Biological Information

The relations between life and cogntion have been addressed through different perspectives [Stewart 1996, Boden 2001, Bourgine and Stewart 2004, van Duijn & all 2006, Di Paolo 2009]. We would like here to address that subject by relating life to cognition through a process of meaning generation. Life emerged on earth as a far from thermodynamic equilibrium performance that had to maintain herself. Life is charactertized by a ‘stay alive’ constraint that has to be satisfied (such constraint can be included (...) in the constraint of being able to maintain far from equilibrium thermodynamic conditions [Bickhard 2011]). The local ‘stay alive‘ constraint has to be satisfied in an environment containing elements potentially supportive or harmfull. A key activity for the living entity is to characterize these elements in terms of meaningfulness relatively to the ‘stay alive’ constraint. This process can be modeled with an existing tool where a system submitted to an internal constraint generates meaningful information characterizing elements of the environment: the Meaning Generator System (MGS) [Menant, 2003, 2014 a]. In a few words: when a system submitted to an internal constraint receives from the environment an information that has a connection with the constraint it generates a meaning usable for the implementation of an action satisfying the constraint.The generated meaning is the connection existing between the received information and the constraint. The MGS models this process and interfaces to the action implementation for constraint satisfaction The meaning is generated by and for the system. The MGS grounds meaning generation in constraint satisfaction and links the living entity to her environment in a relational process. A simple example is with a paramecium close to a drop of acid. The paramecium which is submitted to a ‘stay alive’ constraint will move away from the acid area. The received information ‘presence of acid’ generates the meaning ‘acid not compatible with the ‘stay alive’ constraint‘ which triggers the moving away action (that example is close to Varela’s bacteria swimming up a sugar gradient. What the MGS brings in addition is a modeling of the significance of the chemical gradient for the organism). The action implemented to satisfy the constraint modifies the environment and the received information, establishing an interactive process linking the living entity to her environment. During its evolution animal life has elaborated new constraints (like ‘live group life’) and new functions enriching meaning generation and action scenarios. As a result the build up of meaningful representations has improved the constraint satisfaction processes of animals, embedding them in their environments in relational and interactive terms [Menant, 2011]. Cognition can be defined by proposing that ‘a system is cognitive if and only if sensory inputs serve to trigger actions in a specific way, so as to satisfy a viability constraint’ [Bourgine, Stewart 2004]. Cognition can also be considered as exemplifying a ‘vital criterion of responsiveness’ [Boden, 2001 ]. Consequently the MGS can be positioned as an elementary and generic version of animal cognition. For animal life, meaning generation for internal constraint satisfaction links life and cognition in a relational and interactive process. Cognition for human life is more complex as new performances have to be taken into account like self-consciousness and free-will. Meaning generation at human level is a challenging subject as human constraints are not clearly understood [Menant, 2011]. Many research activities are in process looking for some understanding of human mind [Philpapers]. One area of investigation is an evolutionary approach to self-consciousness using meaning generation where anxiety limitation comes up as a generic human constraint [Menant, 2014 b]. Assuming that we can have clear enough an understanding of some human constraints, we can look at the MGS for partly extending to humans the link between life and cognition that has been established for animals. So overall, we can consider that the MGS approach makes available an evolutionary link between life and cognition for animals, and partly for humans. A characteristic of the proposed system approach to meaning generation is the possibility to use it for any type of agent, be it organic (with intrinsic constraints ) or artificial (with derived constraints). Such characterization of agents through meaning generation can be used to discriminate artificial itelligence from human intelligence (see the MGS usage to support Searle’s chinese room argument [Menant, 2013]). On a more general basis, the proposed system approach can positions the MGS as a simple model for an internal source of normativity. It’s usage as a simple building block allows a bottom-up modeling for normativity in the sensorimotor approach. The ‘stay alive’ constraint could also be taken as a starting point for an evolutionary grounding of sensorimotor norms ‘in the biological normativity of the agent as a whole’ [Di Paolo & all 2014]. The proposed presentation will develop the points summarized here above and position them relatively to the autopoietic and enactive approaches. Several possible continuations will also be highlighted. (shrink)

There is an increasing agreement in the cognitive sciences community that our sensations are closely related to our actions. Our actions impact our sensations from the environment and the knowledge we have of it. Cognition is grounded in sensori-motor coordination. In the perspective of implementing such a performance in artificial systems, there is a need for a model of sensori-motor coordination. We propose here such a model as based on the generation of meaningful information by a system submitted to a (...) constraint [1]. Systems and agents have constraints to satisfy which are related to their nature (stay alive for an organism, avoid obstacle for a robot, …). We propose here to use an existing meaning generation process where a system submitted to a constraint generates a meaningful information (a meaning) when it receives an information that has a connection with the constraint [2]. The generated meaning is precisely the connection existing between the received information and the constraint of the system. The generated meaning is used to trigger an action that will satisfy the constraint. The generated meaning links the system to its environment. A Meaning Generator System (MGS) has been introduced as a building block for higher level systems (agents). The MGS allows to link sensation and action through the satisfaction of the constraint of the system/agent. We use the MGS in a model which is based on constraint satisfaction for sensori-motor coordination in agents, be they organic or artificial. The meaning is generated by and for the agent that hosts the MGS. Such approach makes possible an addressing of the concept of autonomy through the intrinsic or artificial nature of the constraint to be satisfied (organisms with intrinsic constraints/autonomy, artificial systems with artificial constraints/autonomy). The systemic nature of the MGS also allows to position the groundings of the generated meaning as being in or out of the MGS, and correspondingly identify the constructivist and objectivist components of the generated meaning. The approach presented here makes available a sensori-motor coordination by meaning generation through constraint satisfaction with groundings of the generated meaning. (shrink)

