Neo-Aristotelian ethical naturalism aims to place moral virtue in the natural world by showing that moral goodness is an instance of natural goodness—a kind of goodness supposedly also found in the biological realm of plants and non-human animals. One of the central issues facing neo-Aristotelian naturalists concerns their commitment to a kind of function ascription based on the concept of the flourishing of an organism that seems to have no place in modern biology. In this paper, I offer (...) a novel defense of this functional commitment by appealing to the organizational account of biological function. I argue that the flourishing-based concept of function that forms the basis of the neo-Aristotelian account of natural goodness is explanatorily indispensable to biology, and therefore essential to the understanding of living things. (shrink)

We introduce a new type of pluralism about biological function that, in contrast to existing, demonstrates a practical integration among the term’s different meanings. In particular, we show how to generalize Sandra Mitchell’s notion of integrative pluralism to circumstances where multiple epistemic tools of the same type are jointly necessary to solve scientific problems. We argue that the multiple definitions of biological function operate jointly in this way based on how biologists explain the evolution of protein (...) function. To clarify how our account relates to existing views, we introduce a general typology for monist and pluralist accounts along with standardized criteria for judging which is best supported by evidence. (shrink)

A new theory that naturalizes biological function is explained and compared with earlier etiological and causal role theories. Etiological theories explain functions from how they are caused over their evolutionary history. Causal role theories analyze how functional mechanisms serve the current capacities of their containing system. The new proposal unifies the key notions of both kinds of theories, but goes beyond them by explaining how functions in an organism can exist as factors with autonomous causal efficacy. The goal-directedness (...) and normativity of functions exist in this strict sense as well. The theory depends on an internal physiological or neural process that mimics an organism’s fitness, and modulates the organism’s variability accordingly. The structure of the internal process can be subdivided into subprocesses that monitor specific functions in an organism. The theory matches well with each intuition on a previously published list of intuited ideas about biological functions, including intuitions that have posed difficulties for other theories. (shrink)

In this essay I introduce the question of artifactual functions in the context of the recent debate on the notion of function. I discuss some of the desiderata a satisfactory account should fulfill and compare them to the desiderata for a theory of biological functions. Finally, within this general framework, I briefly present the three papers included in this volume.

In Origins of Objectivity, Burge presents three arguments against what he calls ‘deflationism’: the project of explaining the representational function in terms of the notion of biological function. I evaluate these arguments and argue that they are not convincing.

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. (shrink)

Bodily sensations, such as pain, hunger, itches, or sexual feelings, are commonly characterized in terms of their phenomenal character. In order to account for this phenomenal character, many philosophers adopt strong representationalism. According to this view, bodily sensations are essentially and entirely determined by an intentional content related to particular conditions of the body. For example, pain would be nothing more than the representation of actual or potential tissue damage. In order to motivate and justify their view, strong representationalists often (...) appeal to the reliable causal covariance between bodily sensations and certain kinds of bodily conditions or to the corresponding biological function that these bodily sensations are supposed to fulfill. In this paper, I argue on the basis of recent empirical research that arguments from reliable causal covariance and biological function cannot motivate the introduction of corresponding intentional content. In particular, I argue that bodily sensations are caused by a heterogeneous class of physiological and psychological factors and their biological functions are too diverse to be reduced to the representation of a particular bodily condition. Responses are available to strong representationalists, but they either require substantial alterations to their core assumptions or incur a significant empirical burden. (shrink)

Within the sedimentation diagram of infective RNA preparations isolated from Tobacco Mosaic Virus, undegraded molecules form a sharp peak with a molecular weight corresponding to the total RNA content of the virus particle. Degradation kinetics by ribonuclease is of the linear, single-target type, indicating that the RNA is single-stranded. The intact RNA of a virus particle thus forms one big single-stranded molecule. Quantitative evaluation of the effect degradation by RNA-ase on the infectivity of the RNA shows that the integrity of (...) the entire molecule is required for its biological activity. (shrink)

In this paper, I discuss the question whether objective criteria could be provided for judging something to be a mental illness. I consider the two most prominent objectivist or naturalistic accounts of mental illness, evolutionary and bio-statistical account, which offer such a criterion by relying on the notion of biological function. According to such suggestions, illness is a condition in which there is dysfunciton in some feature of an organism. In this context, I consider different accounts for ascribing (...) functions in biologyand their relationship with the suggested accounts of illnesses. Special focus is placed on the objections according to which the ascription of functions, as envisaged in naturalistic accounts of illness, is incompatible with actual medical and psychiatric practice. I conclude that these objections are legitimate insofar we want to an account of illness that preserves the current practice of ascribing illness. However, the question remains, could a theory that tries to capture the actual medical practice be value-neutral, since our ordinary conception of illness is permeated with value judgments that indirectly enter into medical practice. In that respect, it seems that the requirement for pure objectivity is too strong and thus, it is not reasonable to expect that naturalistic accounts can satisfy it. (shrink)

