a biblical and scientific exploration of postlapsarian humanity's self-willed state, ‘East of Eden.’. (shrink)

The Cell Cycle Ontology (CCO) has the aim to provide a 'one stop shop' for scientists interested in the biology of the cell cycle that would like to ask questions from a molecular and/or systems perspective: what are the genes, proteins, and so on involved in the regulation of cell division? How do they interact to produce the effects observed in the regulation of the cell cycle? To answer these questions, the CCO must integrate a large amount of knowledge (...) from diverse sources; the irregularity and incompleteness of this information suggests an ontology can act as the means of this integration. The volatility and continued expansion of biological knowledge means the content and modelling of the CCO will have to be frequently changed and updated. The CCO is generated from the input data automatically once every two months. This makes it easy to change the representation to enable certain queries; incorporate new knowledge; and consistently apply design patterns across the CCO. The automatic process also allows the CCO to be delivered in a variety of representations that suit the needs of various CCO customers and the abilities of existing toolsets. In this paper we present the CCO and its characteristics of utility and flexibility, that, from our perspective, make it a beautiful ontology. (shrink)

Gene drives are potentially ontologically and morally disruptive technologies. The potential to shape evolutionary processes and to eradicate (e.g. malaria-transmitting or invasive) populations raises ontological questions about evolution, nature, and wilderness. The transformative promises and perils of gene drives also raise pressing ethical and political concerns. The aim of this article is to arrive at a better understanding of the gene drive debate by analysing how ontological and moral assumptions are coproduced in this debate. Combining philosophical analysis (...) with a critical reading of the gene drive literature and an ethnographic study of two leading research groups, the article explores the hypothesis that the development of and debate about gene drives are characterized by a particular intervention-oriented mode of coproduction. Based on the results of this exploration, we highlight the need for a broadening of the perspective on gene drives in which empirical, moral, and ontological concerns are addressed explicitly in their interplay rather than in (disciplinary) isolation from each other. (shrink)

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry (...) ontology that provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

Biologists explain organisms’ behavior not only as having been programmed by genes and shaped by natural selection, but also as the result of an organism’s agency: the capacity to react to environmental changes in goal-driven ways. The use of such ‘agential explanations’ reopens old questions about how justified it is to ascribe agency to entities like bacteria or plants that obviously lack rationality and even a nervous system. Is organismic agency genuinely ‘real’ or is it just a useful fiction? In (...) this paper we focus on two questions: whether agential explanations are to be interpreted ontically, and whether they can be reduced to non-agential explanations (thereby dispensing with agency). The Kantian approach we identify interprets agential explanations non-ontically, yet holds agency to be indispensable. Attributing agency to organisms is not to be taken literally in the way we attribute physical properties such as mass or acceleration, but nor is it a mere heuristic or predictive tool. Rather, it is an inevitable consequence of our own rational capacity: as long as we are rational agents ourselves, we cannot avoid seeing agency in organisms. (shrink)

The automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is rapidly (...) acquiring the status of a de facto standard in the field of gene and gene product annotations, and whose methodology has been much intimated in attempts to develop controlled vocabularies for shared use in different domains of biology. The GO Consortium has recognized, however, that its controlled vocabulary as currently constituted is marked by several problematic features - features which are characteristic of much recent work in bioinformatics and which are destined to raise increasingly serious obstacles to the automatic integration of biomedical information in the future. Here, we survey some of these problematic features, focusing especially on issues of compositionality and syntactic regimentation. (shrink)

The usual interpretation of Republic 10 takes it as Socrates’ multilevel philosophical demonstration of the untruth and dangerousness of mimesis and its required excision from a well ordered polity. Such readings miss the play of the Platonic mimesis which has within it precisely ordered antistrophes which turn its oft remarked strophes perfectly around. First, this argument, famously concluding to the unreliability of image-makers for producing knowledge begins with two images—the mirror (596e) and the painter. I will show both undercut the (...) argument they introduce. Secondly, Socrates repeats the “three removes” argument three times. Each has its own object and philosophical axis. The “bed” argument (596a-598d) concerns the ontological status of images vis-à-vis human makers and the divine idea. The bit and bridle,” 601b-601d) emphasizes the epistemological status of image-making as beneath the human maker of bridles (having correct opinion) and the human user, who knows. This second takes away the ontological distinction which was the point of the first. Thus, any human being could be in any of the three positions—user, maker, imitator. This dance might bring one to doubt the conclusion that the imitator has “neither knowledge nor right opinion” (602a). Plato leads into his concluding psychological and moral argument (602c-605c) after a third variation of the 3 removes. This last gives us the image of the flute player (601d-602) as the one who knows and so can order the flute maker. We will conclude by considering what it is this flutist could know, and given that his art is itself a mimesis, who the imitator of this imitative artist could be. Thus attention to the differences among these examples opens a defense of the arts, which reverses many of the claims made against the arts within the ostensible “Platonic” argument. (shrink)