Humans are cognitive entities. Our ongoing interactions with the environment are threaded with creations and usages of meaningful information. Animal life is also populated with meaningful information related to survival constraints. Information managed by artificial agents can also be considered as having meanings, as derived from the designer. Such perspective brings us to propose an evolutionary approach to cognition based on meaningful information management. We use a systemic tool, the Meaning Generator System (MGS), and apply it consecutively to animals, humans (...) and artificial agents [1, 2]. The MGS receives information from its environment and compares it with its constraint. The generated meaning is the connection existing between the received information and the constraint. It triggers an action aimed at satisfying the constraint. The action modifies the environment and the generated meaning. Meaning generation links agents to their environments. The MGS is a system: a set of elements linked by a set of relations. Any system submitted to a constraint and capable of receiving information can lead to a MGS. Animals, humans and robots are agents containing MGSs dealing with different constraints. Similar MGSs carrying different constraints will generate different meanings. Cognition is system dependent. Contrary to approaches on meaning generation based on psychology or linguistics, the MGS approach is not based on human mind. We want to avoid the circularity of taking human mind as a starting point. Free will and self-consciousness participate to the management of human meanings. They do not exist for animals or robots. Staying alive is a constraint that we share with animals. Robots ignore that constraint. We first use the MGS for animals with “stay alive” and “group life” constraints. The analysis of meaning and cognition in animals is however limited by our un-complete understanding of the nature of life (the question of final causes). Extending the analysis of meaning generation and cognition to humans is complex and has some true limitations as the nature of human mind is a mystery for today science and philosophy. The natures of our feelings, free will or self-consciousness are unknown. Approaches to identify human constraints are however possible, where the MGS can highlight some openings [3, 4]. Modeling meaning management in artificial agents is rather straightforward with the MGS. We, the designers, know the agents and the constraints. The derived nature of constraints, meaning and cognition is however to be highlighted. We define a meaningful representation of an item for an agent as being the networks of meanings relative to the item for the agent, with the action scenarios involving the item. Such meaningful representations embed the agents in their environments and are far from the GOFAI type of representations. Cognition, meanings and representations exist by and for the agents. We finish by summarizing the points presented here and highlight possible continuations . [1] “Information and Meaning” [2] “Introduction to a systemic theory of meaning” [3] “Computation on Information, Meaning and Representations. An Evolutionary Approach” [4] “Proposal for a shared evolutionary nature of language and consciousness”. (shrink)

The presentation proposes to complement an existing development on meaning generation for animals, humans and artificial agents by looking at what could have existed at pre-biotic times and what could be a post-human meaning generation. The core of the approach is based on an existing model for meaning generation: the Meaning Generator System (MGS). The MGS is part of an agent submitted to an internal constraint. The MGS generates a meaning when it receives an information that has a connection with (...) the constraint. The generated meaning is used by the agent to implement an action (physical, biological or mental) aimed at satisfying the constraint. The action can be in or out the agent. The purpose of the presentation is to widen the MGS approach in order to reach a coverage for information, constraint and meaning from a pre-biotic level to a possible post-human one. We present the MGS for animals, humans and artificial agents with the corresponding constraints. We then look at what could have been a constraint at a pre-biotic far from thermodynamic equilibrium level. At the other end of the spectrum we look at a possible post-human status with an evolution of a ‘limit anxiety’ human constraint and also with AAs submitted to animal or human type constraints. Such approach links information science with physics, evolution, anthropology, semiotics and human mind. Continuations are proposed. (shrink)

Information and Meaning are present everywhere around us and within ourselves. Specific studies have been implemented in order to link information and meaning: - Semiotics - Phenomenology - Analytic Philosophy - Psychology No general coverage is available for the notion of meaning. We propose to complement this lack by a systemic approach to meaning generation.