The survival enhancing propensity (SEP) account has a crucial role to play in the analysis of proper function. However, a central feature of the account, its specification of the proper environment to which functions are relativized, is seriously underdeveloped. In this paper, I argue that existent accounts of proper environment fail because they either allow too many or too few characters to count as proper functions. While SEP accounts retain their promise, they are unworkable because of their inability to (...) specify this important feature. However, I suggest that this problem can be overcome by the application of a new strategy for specifying proper environment that is grounded in the operation of natural selection and I conclude by offering a first approximation of such an account. (shrink)

The book A critical overview of biological functions is a short monograph by J. Garson, which provides a survey of the views on biological functions in the analytic tradition of philosophy. The notion of function is ubiquitous in biology and all of its subfields. Behind the notion of biological functions lurks the shadow of final causes. Overcoming this shadow is a challenge that has stimulated many philosophers and the literature on this topic is very rich. In (...) the analytic tradition, researchers focus on providing naturalized accounts of functions. To do so, the main difficulty is to provide accounts of functions that exclude the use of final causes. The outcome of this collective work is a diversity of accounts of functions. Some of these accounts are fairly recent while others have been proposed several decades ago and are the object of many discussions. (shrink)

Neurological syndromes in which consciousness seems to malfunction, such as temporal lobe epilepsy, visual scotomas, Charles Bonnet syndrome, and synesthesia offer valuable clues about the normal functions of consciousness and ‘qualia’. An investigation into these syndromes reveals, we argue, that qualia are different from other brain states in that they possess three functional characteristics, which we state in the form of ‘three laws of qualia’. First, they are irrevocable: I cannot simply decide to start seeing the sunset as green, or (...) feel pain as if it were an itch; second, qualia do not always produce the same behaviour: given a set of qualia, we can choose from a potentially infinite set of possible behaviours to execute; and third, qualia endure in short-term memory, as opposed to non-conscious brain states involved in the on-line guidance of behaviour in real time. We suggest that qualia have evolved these and other attributes because of their role in facilitating non-automatic, decision-based action. We also suggest that the apparent epistemic barrier to knowing what qualia another person is experiencing can be overcome by using a ‘bridge’ of neurons; and we offer a hypothesis about the relation between qualia and one's sense of self. (shrink)

It has been claimed that the intentional stance is necessary to individuate behavioral traits. This thesis, while clearly false, points to two interesting sets of problems concerning biological explanations of behavior: The first is a general in the philosophy of science: the theory-ladenness of observation. The second problem concerns the principles of trait individuation, which is a general problem in philosophy of biology. After discussing some alternatives, I show that one way of individuating the behavioral traits of an organism (...) is by a special use of the concept of biological function, as understood in an enriched causal role (not selected effect) sense. On this view, a behavioral trait is essentially a special kind of regularity, namely a regularity that is produced by some regulatory mechanism. Regulatory mechanisms always require goal states, which can only be provided by functional considerations. As an example from actual (as opposed to folk) science, I examine the case of social behavior in nematodes. I show that the attempt to explain this phenomenon actually transformed it. This supports the view that scientific explanation does not explain an explanandum phenomenon that is given prior to the explanation; rather, the explanandum is changed by the explanation. This means that there could be a plurality of stances that have some heuristic value initially, but which will be abandoned in favor of a functional characterization eventually. (shrink)

In this paper, I discuss the question whether objective criteria could be provided for judging something to be a mental illness. I consider the two most prominent objectivist or naturalistic accounts of mental illness, evolutionary and bio-statistical account, which offer such a criterion by relying on the notion of biological function. According to such suggestions, illness is a condition in which there is dysfunciton in some feature of an organism. In this context, I consider different accounts for ascribing (...) functions in biologyand their relationship with the suggested accounts of illnesses. Special focus is placed on the objections according to which the ascription of functions, as envisaged in naturalistic accounts of illness, is incompatible with actual medical and psychiatric practice. I conclude that these objections are legitimate insofar we want to an account of illness that preserves the current practice of ascribing illness. However, the question remains, could a theory that tries to capture the actual medical practice be value-neutral, since our ordinary conception of illness is permeated with value judgments that indirectly enter into medical practice. In that respect, it seems that the requirement for pure objectivity is too strong and thus, it is not reasonable to expect that naturalistic accounts can satisfy it. (shrink)