Beneath important ethical questions about the impacts of de-extinct species on ecosystems and the potential harms to individual organisms lies a more fundamental assumption; namely, that the thing being "de-extinct-ed" is indeed a member of previously existing species. This is the ontological assumption: that genetic make-up of the individual is both a necessary and sufficient condition for species membership. Questioning this ontological assumption poses an even more critical challenge for de-extinction. Genes a member of a species do not make. They (...) represent a mere necessary condition. Sufficiency entails a broad set of ecological connections, inside and out. In this commentary on Kasperbauer’s target article, I argue for the primacy of ontology in the ethical analysis of de-extinction. (shrink)

The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on all occasions of use. In the (...) naming of genes, proteins, and other molecular structures, considerable efforts are under way to reduce the effects of the different naming conventions which have been spawned by different groups of researchers. Electronic patient records, too, increasingly involve the use of standardized terminologies, and tremendous efforts are currently being devoted to the creation of terminology resources that can meet the needs of a future era of personalized medicine, in which genomic and clinical data can be aligned in such a way that the corresponding information systems become interoperable. (shrink)

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

The Unified Medical Language System and the Gene Ontology are among the most widely used terminology resources in the biomedical domain. However, when we evaluate them in the light of simple principles for wellconstructed ontologies we find a number of characteristic inadequacies. Employing the theory of granular partitions, a new approach to the understanding of ontologies and of the relationships ontologies bear to instances in reality, we provide an application of this theory in relation to an example drawn (...) from the context of the pathophysiology of hypertension. This exercise is designed to demonstrate how, by taking ontological principles into account we can create more realistic biomedical ontologies which will also bring advantages in terms of efficiency and robustness of associated software applications. (shrink)

What has been called the new mechanistic philosophy conceives of mechanisms as the main providers of biological explanation. We draw on the characterization of the p53 gene in molecular oncology, to show that explaining a biological phenomenon implies instead a dynamic interaction between the mechanistic level—rendered at the appropriate degree of ontological resolution—and far more general explanatory tools that perform a fundamental epistemic role in the provision of biological explanations. We call such tools “explanatory frameworks”. They are called frameworks (...) to stress their higher level of generality with respect to bare mechanisms; on the other hand, they are called explanatory because, as we show in this paper, their importance in explaining biological phenomena is not secondary with respect to mechanisms. We illustrate how explanatory frameworks establish selective and local criteria of causal relevance that drive the search for, characterisation and usage of biological mechanisms. Furthermore, we show that explanatory frameworks allow for changes of scientific perspective on the causal relevance of mechanisms going beyond the account provided by the new mechanistic philosophy. (shrink)

Where humans can manipulate and integrate the information they receive in subtle and ever-changing ways from context to context, computers need structured and context-free background information of a sort which ontologies can help to provide. A domain ontology captures the stable, highly general and commonly accepted core knowledge for an application domain. The domain at issue here is that of the life sciences, in particular molecular biology and bioinformatics. Contemporary life science research includes components drawn from physics, chemistry, mathematics, (...) medicine and many other areas, and all of these dimensions, as well as fundamental philosophical issues, must be taken into account in the construction of a domain ontology. Here we describe the basic features of domain ontologies in the life sciences and show how they can be used. (shrink)

It took a long time for humanity to know about biogenetics. And yet its role as a determinant in the living system was not proven until the twentieth century when DNA was discovered. Similarly, it took a long time for humanity to know about culture and civilization. And yet until now there is neither definite standards for differentiating them nor a definition that is commonly acceptable. By taking an evolutionary pluralism as ontology framework and the transdisciplinary research method of (...) the systems science, we have in the new social system model discovered the central rules that govern the social?cultural heredity: Culture?Production?Civilization. The relationship between culture and civilization is exactly that of genotype and phenotype. Culture is the S-cDNA within the social system while civilization is the social phenotype. Culture is a determinant that ultimately determines the existence, stagnation, change, and evolution of the social system. (shrink)

