The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (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)

This project continues our interdisciplinary research into computational and cognitive aspects of narrative comprehension. Our ultimate goal is the development of a computational theory of how humans understand narrative texts. The theory will be informed by joint research from the viewpoints of linguistics, cognitive psychology, the study of language acquisition, literary theory, geography, philosophy, and artificial intelligence. The linguists, literary theorists, and geographers in our group are developing theories of narrative language and spatial understanding that are being tested by the (...) cognitive psychologists and language researchers in our group, and a computational model of a reader of narrative text is being developed by the AI researchers, based in part on these theories and results and in part on research on knowledge representation and reasoning. This proposal describes the knowledge-representation and natural-language-processing issues involved in the computational implementation of the theory; discusses a contrast between communicative and narrative uses of language and of the relation of the narrative text to the story world it describes; investigates linguistic, literary, and hermeneutic dimensions of our research; presents a computational investigation of subjective sentences and reference in narrative; studies children’s acquisition of the ability to take third-person perspective in their own storytelling; describes the psychological validation of various linguistic devices; and examines how readers develop an understanding of the geographical space of a story. This report is a longer version of a project description submitted to NSF. This document, produced in May 2007, is a L ATEX version of Technical Report 89-07 (Buffalo: SUNY Buffalo Department of Computer Science, August 1989), with slightly.. (shrink)

How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on "Microbiota, Symbiosis and Individuality: Conceptual and Philosophical Issues" (July 2019), which was supported by a European Research Council starting grant project "Immunity, DEvelopment, and the Microbiota" (IDEM). The summer school centered around interdisciplinary group work on four facets of microbiota research: holobionts, individuality, causation, and human health. The conceptual discussion of cutting-edge empirical research provided new insights into microbiota and highlights the value of (...) incorporating into meetings experts from other disciplines, such as philosophy and history of science. (shrink)

1. First there is an outline of the libertarian approach taken here. 2. On the assumption of personhood, it is explained how there need be no overall inflicted harm and no proactive killing with abortion and infanticide. This starts with an attached-adult analogy and transitions to dealing directly with the issues. Various well-known criticisms are answered throughout. 3. There is then a more-abstract explanation of how it is paradoxical to assume a duty to do more than avoid inflicting overall harm (...) and, instead, positively benefit. A putative counterexample is explained away. 4. A positive theory of intellectual personhood is defended in principle, but not made precise, which is sufficient to be practical. The greater moral value of intellectual-personhood is defended. An important putative reductio of the potential-personhood argument is refuted. 5. Several further criticisms that apply to both types of defences are answered. 6. Conclusion. (shrink)

Judith Butler’s influential work in feminist theory is significant for its insight that sexist discourse in popular culture affects the agency and consciousness of individuals, but offers an inadequate account of how such discourse might be said to touch, shape, or affect selves. Supplementing Butler’s account of signification with a Deweyan pragmatic account of meaning-making and selective emphasis enables a consistent account of the relationship between discourse and subjectivity with a robust conception of the bodily organism. An analysis of (...) the popular discourse surrounding Hillary Clinton in the 2008 Presidential campaign demonstrates why this hybrid pragmatic/poststructuralist account is necessary. (shrink)

Whenever science returns a confident and univocal answer to a question, Trumping Naturalism enjoins us to accept it. The majority of contemporary philosophers are sympathetic to this sort of position. Indeed, several have endorsed it or something very close to it. Arguments for Trumping Naturalism, however, are scant, the principal one being the Track Record Argument. The argument is based on the fact that in cases of conflict, science has a better track record than non-scientific forms of inquiry such as (...) philosophy. My chapter investigates this argument. I enumerate and assess several objections to the argument, from footling objections to stronger ones. My conclusion is that the Track Record Argument is not as strong as imagined. (shrink)