Several authors have used the notion of causal specificity in order to defend non-parity about genetic causes (Waters 2007, Woodward 2010, Weber 2017, forthcoming). Non-parity in this context is the idea that DNA and some other biomolecules that are often described as information-bearers by biologists play a unique role in life processes, an idea that has been challenged by Developmental Systems Theory (e.g., Oyama 2000). Indeed, it has proven to be quite difficult to state clearly what the alleged special role (...) of genetic causes consists in. In this paper, I show that the set of biomolecules that are normally considered to be information-bearers (DNA, mRNA) can be shown to be the most specific causes of protein primary structure, provided that causal specificity is measured over a relevant space of biological possibilities, disregarding physical as well as logically possible states of the causal variables. (shrink)

In spite of being ubiquitous in life sciences, the concept of information is harshly criticized. Uses of the concept other than those derived from Shannon's theory are denounced as pernicious metaphors. We perform a computational experiment to explore whether Shannon's information is adequate to describe the uses of said concept in commonplace scientific practice. Our results show that semantic sequences do not have unique complexity values different from the value of meaningless sequences. This result suggests that quantitative theoretical frameworks do (...) not account fully for the complex phenomenon that the term “information” refers to. We propose a restructuring of the concept into two related, but independent notions, and conclude that a complete theory of biological information must account completely not only for both notions, but also for the relationship between them. (shrink)

Forty-two years ago, Capra published “The Tao of Physics” (Capra, 1975). In this book (page 17) he writes: “The exploration of the atomic and subatomic world in the twentieth century has …. necessitated a radical revision of many of our basic concepts” and that, unlike ‘classical’ physics, the sub-atomic and quantum “modern physics” shows resonances with Eastern thoughts and “leads us to a view of the world which is very similar to the views held by mystics of all ages and (...) traditions.“ This article stresses an analogous situation in biology with respect to a new theoretical approach for studying living systems, Integral Biomathics (IB), which also exhibits some resonances with Eastern thought. Stepping on earlier research in cybernetics1 and theoretical biology,2 IB has been developed since 2011 by over 100 scientists from a number of disciplines who have been exploring a substantial set of theoretical frameworks. From that effort, the need for a robust core model utilizing advanced mathematics and computation adequate for understanding the behavior of organisms as dynamic wholes was identified. At this end, the authors of this article have proposed WLIMES (Ehresmann and Simeonov, 2012), a formal theory for modeling living systems integrating both the Memory Evolutive Systems (Ehresmann and Vanbremeersch, 2007) and the Wandering Logic Intelligence (Simeonov, 2002b). Its principles will be recalled here with respect to their resonances to Eastern thought. (shrink)

We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use of (...) the term 'concept' in ontology development, influenced SNOMED CT and other medical terminologies. Against this background we then show how the Foundational Model of Anatomy, the Gene Ontology, Basic Formal Ontology and other OBO Foundry ontologies came into existence and discuss their role in the development of contemporary biomedical informatics. (shrink)

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we (...) present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research. (shrink)

The primary focus of this project is the silent and subvocal speech-recognition interface unveiled in 2018 as an ambulatory device wearable on the neck that detects a myoelectrical signature by electrodes worn on the surface of the face, throat, and neck. These emerge from an alleged “intending to speak” by the wearer silently-saying-something-to-oneself. This inner voice is believed to occur while one reads in silence or mentally talks to oneself. The artifice does not require spoken sounds, opening the mouth, or (...) any explicit or external movement of the lips. The essay then considers such subvocal “speech” as a mode of writing or saying and the interior of the mouth or oral cavity as its writing surface. It briefly revisits discussions of telepathy to recontextualize Heidegger’s warning against enframing language exclusively within calculative technics and physiology, which he suggests is detrimental to Mundarten (mouth-modes of regional dialects). It closes in reconsideration of Husserl’s phenomenology of language and meaning in Ideas as it might apply to subvocal speech-recognition interfaces. It suggests ways by which the electrophysiology that the device detects and deciphers (as an alleged intention of a presumed natural language unspoken vocally or aloud) might supplement Husserl’s insinuation of the Leiblichkeit of language through a self-stamping extraction of an extension of meaning. (shrink)

The free-energy principle states that all systems that minimize their free energy resist a tendency to physical disintegration. Originally proposed to account for perception, learning, and action, the free-energy principle has been applied to the evolution, development, morphology, anatomy and function of the brain, and has been called a postulate, an unfalsifiable principle, a natural law, and an imperative. While it might afford a theoretical foundation for understanding the relationship between environment, life, and mind, its epistemic status is unclear. Also (...) unclear is how the free-energy principle relates to prominent theoretical approaches to life science phenomena, such as organicism and mechanism. This paper clarifies both issues, and identifies limits and prospects for the free-energy principle as a first principle in the life sciences. (shrink)

Rapidly, accurately and easily interpreting generated data is of fundamental concern. Ontologies – structured controlled vocabularies – support interoperability and prevent the development of data silos which undermine interoperability. The Open Biological and Biomedical Ontologies (OBO) Foundry serves to ensure ontologies remain interoperable through adherence by its members to core ontology design principles. For example, the Infectious Disease Ontology (IDO) Core includes terminological content common to investigations of all infectious diseases. Ontologies covering more specific infectious diseases in turn extend from (...) IDOCore, such as the Coronavirus Infectious Disease Ontology (CIDO). The growing list of virus-specific IDO extensions has motivated construction of a reference ontology covering content common to viral infectious disease investigations: the Virus Infectious Disease Ontology (VIDO). Additionally the present pandemic has motivated construction of a more specific extension of CIDO covering terminological contents specific to the pandemic: the COVID-19 Infectious Disease Ontology (IDO-COVID-19). We report here the development of VIDO and IDO-COVID-19. More specifically we examine newly minted terms for each ontology, showcase reuse of terms from existing OBO ontologies, motivate choicepoints for ontological decisions based on research from relevant life sciences, apply ontology terms to explicate viral pathogenesis, and discuss the annotating power of virus ontologies for use in machine-learning projects. (shrink)