Over the last hundred years, competing and incompatible positions in relation to basic problems of knowledge and the use of the verb ‘to know’ have multiplied; and the prospect of a consensus solution emerging with respect to any of the problems has not seemed particularly good. We have a Gordian knot. Even so, I suggest that we also have a way to cut it. This will involve identifying why the cognitive mechanism that produces our intuitions of knowing evolved and was (...) maintained (by natural selection), i.e., identifying the ‘teleonomic function’ of that cognitive mechanism. Also, it will involve predicting, on the basis of this teleonomic function, the triggering-conditions of these natural knowledge intuitions. In this thesis, I develop a general theory of the origin, function and triggering-conditions of knowledge intuitions that will allow us to cut that knot. That theory follows basic biological theory (including that which pertains to natural altruism) and also signal detection theory. -/- My theory identifies a number of different circumstances under which the triggering-conditions of knowledge intuitions are different. Strikingly, these different circumstances (and their associated triggering-conditions) map onto the different competing and incompatible epistemological positions to which I referred. This suggests that these positions are all correct within the boundaries of one of the circumstances that my theory identifies; and that the Gordian knot is largely the result of epistemologists claiming universal applicability of a theory that in fact only applies under particular circumstances. We cut the knot by specifying the different circumstances under which each of the different epistemological positions will hold, and the reason we should expect it to hold in just these circumstances, in light of the teleonomic function of knowledge intuitions. (shrink)

The selected effects or ‘etiological’ theory of Proper function is a naturalistic and realist account of biological teleology. It is used to analyse normativity in philosophy of language, philosophy of mind, philosophy of medicine and elsewhere. The theory has been developed with a simple and intuitive view of natural selection. Traits are selected because of their positive effects on the fitness of the organisms that have them. These ‘selected effects’ are the Proper functions of the traits. Proponents argue (...) that this analysis of biological teleology has the unique advantage that the selected effect function of a trait is also a causal explanation of the trait: the trait exists because it performs this function. We show, however, that selected effect functions as currently defined explain the existence of traits only under highly restrictive assumptions about evolutionary dynamics. In many common scenarios in which traits evolve by natural selection, selected effect functions do not explain those traits. This is because definitions of selected effect function extract from any evolutionary scenario only the information that would be explanatorily relevant in the simple evolutionary scenario implicit in those definitions. When applied to more complex scenarios selected effect functions omit the key information that is explanatorily relevant in those scenarios. The assumptions required for selected effect functions to be explanatory are particularly unlikely to hold in the domain that its proponents care most about - the evolution of representation. A more adequate selected effects theory of Proper functions may be possible, but will require much greater attention to the structure of actual evolutionary explanations. (shrink)

A model of brain function is presented that is consistently based on the biological principle of equilibrium. The neuronal modules of the cerebral cortex are proposed as units in which equilibrium between incoming signals and the synaptic structure is determined or established. Because of the electromagnetic activity of the brain, the electromagnetic properties of thecells are brought into focus. Due to the synaptic changes of the modules -essentially during sleep -an electromagnetic resting balance between the modules is established. (...) Incoming signals during the day, disturb the electromagnetic resting equilibrium and are detected and understood by this. The connecting nodes within the neuronal network are given by the equilibrium modules. Incoming information is represented in the form of the specific pathway of the network, while recognized information is represented by the equilibrium states within the modules. The paper leads to an understanding of information storage and processing in the brain. It even provides a hypothesis for understanding the emergence of the "self". Finally, the consideration of electromagnetic wave properties of neurons opens up a biophysical starting point to understanding conscious perceptions. In neuroscience, we lack a unifying theory of the brain. The reason for this may be an important detail –a missing link –that we do not yet see. Following the "track of biological equilibrium" in this paper leads to the hypothesis that the electromagnetic properties of the neurons are potential candidates to fill that gap. A hypothesis is developed describing their physiological significance in the processing of neurological information. (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)

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)