L’œuvre de Judith Butler, largement reconnue pour son apport en études de genre, recèle d’ouvertures nombreuses sur l’animalité et à son rôle dans la constitution de l’humain. Construite en patchwork et sans prétention à la systématicité théorique, elle repose, dans des contextes toujours différents, la problématique de la régulation normative de la vie et de la mort. Aussi, c’est en prenant au sérieux la marge constituante qu’y représente la question animale et par la (re)lecture de ses textes consacrés à (...) l’étude de pratiques esthétiques et artistiques, que cet article propose un décentrement théorique pour penser la question politique des corps qui comptent des animaux. Il étudie, de manière comparée, les happenings publics de L214, 269Life, 269 Libération Animale et Anonymous for the Voiceless. Il suggère que les choix esthétiques de ces différents collectifs reflètent et alimentent un certain regard politique porté sur la cause animale et sa finalité aussi bien que sur le genre de subjectivité politique attribuée ou non aux animaux non-humains. Il montre d’abord que les animaux constituent, chez Judith Butler, d’autres corps qui comptent : il s’agit alors d’introduire la diversité des outils théoriques de læ philosophe qui articulent la dimension publique, esthétique et souvent même artistique de la vie des corps avec la question du politique. C’est cette fondation qui lui permet, ensuite, de s’atteler à l’élaboration d’une cartographie des articulations esthético-politiques dans les performances militantes antispécistes. Y sont discutées une esthétique humanimale subversive et critique du binarisme humain/animal, une esthétique de l’« horreur morale » qui appelle au changement de comportement individuel par la mise en évidence de la violence, et une esthétique de la reconnaissance, qui valorise la possibilité d’une égalité radicale entre humains et non-humains dans le partage de la précarité de toute vie et du deuil public de chaque mort. (shrink)

Recent research has relied on trolley-type sacrificial moral dilemmas to study utilitarian versus nonutili- tarian modes of moral decision-making. This research has generated important insights into people’s attitudes toward instrumental harm—that is, the sacrifice of an individual to save a greater number. But this approach also has serious limitations. Most notably, it ignores the positive, altruistic core of utilitarianism, which is characterized by impartial concern for the well-being of everyone, whether near or far. Here, we develop, refine, and validate a (...) new scale—the Oxford Utilitarianism Scale—to dissociate individual differences in the ‘negative’ (permissive attitude toward instrumental harm) and ‘positive’ (impartial concern for the greater good) dimensions of utilitarian thinking as manifested in the general population. We show that these are two independent dimensions of proto-utilitarian tendencies in the lay population, each exhibiting a distinct psychological profile. Empathic concern, identification with the whole of humanity, and concern for future generations were positively associated with impartial beneficence but negatively associated with instrumental harm; and although instrumental harm was associated with subclinical psychopathy, impartial beneficence was associated with higher religiosity. Importantly, although these two dimensions were independent in the lay population, they were closely associated in a sample of moral philosophers. Acknowledging this dissociation between the instrumental harm and impartial beneficence components of utilitarian thinking in ordinary people can clarify existing debates about the nature of moral psychology and its relation to moral philosophy as well as generate fruitful avenues for further research. (shrink)

Euclid’s Elements inspired a number of foundationalist accounts of mathematics, which dominated the epistemology of the discipline for many centuries in the West. Yet surprisingly little has been written by recent philosophers about this conception of mathematical knowledge. The great exception is Imre Lakatos, whose characterisation of the Euclidean Programme in the philosophy of mathematics counts as one of his central contributions. In this essay, we examine Lakatos’s account of the Euclidean Programme with a critical eye, and suggest an alternative (...) picture which builds on his work, but differs in a number of important respects. (shrink)

