Functions

We propose a definition of capability as a class intermediate between function and disposition as the latter are defined in Basic Formal Ontology (BFO). A disposition inheres in a material entity and is realized in a certain kind of process. An example is the disposition of a glass to break when struck, which is realized when it shatters. A function is a disposition which is (simply put) the rationale for the existence of its bearer. To say for example that a (...) water pump has the function to pump water is to say that the pump exists because something was needed that would pump water. Capabilities are a special sort of disposition in that that, like functions, they can be evaluated on the basis of how well they are realized. They differ from functions in that their realizations are not the rationale – not the primary reason – for the existence of their bearers. Thus, a water pump may have many capabilities, including to be weatherproof, to run without lubricant, and so forth, but only one function. All functions are capabilities on the view we defend, but not all capabilities are functions. We develop a series of axioms to distinguish capabilities formally from both dispositions and functions and provide examples of the use of ‘capability’ in a variety of domains. (shrink)

Philosophers of biology usually distinguish historical and systemic accounts of functions. In many areas of experimental biology the "systemic" account is often the most relevant. Yet there are problems this account does admittedly not face up to very well. My contention is that, though two minor problems are irredeemably unsolvable for the systemic account of function, the major ones can be solved by assuming that 'function' denotes (directly) a causal role in a model and (indirectly) the corresponding process in nature. (...) I try to show this through the analysis of the hypothalamus-pituitary-adrenal axis of stress. (shrink)

The notion of malfunction is critical to biological explanation. It provides a test-bed for the normative character of functional attribution. Theories of biological functioning must permit traits to operate but, at the same time, be judged as malfunctioning (in some naturalized, non-arbitrary sense). Whereas malfunctioning has attracted most attention and discussion in evolutionary etiological approaches, systemic and organizational ones have been less discussed. The most influential of the organizational approaches (by Saborido, Moreno and Mossio) takes a dual-order approach to malfunctions, (...) as a set of functions that fit first-order constitutive norms but fail to obey second-order regulatory ones. We argue that this conception is unnecessarily complicated (malfunctions do not need to arise as a result of two conflicting orders of norms) and too narrow (it excludes canonical cases of malfunctioning). We provide an alternative organizational account grounded on viability theory. The dynamics of the traits that constitute an organism define the normative field of its viability space: sugar must be replaced at certain rate, blood must be pumped at a certain pace, etc. A trait operates normatively when its effects on the viability space correlate positively with the normative field. Three senses of dysfunctionality might be distinguished: subfunctional operations are those that positively correlate with the normative field but quantitatively fail to match the required speed; malfunctional operations are those that do not positively correlate with the normative field; and, nonfunctional traits either don’t operate at all or operate with null effect on the normative field. (shrink)

Episodic memory is memory for past events. It’s characteristically associated with an experience of ‘mentally replaying’ one’s experiences in the mind’s eye. This biological phenomenon has inspired the development of several ‘experience replay’ algorithms in AI. In this chapter, I ask whether experience replay algorithms might shed light on a puzzle about episodic memory’s function: what does episodic memory contribute to the cognitive systems in which it is found? I argue that experience replay algorithms can serve as idealized models of (...) episodic memory for the purposes of addressing this question. Taking the DQN algorithm as a case study, I suggest that these algorithms provide some support for mnemonic accounts, on which episodic memory’s function lies in the storage, encoding and retrieval of information. By extending and adapting experience replay algorithms, we might gain further insight into episodic memory’s operations and contributions to cognition. (shrink)

Ruth Millikan and Mark Bickhard both offer theories of representation that can be understood as broadly teleosemantic. Both agree that representations have an essentially normative character and that their normativity should be understood by appealing to some biological notion of function. Their fundamental difference has to do with their accounts of biological function. Millikan offers an etiological account of function, according to which the function of a thing is to be understood in terms of what is has been designed to (...) do, or been selected for. According to such an account, whether or not a thing has a particular function depends on the history of the thing. Bickhard, in contrast, argues that we should understand function in non-etiological terms. Instead of appealing to design or selection, Bickhard appeals to the notion of dynamic presuppositions. Living beings are complex systems that involve multiple interconnected processes and there are dynamic presuppositions between the various processes. So according to such an account the reason why the function of the heart is to pump blood, is not because it was selected for this task, but that if it stopped pumping blood the whole organism would die, including the heart itself. I will argue that both Bickhard and Millikan are substantially correct in their positive theses. Rather than being incompatible theories that are attempting to explain the same thing, they offer distinct notions of function, biological normativity and representation that both have their place and provide for distinct, but equally valid and non-competing types of explanation. (shrink)

