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)

A phenome occurs through the many pathways of the complex net of interaction between the phenome and its environment; therefore researching and understanding how it arises requires investigation into many possible causes that are in constant interaction with each other. The most comprehensive investigations in biology are the ones in which many biologists from different sub-areas—evolutionary biology, developmental biology, molecular biology, physiology, genetics, epigenetics, ecology—have collaborated. Still, biologists do not always need to collaborate or look for the most comprehensive explanations. (...) A more standard investigation in biology occurs within a single subarea, and uses well-defined experiments with very specific conditions. This paper is about causation and related explanation in plant phenome research and its relevance to Aristotle’s Theory of Four Causes. I argue that there are causes which resemble Aristotle’s formal, material, and efficient causes in phenotype explanation and occurrence; but causes which resemble Aristotle’s final causes occur in phenotype explanation only, not in the occurrence. (shrink)

There have been constant and multiple endeavours to argue for Darwin's both epistemic and practical debt to Romanticism. Almost all of these arguments emphasise Darwin's theoretical and aesthetic associations with Alexander von Humboldt, who, from a prevailing Darwin-centred perspective, is in turn usually oversimplified as an undisputed incarnation of Romanticism. The antagonistic view, however, develops nothing other than another stereotype of Humboldt as an anti-idealistic, pro-French, and even highly Anglophone empiricist naturalist, and accordingly rejects the claim of a romantic Darwin (...) in terms of his Humboldtian inheritance. In this paper, I will first portray a balanced figure of Humboldt in terms of both his critical incorporation of romantic philosophy and the idiosyncratic history of his science. Then, I will thematically compare Darwin with Humboldt and other romantics so as to elucidate Darwin's peculiar appropriation of romantic tenets. Three interrelated romantic themes are examined, along with a discrimination of different senses in which the term romanticism is used: a) the literature-science relation, b) the pursuit of the unity in and through multiplicity, and c) the epistemic role of imagination. On the basis of this triadic dissection, both Humboldt's and Darwin's adherence to and departure from romanticism are reevaluated. (shrink)

In a short work called De conceptione appended to the end of his Exercitationes de generatione animalium , William Harvey developed a rather strange analogy. To explain how such marvelous productions as living beings were generated from the rather inauspicious ingredients of animal reproduction, Harvey argued that conception in the womb was like conception in the brain. It was mostly rejected at the time; it now seems a ludicrous theory based upon homonymy. However, this analogy offers insight into the structure (...) and function of analogies in early modern natural philosophy. In this essay I hope to not only describe the complex nature of Harvey’s analogy, but also offer a novel interpretation of his use of analogical reasoning, substantially revising the account offered by Guido Giglioni . I discuss two points of conceptual change and negotiation in connection with Harvey’s analogy, understanding it as both a confrontation between the border of the natural and the supernatural, as well as a moment in the history of psychology. My interpretation touches upon a number of important aspects, including why the analogy was rejected, how Harvey systematically deployed analogies according to his notions of natural philosophical method, how the analogy fits into contemporary discussions of analogies in science, and finally, how the analogy must be seen in the context of changing Renaissance notions of the science of the soul, ultimately confronting the problem of how to understand final causality in Aristotelian science. In connection with the last, I conclude the essay by turning to how Harvey embeds the analogy within a natural theological cosmology. (shrink)

Teleology has a complicated history in the biological sciences. Some have argued that Darwin’s theory has allowed biology to purge itself of teleological explanations. Others have been content to retain teleology and to treat it as metaphorical, or have sought to replace it with less problematic notions like teleonomy. And still others have tried to naturalize it in a way that distances it from the vitalism of the nineteenth century, focusing on the role that function plays in teleological explanation. No (...) consensus has seemed possible in this debate. This paper takes a different approach. It argues that teleology is a perfectly acceptable scientific notion, but that the debate took an unfortunate misstep some 2300 years ago, one that has confused things ever since. The misstep comes in the beginning of Aristotle’s Physics when a distinction is made between two types of teleological explanation. One type pertains to artifacts while the other pertains to entities in nature. For Aristotle, artifacts are guided by something external to themselves, human intentions, while natural entities are guided by an internal nature. We aim to show that there is, in fact, only one type of legitimate teleological explanation, what Aristotle would have considered a variant of an artifact model, where entities are guided by external fields. We begin with an analysis of the differences between the two types of explanation. We then examine some evidence in Aristotle’s biological works suggesting that on account of his natural-artifactual distinction, he encountered difficulties in trying to provide teleological accounts of spontaneous generation. And we show that it is possible to resolve these difficulties with a more robust version of an artifact model of teleology, in other words, with an externalist teleology. This is McShea’s model, in which goal-directed entities are guided by a nested series of upper-level fields. To explain teleological behavior, this account invokes only external physical forces rather than mysterious internal natures. We then consider how field theory differs from other efforts to naturalize teleology in biology. And finally, we show how the account enables us to grapple with certain difficult cases – genes and intentions – where, even in biology today, the temptation to posit internal natures remains strong. (shrink)

This dissertation examines Avicenna's theory of efficient causation in light of his approach to central problems in metaphysics, from the proof of the Necessary Existent to his emanative cosmology. Avicenna provides an internally coherent metaphysical account of efficient causation. A metaphysical account of the efficient cause explains the existence of the effect or essence in a way that is not explained by the causes of motion, as investigated in physics. That is, a full explanation of the cause of the existence (...) of an essence is not found in the four causes of natural change and motion. Avicenna aims to clarify what the explanatory division of labor is between the account of the natural philosopher and that of the metaphysician. In so doing, Avicenna develops a theory of causation that ties his innovative concepts of the contingent in itself and necessary in itself to the concept of efficient causation. A central distinction that Avicenna advances in relation to the efficient cause is that between the cause of the effect qua species and the cause of the effect qua individual. The distinction is relevant to understanding his view of the role of the causes of the essence, including the Active Intellect. Drawing on the above theory of efficient causation, the study reexamines Avicenna's famous proof for the Necessary Existent. The analysis shows that his metaphysical account of efficient causation is at the heart of his proof for a Necessary Existent. The "cause of persistence", in particular, is argued to have a more critical role than previously acknowledged, and is explicated in the context of his theory of efficient causation in metaphysics. (shrink)