The revival of the philosophy of mathematics in the 60s following its post-1931 slump left us with two conflicting positions on arithmetic’s ontological relationship to set theory. W.V. Quine’s view, presented in 'Word and Object' (1960), was that numbers are sets. The opposing view was advanced in another milestone of twentieth-century philosophy of mathematics, Paul Benacerraf’s 'What Numbers Could Not Be' (1965): one of the things numbers could not be, it explained, was sets; the other thing numbers could not be, (...) even more dramatically, was objects. Curiously, although Benacerraf’s article appeared in the heyday of Quine’s influence, it declined to engage the Quinean position squarely, even seemed to think it was not its business to do so. Despite that, in my experience, most philosophers believe that Benacerraf’s article put paid to the reductionist view that numbers are sets (though perhaps not the view that numbers are objects). My chapter will attempt to overturn this orthodoxy. (shrink)

This short article discusses the fact that the word ‘ancestor’ features in certain arguments that a) are apparently logically valid, b) contain infinitely many premises, and c) are such that none of their finite sub-arguments are logically valid. The article's aim is to motivate, within its brief compass, the study of infinitary logics.

In mathematics, the deductive method reigns. Without proof, a claim remains unsolved, a mere conjecture, not something that can be simply assumed; when a proof is found, the problem is solved, it turns into a “result,” something that can be relied on. So mathematicians think. But is there more to mathematical justification than proof? -/- The answer is an emphatic yes, as I explain in this article. I argue that non-deductive justification is in fact pervasive in mathematics, and that it (...) is in good epistemic standing. (shrink)

A focussed issue of The Reasoner on the topic of 'Infinitary Reasoning'. Owen Griffiths and A.C. Paseau were the guest editors.

A brief article introducing *One True Logic*. The book argues that there is one correct foundational logic and that it is highly infinitary.

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)

An essay review of Gila Sher's *Logical Consequence*.

Recent research has begun treating the perennial philosophical question, “what makes a person the same over time?” as an empirical question. A long tradition in philosophy holds that psychological continuity and connectedness of memories are at the heart of personal identity. More recent experimental work, following Strohminger & Nichols (2014), has suggested that persistence of moral character, more than memories, is perceived as essential for personal identity. While there is a growing body of evidence supporting these findings, a critique by (...) Starmans & Bloom (2018) suggests that this research program conflates personal identity with mere similarity. To address this criticism, we explore how loss of someone’s morality or memories influence perceptions of identity change, and perceptions of moral duties towards the target of the change. We present participants with a classic ‘body switch’ thought experiment and after assessing perceptions of identity persistence, we present a moral dilemma, asking participants to imagine that one of the patients must die (Study 1) or be left alone in a care home for the rest of their life (Study 2). Our results highlight the importance of the continuity of moral character, suggesting lay intuitions are tracking (something like) personal identity, not just mere similarity. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

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)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

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.

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)

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)

Judgments of plausibility involve appearance of the truth or reasonableness, which is always a function of background knowledge. What anyone will countenance is conditioned by what they already know (or think they know). Marc Kirschner (professor of systems biology at Harvard) and John Gerhart (professor of molecular and cell biology at the University of California—Berkeley) aim to show that molecular, cellular, and developmental processes relevant to the generation of phenotypic variation in anatomy, physiology, and behavior demonstrate how evolutionary processes, especially (...) the origins of novelty, are plausible. The outstanding question for Kirschner and Gerhart concerns not the modification of structures but their origination—a question unanswered by the theoretical framework of the modern synthesis. (shrink)

Skepticism is one of the most enduring and profound of philosophical problems. With its roots in Plato and the Sceptics to Descartes, Hume, Kant and Wittgenstein, skepticism presents a challenge that every philosopher must reckon with. In this outstanding collection philosophers engage with skepticism in five clear sections: the philosophical history of skepticism in Greek, Cartesian and Kantian thought; the nature and limits of certainty; the possibility of knowledge and related problems such as perception and the debates between objective knowledge (...) and constructivism; the transcendental method as a response to skepticism and the challenge of naturalism; overcoming the skeptical challenge. (shrink)