Do perceptual states necessarily constitute evidence epistemically supporting corresponding perceptual beliefs? Susanna Schellenberg thinks so. She argues that perceptual states, veridical or not, necessarily provide (or constitute) a kind of evidence (for the existence of the truth-maker) supporting corresponding perceptual beliefs. She uses “phenomenal evidence” as a label for this kind of evidence and calls her argument “The Phenomenal Evidence Argument.” Having introduced her project, we offer a reconstruction of Schellenberg’s argument (Sect. 2 ). A key premise has it that, (...) necessarily, for items with a function, fulfillment of the function (the good case) is explanatorily and metaphysically prior to function failure (the bad case). We suggest that the etiological theory of functions renders this key premise plausible (Sect. 3 ). However, Schellenberg rejects the etiological theory of functions (Sect. 4 ) and likewise the idea that the epistemic or warranting force of perceptual states is grounded in their being reliably linked to veridical perception (Sect. 5 ). But then what supports the key premise? Schellenberg argues that accurate perception is a part of the _nature_ of perceptual capacities because the nature of perceptual capacities is explained in terms of their function, and their function is to represent accurately (Sect. 6 ). We suggest that Schellenberg is committed to an understanding of priority which doesn’t require any _actual_ good cases—just possible ones (Sect. 7 ). This reading, we argue, is too weak to support the key premise (Sect. 8 ). Given Schellenberg’s commitments, it is not necessarily the case that perceptual states are evidence for a corresponding perceptual belief. Before concluding we discuss an overgeneralization objection to Schellenberg’s argument (Sect. 9 ). (shrink)

The question “What is it to be an artifact?” must be distinguished from the question “What is it to be an artifact of kind K?”. Failure to distinguish between these two questions leads to an exaggeration of the role of intentions in the philosophy of artifacts. We accept that intentions are necessary to define the category of artifacts, but we reject the view that intentions are constitutive of what makes something a specific kind of artifact. In the first part of (...) this paper, we discuss a series of cases involving what we call “faith-based artifacts” which often exhibit a social dimension. These cases, we argue, constitute counterexamples to the thesis that something is an artifact of a specific kind if it was produced with the intention that it be an object of that kind. In the second part of the paper, we explain how a capacity-based approach to artifacts, by contrast, can accommodate faith-based artifacts. In the last section, we address an objection to the capacity-based approach. (shrink)

Since the early debates on teleosemantics, there have been people objecting that teleosemantics cannot account for evolutionarily novel contents such as “democracy” (e.g., Peacocke in A Study of Concepts, MIT Press, Cambridge, 1992). Most recently, this objection was brought up by Garson (What Biological Functions Are and Why They Matter, Cambridge University Press, Cambridge, 2019.) and in a more moderate form by Garson and Papineau (Biol Philos 34(3):36, 2019.). The underlying criticism is that the traditional selected effects theory of functions (...) on which teleosemantics is built is unable to ascribe new functions to the products of ontogenetic processes and thus unable to ascribe functions to new traits that appear during the lifetime of an individual organism. I will argue that this underlying thought rests on rather common misunderstandings of Millikan’s theory of proper functions, especially her notions of relational, adapted, and derived proper functions (Millikan in Language, Thought, and Other Biological Categories: New Foundations for Realism, MIT Press, Cambridge, 1984: Ch. 2). The notions of relational, adapted, and derived proper functions not only help us solve the problem of novel contents and can ascribe functions to the products of ontogenetic selection mechanisms but are indispensable parts of every selected effects theory. (shrink)

Ruth Millikan and Mark Bickhard both offer theories of representation that can be understood as broadly teleosemantic. Both agree that representations have an essentially normative character and that their normativity should be understood by appealing to some biological notion of function. Their fundamental difference has to do with their accounts of biological function. Millikan offers an etiological account of function, according to which the function of a thing is to be understood in terms of what is has been designed to (...) do, or been selected for. According to such an account, whether or not a thing has a particular function depends on the history of the thing. Bickhard, in contrast, argues that we should understand function in non-etiological terms. Instead of appealing to design or selection, Bickhard appeals to the notion of dynamic presuppositions. Living beings are complex systems that involve multiple interconnected processes and there are dynamic presuppositions between the various processes. So according to such an account the reason why the function of the heart is to pump blood, is not because it was selected for this task, but that if it stopped pumping blood the whole organism would die, including the heart itself. I will argue that both Bickhard and Millikan are substantially correct in their positive theses. Rather than being incompatible theories that are attempting to explain the same thing, they offer distinct notions of function, biological normativity and representation that both have their place and provide for distinct, but equally valid and non-competing types of explanation. (shrink)

In our daily lives, as in science and in all other domains, we encounter huge numbers of dispositions (tendencies, potentials, powers) which are realized in processes such as sneezing, sweating, shedding, melting. Among this plethora of what we can think of as ‘mere dispositions’ is a subset of dispositions in whose realizations we have an interest – a car responding well when driven on ice, a rabbit’s lungs responding well when it is chased by a wolf, and so on. We (...) call the latter ‘capabilities’ and we attempt to provide an ontological account of what capabilities are that is of sufficient generality to serve a variety of purposes, for example by providing a useful extension to ontology-based research in areas where capabilities data are being collected in siloed fashion. (shrink)