Starting from a philosophical perspective, which states that the living structures are actually a combination between matter and information, this article presents the results on an analysis of the bipolar information-matter structure of the human organism, distinguishing three fundamental circuits for its survival, which demonstrates and supports this statement, as a base for further development of the informational model of consciousness to a general informational model of the human organism. For this, it was examined the Informational System of the Human (...) Body and its components from the perspective of the physics/information/neurosciences concepts, showing specific functions of each of them, highlighting the correspondence of these centers with brain support areas and with their projections in consciousness, which are: Center of Acquisition and Storing of Information (CASI) reflected in consciousness as memory, Center of Decision and Command (CDC) (decision), Info-Emotional Center (IES) (emotions), Maintenance Informational System (MIS) (personal status), Genetic Transmission System (GTS) (associativity/genetic transmission) and Info Genetic Generator (IGG) related by the body development and inherited behaviors. The Info Connection (IC), detected in consciousness as trust and confidence can explain the Near-Death Experiences (NDEs) and associated phenomena. This connection is antientropic and informational, because from the multitude of uncertain possibilities is selected a certain one, helping/supporting the survival and life. The human body appears therefore as a bipolar structure, connected to two poles: information and matter. It is argued that the survival, which is the main objective of the organism, is complied in three main ways, by means of: (i) the reactive operation for adaptation by attitude; (ii) the info-genetic integration of information by epigenetic processes and genetic transmission of information for species survival, both circuits (i) and (ii) being associated to the information pole; (iii) maintenance of the material body (defined as informed matter) and its functions, associated to the matter pole of the organism. It results therefore that the informational system of the human body is supported by seven informational circuits formed by the neuro-connections between the specific zones of the brain corresponding to the informational subsystems, the cognitive centers, the sensors, transducers and execution (motor/mobile) elements. The fundamental informational circuits assuring the survival are the reactive circuit, expressible by attitude, the epigenetic/genetic circuit, absorbing and codifying information to be transmitted to the next generations, and the metabolic circuit, connected to matter (matter pole). The presented analysis allows to extend the informational modeling of consciousness to an Informational Model of Consciousness and Organism, fully describing the composition/functions of the organism in terms of information/matter and neurosciences concept. (shrink)

The concept of information and its relation to biosemiotics is a major area of contention among biosemioticians. Biosemioticians influenced by von Uexküll, Sebeok, Bateson and Peirce are critical of the way the concept as developed in information science has been applied to biology, while others believe that for biosemiotics to gain acceptance it will have to embrace information science and distance biosemiotics from Peirce’s philosophical work. Here I will defend the influence of Peirce on biosemiotics, arguing that information science and (...) biosemiotics as these were originally formulated are radically opposed research traditions. Failure to appreciate this will undermine the challenge of biosemiotics and other anti-reductionist traditions to mainstream science with its reductionist ambition to explain everything through physics. However, for this challenge to be successful, it will be necessary to respond to criticisms of Peircian ideas, jettisoning ideas that are no longer defensible and integrating ideas allied to his anti-reductionist agenda. Here I will argue that the natural philosophy of Gilbert Simondon, offering a searching critique of the application of the new concept of information and cybernetics to the life and human sciences, provides the means to defend and advance Peirce’s core ideas and thereby defend post-reductionist biosemiotics. (shrink)

