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)

The concept of a function is central both to biology and to technology. But there is an intricate debate how functions as well as related entities like dispositions and roles are to be represented in top level ontologies and how they are to be related. We review important philosophical accounts and ontological models for functions and roles and discuss three models for the relation of functions and dispositions. We conclude that mainly because of the need to account for malfunctioning, functions (...) should not be treated as a subtype of dispositions, but as their sibling category. (shrink)

This paper proposes a new framework for investigating neural signals sufficient for a conscious sensation of movement and their role in motor control. We focus on signals sufficient for proprioceptive awareness, particularly from muscle spindle activation and from primary motor cortex (M1). Our review of muscle vibration studies reveals that afferent signals alone can induce conscious sensations of movement. Similarly, studies employing peripheral nerve blocks suggest that efferent signals from M1 are sufficient for sensations of movement. On this basis, (...) we show that competing theories of motor control assign different roles to sensation of movement. According to motor command theories, sensation of movement corresponds to an estimation of the current state based on afferent signals, efferent signals, and predictions. In contrast, within active inference architectures, sensations correspond to proprioceptive predictions driven by efferent signals from M1. The focus on sensation of movement provides a way to critically compare and evaluate the two theories. Our analysis offers new insights into the functional roles of movement sensations in motor control and consciousness. (shrink)

In this paper, a theoretical account of the functional role of consciousness in the cognitive system of normal subjects is developed. The account is based upon an approach to consciousness that is drawn from the phenomenological tradition. On this approach, consciousness is essentially peripheral self-awareness, in a sense to be duly explained. It will be argued that the functional role of consciousness, so construed, is to provide the subject with just enough information about her ongoing experience (...) to make it possible for her to easily obtain as much information as she may need. The argument for this account of consciousness' functional role will proceed in three main stages. First, the phenomenological approach to consciousness as peripheral self-awareness will be expounded and endorsed. Second, an account of the functional role of peripheral perceptual awareness will be offered. Finally, the account of the functional role of peripheral self-awareness will be obtained by straightforward extension from the functional role of peripheral perceptual awareness. (shrink)

Exploring emotions, in terms of their evolutionary origin; their basic neurobiological substratum, and their functional significance in autonomous agents, we propose a model of minimal functionality of emotions. Our aim is to provide a naturalized explanation – mostly based on an interactivist model of emergent representation and appraisal theory of emotions – concerning basic aesthetic emotions in the formation of aesthetic judgment. We suggest two processes the Cognitive Variables Subsystem (CVS) which is fundamental for the accomplishment of the function (...) of heuristic learning; and Aesthetic Appraisal Subsystem (AAS) which primarily affects the elicitation of aesthetic emotional meanings. These two subsystems (CVS and AAS) are organizationally connected and affect the action readiness of the autonomous agent. More specifically, we consider the emotional outcome of these two subsystems as a functional indication that strengthens or weakens the anticipation for the resolution of the dynamic uncertainty that emerges in the particular interaction. (shrink)

In this paper it is argued that functional role semantics can be saved from criticisms, such as those raised by Putnam and Fodor and Lepore, by indicating which beliefs and inferences are more constitutive in determining mental content. The Scylla is not to use vague expressions; the Charybdis is not to endorse the analytic/synthetic distinction. The core idea is to use reflective equilibrium as a strategy to pinpoint which are the beliefs and the inferences that constitute the content (...) of a mental state. The beliefs and the inferences that are constitutive are those that are in reflective equilibrium in the process of attributing mental states to others. (shrink)

In synthetic biology the use of engineering metaphors to describe biological organisms and their behavior has become a common practice. The concept of noise provides one of the most compelling examples of such transfer. But this notion is also confusing: While in engineering noise is a destructive force perturbing artificial systems, in synthetic biology it has acquired an additional functional meaning. It has been found out that noise is an important factor in driving biological processes such as gene regulation, (...) development, and evolution. How did noise acquire this dual meaning in the field of synthetic biology? In this paper we study the emergence of the functional meaning of noise in relation to synthetic modeling. We will pay particular attention to the interdisciplinary aspects of this process highlighting the way borrowed concepts, analogical reasoning and the use of cross-disciplinary computational templates were entwined in it. (shrink)