A key source of support for the view that challenging people’s beliefs about free will may undermine moral behavior is two classic studies by Vohs and Schooler (2008). These authors reported that exposure to certain prompts suggesting that free will is an illusion increased cheating behavior. In the present paper, we report several attempts to replicate this influential and widely cited work. Over a series of five studies (sample sizes of N = 162, N = 283, N = 268, N (...) = 804, N = 982) (four preregistered) we tested the relationship between (1) anti-free-will prompts and free will beliefs and (2) free will beliefs and immoral behavior. Our primary task was to closely replicate the findings from Vohs and Schooler (2008) using the same or highly similar manipulations and measurements as the ones used in their original studies. Our efforts were largely unsuccessful. We suggest that manipulating free will beliefs in a robust way is more difficult than has been implied by prior work, and that the proposed link with immoral behavior may not be as consistent as previous work suggests. (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 this chapter, we outline the interdisciplinary contributions that philosophy, psychology, and neuroscience have provided in the understanding of the self and identity, focusing on one specific line of burgeoning research: the importance of morality to perceptions of self and identity. Of course, this rather limited focus will exclude much of what psychologists and neuroscientists take to be important to the study of self and identity (that plethora of self-hyphenated terms seen in psychology and neuroscience: self-regulation, self-esteem, self-knowledge, self-concept, self-perception, (...) and more). We will likewise not engage with many canonical philosophical treatments of self and identity. But we will lay out a body of research that brings together classic themes in philosophy, psychology, and neuroscience to raise empirically tractable philosophical questions, and philosophically rigorous empirical questions about self and identity. More specifically, in section 4.2, we will review some recent research that has treated traditional philosophical questions about self and identity as empirical questions. Within this body of work, we will be primarily concerned with the finding that morality (more so than memory) is perceived to be at the core of self and identity. Then, in section 4.3, we raise and respond to a variety of questions and criticisms: first, about the operationalization of identity concepts in the empirical literature; second, about the generalizability of the moral self effect; third, about the direction of change; fourth, about connections with recent work in neuroscience; and fifth, about the target of evaluation. Finally, in section 4.4, we consider a variety of implications and applications of this work on the moral self. Throughout, we aim to highlight connections between classical themes in philosophy, psychology, and neuroscience, while also suggesting new directions for interdisciplinary collaboration. (shrink)

This chapter describes the potential far‐reaching consequences of contemplative higher education for the fields of science and medicine.

In this paper, we intend to promote an analysis of the use of the artificial language Heptapod B in Story of Your Life written by Ted Chiang and in its filmic adaptation, Arrival, written by Eric Heisserer and directed by Denis Villeneuve in relation to the authors’ views on the metaphysics of time. In both literary and filmic texts, the glossopoeia is used as a plot device upon which the alien race’s time perception is constructed and explicated in connexion with (...) the strong metaphor provided by Fermat’s principle of least time. Throughout the article, we discuss these hybrid interfaces of literature, cinema and science, researching the stories’ specific diegeses, the writers’ own elicitations as well as various texts on the Philosophy of time. The result consists of a comprehensive exegesis of the problematics generated by the narratives and an extensive philosophical debate on the subject. (shrink)

Background: Recent literature on addiction and judgments about the characteristics of agents has focused on the implications of adopting a ‘brain disease’ versus ‘moral weakness’ model of addiction. Typically, such judgments have to do with what capacities an agent has (e.g., the ability to abstain from substance use). Much less work, however, has been conducted on the relationship between addiction and judgments about an agent’s identity, including whether or to what extent an individual is seen as the same person after (...) becoming addicted. Methods: We conducted a series of vignette-based experiments (total N = 3,620) to assess lay attitudes concerning addiction and identity persistence, systematically manipulating key characteristics of agents and their drug of addiction. Conclusions: In Study 1, we found that US participants judged an agent who became addicted to drugs as being closer to ‘a completely different person’ than ‘completely the same person’ as the agent who existed prior to the addiction. In Studies 2-6, we investigated the intuitive basis for this result, finding that lay judgments of altered identity as a consequence of drug use and addiction are driven primarily by perceived negative changes in the moral character of drug users, who are seen as having deviated from their good true selves. (shrink)