We undeniably live in an information age—as, indeed, did those who lived before us. After all, as the cultural historian Robert Darnton pointed out: ‘every age was an age of information, each in its own way’ (Darnton 2000: 1). Darnton was referring to the news media, but his insight surely also applies to the sciences. The practices of acquiring, storing, labeling, organizing, retrieving, mobilizing, and integrating data about the natural world has always been an enabling aspect of scientific work. Natural (...) history and its descendant discipline of biological taxonomy are prime examples of sciences dedicated to creating and managing systems of ordering data. In some sense, the idea of biological taxonomy as an information science is commonplace. Perhaps it is because of its self-evidence that the information science perspective on taxonomy has not been a major theme in the history and philosophy of science. The botanist Vernon Heywood once pointed out that historians of biology, in their ‘preoccupation with the development of the sciences of botany and zoology… [have] diverted attention from the role of taxonomy as an information science’ (Heywood 1985: 11). More specifically, he argued that historians had failed to appreciate how principles and practices that can be traced to Linnaeus constituted ‘a change in the nature of taxonomy from a local or limited folk communication system and later a codified folk taxonomy to a formal system of information science [that] marked a watershed in the history of biology’ (ibid.). A similar observation could be made about twentieth-century philosophy of biology, which mostly skipped over practical and epistemic questions about information management in taxonomy. The taxonomic themes that featured in the emerging philosophy of biology literature in the second half of the twentieth century were predominantly metaphysical in orientation. This is illustrated by what has become known as the ‘essentialism story’: an account about the essentialist nature of pre- Darwinian taxonomy that used to be accepted by many historians and philosophers, and which stimulated efforts to document and interpret shifts in the metaphysical understanding of species and (natural) classification (Richards 2010; Winsor 2003; Wilkins 2009). Although contemporary debates in the philosophy of taxonomy have moved on, much discussion continues to focus on conceptual and metaphysical issues surrounding the nature of species and the principles of classification. Discussions centring on whether species are individuals, classes, or kinds have sprung up as predictably as perennials. Raucous debates have arisen even with the aim of accommodating the diversity of views: is monism, pluralism, or eliminativism about the species category the best position to take? In addition to these, our disciplines continue to interrogate what is the nature of these different approaches to classification: are they representational or inferential roles of different approaches to classification (evolutionary taxonomy, phenetics, phylogenetic systematics)? While there is still much to learn from these discussions—in which we both actively participate—our aim with this topical collection has been to seek different entrypoints and address underexposed themes in the history and philosophy of taxonomy. We believe that approaching taxonomy as an information science prompts new questions and can open up new philosophical vistas worth exploring. A twenty-first century information science turn in the history and philosophy of taxonomy is already underway. In scientific practice and in daily life it is hard to escape the imaginaries of Big Data and the constant threats of being ‘flooded with data’. In the life sciences, these developments are often associated with the socalled bioinformatics crisis that can hopefully be contained by a new, interdisciplinary breed of bioinformaticians. These new concepts, narratives, and developments surrounding the centrality of data and information systems in the biological and biomedical sciences have raised important philosophical questions about their challenges and implications. But historical perspectives are just as necessary to judge what makes our information age different from those that preceded us. Indeed, as the British zoologist Charles Godfray has often pointed out, the piles of data that are being generated in contemporary systematic biology have led to a second bioinformatics crisis, the first being the one that confronted Linnaeus in the mid-18th century (Godfray 2007). Although our aim is to clear a path for new discussions of taxonomy from an information science-informed point of view, we continue where others in the history, philosophy, and sociology of science have already trod. We believe that an appreciation of biological taxonomy as an information science raises many questions about the philosophical, theoretical, material, and practical aspects of the use and revision of biological nomenclatures in different local and global communities of scientists and citizen scientists. In particular, conceiving of taxonomy as an information science directs attention to the temporalities of managing an accumulating data about classified entities that are themselves subject to revision, to the means by which revision is accomplished, and to the semantic, material, and collaborative contexts that mediate the execution of revisions. (shrink)

Epidemiological crisis during recrudescence of pandemic like COVID-19 may stir fear and anxiety leading to prejudices against people and communities, social isolation and stigma. Such behavioral change may wind up into increased hostility, chaos and unnecessary social disruptions. A qualitative exploratory approach was utilized to conduct an extensive review of secondary literature. The case-studies were gathered from academic literature like articles, opinions and perspective pieces published in journals and in grey literature like publications in humanitarian agencies and media reports. Grey (...) literature was included in the scope as the COVID-19 situation is still evolving. I discuss some of the mechanisms of stigmatization and how social connectedness and empathetic understandings can be a way out of negative stereotyping and discrimination met out to the sufferer of the communicable diseases as COVID-19. Empathetic understanding paves a way to approach a problem from the perspective of ‘we’ not limiting one only to ‘I’. The moment when we make an approach from ‘I’ to ‘We’ actually then we embark on a journey of illness to wellness. Keywords: COVID-19, pandemic, stigma, discrimination, mental health, empathy, India, Face-to-face communication, social distancing, suicide. (shrink)

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established (...) ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (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)

Immunology researchers are beginning to explore the possibilities of reproducibility, reuse and secondary analyses of immunology data. Open-access datasets are being applied in the validation of the methods used in the original studies, leveraging studies for meta-analysis, or generating new hypotheses. To promote these goals, the ImmPort data repository was created for the broader research community to explore the wide spectrum of clinical and basic research data and associated findings. The ImmPort ecosystem consists of four components–Private Data, Shared Data, Data (...) Analysis, and Resources—for data archiving, dissemination, analyses, and reuse. To date, more than 300 studies have been made freely available through the ImmPort Shared Data portal , which allows research data to be repurposed to accelerate the translation of new insights into discoveries. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