One strategy for providing an analysis of practical rationality is to start with the notion of a practical reason as primitive. Then it will be quite tempting to think that the rationality of an action can be defined rather simply in terms of ‘the balance of reasons’. But just as, for many philosophical purposes, it is extremely useful to identify the meaning of a word in terms of the systematic contribution the word makes to the meanings of whole sentences, this (...) paper argues that it is extremely useful to explain the nature of practical reasons in terms of the systematic contributions that such reasons make to the wholesale rational statuses of actions. This strategy gives us a clear view of two logically distinct normative roles for practical reasons – justifying and requiring – that are often conflated, and it allows us to give clear definitions of what ‘the strength of a reason’ means within each of these roles. The final section of the paper explores some implications of the resulting view for the internalism/externalism debate about practical reasons, and for the practical significance of moral theory. (shrink)

Our aim is to point out the role of scientific research in contemporary technological developments. Interactions between science and technology in the context of application-driven research projects of the 20th century are discussed. We define science and technology as two separate domains, and provide elementary models for their interaction by the means of applied and engineering sciences. These elementary models constitute linear and cascade models of science-technology interaction. We apply these elementary models for the purpose of further methodological analysis (...) of Soviet nuclear warfare project. The special role of organization and management in research and development activities is being emphasized. The new science-technology interaction model is devised in the course of nuclear project. This new interaction model is referred as non-linear or spiral. The model is seen as more collaborative and risk aware than linear and cascade interaction models present in twentieth century. The conclusion is the new model was of great impact to modern social forms in which research is carried out in the present. (shrink)

The propositional account of explicit and implicit knowledge interprets cognitive differences between direct and indirect test performance as emerging from the elements in different hierarchical levels of the propositional representation that have been made explicit. The hierarchical nature of explicitness is challenged, however, on the basis of neuropsychological dissociations between direct and indirect tests of memory, as well as the stochastic independence that has been observed between these two types of tests. Furthermore, format specificity on indirect test of memory challenges (...) the basic notion of a propositional theory of implicit and explicit knowledge. (shrink)

While the claim that certain functional states are sufficient for conscious experience has received substantial critical attention, the claim that functional states are necessary is rarely addressed. Yet the latter claim is perhaps now more common than the former. I aim to revive and revise a neglected argument against the necessity claim, by Michael Antony. The argument involves manipulating a conscious subject's brain so as to cancel a disposition which is supposedly crucial to the realization of an experience (...) that the subject is having at the time. The key step in the argument is to show that, contrary to what the functional necessity claim implies, the experience can survive such a manipulation. I defend that key step in a new way, by arguing that since the manipulation cannot influence the subject's thoughts, emotions, or behavior, there is no reason to suppose that it alters his conscious experience. (shrink)

Pro Doernberg and Truog (2023), we recognize and acknowledge five spheres of morality in medicine. We posit that these spheres represent domains of practical engagement, which, as the authors note,...

Molday and Hsu review results from in vitro experiments, which indicate that Ca-bound calmodulin reduces the cGMP sensitivity of the cyclic nucleotide-gated channel of photoreceptor cells, and speculate about the role they might play in the recovery of the light response. We discuss results from in vivo experiments that argue against the participation of Ca-calmodulin in photorecovery.

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 KCTD family includes tetramerization (T1) domain containing proteins with diverse biological effects. We identified a novel member of the KCTD family, BTBD10. A comprehensive analysis of protein‐protein interactions (PPIs) allowed us to put forth a number of testable hypotheses concerning the biological functions for individual KCTD proteins. In particular, we predict that KCTD20 participates in the AKT‐mTOR‐p70 S6k signaling cascade, KCTD5 plays a role in cytokinesis in a NEK6 and ch‐TOG‐dependent manner, KCTD10 regulates the RhoA/RhoB pathway. Developmental regulator (...) KCTD15 represses AP‐2α and contributes to energy homeostasis by suppressing early adipogenesis. TNFAIP1‐like KCTD proteins may participate in post‐replication DNA repair through PCNA ubiquitination. KCTD12 may suppress the proliferation of gastrointestinal cells through interference with GABAb signaling. KCTD9 deserves experimental attention as the only eukaryotic protein with a DNA‐like pentapeptide repeat domain. The value of manual curation of PPIs and analysis of existing high‐throughput data should not be underestimated. (shrink)