The Gene Ontology is an important tool for the representation and processing of information about gene products and functions. It provides controlled vocabularies for the designations of cellular components, molecular functions, and biological processes used in the annotation of genes and gene products. These constitute three separate ontologies, of cellular components), molecular functions and biological processes, respectively. The question we address here is: how are the terms in these three separate ontologies related to each other? We (...) use statistical methods and formal ontological principles as a first step towards finding answers to this question. (shrink)

Definitions of the term gene typically superimpose molecular genetics onto Mendelism. What emerges are persistent attempts to regard the gene as a unit of structure and/or function, language that creates multiple meanings for the term and fails to acknowledge the diversity of gene architecture. I argue that coherence at the molecular level requires abandonment of the classical unit concept and recognition that a gene is constructed from an assemblage of domains. Hence, a domain set (1) conforms (...) more closely to empirical evidence for genetic organization of DNA regions capable of transcription and (2) has ontological properties lacking in the traditional unit definition. (shrink)

This article examines how minimal genome research mobilizes philosophical concepts such as minimality and essentiality. Following a historical approach the article aims to uncover what function this terminology plays and which problems are raised by them. Specifically, four historical moments are examined, linked to the work of Harold J. Morowitz, Mitsuhiro Itaya, Eugene Koonin and Arcady Mushegian, and J. Craig Venter. What this survey shows is a historical shift away from historical questions about life or descriptive questions about specific organisms (...) towards questions that explore biological possibilities: what are possible forms of minimal genomes, regardless of whether they exist in nature? Moreover, it highlights a fundamental ambiguity at work in minimal genome research between a universality claim and a standardization claim: does a minimal genome refer to the minimal gene set for any organism whatsoever? Or does it refer rather to a gene set that will provide stable, robust and predictable behaviour, suited for biotechnological applications? Two diagnoses are proposed for this ambiguity: a philosophical diagnosis of how minimal genome research either misunderstands the ontology of biological entities or philosophically misarticulates scientific practice. Secondly, a historical diagnosis that suggests that this ambiguity is part of a broader shift towards technoscience. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and (...) developmental stages across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

The organism is neither a discovery like the circulation of the blood or the glycogenic function of the liver, nor a particular biological theory like epigenesis or preformationism. It is rather a concept which plays a series of roles, sometimes masked, often normative, throughout the history of biology. Indeed, it has often been presented as a key-concept in life science and its ‘theorization’, but conversely has also been the target of influential rejections: as just an instrument of transmission for the (...) selfish gene, but also, historiographically, as part of an outdated ‘vitalism’. Indeed, the organism, perhaps because it is experientially closer to the ‘body’ than to the ‘molecule’, is often the object of quasi-affective theoretical investments presenting it as essential, as the pivot of a science or a particular approach to nature, while other approaches reject or attack it with equal force, assimilating it to a mysterious ‘vitalist’ ontology of extra-causal forces, or other pseudo-scientific doctrines. I do not seek to adjudicate between these debates, either regarding scientific validity or historical coherence; nor do I return to the well-studied issue of the organism-mechanism tension in biology. Recent scholarship has begun to discuss the emergence and transformation of the organism concept, but has not emphasized the way the latter is a shifting, ‘go-between’ concept – invoked as ‘natural’ by some thinkers to justify their metaphysics, but then presented as value-laden by others, over and against the natural world. The organism as go-between concept is also a hybrid, a boundary concept or a limit case, which continues to function in different contexts – as a heuristic, an explanatory challenge, a model of order, of regulation, etc. – despite having frequently been pronounced irrelevant and reduced to molecules or genes. Yet this perpetuation is far removed from any ‘metaphysics of organism’, or organismic biology. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all (...) plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