Description courte (Électre, 2019) : Une étude d'un des principaux axes de réflexion du philosophe des sciences et de la nature Raymond Ruyer (1902-1987). À la lumière des découvertes de l'embryogenèse et en s'appuyant par ailleurs sur la théorie de l'information, il proposa une interprétation des concepts unificateurs de la cybernétique mécaniste. -/- Short Descriptor (Electre 2019): A study of one of the main axes of reflection of the French philosopher of science and of nature Raymond Ruyer (1902-1987). Relying on (...) the discoveries about embryogenesis, and also with the use of information theory, Ruyer proposed an interpretation of the main unifying concepts of mechanistic cybernetics. -/- Cet ouvrage propose une étude fouillée d'un des principaux axes de réflexion du philosophe des sciences et de la nature français Raymond Ruyer (1902–1987) : la cybernétique. Après avoir proposé une philosophie structuraliste, Ruyer la modifia à la lumière des découvertes de l'embryogenèse, puis il proposa une interprétation des concepts unificateurs de la cybernétique mécaniste. Réfléchissant sur cette dernière et sur la théorie de l'information, en particulier sur l'origine de l'information, il défendit que cette cybernétique n'était qu'une lecture inversée de la vraie cybernétique, qui nous donnerait de lire dans l'expérience même les traces du pouvoir morphogénétique, appréhendé comme un champ axiologique. Dans un texte résumant son propre parcours, Ruyer affirma finalement que la critique de la théorie de l'information « peut donner […] l'espoir d'aboutir à quelque chose comme une nouvelle théologie. » Les idées directrices de Ruyer sont tout particulièrement contextualisées ici à partir de la question du développement des formes en biologie, et de celles de la génétique, de la genèse stochastique de l'ordre, et de l'identification mentale ou physique de l'information. Il se termine en départageant ce qui est théologique et axiologique dans ce projet de métaphysique qui, bien que resté inachevé, n'en représente pas moins le plus impressionnant conçu en France au siècle dernier. – This book offers an in-depth study of one of the main axes in the reflection of French philosopher of science and nature Raymond Ruyer. In a text summarising his own development, Ruyer stated about the philosophical critique of information theory that it "is what can give the most long-lasting hope of getting to something like a new theology." After propounding a structuralist philosophy, and distinguishing between form and structure, to then modify it in the light of discoveries in embryogenesis, Ruyer offered a re-evaluation of the unifying concepts of mechanistic cybernetics. Thinking about it and about information theory, he defended the idea that this cybernetics was in reality an inverted reading of the real one, which would allow us to read in experience itself traces of the morphogenetic power, apprehended as the axiological field. On some transversal points, the development of forms in biology and genetics, the stochastic genesis of order, the identification of information with either psychological and mental, or physical reality, behaviour, and the access to meaning, this work exposes the main ideas of Ruyer while situating them in the context of the breadth of others' contributions. It ends by determining what is theological and axiological in this project for a metaphysics which, although unfinished, is nevertheless the most impressive effort done in France in the last century. – Available on i6doc dot com (ISBN 978-2-930517-56-8 ; pdf 978-2-930517-57-5). (shrink)

While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through which semantic (...) similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results. (shrink)

The idea of homesteading can be extended to the realm of biological entities, to the ownership of information wherein organisms perform artifactual functions as a result of human development. Can the information of biological entities be ethically “homesteaded”: should humans (or businesses) have ownership rights over this information from the basis of mere development and possession, as in Locke’s theory of private property? I offer three non-consequentialist arguments against such homesteading: the information makeup of biological entities is not commonly owned, (...) and thus is not available for homesteading; the value of the individual biological entity extends to the information whereby it is constituted, and includes inalienable rights of an entity over itself and its information; and use of life as an information artifact makes an organism an unending means to an end rather than an end itself. I conclude that the information space of biological entities is not open for homesteading, not liable to private ownership, and should not be available for perpetual exploitation. (shrink)

Path-dependence offers a promising way of understanding the role historicity plays in explanation, namely, how the past states of a process can matter in the explanation of a given outcome. The two main existing accounts of path-dependence have sought to present it either in terms of dynamic landscapes or branching trees. However, the notions of landscape and tree both have serious limitations and have been criticized. The framework of causal networks is both more fundamental and more general that that of (...) landscapes and trees. Within this framework, I propose that historicity in networks should be understood as symmetry breaking. History matters when an asymmetric bias towards an outcome emerges in a causal network. This permits a quantitative measure for how path-dependence can occur in degrees, and offers suggestive insights into how historicity is intertwined both with causal structure and complexity. (shrink)

The idea that development is the expression of information accumulated during evolution and that heredity is the transmission of this information is surprisingly hard to cash out in strict, scientific terms. This paper seeks to do so using the sense of information introduced by Francis Crick in his sequence hypothesis and central dogma of molecular biology. It focuses on Crick's idea of precise determination. This is analysed using an information-theoretic measure of causal specificity. This allows us to reconstruct some of (...) Crick's claims about information in transcription and translation. Crick's approach to information has natural extensions to non-coding regions of DNA, to epigenetic marks, and to the genetic or environmental upstream causes of those epigenetic marks. Epigenetic information cannot be reduced to genetic information. The existence of biological information in epigenetic and exogenetic factors is relevant to evolution as well as to development. (shrink)

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with (...) the goal of enhancing reliability of detection by promoting the sharing of data between image analysts. (shrink)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

In his book "A Brief History of Time", Stephen Hawking says "If a complete unified theory was discovered, it would only be a matter of time before it was digested and simplified - and taught in schools, at least in outline. We should then all be able to have some understanding of the laws that govern the universe and are responsible for our existence." If complete, a unified theory would be physical and embrace all the space, matter and time of (...) the entire universe. It could not be partial and, as often interpreted, restricted to mathematics. -/- A complete unified theory that includes everything in space-time has practical applications for the matter called children who live today or in the past. They'd have "some understanding of the laws that govern the universe" at least from conception and associations formed at childhood would not always be "simpler". Pruning of nerve connections deprives us, in an intuitive sense, of "some understanding of the laws that govern the universe". Pruning prepares us for this part of existence - to attend school and university, and to develop the physics and maths that leads to discovery of the complete unified theory which, in their earliest years, children have some intuitive knowledge of. (shrink)

