To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

The pathbreaking scientific advances of recent years call for a new philosophical consideration of the fundamental categories of biology and its neighboring disciplines. Above all, the new information technologies used in biomedical research, and the necessity to master the continuously growing flood of data that is associated therewith, demand a profound and systematic reflection on the systematization and classification of biological data. This, however, demands robust theories of basic concepts such as kind, species, part, whole, function, process, fragment, sequence, expression, (...) boundary, locus, environment, system, and so on. Concepts which belong to the implicit stock of knowledge of every biologist. They amount to a dimension of biological reality which remains constant in the course of biological evolution and whose theoretical treatment requires contemporary analogues of the tools developed in traditional Aristotelian metaphysics. To provide the necessary theories and definitions is a task for philosophy, which is thus called upon to play an important role as intermediary between biology and informatics. (shrink)

Die bahnbrechenden wissenschaftlichen Ergebnisse der letzten Jahre erzwingen eine neue philosophische Auseinandersetzung mit den Grundkategorien der Biologie und der benachbarten Disziplinen. Insbesondere die Anwendung neuer informationstechnischer Mittel in der biomedizinischen Forschung und die damit verbundene, kontinuierlich zunehmende Datenflut sowie die Notwendigkeit, ihrer Herr zu werden, erfordern ein konsequentes Nachdenken darüber, wie biologische Daten systematisiert und klassifiziert werden können. Dafür wiederum bedarf es robuster Theorien von Grundbegriffen wie Art, Spezies, Teil, Ganzes, Funktion, Prozess, Fragment, Sequenz, Expression, Grenze, Locus, Umwelt, System usw. (...) Solche Begriffe gehören zum impliziten Wissen jedes Biologen. Sie spiegeln einerseits eine Dimension der biologischen Wirklichkeit wider, die auch vor dem Hintergrund der biologischen Evolution unverändert bleibt. Andererseits verlangt deren theoretische Behandlung nach zeitgemäßen Analoga der in der traditionellen aristotelischen Metaphysik entwickelten Methoden. Zugleich können so die explizit formulierten Theorien und Definitionen bereitgestellt werden, die für computergestützte Informationssysteme unabdingbar sind. Das Entwickeln derartiger Theorien und Definitionen ist eine Aufgabe der Philosophie, die in diesem Sinne herausgefordert ist, zwischen Biologie und Informatik zu vermitteln. (shrink)

In their responses to my article “Epistemically Pernicious Groups and the Groupstrapping Problem” (Boyd, 2018), Bert Baumgaertner (“Groupstrapping, Boostrapping, and Oops-strapping: A Reply to Boyd”) and C. Thi Nguyen (“Group-strapping, Bubble, or Echo Chamber?”) have raised interesting questions and opened lines of inquiry regarding my discussion of what I hope to be a way to help make sense of how members of groups can continue to hold beliefs that are greatly outweighed by countervailing evidence (e.g. antivaxxers, climate-change deniers, etc.). (...) Here I respond to these arguments and suggestions by providing three new reasons to believe that groupstrapping as I describe it occurs in epistemically pernicious groups. (shrink)

Spatially situated opinions that can be held with different degrees of conviction lead to spatiotemporal patterns such as clustering (homophily), polarization, and deadlock. Our goal is to understand how sensitive these patterns are to changes in the local nature of interactions. We introduce two different mixing mechanisms, spatial relocation and nonlocal interaction (“telephoning”), to an earlier fully spatial model (no mixing). Interestingly, the mechanisms that create deadlock in the fully spatial model have the opposite effect when there is a sufficient (...) amount of mixing. With telephoning, not only is polarization and deadlock broken up, but consensus is hastened. The effects of mixing by relocation are even more pronounced. Further insight into these dynamics is obtained for selected parameter regimes via comparison to the mean-field differential equations. (shrink)

Voting Advice Applications (VAAs) are online tools designed to help citizens decide how to vote. They typically offer their users a representation of what is at stake in an election by matching user preferences on issues with those of parties or candidates. While the use of VAAs has boomed in recent years in both established and new democracies, this new phenomenon in the electoral landscape has received little attention from political theorists. The current academic debate is focused on epistemic aspects (...) of the question how a VAA can adequately represent electoral politics. We argue that conceptual and normative presuppositions at play in the background of the tool are at least as important. Even a well-developed VAA does not simply reflect what is at stake in the election by neutrally passing along information. Rather, it structures political information in a way that is informed by the developers’ presuppositions. Yet, these presuppositions remain hidden if we interpret the tool as a mirror that offers the user a reflection of him/herself situated within the political landscape. VAAs should therefore be understood as electoral dioramas, staged according to a contestable picture of politics. (shrink)