Much of cognitive science is committed to the modular approach to the study of cognition. The core of this approach consists of a pair of assumptions - the anatomical and the functional modularity assumptions - which motivate two kinds of inference: the anatomical and the functional modularity inferences. The legitimacy of both of these inferences has been strongly challenged, a situation that has had surprisingly little impact on most theorizing in the field. Following the introduction of an important, (...) yet rarely made, distinction between two functional concepts - the distinction between cognitive working and cognitive role - this paper analyses these kinds of inference, and refocuses the attention on new aspects of their main limitations. It is argued that both the anatomical and functional modularity inferences can, and do, operate in three distinct modes in contemporary cognitive science, and that seeing this is essential to understanding both the power and the limitations of these methodological tools. (shrink)

A single physical process may often be described equally well as computing several different mathematical functions—none of which is explanatorily privileged. How, then, should the computational identity of a physical system be determined? Some computational mechanists hold that computation is individuated only by either narrow physical or functional properties. Even if some individuative role is attributed to environmental factors, it is rather limited. The computational semanticist holds that computation is individuated, at least in part, by semantic properties. She (...) claims that the mechanistic account lacks the resources to individuate the computations performed by some systems, thereby leaving interesting cases of computational indeterminacy unaddressed. This article examines some of these views, and claims that more cases of computational indeterminacy can be addressed, if the system-environment interaction plays a greater role in individuating computations. A new, long-arm functional strategy for individuating computation is advanced. (shrink)

Online support groups are common sources of both health information and social support. To augment existing qualitative understandings of member roles and identities in OSGs, this article presents a corpus-based investigation of shifts in member lexicogrammatical and discourse-semantic choices in a bipolar disorder OSG. In total, 8.4 million words in 57,000 posts were transformed into a structured, grammatically annotated corpus and investigated using systemic functional linguistics as a theoretical framework, focusing on interpersonal and experiential meanings. The findings of mood (...) and transitivity analyses show marked differences between new and veteran members’ language choices over the course of membership in the OSG: particularly, in how veteran members provide advice, and in how new and veteran members ascribe and attribute bipolar disorder to both the self and others. Discussion addresses the affordances and limitations of corpus linguistics and SFL as strategies for providing quantitative support for key claims of earlier research in this field. (shrink)

Functional information means an encoded network of functions in living organisms from molecular signaling pathways to an organism’s behavior. It is represented by two components: code and an interpretation system, which together form a self-sustaining semantic closure. Semantic closure allows some freedom between components because small variations of the code are still interpretable. The interpretation system consists of inference rules that control the correspondence between the code and the function (phenotype) and determines the shape of the fitness landscape. The (...) utility factor operates at multiple time scales: short-term selection drives evolution towards higher survival and reproduction rate within a given fitness landscape, and long-term selection favors those fitness landscapes that support adaptability and lead to evolutionary expansion of certain lineages. Inference rules make short-term selection possible by shaping the fitness landscape and defining possible directions of evolution, but they are under control of the long-term selection of lineages. Communication normally occurs within a set of agents with compatible interpretation systems, which I call communication system. Functional information cannot be directly transferred between communication systems with incompatible inference rules. Each biological species is a genetic communication system that carries unique functional information together with inference rules that determine evolutionary directions and constraints. This view of the relation between utility and inference can resolve the conflict between realism/positivism and pragmatism. Realism overemphasizes the role of inference in evolution of human knowledge because it assumes that logic is embedded in reality. Pragmatism substitutes usefulness for truth and therefore ignores the advantage of inference. The proposed concept of evolutionary pragmatism rejects the idea that logic is embedded in reality; instead, inference rules are constructed within each communication system to represent reality, and they evolve towards higher adaptability on a long time scale. (shrink)

Many areas of science develop by discovering mechanisms and role functions. Cummins' (1975) analysis of role functions-according to which an item's role function is a capacity of that item that appears in an analytic explanation of the capacity of some containing system-captures one important sense of "function" in the biological sciences and elsewhere. Here I synthesize Cummins' account with recent work on mechanisms and causal/mechanical explanation. The synthesis produces an analysis of specifically mechanistic role functions, one (...) that uses the characteristic active, spatial, temporal, and hierarchical organization of mechanisms to add precision and content to Cummins' original suggestion. This synthesis also shows why the discovery of role functions is a scientific achievement. Discovering a role function (i) contributes to the interlevel integration of multilevel mechanisms, and (ii) provides a unique, contextual variety of causal/mechanical explanation. (shrink)