We approach the notion of general (global) human intelligence as a prominently multifaceted concept which can be tested in at least seventy specific scenarios. We say that an agent has Artificial Global Intelligence (AGLI), if it is able to perform in an intelligent manner for at least the collection of tasks defining the former scenarios. In particular, based on Gartner's multiple intelligences theory, we describe the design of a concrete test for AGLI made in such a way that an ‘average’ (...) young human being should, per diffinitionem, pass it. We compare our holistic test with several highly representative human and artificial intelligence tests for deducing that our AGLI test is the one with the broader scope of the whole range of intelligence. However, we claim as a plausible hypothesis and based on the wide thematic spectrum of the test that the most outstanding inventions of AI currently available are far from getting a high score on it. Finally, we open a discussion about the fact that, although there are artificial agents being able to simulate intelligent behaviour at a perfect level for several local tasks, this seems not to be the case for AGLI. This would imply, in particular, a kind of practical implausibility of the notion of intelligence explosion coming from philosophy of AI. (shrink)

The role of evolutionary theory at the origin of life is an extensively debated topic. The origin and early development of life is usually separated into a prebiotic phase and a protocellular phase, ultimately leading to the Last Universal Common Ancestor. Most likely, the Last Universal Common Ancestor was subject to Darwinian evolution, but the question remains to what extent Darwinian evolution applies to the prebiotic and protocellular phases. In this review, we reflect on the current status of evolutionary theory (...) in origins of life research by bringing together philosophy of science, evolutionary biology, and empirical research in the origins field. We explore the various ways in which evolutionary theory has been extended beyond biology; we look at how these extensions apply to the prebiotic development of (proto)metabolism; and we investigate how the terminology from evolutionary theory is currently being employed in state-of-the-art origins of life research. In doing so, we identify some of the current obstacles to an evolutionary account of the origins of life, as well as open up new avenues of research. (shrink)

Ever since its inception, the theory of evolution has been reified into an “-ism”: Darwinism. While biologists today tend to shy away from the term in their research, the term is still actively used in the broader academic and societal contexts. What exactly is Darwinism, and how precisely are its various uses and abuses related to the scientific theory of evolution? Some call for limiting the meaning of the term “Darwinism” to its scientific context; others call for its abolition; yet (...) others claim the term refers to a myth-like story. In this paper we propose a conceptually grounded overview of the term. We show how the scientific dimension of Darwinism feeds into, and is influenced by, guises of Darwinism as a methodology and as an ethically and politically charged “worldview”. The full meaning of Darwinism, as well as how this meaning has changed over time, can only be understood through the complex interaction between these three dimensions. (shrink)

This volume provides a broad overview of issues in the philosophy of behavioral biology, covering four main themes: genetic, developmental, evolutionary, and neurobiological explanations of behavior. It is both interdisciplinary and empirically informed in its approach, addressing philosophical issues that arise from recent scientific findings in biological research on human and non-human animal behavior. Accordingly, it includes papers by professional philosophers and philosophers of science, as well as practicing scientists. Much of the work in this volume builds on presentations given (...) at the international conference, “Biological Explanations of Behavior: Philosophical Perspectives”, held in 2008 at the Leibniz Universität Hannover in Germany. The volume is intended to be of interest to a broad range of audiences, which includes philosophers (e.g., philosophers of mind, philosophers of biology, and metaethicists), as well as practicing scientists, such as biologists or psychologists whose interests relate to biological explanations of behavior. (shrink)