The etiological account of teleological function is beset by several difficulties, which I propose to solve by grafting onto the etiological theory a subordinated goal-contribution clause. This approach enables us to ascribe neither too many teleofunctions nor too few; to give a unitary, one-clause analysis that works just as well for teleological functions derived from Darwinian evolution, as for those derived from human intention; and finally, to save the etiological theory from falsification, by explaining how, in spite of appearances, the (...) theory can allow for evolutionary function loss. (shrink)

Anna Smajdor and Joona Räsänen argue that we have good reason to classify pregnancy as a disease. They discuss five accounts of disease and argue that each account either implies that pregnancy is a disease or, if it does not, it faces problems. This strategy allows Smajdor and Räsänen to avoid articulating their own account of disease. Consequently, they cannot establish that pregnancy is a disease, only that plausible accounts of disease suggest this. Some readers will dismiss Smajdor and Räsänen’s (...) claims as counterintuitive. By analogy, if a mathematical proof concludes ‘2+2=5’, readers will know—without investigation—that an error occurred. Rather than dismiss Smajdor and Räsänen’s work, however, the easiest way to undermine their argument is to describe at least one plausible account of disease that (i) excludes pregnancy and (ii) avoids the problems they raise for it. This is our strategy. We focus on dysfunction accounts of disease. After outlining Smajdor and Räsänen’s main arguments against dysfunction accounts, we explain why pregnancy is not a disease on these accounts. Next, we defend dysfunction accounts against the three problems that Smajdor and Räsänen raise. If successful, then contra Smajdor and Räsänen, at least one plausible account of disease does not imply that pregnancy is a disease. We suspect that defenders of other accounts can respond similarly. Yet, we note that insofar as dysfunction accounts align with the commonsense intuition that pregnancy is not a disease, this, all else being equal, seems like a point in their favour. (shrink)

Teleosemantic theories aim to naturalize mental representation through the use of functions, typically based on past selection processes. However, the historical dependence of these theories has faced severe criticism, leading some philosophers to develop ahistorical alternatives. -/- This paper presents a new dilemma for all ahistorical teleosemantic theories, focusing in particular on the theories proposed by Timothy Schroeder and Bence Nanay. These theories require certain dispositions in the producers or consumers of mental representations. But the appeal to dispositions puts the (...) proponents in an undesirable position: mental content is either overly dependent on current circumstances or ultimately dependent on historical factors. (shrink)

In her book “Are Mental Disorders Brain Disorders?” (2022), Anneli Jefferson proposes that brain processes that always realize mental dysfunctions are brain dysfunctions. This paper explores possible interpretations of two underdeveloped aspects of this thesis. First, it argues that “realization” should be interpreted as partial rather than full realization. Second, it argues that the “always” should only quantify over biologically normal situations. Taken together, these changes can account for the fact that some psychological dysfunctions are partially realized by functional mechanisms, (...) for the existence of psychological dysfunctions due to mismatches rather than brain dysfunctions, and for the fact that brain dysfunctions do not cease to be brain dysfunctions just because they can be compensated. (shrink)

Justin Garson has recently argued that proper functions are proximal activities of traits selected by phylogenetic or ontogenetic selection processes, and that traits are dysfunctional only if they cannot perform their proper functions for constitutional reasons. We partially agree with Garson, but reject the view that functions are proximal activities, as well as his account of dysfunctions. Instead, we propose our own theory that biological functions are selected dispositions and that a trait is dysfunctional in virtue of not having the (...) dispositions for which it was selected. This account can explain both defects (or dysfunctions in Garson’s sense) and dysfunctions due to environmental factors. Moreover, it offers a neat way to explain the graduality of dysfunction. (shrink)

A satisfactory analysis of human deception must rule out cases where it is a mistake or an accident that person B was misled by person A's behavior. Therefore, most scholars think that deceivers must intend to deceive. This article argues that there is a better solution: rather than appealing to the deceiver's intentions, we should appeal to the function of their behavior. After all, animals and plants engage in deception, and most of them are not capable of forming intentions. Accordingly, (...) certain human behavior is deceptive if and only if its function is to mislead. This solves our problem because if the function of A's behavior was to mislead, B's ending up misled was not an accident or a mere mistake even if A did not intend to deceive B. (shrink)

Philosophers tend to focus on the metaphysics of functions: establishing unifying theories employing general criteria for being a function, avoiding spooky backward causation, distinguishing functions from accidents, and correctly representing the functional structure of the world. We show that there is a need for localized, practice-sensitive accounts of the epistemology of functions—accounts that explain the identification, justification, and explanatory applications of function attributions in particular scientific contexts—and that this need is best met alongside a plurality of unifying metaphysical theories of (...) functions. Our argument begins with the observation that unifying theories assume that (i) functions are discovered or justified by criteria for being a function and (ii) criteria identified in a theory are generally applicable across target systems. We then draw on examples from cognitive science and ecology to show that function ascriptions are sometimes presupposed or assigned based on highly contextual epistemic factors not described in unifying metaphysical theories. (shrink)