Section 10.1 introduces generalized evolution (GE) theory. Here, the three core principles of the theory of evolution − reproduction, variation and selection − are detached from their biological basis, abstracted and extended to other domains, in particular to the domain of cultural evolution (CE). Section 10.2 investigates the ontological foundations of GE and CE theory. They consist in entities and structures that must be realized to get the three modules of evolution running. These entities include self-reproducing systems with variation, and (...) populations of such systems in environments with limited resources. A difference between the reproductive units of BE (biological evolution) and CE consists in the fact that genes act as constructors of evolutionary systems, while memes play the role of modifiers. Section 10.3 is devoted to the abductive justification of GE and CE theory that proceeds in three steps: First, CE theory is justified; second, based on the first step GE theory is abductively justified as the common core of BE and CE; and thirdly, the fruitfulness of GE theory is demonstrated by its applicability to further domains. (shrink)

Scientific conflicts often stem from differences in the conceptual framework through which scientists view and understand their own field. In this chapter, I analyze the ontological and methodological assumptions of three traditions in evolutionary biology, namely, Ernst Mayr’s population thinking, the gene-centered view of the Modern Syn thesis, and the Extended Evolutionary Synthesis. Each of these frameworks presupposes a different account of "evolutionary causes," and this discrepancy prevents mutual understanding and objective evaluation in the recent contention surrounding the EES. (...) From this perspective, the chapter characterizes the EES research program as an attempt to introduce causal structures beyond genes as additional units of evolution, and compares its research methodology and objectives with those of the traditional MS framework. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological (...) reality through both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

The organism is neither a discovery like the circulation of the blood or the glycogenic function of the liver, nor a particular biological theory like epigenesis or preformationism. It is rather a concept which plays a series of roles – sometimes overt, sometimes masked – throughout the history of biology, and frequently in very normative ways, also shifting between the biological and the social. Indeed, it has often been presented as a key-concept in life science and the ‘theorization’ of Life, (...) but conversely has also been the target of influential rejections: as just an instrument of transmission for the selfish gene, but also, historiographically, as part of an outdated ‘vitalism’. Indeed, the organism, perhaps because it is experientially closer to the ‘body’ than to the ‘molecule’, is often the object of quasi-affective theoretical investments presenting it as essential, sometimes even as the pivot of a science or a particular approach to nature, while other approaches reject or attack it with equal force, assimilating it to a mysterious ‘vitalist’ ontology of extra-causal forces, or other pseudo-scientific doctrines. This paper does not seek to adjudicate between these debates, either in terms of scientific validity or historical coherence; nor does it return to the well-studied issue of the organism-mechanism tension in biology. Recent scholarship has begun to focus on the emergence and transformation of the concept of organism, but has not emphasized so much the way in which organism is a shifting, ‘go-between’ concept – invoked as ‘natural’ by some thinkers to justify their metaphysics, but then presented as value-laden by others, over and against the natural world. The organism as go-between concept is also a hybrid, a boundary concept or an epistemic limit case, all of which partly overlap with the idea of ‘nomadic concepts’. Thereby the concept of organism continues to function in different contexts – as a heuristic, an explanatory challenge, a model of order, of regulation, etc. – despite having frequently been pronounced irrelevant and reduced to molecules or genes. Yet this perpetuation is far removed from any ‘metaphysics of organism’, or organismic biology. (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)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. (...) Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

In order to tackle the question posed by the title – notoriously answered in the positive, among others, by Heisenberg, Margenau, Popper and Redhead – I first discuss some attempts at distinguishing dispositional from non-dispositional properties, and then relate the distinction to the formalism of quantum mechanics. Since any answer to the question titling the paper must be interpretation-dependent, I review some of the main interpretations of quantum mechanics in order to argue that the ontology of theories regarding “wave (...) collapse” as a genuine physical process could be interpreted as being irreducibly dispositional. In non-collapse interpretations, on the contrary, the appeal to dispositions is simply a way to reformulate the predictive content of the algorithm of the theory in a fancier metaphysical language. (shrink)

What are words? What makes two token words tokens of the same word-type? Are words abstract entities, or are they (merely) collections of tokens? The ontology of words tries to provide answers to these, and related questions. This article provides an overview of some of the most prominent views proposed in the literature, with a particular focus on the debate between type-realist, nominalist, and eliminativist ontologies of words.

In previous work on biomedical ontologies we showed how the provision of formal definitions for relations such as is_a and part_of can support new types of auto-mated reasoning about biomedical phenomena. We here extend this approach to the transformation_of characteristic of pathologies.