This document presents the Bonn PRINTEGER Consensus Statement: Working with Research Integrity—Guidance for research performing organisations. The aim of the statement is to complement existing instruments by focusing specifically on institutional responsibilities for strengthening integrity. It takes into account the daily challenges and organisational contexts of most researchers. The statement intends to make research integrity challenges recognisable from the work-floor perspective, providing concrete advice on organisational measures to strengthen integrity. The statement, which was concluded February 7th 2018, provides guidance on (...) the following key issues: § 1.Providing information about research integrity § 2.Providing education, training and mentoring § 3.Strengthening a research integrity culture § 4.Facilitating open dialogue § 5.Wise incentive management § 6.Implementing quality assurance procedures § 7.Improving the work environment and work satisfaction § 8.Increasing transparency of misconduct cases § 9.Opening up research § 10.Implementing safe and effective whistle-blowing channels § 11.Protecting the alleged perpetrators § 12.Establishing a research integrity committee and appointing an ombudsperson § 13.Making explicit the applicable standards for research integrity. (shrink)

Information Theory, Evolution and The Origin ofLife: The Origin and Evolution of Life as a Digital Message: How Life Resembles a Computer, Second Edition. Hu- bert P. Yockey, 2005, Cambridge University Press, Cambridge: 400 pages, index; hardcover, US $60.00; ISBN: 0-521-80293-8. The reason that there are principles of biology that cannot be derived from the laws of physics and chemistry lies simply in the fact that the genetic information content of the genome for constructing even the simplest organisms is (...) much larger than the information content of these laws. Yockey in his previous book (1992, 335) In this new book, Information Theory, Evolution and The Origin ofLife, Hubert Yockey points out that the digital, segregated, and linear character of the genetic information system has a fundamental significance. If inheritance would blend and not segregate, Darwinian evolution would not occur. If inheritance would be analog, instead of digital, evolution would be also impossible, because it would be impossible to remove the effect of noise. In this way, life is guided by information, and so information is a central concept in molecular biology. The author presents a picture of how the main concepts of the genetic code were developed. He was able to show that despite Francis Crick's belief that the Central Dogma is only a hypothesis, the Central Dogma of Francis Crick is a mathematical consequence of the redundant nature of the genetic code. The redundancy arises from the fact that the DNA and mRNA alphabet is formed by triplets of 4 nucleotides, and so the number of letters (triplets) is 64, whereas the proteome alphabet has only 20 letters (20 amino acids), and so the translation from the larger alphabet to the smaller one is necessarily redundant. Except for Tryptohan and Methionine, all amino acids are coded by more than one triplet, therefore, it is undecidable which source code letter was actually sent from mRNA. This proof has a corollary telling that there are no such mathematical constraints for protein-protein communication. With this clarification, Yockey contributes to diminishing the widespread confusion related to such a central concept like the Central Dogma. Thus the Central Dogma prohibits the origin of life "proteins first." Proteins can not be generated by "self-organization." Understanding this property of the Central Dogma will have a serious impact on research on the origin of life. (shrink)

Opinions are rarely binary; they can be held with different degrees of conviction, and this expanded attitude spectrum can affect the influence one opinion has on others. Our goal is to understand how different aspects of influence lead to recognizable spatio-temporal patterns of opinions and their strengths. To do this, we introduce a stochastic spatial agent-based model of opinion dynamics that includes a spectrum of opinion strengths and various possible rules for how the opinion strength of one individual affects the (...) influence that this individual has on others. Through simulations, we find that even a small amount of amplification of opinion strength through interaction with like-minded neighbors can tip the scales in favor of polarization and deadlock. (shrink)

One feature of vague predicates is that, as far as appearances go, they lack sharp application boundaries. I argue that we would not be able to locate boundaries even if vague predicates had sharp boundaries. I do so by developing an idealized cognitive model of a categorization faculty which has mobile and dynamic sortals (`classes', `concepts' or `categories') and formally prove that the degree of precision with which boundaries of such sortals can be located is inversely constrained by their flexibility. (...) Given the literature, it is plausible that we are appropriately like the model. Hence, an inability to locate sharp boundaries is not necessarily because there are none; boundaries could be sharp and it is plausible that we would nevertheless be unable to locate them. (shrink)

Das Wiskott-Aldrich-Syndrom (WAS), ein genetisch bedingter Immundefekt mit klinischer Manifestation im Kleinkindalter, wird voraussichtlich in näherer Zukunft erstmals versuchsweise durch eine somatische Gentherapie behandelt werden. Im vor- liegenden Beitrag werden die wichtigsten medizinisch-naturwissenschaftlichen Fakten dieses Krankheitsbildes sowie die bisherigen Erfahrungen mit somatischen Gentherapien bei anderen Immunmangelsyndromen ausführlich dargestellt. Sodann erfolgt eine ethische Analyse eines möglichen gentherapeutischen Eingriffs bei WAS-Patienten, bei der die spezifischen Aspekte des Wiskott-Aldrich-Syndroms – insbesondere die fast ausschließliche Betroffenheit von Kindern sowie die unterschiedlich aussichtsreiche Alter- nativoption einer (...) allogenen Knochenmarktransplantation–wesentliche Aspekte der Beurteilung sind. Im Ergebnis zeigt sich, dass ein gentherapeutischer Eingriff im vorliegenden Fall nicht im Rahmen einer Forschungsstudie, d.h. als Humanexperiment, gerechtfertigt werden kann, sondern allein als individueller Heilversuch. Gleichwohl las- sen die besonderen Risiken und die Innovativität eines solchen Eingriffs es notwendig erscheinen, diesen Heilversuch – anders als andere Heilbehandlungen mit bislang unerprobten Mitteln – in streng kontrollierter Form durchzuführen. Der neuartige Gedanke eines kontrollierten individuellen Heilversuchs zeichnet sich daher für den vorliegenden Fall, und womöglich auch für vergleichbare risikoreiche Behandlungsansätze namentlich im Bereich der Gentherapie, als geeignetes Instrument der Konzeption und Beurteilung ab. (shrink)