In recent times, the exponential growth of sequenced genomes and structural knowledge of proteins, as well as the development of computational tools and controlled vocabularies to deal with this growth, has fueled a demand for conceptual clarification regarding the concept of function in molecular biology. In this article, we will attempt to develop an account of function fit to deal with the conceptual/philosophical problems in that domain, but which can be extended to other areas of biology. To provide this account, (...) we will argue for three theses: (1) some authors have confused metatheoretical issues (about the meaning and application criteria of terms) with metaphysical ones (about teleology); this led them to (2) look for explicit definitions of “function”, in terms of necessary and sufficient criteria of application, in order to make the concept of function eliminable; however, (3) if one leaves metaphysical worries aside and focuses on functional attribution practices, it is more adequate to say that the concept of function has an open texture. That is, that a multiplicity of application criteria is available, none of which is sufficient nor necessary to attribute a function to a trait, and which only in concert form a clear picture. We distinguish this thesis from some usual forms of pluralism. Finally, we will illustrate this account with a historical reconstruction of the ascription of a water transport function to aquaporins. (shrink)

In this paper we provide an ontological analysis of so-called “artifactual functions” by deploying a realizable-centered approach to artifacts which we have recently developed within the framework of the upper ontology Basic Formal Ontology (BFO). We argue that, insofar as material artifacts are concerned, the term “artifactual function” can refer to at least two kinds of realizable entities: novel intentional dispositions and usefactual realized entities. They inhere, respectively, in what we previously called “canonical artifacts” and “usefacts”. We show how this (...) approach can help to clarify functions in BFO, whose current elucidation includes reference to the term “artifact”. In our framework, having an artifactual function implies being an artifact, but not vice versa; in other words, there are artifacts that lack an artifactual function. (shrink)

Artifacts remain nebulous entities, notwithstanding their relevance to various domains such as engineering, art and archeology. In this paper we investigate the interconnection between artifacts and realizable entities, as illustrated by dispositions, functions, and roles within the framework of the upper ontology Basic Formal Ontology (BFO). More concretely, we propose the notions of canonical artifact (something that is intentionally produced for some purpose) and usefact (something that is intended to be used for some non-original purpose) which can correspond to various (...) usages of the term “artifact”. We also characterize them in terms of intentional realizable entities and novel realizable entities: material canonical artifacts and material usefacts can be analyzed in terms of novel intentional realizable entities and a special kind of non-novel intentional realizable entities, respectively. (shrink)

There are three main accounts of the proper function of the low mood system (LMS): the social risk theory, the disease theory, and the propitiousness theory. Adjudicating between these accounts has proven difficult, as there is little agreement in the literature about what a theory of the LMS’s proper function is supposed to explain. In this article, drawing upon influential work on the evolution of other affective systems, such as the disgust system and the fear system, I argue that a (...) theory of the proper function of the low mood system should: (i) account for the reliable, distal causes and effects of the system’s activation, and (ii) explain how having a system that performed such a function increased fitness in ancestral environments. On this basis, I show that the proper function of the low mood system is to limit resource expenditure in relatively unpropitious circumstances, exactly as hypothesised by the propitiousness theory. (shrink)

Cancer biology features the ascription of normal functions to parts of cancers. At least some ascriptions of function in cancer biology track local normality of parts within the global abnormality of the aberration to which those parts belong. That is, cancer biologists identify as functions activities that, in some sense, parts of cancers are supposed to perform, despite cancers themselves having no purpose. The present paper provides a theory to accommodate these normal function ascriptions—I call it the Modeling Account of (...) Normal Function (MA). MA comprises two claims. First, normal functions are activities whose performance by the function-bearing part contributes to the self-maintenance of the whole system and, thereby, results in the continued presence of that part. Second, MA holds that models of system-level activities that are (partly) constitutive of self-maintenance are improved by including a representation of the relevant function-bearing part and by making reference to the activity/activities that part performs which contribute(s) to those system-level activities. I contrast MA with two other accounts that seek to explicate the ascription of normal functions in biology, namely, the organizational account and the selected effects account. Both struggle to extend to cancer biology. However, I offer ecumenical readings which allow them to recover some ascriptions of normal function to parts of cancers. So, though I contend that MA excels in this respect, the purpose of this paper is served if it provides materials for bridging the gap between cancer biology, philosophy of cancer, and the literature on function. (shrink)