The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the (...) model organism communities to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

In this paper, rather than focusing on genes as an organising concept around which historical considerations of theory and practice in genetics are elucidated, we place genetic markers at the heart of our analysis. This reflects their central role in the subject of our account, livestock genetics concerning the domesticated pig, Sus scrofa. We define a genetic marker as a element existing in different forms in the genome, that can be identified and mapped using a variety of quantitative, classical and (...) molecular genetic techniques. The conjugation of pig genome researchers around the common object of the marker from the early-1990s allowed the distinctive theories and approaches of quantitative and molecular genetics concerning the size and distribution of gene effects to align in projects to populate genome maps. Critical to this was the nature of markers as ontologically inert, internally heterogeneous and relational. Though genes as an organising and categorising principle remained important, the particular concatenation of limitations, opportunities, and intended research goals of the pig genetics community, meant that a progressively stronger focus on the identification and mapping of markers rather than genes per se became a hallmark of the community. We therefore detail a different way of doing genetics to more gene-centred accounts. By doing so, we reveal the presence of practices, concepts and communities that would otherwise be hidden. (shrink)

Vitalism was long viewed as the most grotesque view in biological theory: appeals to a mysterious life-force, Romantic insistence on the autonomy of life, or worse, a metaphysics of an entirely living universe. In the early twentieth century, attempts were made to present a revised, lighter version that was not weighted down by revisionary metaphysics: " organicism ". And philosophers since the Vienna Circle (Schlick, Frank and later Nagel) criticized Driesch and Bergson's " neovitalism " as a too-strong ontological commitment (...) to the existence of certain entities or " forces ", over and above the system of causal relations studied by mechanistic science, rejecting the weaker form, organicism, as well. But there has been some significant scholarly " push-back " against this orthodox attitude, notably pointing to the 18th-century Montpellier vitalists to show that there are different historical forms of vitalism, including how they relate to mainstream scientific practice (Wolfe and Normandin, eds. 2013). Additionally, some trends in recent biology that run counter to genetic reductionism and the informational model of the gene present themselves as organicist (Gilbert and Sarkar 2000, Moreno and Mossio 2015). Here, we examine some cases of vitalism in the twentieth century and today, not just as a historical form but as a significant metaphysical and scientific model. We argue for vitalism's conceptual originality without either reducing it to mainstream models of science or presenting it as an alternate model of science, by focusing on historical forms of vitalism, logical empiricist critiques thereof and the impact of synthetic biology on current (re-)theorizing of vitalism. (shrink)

Social groups—like teams, committees, gender groups, and racial groups—play a central role in our lives and in philosophical inquiry. Here I develop and motivate a structuralist ontology of social groups centered on social structures (i.e., networks of relations that are constitutively dependent on social factors). The view delivers a picture that encompasses a diverse range of social groups, while maintaining important metaphysical and normative distinctions between groups of different kinds. It also meets the constraint that not every arbitrary collection (...) of people is a social group. In addition, the framework provides resources for developing a broader structuralist view in social ontology. (shrink)

The paper points out that the modern formulation of Bohm’s quantum theory known as Bohmian mechanics is committed only to particles’ positions and a law of motion. We explain how this view can avoid the open questions that the traditional view faces according to which Bohm’s theory is committed to a wave-function that is a physical entity over and above the particles, although it is defined on configuration space instead of three-dimensional space. We then enquire into the status of the (...) law of motion, elaborating on how the main philosophical options to ground a law of motion, namely Humeanism and dispositionalism, can be applied to Bohmian mechanics. In conclusion, we sketch out how these options apply to primitive ontology approaches to quantum mechanics in general. (shrink)

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...) insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (shrink)

Denis Noble suggests that biologists who created the Modern Synthesis were taken in by conceptual traps and illusions hidden in the language they used. Rather than blame language itself, my response counters that all writers are responsible for careful attention to the implications of the metaphors they use, and that Richard Dawkins deliberately chose “the selfish gene.” Noble’s concept of biological relativity restores Darwin’s fuller and more nuanced definition of natural selection and shows how it also accounts for Lamarck’s (...) assertion that acquired characteristics can be inherited. Biological relativity is supported by Maurice Merleau- Ponty’s chiasmic ontology. (shrink)