A number of debates in philosophy of biology and psychology, as well as in their respective sciences, hinge on particular views about the relationship between genotypes and phenotypes. One such view is that the genotype-phenotype relationship is relatively straightforward, in the sense that a genome contains the ?genes for? the various traits that an organism exhibits. This leads to the assumption that if a particular set of traits is posited to be present in an organism, there must be a corresponding (...) number of genes in that organism's genome to account for those traits. This assumption underlies what can be called the ?counting argument,? in which empirical estimates of the number of genes in a genome are used to support or refute particular hypotheses in philosophical debates about biology and psychology. In this paper, we assess the counting argument as it is used in discussions of the alleged massive modularity of the brain, and conclude that this argument cannot be upheld in light of recent philosophical work on gene concepts and empirical work on genome complexity. In doing so, we illustrate that there are those on both sides of the debate about massive modularity who rely on an incorrect view of gene concepts and the nature of the genotype-phenotype relationship. (shrink)

Visual imagery is a form of sensory imagination, involving subjective experiences typically described as similar to perception, but which occur in the absence of corresponding external stimuli. We used the Activation Likelihood Estimation algorithm (ALE) to identify regions consistently activated by visual imagery across 40 neuroimaging studies, the first such meta-analysis. We also employed a recently developed multi-modal parcellation of the human brain to attribute stereotactic co-ordinates to one of 180 anatomical regions, the first time this approach has been combined (...) with the ALE algorithm. We identified a total 634 foci, based on measurements from 464 participants. Our overall comparison identified activation in the superior parietal lobule, particularly in the left hemisphere, consistent with the proposed ‘top-down’ role for this brain region in imagery. Inferior premotor areas and the inferior frontal sulcus were reliably activated, a finding consistent with the prominent semantic demands made by many visual imagery tasks. We observed bilateral activation in several areas associated with the integration of eye movements and visual information, including the supplementary and cingulate eye fields (SCEFs) and the frontal eye fields (FEFs), suggesting that enactive processes are important in visual imagery. V1 was typically activated during visual imagery, even when participants have their eyes closed, consistent with influential depictive theories of visual imagery. Temporal lobe activation was restricted to area PH and regions of the fusiform gyrus, adjacent to the fusiform face complex (FFC). These results provide a secure foundation for future work to characterise in greater detail the functional contributions of specific areas to visual imagery. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

Faculty resistance to Writing Across the Curriculum (WAC) is an issue that has been recognized by WAC program directors and practitioners for decades, yet it remains unresolved. Perhaps the problem is not resistance per se, but how we interpret and react to it. Faculty resistance is typically viewed as an impediment to the pedagogical change WAC programs hope to achieve. Moreover, the label of "resistance" is often used without further examination of the underlying causes. Based on research and experience as (...) doctoral Writing Fellows in the Borough of Manhattan Community College WAC Program, we argue that so-called resistances are often justified concerns in regard to implementing WAC under given institutional, disciplinary, departmental, and personal constraints. We also suggest that if we listen and respond to these concerns, they become means to facilitate faculty engagement with WAC. By working through their concerns and adapting WAC to their context, faculty can take ownership of WAC and further develop the practice. Thus, what at first appears to be an impediment to deep-rooted pedagogical change ”resistance” can be used to encourage faculty to make WAC their own. (shrink)

A graph-theoretic account of logics is explored based on the general notion of m-graph (that is, a graph where each edge can have a finite sequence of nodes as source). Signatures, interpretation structures and deduction systems are seen as m-graphs. After defining a category freely generated by a m-graph, formulas and expressions in general can be seen as morphisms. Moreover, derivations involving rule instantiation are also morphisms. Soundness and completeness theorems are proved. As a consequence of the generality of the (...) approach our results apply to very different logics encompassing, among others, substructural logics as well as logics with nondeterministic semantics, and subsume all logics endowed with an algebraic semantics. (shrink)

This paper focuses on invasive therapeutic procedures, defined as procedures requiring the introduction of hands, instruments, or devices into the body via incisions or punctures of the skin or mucous membranes performed with the intent of changing the natural history of a human disease or condition for the better. Ethical and methodological concerns have been expressed about studies designed to evaluate the effects of invasive therapeutic procedures. Can such studies meet the same standards demanded of those, for example, evaluating pharmaceutical (...) agents? This paper describes a research project aimed at examining the interplay and sometimes apparent conflict between ethical standards for human research and standards for methodological rigor in trials of invasive procedures. The paper discusses how the authors plan to develop a set of consensus standards that, if met, would result in substantial and much-needed improvements in the methodological and ethical quality of such trials. (shrink)

