‘Natural selection’ is, it seems, an ambiguous term. It is sometimes held to denote a consequence of variation, heredity, and environment, while at other times as denoting a force that creates adaptations. I argue that the latter, the force interpretation, is a redundant notion of natural selection. I will point to difficulties in making sense of this linguistic practise, and argue that it is frequently at odds with standard interpretations of evolutionary theory. I provide examples to show this; one example (...) involving the relation between adaptations and other traits, and a second involving the relation between selection and drift. (shrink)

It is a plain fact that biology makes use of terms and expressions commonly spoken of as teleological. Biologists frequently speak of the function of biological items. They may also say that traits are 'supposed to' perform some of their effects, claim that traits are 'for' specific effects, or that organisms have particular traits 'in order to' engage in specific interactions. There is general agreement that there must be something useful about this linguistic practice but it is controversial whether it (...) is entirely appropriate, and if so why it is.Many theorists have defended the use of seemingly teleological terms by appeal to an etiological notion of function (Wright, 1973; Millikan, 1984, 2002; Neander, 1991; .. (shrink)

It is commonly thought that natural selection explains the rise of adaptive complexity. Razeto-Barry and Frick have recently argued in favour of this view, dubbing it the Creative View. I argue that the Creative View is mistaken if it claims that natural selection serves to answer Paley’s question. This is shown by a case that brings out the contrastive structure inherent in this demand for explanation. There is, however, a rather trivial sense in which specific environmental conditions are crucial for (...) the rise of specific adaptations, but this is hardly what opponents of the Creative View are denying. (shrink)

It is commonly thought that natural selection explains the rise of adaptive complexity. Razeto-Barry and Frick have recently argued in favour of this view, dubbing it the Creative View. I argue that the Creative View is mistaken if it claims that natural selection serves to answer Paley’s question. This is shown by a case that brings out the contrastive structure inherent in this demand for explanation. There is, however, a rather trivial sense in which specific environmental conditions are crucial for (...) the rise of specific adaptations, but this is hardly what opponents of the Creative View are denying. (shrink)

The target of this article is the claim that natural selection accounts for the multiple realisation of biological and psychological kinds. I argue that the explanation actually offered does not provide any insight about the phenomenon since it presupposes multiple realisation as an unexplained premise, and this is what does all the work. The purported explanation mistakenly invokes the ?indifference? of selection to structure as an additional explanatorily relevant factor. While such indifference can be explanatory in intentional contexts, it is (...) not a causal factor at all in non-intentional nature. The upshot is that, once the necessary initial assumption about heterogeneity is accepted, there is no further explanation to do. (shrink)

It is commonly thought that natural selection explains the rise of adaptive complexity. Razeto-Barry and Frick have recently argued in favour of this view, dubbing it the Creative View. I argue that the Creative View is mistaken if it claims that natural selection serves to answer Paley’s question. This is shown by a case that brings out the contrastive structure inherent in this demand for explanation. There is, however, a rather trivial sense in which specific environmental conditions are crucial for (...) the rise of specific adaptations, but this is hardly what opponents of the Creative View are denying. (shrink)

The language of intentional psychology is commonly used as a means of addressing issues concerning selection. This habit is generally considered an efficient shorthand, but oft-reported misunderstandings leave room for doubt. I stress the general point that efficiency of a mode of expression is an empirical matter, deserving the same treatment, theoretically and methodologically, as other such matters. Mistaken assumptions regarding the relevant cognitive capacities may make for inefficient communication, and discourse about human evolution is a plausible case in point.

The language of intentional psychology is commonly used as a means of addressing issues concerning selection. This habit is generally considered an efficient shorthand, but oft-reported misunderstandings leave room for doubt. I stress the general point that efficiency of a mode of expression is an empirical matter, deserving the same treatment, theoretically and methodologically, as other such matters. Mistaken assumptions regarding the relevant cognitive capacities may make for inefficient communication, and discourse about human evolution is a plausible case in point.

Abstract: By focusing on contributions to the literature on function ascription, this article seeks to illustrate two problems with philosophical accounts that are presented as having descriptive aims. There is a motivational problem in that there is frequently no good reason why descriptive aims should be important, and there is a methodological problem in that the methods employed frequently fail to match the task description. This suggests that the task description as such may be the result of “default descriptivism,” a (...) tendency to take considerations that make sense of a practice to be the very considerations that generate it. Although such hypotheses are frequently quite plausible, the fact of the matter may not be very important for the pursuits of philosophers. (shrink)

For researchers who study technology designs, the application and execution of so-called design-oriented research projects are a common way of funding their research. Against this background, we propose a new methodical approach with which VSD can easily be implemented in such projects and which we call “value declaration”. We share our experience with this method which we gained in two design-oriented research projects.

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)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

Distractibility is one of the key features of attention deficit hyperactivity disorder and has been associated with alterations in the neural orienting and alerting networks. Task-irrelevant stimuli are thus expected to have detrimental effects on the performance of patients with ADHD. However, task-irrelevant presentation of novel sounds seems to have the opposite effect and improve subsequent attentional performance particularly in patients with ADHD. Here, we aimed to understand the neural modulations of the attention networks underlying these improvements. Fifty boys participated (...) in a functional magnetic resonance imaging study in which unique or repeatedly presented sounds were placed before a visual flanker task in 2/3 of the trials. We found that presenting any sound improved task performance in all participants, but the underlying neural mechanisms differed for the type of sound. Familiar sounds led to a stronger increase in activity in the left posterior insula in patients with ADHD compared to typically developing peers. Novel sounds led to activations of the fronto-temporoparietal ventral attention network, likewise in ADHD and TD. These changes in signaling by novelty in the right inferior frontal gyrus were directly related to improved response speed showing that neural orienting network activity following novel sounds facilitated subsequent attentional performance. This mechanism of behavioral enhancement by short distractions could potentially be useful for cognitive trainings or homework situations. (shrink)

The 10th International Conference on Biomedical Ontology (ICBO 2019), was held at the Jacobs School of Medicine and Biomedical Sciences of the University at Buffalo, in Buffalo, NY, USA. It was the 10-year anniversary of the ICBO series, and the return of the conference to Buffalo after the first two ICBO conferences were held in Buffalo in 2009 and 2011. ICBO 2019 was well attended, with 115 registered attendees and additional walk-ins from the local academic community. The program included excellent (...) keynote talks by Barry Smith, “International Standard Ontology,” and Bjoern Peters, “Putting principles into practice: OBO ontologies and applications in immunology,” as well as 23 oral presentations, 26 posters, and one software presentation. There were 53 papers and abstracts submitted for peer-review to ICBO 2019. Each submission was reviewed by three members chosen from the Program Committee. Of these submissions, 43 were accepted for this volume: 19 full papers, 23 poster abstracts, and 1 software demonstration extended abstract. We thank our program committee for their thoughtful reviews. There were also three workshops and four tutorials (listed below) held in conjunction with the main ICBO 2019 meeting. (shrink)