This article argues for an epistemology of music, stating that dealing with music can be considered as a process of knowledge acquisition. What really matters is not the representation of an ontological musical reality, but the generation of music knowledge as a tool for adaptation to the sonic world. Three major positions are brought together: the epistemological claims of Jean Piaget, the biological methodology of Jakob von Uexküll, and the constructivistic conceptions of Ernst von Glasersfeld, each ingstress the role (...) of the music user rather than the music. Dealing with music, in this view, is not a matter of representation, but a process of semiotization of the sonorous environment as the outcome of interactions with the sound. Hence the role of enactive cognition and perceptual-motor interaction with the sonic environment. What is considered a central issue is the way how listeners as subjects experience their own phenomenal world or Umwelt, and how they can make sense out of their sonic environment. Umwelt-research, therefore, is highly relevant for music education in stressing the role of the listener and his/her listening strategies. (shrink)

This is a short overview of the biological functions debate in philosophy. While it was fairly comprehensive when it was written, my short book ​A Critical Overview of Biological Functions has largely supplanted it as a definitive and up-to-date overview of the debate, both because the book takes into account new developments since then, and because the length of the book allowed me to go into substantially more detail about existing views.

Various prominent theories of pain assume that it is pain’s biological function to inform organisms about damage to their bodies. I argue that this is a mistake. First, there is no biological evidence to support the notion that pain was originally selected for its informative capacities, nor that it currently contributes to the fitness of organisms in this specific capacity. Second, neurological evidence indicates that modulating mechanisms in the nociceptive system systematically prevent pain from serving a primarily (...) informative role. These considerations threaten to undermine standard perceptual and representational accounts of pain. (shrink)

The function of a trait token is usually defined in terms of some properties of other (past, present, future) tokens of the same trait type. I argue that this strategy is problematic, as trait types are (at least partly) individuated by their functional properties, which would lead to circularity. In order to avoid this problem, I suggest a way to define the function of a trait token in terms of the properties of the very same trait token. To (...) able to allow for the possibility of malfunctioning, some of these properties need to be modal ones: a function of a trait is to do F just in case its doing F would contribute to the inclusive fitness of the organism whose trait it is. Function attributions have modal force. Finally, I explore whether and how this theory of biological function could be modified to cover artifact function. (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 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)

I clarify some of the details of the modal theory of function I outlined in Nanay (2010): (a) I explicate what it means that the function of a token biological trait is fixed by modal facts; (b) I address an objection to my trait type individuation argument against etiological function and (c) I examine the consequences of replacing the etiological theory of function with a modal theory for the prospects of using the concept of (...) class='Hi'>biological function to explain mental content. (shrink)

This paper argues that proper functions are proximal functions. In other words, it rejects the notion that there are distal biological functions – strictly speaking, distal functions are not functions at all, but simply beneficial effects normally associated with a trait performing its function. Once we rule out distal functions, two further positions become available: dysfunctions are simply failures of proper function, and pathological conditions are dysfunctions. Although elegant and seemingly intuitive, this simple view has had surprisingly (...) little uptake in the literature. Indeed, our position departs from that of almost every theorist who has engaged with the issue at any depth. We start by presenting three arguments for the position that proper functions are proximal: one from the specificity of functions, one from their relation to intervention, and one from their relation to pathology. We then consider two case studies evidencing the trouble that accepting distal functions causes for philosophical reflection on the nature of pathological conditions. Finally, we anticipate and respond to three objections: that there can be failure of function without dysfunction; that our account is unacceptably revisionary in respect of normal function-talk; and that our thesis over-generalises from a narrow set of cases. (shrink)

We provide a new perspective on the relation between the space of description of an object and the appearance of novelties. One of the aims of this perspective is to facilitate the interaction between mathematics and historical sciences. The definition of novelties is paradoxical: if one can define in advance the possibles, then they are not genuinely new. By analyzing the situation in set theory, we show that defining generic (i.e., shared) and specific (i.e., individual) properties of elements of a (...) set are radically different notions. As a result, generic and specific definitions of possibilities cannot be conflated. We argue that genuinely stating possibilities requires that their meaning has to be made explicit. For example, in physics, properties playing theoretical roles are generic; then, generic reasoning is sufficient to define possibilities. By contrast, in music, we argue that specific properties matter, and generic definitions become insufficient. Then, the notion of new possibilities becomes relevant and irreducible. In biology, among other examples, the generic definition of the space of DNA sequences is insufficient to state phenotypic possibilities even if we assume complete genetic determinism. The generic properties of this space are relevant for sequencing or DNA duplication, but they are inadequate to understand phenotypes. We develop a strong concept of biological novelties which justifies the notion of new possibilities and is more robust than the notion of changing description spaces. These biological novelties are not generic outcomes from an initial situation. They are specific and this specificity is associated with biological functions, that is to say, with a specific causal structure. Thus, we think that in contrast with physics, the concept of new possibilities is necessary for biology. (shrink)