Proper functionalism explicates epistemic warrant in terms of the function and normal functioning of the belief-forming process. There are two standard substantive views of the sources of functions in the literature in epistemology: God (intelligent design) or Mother Nature (evolution by natural selection). Both appear to confront the Swampman objection: couldn’t there be a mind with warranted beliefs neither designed by God nor the product of evolution by natural selection? Is there another substantive view that avoids the Swampman objection? There (...) are two. The first is the generalized selected-effects theory of functions. The second is the organizational theory of functions. Both, however, require some history to assign functions, for both are etiological theories of functions: past effects help explain current function. Swampman can then acquire functions, perhaps soon after creation, though he has none at the moment of inception. (shrink)

Perception provides us with access to the external world, but that access is shaped by our own experiential histories. Through perceptual learning, we can enhance our capacities for perceptual discrimination, categorization, and attention to salient properties. We can also encode harmful biases and stereotypes. This article reviews interdisciplinary research on perceptual learning, with an emphasis on the implications for our rational and normative theorizing. Perceptual learning raises the possibility that our inquiries into topics such as epistemic justification, aesthetic criticism, and (...) moral knowledge should include not only an examination of cognition but also of perception. (shrink)

Our perceptual systems are not stagnant but can learn from experience. Why is this so? That is, what is the function of perceptual learning? I consider two answers to this question: The Offloading View, which says that the function of perceptual learning is to offload tasks from cognition onto perception, thereby freeing up cognitive resources (Connolly, 2019) and the Perceptual View, which says that the function of perceptual learning is to improve the functioning of perception. I argue that the Perceptual (...) View better explains data from infants and animals, and better accounts for learned tasks that only perception could perform. (shrink)

According to recent work in experimental philosophy, folk intuitions concerning various metaphysical issues are heavily teleological. The experiments in question, which belong to a broader research program in psychology about ‘promiscuous teleology’, have featured prominently in debates about the methodology of metaphysics, with some authors claiming that the folk’s teleological bias debunks everyday intuitions concerning composition, persistence, and organisms. The present paper argues for a possibility that is very rarely discussed in that debate, namely the idea that the folk’s intuitions (...) could be veridical. Our argument is based on an emerging naturalistic theory of biological functions called “the organismic view”. The gist of the organismic view is that biological systems are characterized by a special circular causal regime where each part of the system contributes to the boundary conditions of some other parts, as well as of the whole. We argue that teleological folk intuitions are veridical in the biological domain under such a view, and they are veridical in the social and artefactual domains under coherent extensions of the organismic view. (shrink)

Since the ENCODE project published its final results in a series of articles in 2012, there is no consensus on what its implications are. ENCODE’s central and most controversial claim was that there is essentially no junk DNA: most sections of the human genome believed to be «junk» are functional. This claim was met with many reservations. If researchers disagree about whether there is junk DNA, they have first to agree on a concept of function and how function, given a (...) particular definition, can be discovered. The ENCODE debate centered on a notion of function that assumes a strong dichotomy between evolutionary and non-evolutionary function and causes, prevalent in the Modern Evolutionary Synthesis. In contrast to how the debate is typically portrayed, both sides share a commitment to this distinction. This distinction is, however, much debated in alternative approaches to evolutionary theory, such as the EES. We show that because the ENCODE debate is grounded in a particular notion of function, it is unclear how it connects to broader debates about what is the correct evolutionary frame- work. Furthermore, we show how arguments brought forward in the controversy, particularly arguments from mathematical population genetics, are deeply embedded in their particular disciplinary contexts, and reflect substantive assumptions about the evolution of genomes. With this article, we aim to provide an anatomy of the ENCODE debate that offers a new perspective on the notions of function both sides employed, as well as to situate the ENCODE debate within wider debates regarding the forces operating in evolution. (shrink)

The classification of preserved hypothalamic activity in brain death and brainstem death as functional or non-functional has become a subject of debate. While proponents of the neurological criterion claim that these activities lack functional significance (Shemie et al. 2014), Nair-Collins and Joffe (2023) argue for their functional physiological role. However, the interpretation of the term "function" within the medico-legal framework, where death is characterized by the irreversible cessation of all brain functions, remains unclear. -/- My intention here is not to (...) engage in a debate over the validity of different viewpoints regarding the functional significance of preserved activities in the hypothalamus or the heart. Rather, I aim to highlight the critical importance of exploring and defining the concept of function in medicine, which currently lacks clarity. My point is that, whatever our position in the brain death debate, reaching a consensus on this conceptual matter would minimize misunderstandings and establish a robust foundation for further insightful analysis. (shrink)

The Uniform Determination of Death Act (UDDA) provides that “an individual who has sustained either (1) irreversible cessation of circulatory and respiratory functions or (2) irreversible cessation of all functions of the entire brain, including the brain stem, is dead.” We show that the UDDA contains two conflicting interpretations of the phrase “cessation of functions.” By one interpretation, what matters for the determination of death is the cessation of spontaneous functions only, regardless of their generation by artificial means. By the (...) other, what matters is the cessation of both spontaneous and artificially supported functions. Because each UDDA criterion uses a different interpretation, the law is conceptually inconsistent. A single consistent interpretation would lead to the conclusion that conscious individuals whose respiratory and circulatory functions are artificially supported are actually dead, or that individuals whose brain is entirely and irreversibly destroyed may be alive. We explore solutions to mitigate the inconsistency. (shrink)