In this chapter we examine the relationship between biological information, the key biological concept of specificity, and recent philosophical work on causation. We begin by showing how talk of information in the molecular biosciences grew out of efforts to understand the sources of biological specificity. We then introduce the idea of ‘causal specificity’ from recent work on causation in philosophy, and our own, information theoretic measure of causal specificity. Biological specificity, we argue, is simple the causal specificity of certain biological (...) processes. This, we suggest, means that causal relationships in biology are ‘informational’ relationships simply when they are highly specific relationships. Biological information can be identified with the storage, transmission and exercise of biological specificity. It has been argued that causal relationships should not be regarded as informational relationship unless they are ‘arbitrary’. We argue that, whilst arbitrariness is an important feature of many causal relationships in living systems, it should not be used in this way to delimit biological information. Finally, we argue that biological specificity, and hence biological information, is not confined to nucleic acids but distributed among a wide range of entities and processes. (shrink)

We describe an approach to measuring biological information where ‘information’ is understood in the sense found in Francis Crick’s foundational contributions to molecular biology. Genes contain information in this sense, but so do epigenetic factors, as many biologists have recognized. The term ‘epigenetic’ is ambiguous, and we introduce a distinction between epigenetic and exogenetic inheritance to clarify one aspect of this ambiguity. These three heredity systems play complementary roles in supplying information for development. -/- We then consider the evolutionary significance (...) of the three inheritance systems. Whilst the genetic inheritance system was the key innovation in the evolution of heredity, in modern organisms the three systems each play important and complementary roles in heredity and evolution. -/- Our focus in the earlier part of the paper is on ‘proximate biology’, where information is a substantial causal factor that causes organisms to develop and causes offspring to resemble their parents. But much philosophical work has focused on information in ‘ultimate biology’. Ultimate information is a way of talking about the evolutionary design of the mechanisms of development and inheritance. We conclude by clarifying the relationship between the two. Ultimate information is not a causal factor that acts in development or heredity, but it can help to explain the evolution of proximate information, which is. (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)

Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

This paper presents the Obstetric and Neonatal Ontology (OntONeo). This ontology has been created to provide a consensus representation of salient electronic health record (EHR) data and to serve interoperability of the associated data and information systems. More generally, it will serve interoperability of clinical and translational data, for example deriving from genomics disciplines and from clinical trials. Interoperability of EHR data is important to ensuring continuity of care during the prenatal and postnatal periods for both mother and child. As (...) a strategy to advance such interoperability we use an approach based on ontological realism and on the ontology development principles of the Open Biomedical Ontologies Foundry, including reuse of reference ontologies wherever possible. We describe the structure and coverage domain of OntONeo and the process of creating and maintaining the ontology. (shrink)

Electronic health records (EHRs) serve as repositories of documented data collected in a health care encounter. An EHR records information about who receives, who provides the health care and about the place where the encounter happens. We also observe additional elements relating to social relations in which the healthcare consumer is involved. To provide a consensus representation of common data and to enhance interoperability between different EHR repositories we have created a solution grounded in formal ontology. Here, we present how (...) an ontology for the obstetric and neonatal domain deals with these general elements documented in health care encounters. Our goal is to promote the interoperability of information among EHRs created in different specialties. To develop our ontology, we used two main approaches: one based on ontological realism, the other based on the principles of the OBO Foundry, including reuse of reference ontologies. (shrink)

The concepts of the origin of the genetic code and the definitions of life changed dramatically after the RNA world hypothesis. Main narratives in molecular biology and genetics such as the “central dogma,” “one gene one protein” and “non-coding DNA is junk” were falsified meanwhile. RNA moved from the transition intermediate molecule into centre stage. Additionally the abundance of empirical data concerning nonrandom genetic change operators such as the variety of mobile genetic elements, persistent viruses and defectives do not fit (...) with the dominant narrative of error replication events (mutations) as being the main driving forces creating genetic novelty and diversity. The reductionistic and mechanistic views on physico-chemical properties of the genetic code are no longer convincing as appropriate descriptions of the abundance of non-random genetic content operators which are active in natural genetic engineering and natural genome editing. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (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. (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)

Organisms actively compete for environmental resources. They assess their surroundings, estimate how much energy they need for particular goals, and then realize the optimum variant. They take measures to control certain environmental resources. They perceive themselves and can distinguish between “self” and “non-self.” Current empirical data on all domains of life indicate that unicellular organisms such as bacteria, archaea, giant viruses, and protozoa as well as multicellular organisms such as animals, fungi, and plants coordinate and organize their essential life functions (...) through signaling processes. Signaling allows for real life coordination and organization and is a communicative action in which speciesspecific behavioral patterns and sign repertoires are used. Cells, tissues, organs, and organisms that communicate share several key levels that are essential to all life forms and which serve as a uniform tool for investigating biocommunication. (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)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