I explore the view that the imago Dei is essential to us as humans but accidental to us as persons. To image God is to resemble God, and resemblance comes in degrees. This has the straightforward—and perhaps disturbing—implication that we can be more or less human, and possibly cease to be human entirely. Hence, I call it the spectrum view. I argue that the spectrum view is complementary to the Biblical data, helps explain the empirical reality of horrendous evil, and (...) offers an elegant rapprochement between the traditional view of hell and its rivals. (shrink)

Would the existence of extraterrestrial intelligent life conflict in any way with Christian belief? We identify six areas of potential conflict. If there be no conflict in any of these areas—and we argue ultimately there is not—we are confident in declaring that there is no conflict, period. This conclusion underwrites the integrity of theological explorations into the existence of ETI, which has become a topic of increasing interest among theologians in recent years.

Background If trials of therapeutic interventions are to serve society's interests, they must be of high methodological quality and must satisfy moral commitments to human subjects. The authors set out to develop a clinical - trials compendium in which standards for the ethical treatment of human subjects are integrated with standards for research methods. Methods The authors rank-ordered the world's nations and chose the 31 with >700 active trials as of 24 July 2008. Governmental and other authoritative entities of the (...) 31 countries were searched, and 1004 English-language documents containing ethical and/or methodological standards for clinical trials were identified. The authors extracted standards from 144 of those: 50 designated as ‘core’, 39 addressing trials of invasive procedures and a 5% sample of the remainder. As the integrating framework for the standards we developed a coherent taxonomy encompassing all elements of a trial's stages. Findings Review of the 144 documents yielded nearly 15 000 discrete standards. After duplicates were removed, 5903 substantive standards remained, distributed in the taxonomy as follows: initiation, 1401 standards, 8 divisions; design, 1869 standards, 16 divisions; conduct, 1473 standards, 8 divisions; analysing and reporting results, 997 standards, four divisions; and post-trial standards, 168 standards, 5 divisions. Conclusions The overwhelming number of source documents and standards uncovered in this study was not anticipated beforehand and confirms the extraordinary complexity of the clinical trials enterprise. This taxonomy of multinational ethical and methodological standards may help trialists and overseers improve the quality of clinical trials, particularly given the globalisation of clinical research. (shrink)

Many philosophers have appealed to the PSR in arguments for a being that exists a se, a being whose explanation is in itself. But what does it mean, exactly, for something to have its explanation ‘in itself’? Contemporary philosophers have said next to nothing about this, relying instead on phrases plucked from the accounts of various historical figures. In this article, I analyse five such accounts – those of Anselm, Aquinas, Descartes, Spinoza, and Leibniz – and argue that none are (...) satisfactory. Should we abandon or restrict the PSR, then? I think that would be hasty, for many reasons. I therefore consider the prospects of explaining everything, including God, given the constraints of certain features of good explanations, and conclude with several observations about future approaches. (shrink)

Abstract: Tomatoes are part of the major crops in food security. Tomatoes are plants grown in temperate and hot regions of South American origin from Peru, and then spread to most countries of the world. Tomatoes contain a lot of vitamin C and mineral salts, and are recommended for people with constipation, diabetes and patients with heart and body diseases. Studies and scientific studies have proven the importance of eating tomato juice in reducing the activity of platelets in diabetics, which (...) helps in protecting them from developing deadly blood clots. A tomato classification approach is presented with a data set containing approximately 5,266 images with 7 species belonging to tomatoes. The Neural Network Algorithms (CNN), a deep learning technique applied widely in image recognition, is used for this task. (shrink)