This paper aims to provide a philosophical and theoretical account of biological communication grounded in the notion of organisation. The organisational approach characterises living systems as organised in such a way that they are capable to self-produce and self-maintain while in constant interaction with the environment. To apply this theoretical framework to the study of biological communication, we focus on a specific approach, based on the notion of influence, according to which communication takes place when a signal emitted (...) by a sender triggers a change in the behaviour of the receiver that is functional for the sender itself. We critically analyse the current formulations of this account, that interpret what is functional for the sender in terms of evolutionary adaptations. Specifically, the adoption of this etiological functional framework may lead to the exclusion of several phenomena usually studied as instances of communication, and possibly even of entire fields of investigation such as synthetic biology. As an alternative, we reframe the influence approach in organisational terms, characterising functions in terms of contributions to the current organisation of a biological system. We develop a theoretical account of biological communication in which communicative functions are distinguished from other types of biological functions described by the organisational account (e.g. metabolic, ecological, etc.). The resulting organisational-influence approach allows to carry out causal analyses of current instances of phenomena of communication, without the need to provide etiological explanations. In such a way it makes it possible to understand in terms of communication those phenomena which realise interactive patterns typical of signalling interactions – and are usually studied as such in scientific practice – despite not being the result of evolutionary adaptations. Moreover, this approach provides operational tools to design and study communicative interactions in experimental fields such as synthetic biology. (shrink)

This article presents a distinct sense of ‘mechanism’, which I call the functional sense of mechanism. According to this sense, mechanisms serve functions, and this fact places substantive restrictions on the kinds of system activities ‘for which’ there can be a mechanism. On this view, there are no mechanisms for pathology; pathologies result from disrupting mechanisms for functions. Second, on this sense, natural selection is probably not a mechanism for evolution because it does not serve a function. After distinguishing (...) this sense fromsimilar explications of ‘mechanism’, I argue that it is ubiquitous in biology and has valuable epistemic benefits. (shrink)

Function talk is a constant across different life sciences. From macro-evolution to genetics, functions are mentioned everywhere. For example, a limb’s function is to allow movement and RNA polymerases’ function is to transcribe DNA. Biochemistry is not immune from such a characterization; the biochemical world seems to be a chemical world embedded within biological processes. Specifically, biochemists commonly ascribe functions to biomolecules and classify them accordingly. This has been noticed in the recent philosophical literature on biochemical (...) kinds. But while a lot has been written on biological and psychological functions, little has been said explicitly about biochemical fuctions. Here, I explore functional attribution to biochemical molecules. I argue that if we accept this attribution, then biochemical functions are constituted by chemical dispositional properties that causally contribute to selected biological processes. In section 2, I discuss the controversy concerning the characterization of biochemical functions. In section 3, I consider whether a biological or a chemical under- standing of function can be applied to biochemical functions, illustrating the account with the example of vitamin B12. The result is that none of the theories on their own provides an adequate characterization. In section 4, I present an account of biochemical functions. In section 5, I assess this account taking into consideration common requirements for a theory of functions and an objection. (shrink)

What is the biological function of perception? I hold perception, especially visual perception in humans, has the biological function of accurately representing the environment. Tyler Burge argues this cannot be so in Origins of Objectivity (Oxford, 2010), for accuracy is a semantical relationship and not, as such, a practical matter. Burge also provides a supporting example. I rebut the argument and the example. Accuracy is sometimes also a practical matter if accuracy partly explains how perception contributes (...) to survival and reproduction. (shrink)

Representations are not only used in our folk-psychological explanations of behaviour, but are also fruitfully postulated, for example, in cognitive science. The mainstream view in cognitive science maintains that our mind is a representational system. This popular view requires an understanding of the nature of the entities they are postulating. Teleosemantic theories face this challenge, unpacking the normativity in the relation of representation by appealing to the teleological function of the representing state. It has been argued that, if intentionality (...) is to be explained in teleological terms, then the function of a state cannot depend on its phylogenetical history, given the metaphysical possibility of a duplicate of an intentional being that lacks an evolutionary history. In this paper, I present a method to produce, according to our current knowledge in genetic engineering, human-like individuals who are not the product of natural selection in the required sense. This variation will be used to shed light on the main replies that have been offered in the literature to the Swampman thought experiment. I argue that these replies are not satisfactory: representations should better not depend on natural selection. I conclude that a non-etiological notion of function is to be preferred for characterizing the relation of representation. (shrink)