Disputes about the causal structure of natural selection have implications for teleosemantics. Etiological, mainstream teleosemantics is based on a causalist view of natural selection. The core of its solution to Brentano’s Problem lies in the solution to Kant’s Puzzle provided by the Modern Synthesis concerning populational causation. In this paper, I suggest that if we adopt an alternative, statisticalist view on natural selection, the door is open for two reflections. First, it allows for setting different challenges to etiological teleosemantics that (...) arise if a statisticalist reading of natural selection is right. Second, by providing a different solution to Kant’s Puzzle based on individual causes of evolution, statisticalism promotes a different answer to Brentano’s Problem, what I label as Agential Teleosemantics. (shrink)

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)

We characterize a type of functional explanation that addresses why a homologous trait originating deep in the evolutionary history of a group remains widespread and largely unchanged across the group’s lineages. We argue that biologists regularly provide this type of explanation when they attribute conserved functions to phenotypic and genetic traits. The concept of conserved function applies broadly to many biological domains, and we illustrate its importance using examples of molecular sequence alignments at the intersection of evolution and cell biology. (...) We use these examples to show how the study of conserved functions can integrate knowledge of a trait’s causal effects on fitness and its history of natural selection without invoking adaptation. We also show how conserved function provides a novel basis for addressing objections against evolutionary functions raised by Robert Cummins. (shrink)

The theoretical biology movement originating in Britain in the early 1930’s and the biosemiotics movement which took off in Europe in the 1980’s have much in common. They are both committed to replacing the neo-Darwinian synthesis, and they have both invoked theories of signs to this end. Yet, while there has been some mutual appreciation and influence, particularly in the cases of Howard Pattee, René Thom, Kalevi Kull, Anton Markoš and Stuart Kauffman, for the most part, these movements have developed (...) independently of each other. Focussing on morphogenesis understood as vegetative semiosis, in this paper I will argue that the ideas of these movements are commensurate. Furthermore, synthesising them would enable us to see life processes as proto-narratives. Doing so will involve synthesising biohermeneutics, Peircian biosemiotics with Waddington’s theoretical biology and Piagetian genetic structuralism, and this, I claim, would strengthen the challenge of these traditions to mainstream biology. At the same time, this should contribute to overcoming the opposition between the sciences and the humanities, developing a broader tradition of Schellingian thought which involves developing the humanities and then demanding of the physical and biological sciences that they are consistent with and can make intelligible the emergence of humans as conceived by the humanities. (shrink)

The culturally pervasive tendency to identify aspects of the body as aesthetically imperfect harms individuals and scaffolds injustice related to disability, race, gender, LGBTQ+ identities, and fatness. But abandoning the notion of imperfection may not respect people’s reasonable understandings of their own bodies. I examine the prospects for a practice of aesthetic assessment grounded in a notion of the body’s function. I argue that functional aesthetic assessment, to be respectful, requires understanding the body’s functions as complex, malleable, and determined by (...) the projects and interests of the person whose body it is. Aesthetically relevant functions, on this account, are determined neither by the body’s status as organism nor by cultural assumptions about how bodies should function or be used. (shrink)

The proper function of the heart is pumping the blood. According to what we call the type etiological view, this is because previous tokens of the type HEART were selected for pumping the blood. Nanay :412–431, 2010) argues that the type etiological view is viciously circular. He claims that the only plausible accounts of trait type individuation use proper functions, such that whenever the type etiological view is supplemented with a plausible account of trait type individuation, the result is a (...) view that uses proper functions to explain proper functions. We refine this objection, and argue that Nanay at most establishes a potentially benign definitional circularity. However, we show that the type etiological view’s reliance on types nevertheless generates a vicious regress. Hence the type etiological view is false. We reject dispositional and modal alternatives to the type etiological view for the reason that they either cannot accommodate malfunction, or do so at the cost of proliferation; and then formulate a novel token etiological view that overcomes both problems because it makes no reference to trait types. (shrink)

Do essence-based accounts of necessity and Vetter’s potentiality-based account of possibility in fact lead to the same result, viz., a single derived notion of necessity that is interdefinable with possibility or vice versa? And does each approach independently have the ability to reach its desired goal without having to rely on the primitive notion utilized by the other? In this essay, I investigate these questions and Vetter’s responses to them. Contrary to the “separatist” position defended by Vetter, I argue that (...) there are reasons to favor “Combination”, according to which an essence-based account of necessity should be combined with a potentiality-based account of possibility, or vice versa. According to this alternative approach, essentialism and potentialism should be regarded as allies, rather than as competitors, in a theory of derived modality, since both notions are needed in order to give a full account of necessity and possibility. Keywords: possibility, necessity, potentiality, essence, interdefinability, actuality, dependence, artifact-functions. (shrink)