According to the proponents of Developmental Systems Theory and the Causal Parity Thesis, the privileging of the genome as “first among equals” with respect to the development of phenotypic traits is more a reflection of our own heuristic prejudice than of ontology - the underlying causal structures responsible for that specified development no more single out the genome as primary than they do other broadly “environmental” factors. Parting with the methodology of the popular responses to the Thesis, this paper offers (...) a novel criterion for ‘causal primacy’, one that is grounded in the ontology of the unique causal role of dispositional properties. This paper argues that, if the genome is conceptualised as realising dispositional properties that are “directed toward” phenotypic traits, the parity of ‘causal roles’ between genetic and extra-genetic factors is no longer apparent, and further, that the causal primacy of the genome is both plausible and defensible. (shrink)

The Information Artifact Ontology (IAO) was created to serve as a domain‐neutral resource for the representation of types of information content entities (ICEs) such as documents, data‐bases, and digital im‐ages. We identify a series of problems with the current version of the IAO and suggest solutions designed to advance our understanding of the relations between ICEs and associated cognitive representations in the minds of human subjects. This requires embedding IAO in a larger framework of ontologies, including most importantly the Mental (...) Func‐tioning Ontology (MFO). It also requires a careful treatment of the aboutness relations between ICEs and associated cognitive representa‐tions and their targets in reality, which implies in turn a new treatment of the relation of truthmaking. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

The rapidly increasing interest in the quantum properties of living matter stimulates a discussion of the fundamental properties of life as well as quantum mechanics. In this discussion often concepts are used that originate in philosophy and ask for a philosophical analysis. In the present work the classic philosophical tradition based on Aristotle and Aquinas is employed which surprisingly is able to shed light on important aspects. Especially one could mention the high degree of unity in living objects and the (...) occurrence of thorough qualitative changes. The latter are outside the scope of classical physics where changes are restricted to geometrical rearrangement of microscopic particles. A challenging approach is used in the philosophical analysis as the empirical evidence is not taken from everyday life but from 20th century science (quantum mechanics) and recent results in the field of quantum biology. In the discussion it is argued that quantum entanglement is possibly related to the occurrence of life. Finally it is recommended that scientists and philosophers should be open for dialogue that could enrich both. Scientists could redirect their investigation, as paradigm shifts like the one originating from philosophical evaluation of quantum mechanics give new insight about the relation between the whole en the parts. Whereas philosophers could use scientific results as a consistency check for their philosophical framework for understanding reality. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

In recent years, the growing academic field called “Data Science” has made many promises. On closer inspection, relatively few of these promises have come to fruition. A critique of Data Science from the phenomenological tradition can take many forms. This paper addresses the promise of “participation” in Data Science, taking inspiration from Paul Majkut’s 2000 work in Glimpse, “Empathy’s Impostor: Interactivity and Intersubjectivity,” and some insights from Heidegger’s "The Question Concerning Technology." The description of Data Science provided in the scholarly (...) literature includes “the study of the generalizable extraction of knowledge from data” (Dhar 2013, 64), “data stewardship and data sharing…access to data at higher volumes and more quickly, and the potential for replication and augmentation of existing research” (Hartter et al., 2013, 1), and “personal information, health status, daily activities and shopping preferences that are recorded and used to give us instant feedback and recommendations based on previous online behavior.” (Shin 2013) United States universities have begun to offer graduate programs in “data science”, anticipating the growth of this field for marketing, national security, and health industries. These universities include New York University, Columbia University, Stanford, Northwestern, and Syracuse. (shrink)

Western science claims to provide unique, objective information about the world. This is supported by the observation that peoples across cultures will agree upon a common description of the physical world. Further, the use of scientific instruments and mathematics is claimed to enable the objectification of science. In this work, carried out by reviewing the scientific literature, the above claims are disputed systematically by evaluating the definition of physical reality and the scientific method, showing that empiricism relies ultimately upon the (...) human senses for the evaluation of scientific theories and that measuring instruments cannot replace the human sensory system. Nativist and constructivist theories of human sensory development are reviewed, and it is shown that nativist claims of core conceptual knowledge cannot be supported by the findings in the literature, which shows that perception does not simply arise from a process of maturation. Instead, sensory function requires a long process of learning through interactions with the environment. To more rigorously define physical reality and systematically evaluate the stability of perception, and thus the basis of empiricism, the development of the method of dimension analysis is reviewed. It is shown that this methodology, relied upon for the mathematical analysis of physical quantities, is itself based upon empiricism, and that all of physical reality can be described in terms of the three fundamental dimensions of mass, length and time. Hereafter the sensory modalities that inform us about these three dimensions are systematically evaluated. The following careful analysis of neuronal plasticity in these modalities shows that all the relevant senses acquire from the environment the capacity to apprehend physical reality. It is concluded that physical reality is acquired rather than given innately, and leads to the position that science cannot provide unique results. Rather, those it can provide are sufficient for a particular environmental setting. (shrink)