Numerous research groups are now utilizing Basic Formal Ontology as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three existing BFO subcategories of realizable entity, namely function, role, and disposition. It proposes one further sub-category of tendency, and considers the merits of recognizing two sub-categories of function for domain ontologies, namely, artifactual and biological function. The motivation is to help advance the coherent ontological treatment of (...) functions, roles, and dispositions, to help provide the potential for more detailed classification, and to shed light on BFO’s general make-up and use. (shrink)

This selective review explores biologically inspired learning as a model for intelligent robot control and sensing technology on the basis of specific examples. Hebbian synaptic learning is discussed as a functionally relevant model for machine learning and intelligence, as explained on the basis of examples from the highly plastic biological neural networks of invertebrates and vertebrates. Its potential for adaptive learning and control without supervision, the generation of functional complexity, and control architectures based on self-organization is brought forward. Learning (...) without prior knowledge based on excitatory and inhibitory neural mechanisms accounts for the process through which survival-relevant or task-relevant representations are either reinforced or suppressed. The basic mechanisms of unsupervised biological learning drive synaptic plasticity and adaptation for behavioral success in living brains with different levels of complexity. The insights collected here point toward the Hebbian model as a choice solution for “intelligent” robotics and sensor systems. Keywords: Hebbian learning; synaptic plasticity; neural networks; self-organization; brain; reinforcement; sensory processing; robot control . (shrink)

Synthetic biology is a field of research that concentrates on the design, construction, and modification of new biomolecular parts and metabolic pathways using engineering techniques and computational models. By employing knowledge of operational pathways from engineering and mathematics such as circuits, oscillators, and digital logic gates, it uses these to understand, model, rewire, and reprogram biological networks and modules. Standard biological parts with known functions are catalogued in a number of registries (e.g. Massachusetts Institute of Technology Registry of (...) Standard Biological Parts). Biological parts can then be selected from the catalogue and assembled in a variety of combinations to construct a system or pathway in a microbe. Through the innovative re-engineering of biological circuits and the optimization of certain metabolic pathways, biological modules can be designed to reprogram organisms to produce products or behaviors. Synthetic biology is what is known as a “platform technology”. That is, it generates highly transferrable theoretical models, engineering principles, and know-how that can be applied to create potential products in a wide variety of industries. Proponents suggest that applications of synthetic biology may be able to provide scientific and engineered solutions to a multitude of worldwide problems from health to energy. Synthetic biology research has already been successful in constructing microbial products which promise to offer cheaper pharmaceuticals such as the antimalarial synthetic drug artemisinin, engineered microbes capable of cleaning up oil spills, and the engineering of biosensors that can detect the presence of high concentrations of arsenic in drinking water. One of the potential benefits of synthetic biology research is in its application to biofuel production. It is this application which is the focus of this entry. The term “biofuel” has referred generally to all liquid fuels that are sourced from plant or plant byproducts and are used for energy necessary for transportation vehicles (Thompson 2012). Biofuels that are produced using synthetic biological techniques re-engineer microbes into biofuel factories are a subset of these. (shrink)

In ‘A modal theory of function’, I gave an argument against all existing theories of function and outlined a new theory. Karen Neander and Alex Rosenberg argue against both my negative and my positive claim. My aim here is not merely to defend my account from their objections, but to (a) very briefly point out that the new account of etiological function they propose in response to my criticism cannot avoid the circularity worry either and, more importantly, (...) to (b) highlight, and attempt to make precise, an important feature of my modal theory that may have been understated in the original paper – that function attributions depend on the explanatory project at hand. (shrink)

Synthetic biology (SynBio) covers two main areas: application engineering, exemplified by metabolic engi- neering, and the design of life from artificial building blocks. As the general public is often reluctant to embrace synthetic approaches, preferring nature to artifice, its immediate future will depend very much on the public’s reaction to the unmet needs created by the pervasive demands of sustainability. On the other hand, this reluctance should not have a negative impact on research that will now take into account the (...) existence of the multiple transitions that cells face over time. The ages of life—birth, development, maturation, senescence and death—reflect specific key transitions and have, until now, rarely been taken into account in SynBio designs. This results in a mismatch between novelty and the very long evolutionary time that led to the existing chassis [remember that this is the common term used to describe the cellular framework as seen by synthetic biologists (de Lorenzo & Danchin, 2008)]. It also implies that, in general, transitions between growth stages will be taken into account with the appro- priate embodiment of highly specific processes. This is particularly important when adapting new models to their host, whether natural or artificial. Adaptation fol- lows two stages, short-term accommodation of new entities and long-term assimilation into the cell as a whole. This requires discrimination between classes of entities. We suggest that proteins playing the essential role of Maxwell’ demons, here named Maxwell’s dis- criminators (MxDs) to refer to their original function, will permit the assimilation and accommodation of artificial constructs. As a consequence, we can foresee that class discrimination, beyond mere recognition, will be implemented in SynBio 2.0, leading to an authentic par- adigm shift (Kuhn, 1996), based on conceptions that embody information as a genuine currency of reality. (shrink)