Does ethics have adequate general theories? Our analysis shows that this question does not have a straightforward answer since the key terms are ambiguous. So we should not concentrate on the answer but on the question itself. “Ethics” stands for many things, but we let that pass. “Adequate” may refer to varied arrays of methodological principles which are seldom fully articulated in ethics. “General” is a notion with at least three meanings. Different kinds of generality may be at cross-purposes, so (...) we must not expect theories to be general in sundry senses. “Theory,” for that matter, is itself ambiguous. Some thinkers say that ethics cannot have theories, while others deny it. We doubt whether opposing parties are talking about the same things.No wonder, then, that controversies in ethics are long-lasting and unproductive. We hope that the methodology we have presented will alleviate some of them. The examples we chose show that this is feasible. Views such as Hare's and Jonsen and Toulmin's which are seemingly wide apart, show convergence if we put them in a methodological perspective.Our analysis also suggests that many alleged differences between science and ethics could fade away if methodology is brought to bear on them. Specifically, the idea that ethics compares poorly with science in view of limited generality, or poor means of justification, is unfounded. Those who defend this view over-rate the powers of science. (shrink)

The theory of proper names proposed by J.S. Mill in A system of logic (1843), and discussed in S. Kripke’s Naming and necessity (1980), is shown to be predated by A. Rosmini’s Nuovo saggio sull’origine delle idee (1830) and T. Reid’s Essays on the intellectual powers of man (1785). For philological reasons, Rosmini probably did not obtain his view of proper names from Reid. For philosophical reasons, it is unlikely that he got it from Hobbes, Locke, Smith, or Stewart. Although (...) not explicitly indicated by Rosmini himself, he may have been influenced by St. Thomas, who in Summa theologica discusses suppositum and natura in relation to the equivocal functions of the terms ”God” and ”sun” as common and proper names. As previously observed, forerunners of the idea can be found in Antiquity, in Plato’s Theaetetus and Aristotle’s Metaphysics. From a historical point of view, the fully developed ”Millian” opinion that connotation is not a fundamental aspect of proper names, and that their referents are not fixed by description, could more accurately be termed the Reid-Rosmini-Mill theory. (shrink)

Antonio Rosmini is practically unknown in Lutheran Sweden. Apparently, only one significant Swedish text has been published about his philosophy, an essay in 1879 by Professor E.O. Burman at the University of Uppsala. After a brief introduction of Burman, some illustrative excerpts from his essay are presented in Italian translation.

Erik Olof Burman (1845–1929) was professor of practical philosophy at the University of Uppsala, Sweden, between 1896 and 1910. In 1879 he published a long essay entitled ”Om den nyare italienska filosofien” (”On recent Italian philosophy”). About half the essay is devoted to the philosophical system of Antonio Rosmini (1797–1855), the second half to that of Vincenzo Gioberti (1801–1852). The text is mainly descriptive, apparently aiming at informing Swedish colleagues about the situation in Italy. However, there are also passages revealing (...) the rationalist-idealist subjectivism of Burman himself as well as his considering Rosmini’s ontology too objectivistic and Gioberti’s idealism insufficiently coherent. A preliminary translation of Burman’s essay into Italian is presented. -/- Erik Olof Burman (1845–1929) fu professore di Filosofia Pratica all’Università di Uppsala negli anni 1896–1910. New 1879 publicò un saggio intitolato ”Om den nyare italienska filosofien” (“Sulla filosofia italiana recente”). Quasi metà di questo lavoro si concentra sul sistema di Antonio Rosmini (1797–1855); la seconda parte verte anzitutto invece su quello di Vincenzo Gioberti (1801–1852). Il testo è principalmente descrittivo, ovviamente mirante a informare filosofi svedesi sulle posizioni attuali in Italia. Vi si trovano anche però commenti sparsi indicanti il razialismo-idealismo soggetivo di Burman stesso e considerazioni riguardo a come egli consideri l’ontologia di Rosmini troppo oggettiva e l’idealismo di Gioberti insufficientemente coerente. Riflettendo l’immagine della filosofia italiana del IX secolo in uno specchio straniero, il lavoro potrebbe essere di un certo valore informativo per moderni filosofi e storici italiani. Per questa ragione una traduzione preliminare del saggio di Burman è presentata. (shrink)