50 years after its introduction, brain death remains controversial among scholars. The debates focus on one question: is brain death a good criterion for determining death? This question has been answered from various perspectives: medical, metaphysical, ethical, and legal or political. Most authors either defend the criterion as it is, propose some minor or major revisions, or advocate abandoning it and finding better solutions to the problems that brain death was intended to solve when it was introduced. Here I plead (...) for a different approach that has been overlooked in the literature: the philosophy of science approach. Some scholars claim that human death is a matter of fact, a biological phenomenon whose occurrence can be determined empirically, based on science. We should take this claim seriously, whether we agree with it or not. The question is: how do we know that human death is a scientific matter of fact? Taking the philosophy of science approach means, among other things, examining how the determination of human death became an object of scientific inquiry, exploring the nature of the brain death criterion itself, and analysing the meaning of its core concepts such as “irreversibility” and “functions”. (shrink)

Abstract One of the most important things that the Darwinian revolution affected is the previous teleological thinking. In particular, the attribution of functions to various entities of the natural world with explanatory pretensions. In this change, his theory of natural selection played an important role. We all agree on that, but the diversity and heterogeneity of the answers that try to explain what Darwin did exactly with functional biology are overwhelming. In this paper I will try to show how Darwin (...) modified previous functional biology. Pre-Darwinian naturalists did not hesitate to attribute functions in which, for example, the traits of one species were in the service of other species. I will try to show that this has consequences on the discussion regarding the nature of functional language, since the main approaches, the systemic and the etiological, do not adequately account for these changes and therefore do not account for the way functional biology regulates the kind of legitimate functions. I will outline a possible new solution to this problem: appropriate functional attributions in Darwinian functional biology could be regulated by a theory or a set of laws that provide the criteria for determining its fundamental concepts. -/- Resumen: Una de las cosas más importantes a las que la revolución darwiniana afectó es el pensamiento teleológico previo. En particular, la atribución de funciones a diversas entidades del mundo natural con pretensiones explicativas. En este cambio, su teoría de la selección natural desempeñó un papel importante. Todos estamos de acuerdo en ello, pero la diversidad y heterogeneidad de las respuestas que tratan de explicar lo que Darwin hizo exactamente con la biología funcional son abrumadoras. En este artículo intentaré mostrar cómo Darwin modificó la biología funcional anterior. Los naturalistas predarwinianos no dudaban en atribuir funciones en las que, por ejemplo, los rasgos de una especie estaban al servicio de otras especies. Intentaré mostrar que esto tiene consecuencias en la discusión sobre la naturaleza del lenguaje funcional, pues los principales enfoques, el sistémico y el etiológico, no dan cuenta adecuadamente de estos cambios y, por tanto, no dan cuenta de la forma en que la biología funcional regula el tipo de funciones legítimas. Esbozaré una posible nueva solución a este problema: las atribuciones funcionales apropiadas en la biología funcional darwiniana podrían estar reguladas por una teoría o un conjunto de leyes que proporcionen los criterios para determinar sus conceptos fundamentales. -/- . (shrink)

In the target article, Christie, Brusse, et al. argue that selected effect functions do not, in general, explain why a trait exists in a population and, therefore, theories of representational content should not rely on selected effect functions. This response focuses on the claim about functions-for-representation. The role of evolutionary functions in a theory of content is to pick out outcomes that have been systematically stabilized by natural selection. Correctness conditions are conditions involved in explaining how that happened. Selected effect (...) functions can play that role in the complex equilibria that Christie, Brusse, et al. identify. Non-equilibrium cases are also discussed. (shrink)

In his _Between Logic and the World_, in the course of presenting his theory of generics, Nickel (Between logic and the world, Oxford University Press, 2016) argues for a theory of characteristicness, or “genericity”, which states that a property is characteristic for a kind if and only if its presence among the members of that kind is explicable by some explanatory domain that recognizes the existence of that kind in the course of engaging the explanatory strategies made available by that (...) explanatory domain. I argue that this notion of genericity is too narrow, excluding properties characteristic for kinds that go unrecognized in such explanatory domains. In particular, Nickel’s theory excludes some characteristic properties of anthropic kinds, such as lilies and cedars, members of which have properties that may be similarly exploited in various human practices despite having divergent geneses. I argue for a generalization of Nickel’s view of genericity where explicability of presence is only one sort of genericity, with others, such as practicability, being possible too. (shrink)

The goal of this essay is to put forward an original theory of artifact function, which takes on board the results of the debate on the notion of biological function and also accommodates the distinctive aspects of artifacts. More precisely, the paper develops and defends the Dual-Aspect Theory, which is a monist account according to which an artifact’s function depends on intentional and reproductive aspects. It is argued that this approach meets a set of theoretical and meta-theoretical desiderata and is (...) superior to alternative views. (shrink)