According to simulationism, the function of episodic memory is not to remember the past, but to help construct representations of possible future episodes, by drawing together features from different experiential sources. This article suggests that the relationship between the traditional storehouse view, on which the function of memory is remembering, and the simulationist approach is more complicated than has been typically acknowledged. This is attributed, in part, to incorrect interpretations of what remembering on the storehouse view requires. Further, (...) by appeal to function pluralism, the article questions both the assumption that the traditional view and simulationism are inconsistent, and the simulationist’s inference to the best explanation strategy that is based upon this assumption. The article then provides an evaluation of the simulationist argument against the traditional view, and finds it in need of further support. (shrink)

Discussions of the functions of biological traits generally take the notion of a trait for granted. Defining this notion is a non-trivial problem. Different approaches to function place different constraints on adequate accounts of the notion of a trait. Accounts of function based on engineering-style analyses allow trait boundaries to be a matter of human interest. Accounts of function based on natural selection have typically been taken to require trait boundaries that are objectively real. After canvassing (...) problems raised by each approach, I conclude with some facts that satisfactory notions of trait must respect. (shrink)

Biological theory demands a clear organism concept, but at present biologists cannot agree on one. They know that counting particular units, and not counting others, allows them to generate explanatory and predictive descriptions of evolutionary processes. Yet they lack a unified theory telling them which units to count. In this paper, I offer a novel account of biological individuality, which reconciles conflicting definitions of ‘organism’ by interpreting them as describing alternative realisers of a common functional role, and then (...) defines individual organisms as essentially possessing some mechanisms that play this role. (shrink)

Philosophers who study the problem of biological function often begin their deliberations by reflecting on the functions of parts of animals, or the behavior of animals. Applying theories of biological function to unconventional or borderline cases can help us to better evaluate and refine those theories. This is the case when we consider whether parts of transposable elements —bits of “selfish” DNA that move about within a host genome—have functions of their own, that is, whether the (...) parts of TEs have the function of helping the TE move about within the genome. Here I argue that whether or not the parts of TEs have functions depends crucially on whether collections of TEs form “populations,” by which I mean, here, a group of individuals of the same type that impact one another’s chances of persistence or multiplication, by impacting one another’s access to a shared resource. I think there is suggestive, but not conclusive, evidence that some TEs have functions of their own. Considering the problem of TE functionality, then, has value both for philosophy and for biology. (shrink)

What is the function of morality? On this question, something approaching a consensus has recently emerged. Impressed by developments in evolutionary theory, many philosophers now tell us that the function of morality is to reduce social tensions, and to thereby enable a society to efficiently promote the well-being of its members. In this paper, I subject this consensus to rigorous scrutiny, arguing that the functional hypothesis in question is not well supported. In particular, I attack the supposed evidential (...) relation between an evolutionary genealogy of morals and the functional hypothesis itself. I show that there are a great many functionally relevant discontinuities between our own culture and the culture within which morality allegedly emerged, and I argue that this seriously weakens the inference from morality’s evolutionary history to its present-day function. (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)

Explanatory Externalism states that the only adaptive force in evolution is natural selection. Explanatory Externalism is a central thesis of the Modern Evolutionary Synthesis. The etiological theory of natural selected-effect functions also advocates Explanatory Externalism. According to this theory, natural selection is the process responsible for determining the proper natural functions of traits. However, I will point out several challenges to Explanatory Externalism that are proposed primarily by developmental biology and its various subfields. Based on these challenges, this paper will (...) argue why biological functions cannot be fully explained by the selected-effect theory, i.e., that a theory of biological functions must adopt some kind of Explanatory Internalism. At the end of this paper, I will discuss whether or not Explanatory Internalism entails a pluralistic view of biological functions, and how this discussion is related to the different explanations of fit and diversity found in evolutionary biology. (shrink)

