How objective are biological functions?

John Searle has argued that functions owe their existence to the value that we put into life and survival. In this paper, I will provide a critique of Searle’s argument concerning the ontology of functions. I rely on a standard analysis of functional predicates as relating not only a biological entity, an activity that constitutes the function of this entity and a type of system but also a goal state. A functional attribution without specification of such a goal state has no truth-value. But if completed with a goal state, functional attributions understood as four-place relations attain a truth-value. The truth conditions of all attributions of function involve a dependence claim of the goal state on the function bearer’s activity. The nature of this dependence may differ; I consider five different possibilities: causality, mechanistic constitution, mereology, supervenience and metaphysical grounding. If these dependency relations are objective, Searle’s central ontological thesis fails. What he ought to have said is that our valuing survival or other goal states may be the reason why biology seeks functional knowledge, but this has nothing to do with ontology. I will show further that Searle also raised an interesting challenge concerning the relationship of functional and causal truths, but it does not threaten the objectivity of functions either. At best, it could show that functional vocabulary is eliminable. However, I will show that functional vocabulary is not so eliminable

Deflating Deflationary Truthmaking

In this paper we confront a challenge to truthmaker theory that is analogous to the objections raised by deflationists against substantive theories of truth. Several critics of truthmaker theory espouse a ‘deflationary’ attitude about truthmaking, though it has not been clearly presented as such. Our goal is to articulate and then object to the underlying rationale behind deflationary truthmaking. We begin by developing the analogy between deflationary truth and deflationary truthmaking, and then show how the latter can be found in the work of Dodd, Hornsby, Schnieder, Williamson, and others. These philosophers believe that the ambitions of truthmaker theory are easily satisfied, without recourse to ambitious ontological investigation—hence the analogy with deflationary truth. We argue that the deflationists’ agenda fails: there is no coherent deflationary theory of truthmaking. Truthmaking, once deflated, fails to address the questions at the heart of truthmaking investigation. Truthmaking cannot be had on the cheap

We don’t need no explanation

Explanation has played myriad roles in truthmaker theory. The notion of explanation is sometimes thought to give content to the very idea of truthmaking, and is sometimes used as a weapon to undermine the entire point of truthmaker theory. I argue that the notion of explanation is dialectically useless in truthmaker theory: while it’s true that truthmaking offers a form of explanation, this claim is theoretically unilluminating, and leaves truthmaker theorists vulnerable to various kinds of attack. I advocate an alternative approach to truthmaker theory that downplays the role of explanation, and show how it releases the enterprise from a variety of problematic commitments that have troubled truthmaker theorists. The “ontology-first” approach to truthmaking that I advocate not only restores the initial impulse behind truthmaking, but also has a number of theoretical advantages. Most prominently, it dodges the infamous problem of negative existentials, and lessens truthmaker theory’s dependence on contentious intuitive judgments about both explanation and truthmaking

The impact of science on metaphysics and its limits

The paper argues for three theses: (1) Metaphysics depends on science as a source of knowledge. Our current scientific theories commit us to certain metaphysical claims. (2) As far as science is concerned, it is sufficient to spell these claims out in such a way that they amount to a parsimonious ontology. That ontology, however, creates a gap between our experience and the scientific view of the world. (3) In order to avoid that gap and to achieve a complete and coherent view of the world including ourselves, we have to enrich that ontology at its foundations, thus making it less parsimonious. The criterion of the integration into a complete and coherent view of the world including ourselves is the way in which the interpretation of scientific theories depends on metaphysics. These three theses are argued for and illustrated by means of two examples from the philosophy of time (eternalism vs. presentism) and the philosophy of mind (mental causation)

Being Emergence vs. Pattern Emergence: Complexity, Control, and Goal-Directedness in Biological Systems

Emergence is much discussed by both philosophers and scientists. But, as noted by Mitchell (2012), there is a significant gulf; philosophers and scientists talk past each other. We contend that this is because philosophers and scientists typically mean different things by emergence, leading us to distinguish being emergence and pattern emergence. While related to distinctions offered by others between, for example, strong/weak emergence or epistemic/ontological emergence (Clayton, 2004, pp. 9–11), we argue that the being vs. pattern distinction better captures what the two groups are addressing. In identifying pattern emergence as the central concern of scientists, however, we do not mean that pattern emergence is of no interest to philosophers. Rather, we argue that philosophers should attend to, and even contribute to, discussions of pattern emergence. But it is important that this discussion be distinguished, not conflated, with discussions of being emergence. In the following section we explicate the notion of being emergence and show how it has been the focus of many philosophical discussions, historical and contemporary. In section 3 we turn to pattern emergence, briefly presenting a few of the ways it figures in the discussions of scientists (and philosophers of science who contribute to these discussions in science). Finally, in sections 4 and 5, we consider the relevance of pattern emergence to several central topics in philosophy of biology: the emergence of complexity, of control, and of goal-directedness in biological systems

Automatic annotation of bioinformatics workflows with biomedical ontologies

Legacy scientific workflows, and the services within them, often present scarce and unstructured (i.e. textual) descriptions. This makes it difficult to find, share and reuse them, thus dramatically reducing their value to the community. This paper presents an approach to annotating workflows and their subcomponents with ontology terms, in an attempt to describe these artifacts in a structured way. Despite a dearth of even textual descriptions, we automatically annotated 530 myExperiment bioinformatics-related workflows, including more than 2600 workflow-associated services, with relevant ontological terms. Quantitative evaluation of the Information Content of these terms suggests that, in cases where annotation was possible at all, the annotation quality was comparable to manually curated bioinformatics resources.Comment: 6th International Symposium on Leveraging Applications (ISoLA 2014 conference), 15 pages, 4 figure

Ontology-based knowledge representation of experiment metadata in biological data mining

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes

A Trope Theoretical Analysis of Relational Inherence

The trope bundle theories of objects are capable of analyzing monadic inherence (objects having tropes), which is one of their main advantage. However, the best current trope theoretical account of relational tropes, namely, the relata specific view leaves relational inherence (a relational trope relating two or more entities) primitive. This article presents the first trope theoretical analysis of relational inherence by generalizing the trope theoretical analysis of inherence to relational tropes. The analysis reduces the holding of relational inherence to the obtaining of certain other facts about entities of the trope theoretical category system. Moreover, I show that the analysis can deal with asymmetric and non-symmetric relations by assuming that all relation-like tropes are quantities. Finally, I provide an account of the spatial location of tropes in the difficult case in which tropes contribute to determining of the location of other entities

Practices of Art

Starting out from the ontology of human work set out by Marx in Das Kapital, the paper seeks to analyse the relations between the artist and his actions and aims, the work of art he produces, and the audience for this work. The paper concludes with a discussion of the problem of creativity in the arts, drawing on ideas of Roman Ingarden and other phenomenologists