Recent research on bacteria and other microorganisms has provided interesting insights into the nature of life, cooperation, evolution, individuality or species. In this paper, I focus on the capacity of bacteria to produce molecules that are usually classified as ’signals’ and I defend two claims. First, I argue that certain interactions between bacteria should actually qualify as genuine forms of communication. Second, I use this case study to revise our general theories of signaling. Among other things, I argue that a (...) plausible requirement for a state to qualify as a signal is that it is a minimal cause. (shrink)

The goal of this essay is to assess the Selected-Effects Etiological Theory of biological function, according to which a trait has a function F if and only if it has been selected for F. First, I argue that this approach should be understood as describing the paradigm case of functions, rather than as establishing necessary and sufficient conditions for function possession. I contend that, interpreted in this way, the selected-effects approach can explain two central properties of functions and can satisfactorily (...) address some recent counterexamples. This reading, however, shows that there is only a partial overlap between biological functions and selected effects, so the former cannot be reduced to the latter. Finally, I maintain that this result is still compatible with a naturalistic theory of function that appeals to some evolutionary process. (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)

The new mechanists and the autonomy approach both aim to account for how biological phenomena are explained. One identifies appeals to how components of a mechanism are organized so that their activities produce a phenomenon. The other directs attention towards the whole organism and focuses on how it achieves self-maintenance. This paper discusses challenges each confronts and how each could benefit from collaboration with the other: the new mechanistic framework can gain by taking into account what happens outside individual mechanisms, (...) while the autonomy approach can ground itself in biological research into how the actual components constituting an autonomous system interact and contribute in different ways to realize and maintain the system. To press the case that these two traditions should be constructively integrated we describe how three recent developments in the autonomy tradition together provide a bridge between the two traditions: (1) a framework of work and constraints, (2) a conception of function grounded in the organization of an autonomous system, and (3) a focus on control. (shrink)

According to Karen Neander’s causal-informational teleosemantics, the contents of perceptual states depend on the etiological response functions of sensory-perceptual systems. In this paper, I argue that this theory is, despite its virtues, unable to explain how humans and other animals are capable of perceiving properties with which no sensory-perceptual system has ever been confronted. After rejecting Neander’s own proposal in terms of second-order similarity and a proposal inspired by Ruth Millikan in terms of simplicity, I offer a solution which equates (...) functions with manifestations of dispositions that made a difference to evolutionary success. My suggestion is able to generate determinate and plausible contents for new perceptual states while still preserving the idea that etiological functions explain evolutionary success. (shrink)

I provide two arguments against value-free naturalism. Both are based on considerations concerning biological teleology. Value-free naturalism is the thesis that both (1) everything is, at least in principle, under the purview of the sciences and (2) all scientific facts are purely non-evaluative. First, I advance a counterexample to any analysis on which natural selection is necessary to biological teleology. This should concern the value-free naturalist, since most value-free analyses of biological teleology appeal to natural selection. My counterexample is unique (...) in that it is likely to actually occur. It concerns the creation of synthetic life. Recent developments in synthetic biology suggest scientists will eventually be able to develop synthetic life. Such life, however, would not have any of its traits naturally selected for. Second, I develop a simple argument that biological teleology is a scientific but value-laden notion. Consequently, value-free naturalism is false. I end with some concluding remarks on the implications for naturalism, the thesis that (1). Naturalism may be salvaged only if we reject (2). (2) is a dogma that unnecessarily constrains our conception of the sciences. Only a naturalism that recognizes value-laden notions as scientifically respectable can be true. Such a naturalism is a functional naturalism. (shrink)

Analytic Philosophy, Volume 62, Issue 4, Page 336-358, December 2021.

I introduce functional powers, i.e., causal powers that play the role of functions. In the first section, I characterize functions and present some desiderata for a good theory of functions. In the second section, I make some assumptions about the ontology of powers, teleology and structures-that will be helpful in order to ground my account of functional powers. In the third section, sixteen different types of functional powers are examined. All such types of functional powers will exhaustively contribute to performing (...) all the ontological and explanatory tasks that may be attributed to functions. Finally, in the fourth section, it is shown how my account of functions as functional powers satisfies all the desiderata presented at the outset. (shrink)

I introduce functional powers, i.e., causal powers that play the role of functions. In the first section, I characterize functions and present some desiderata for a good theory of functions. In the second section, I make some assumptions about the ontology of powers, teleology and structures-that will be helpful in order to ground my account of functional powers. In the third section, sixteen different types of functional powers are examined. All such types of functional powers will exhaustively contribute to performing (...) all the ontological and explanatory tasks that may be attributed to functions. Finally, in the fourth section, it is shown how my account of functions as functional powers satisfies all the desiderata presented at the outset. (shrink)