Millikan’s (1984. Language, Thought, and Other Biological Categories: New Foundations for Realism. MIT Press) selected effects theory of functions states that functions are effects for which the ancestors of a trait were selected for. As the function is an effect a thing’s ancestors produced, only things that are reproductions in some sense can have functions. Against this reproduction requirement, Garson (2019. What Biological Functions Are and Why They Matter. Cambridge University Press) argues that not only processes of (...) differential reproduction but also processes of differential persistence can lead to new functions. Since such “persistence functions” have the same explanatory power as traditional selected effects functions, selected effects theorists should include them in their theory. In this paper, I will defend Millikan’s theory against this argument. I will show that the proponents of the generalized theory have yet to provide a working notion of populations that avoids a liberality problem. Further, I will argue that persistence functions are at best a marginal case of functions due to their restricted explanatory power. (shrink)

The scientific study of living organisms is permeated by machine and design metaphors. Genes are thought of as the ‘‘blueprint’’ of an organism, organisms are ‘‘reverse engineered’’ to discover their functionality, and living cells are compared to biochemical factories, complete with assembly lines, transport systems, messenger circuits, etc. Although the notion of design is indispensable to think about adaptations, and engineering analogies have considerable heuristic value (e.g., optimality assumptions), we argue they are limited in several important respects. In particular, the (...) analogy with human-made machines falters when we move down to the level of molecular biology and genetics. Living organisms are far more messy and less transparent than human-made machines. Notoriously, evolution is an opportunistic tinkerer, blindly stumbling on ‘‘designs’’ that no sensible engineer would come up with. Despite impressive technological innovation, the prospect of artificially designing new life forms from scratch has proven more difficult than the superficial analogy with ‘‘programming’’ the right ‘‘software’’ would suggest. The idea of applying straightforward engineering approaches to living systems and their genomes— isolating functional components, designing new parts from scratch, recombining and assembling them into novel life forms—pushes the analogy with human artifacts beyond its limits. In the absence of a one-to-one correspondence between genotype and phenotype, there is no straightforward way to implement novel biological functions and design new life forms. Both the developmental complexity of gene expression and the multifarious interactions of genes and environments are serious obstacles for ‘‘engineering’’ a particular phenotype. The problem of reverse-engineering a desired phenotype to its genetic ‘‘instructions’’ is probably intractable for any but the most simple phenotypes. Recent developments in the field of bio-engineering and synthetic biology reflect these limitations. Instead of genetically engineering a desired trait from scratch, as the machine/engineering metaphor promises, researchers are making greater strides by co-opting natural selection to ‘‘search’’ for a suitable genotype, or by borrowing and recombining genetic material from extant life forms. (shrink)

One of Clayton’s major contributions to our understanding of animal minds has been her work on episodic-like memory. A central reason for the success of this work was its focus on ecological validity: rather than looking for episodic memory for arbitrary stimuli in artificial contexts, focussing on contexts in which episodic memory would serve a biological function such as food caching. This review aims to deepen this insight by surveying the numerous functions that have been proposed for episodic (...) memory, articulating a philosophically grounded framework for understanding what exactly functions are, and drawing on these to make suggestions for future directions in the comparative cognitive psychology of episodic memory. Our review suggests four key insights. First, episodic memory may have more than one function and may have different functions in different species. Second, cross-disciplinary work is key to developing a functional account of episodic memory. Third, there is scope for further theoretical elaboration of proposals relating episodic memory to food caching and, in particular, future-oriented cognition. Finally, learning-related functions suggested by AI (artificial intelligence)-based models are a fruitful avenue for future behavioural research. (shrink)

Biological conservation practices and approaches take many forms. Conservation projects do not only differ in their aims and methods, but also concerning their conceptual and normative background assumptions and their underlying motivations and objectives. We draw on philosophical distinctions from the ethics of conservation to explain variances of different positions on conservation projects along six dimensions: (1) conservation ideals, (2) intervention intuitions, (3) the moral considerability of nonhuman beings, (4) environmental values, (5) views on nature and (6) human roles (...) in nature. The result is a map of the moral landscape of biological conservation, on which these six dimensions are layered. This map functions as a heuristic tool to understand conceptual and normative foundations of specific conservation projects, which we will illustrate with four paradigmatic examples: the Pisavaara Strict Nature Reserve, Predator Free New Zealand, the Oostvaardersplassen Nature Reserve and the Great Green Wall Project. With this map as a heuristic tool, we aim to conceptually illuminate disagreement and clarify misunderstandings between representatives of different environmental protection strategies and to show that the same project can be supported (or criticised) on different grounds. (shrink)