This essay examines the proposal that psychological essentialism results from a history of natural selection acting on human representation and inference systems. It has been argued that the features that distinguish essentialist representational systems are especially well suited for representing natural kinds. If the evolved function of essentialism is to exploit the rich inductive potential of such kinds, then it must be subserved by cognitive mechanisms that carry out at least three distinct functions: identifying these kinds in the environment, constructing (...) essentialized representations of them, and constraining inductive inferences about kinds. Moreover, there are different kinds of kinds, ranging from nonliving substances to biological taxa to within-species kinds such as sex, and the causal processes that render these categories coherent for the purposes of inductive generalization vary. If the evolved function of essentialism is to support inductive generalization under ignorance of true causes, and if kinds of kinds vary in the implicit assumptions that support valid inductive inferences about them, then we expect different, functionally incompatible modes of essentialist thinking for different kinds. In particular, there should be differences in how biological and nonbiological substances, biological taxa, and biological and social role kinds are essentialized. The functional differences between these kinds of essentialism are discussed. (shrink)

Although infants’ social gaze has specific communicative functions, it remains unclear what they are. In this conceptual analysis paper, we provide a theoretical framework for the study of the functional aspects of eye gaze in early childhood. We argue that studying the communicative functions of infants’ eye gaze involves three premises: the centrality of the object, the importance of common ground on object use, and the role of parental interpretations. The ability to communicate intentionally begins when infants start (...) referring to external objects. Beyond dyadic – infant–parent – emotional sharing, infant social gaze within the infant–parent–object triad becomes an increasingly complex communicative modality. As the predominant type of communicative referents in infancy, objects are thus central to early communication. Although they have affordances, objects are used in conventional ways shared between users (i.e., common ground). Parents transmit to infants the socio-cultural use of objects, which infants progressively learn and master. Accordingly, we argue that within early triadic interactions, the communicative function of infants’ eye gaze is shaped by the knowledge that the infant and the parent share on the socio-cultural use of the referent (i.e., the object). Importantly, before young children develop their ability to convey clear communicative functions, including with eye gaze, the interpretations and responses that parents provide to infants’ early communicative acts play a major role. Relying on these premises, we argue that when referring to objects for which the infant and the parent share common ground, the function of the infant’s social gaze becomes communicatively meaningful for the parent. The knowledge on the communicative referent (i.e., the object) shared between the infant and the parent thus shapes the course of communicative behavior, constitutes and reflects the interactive function of gaze, and cues parents into tailoring their communicative response according to the infant’s developmental needs. Through this theoretical framework for the study of the communicative function of infant eye gaze, an emphasis is put on the key role that socio-materiality plays in early communicative development. (shrink)

Adopting a constructivist stance is not irreconcilable with executive function accounts of emerging social understanding. The executive function view allows for a gradual transition in theory of mind, while specifying the underlying cognitive processes that push that development forward. Executive function abilities can be seen as an important interactional component in the epistemic triangle.

A variety of semiotic resources makes the construction of scientific knowledge possible and meaning-making resources are conveyed by certain semiotic modes. Next, numerous studies have demonstrated the pedagogical importance of gestures in the demonstration of scientific knowledge in the classroom. Drawing on social semiotic systemic functional theory and legitimation code theory, this study explores the types and the role of gestures in the semiotic construction of scientific knowledge in pedagogic semiosis and their pedagogical values for the meaning-making of (...) science content. With this aim, a gesture observation protocol (GOP) is developed to annotate and analyze data. Two science lectures, which are broadcast remotely for middle school students including gifted students, are observed. Systemic Functional Multimodal Discourse Analysis (SF-MDA) method is employed to analyze and evaluate data. Results demonstrated that the deployment of gestures that contributes to the construction of scientific knowledge is low and deployed gestures mostly do not have pedagogical value. It is recommended that teachers should be more conscious and educated about deploying gestures to present scientific knowledge efficiently. (shrink)

What are the functional units of the brain? If the function of the brain is to process information-carrying signals, then the functional units will be the senders and receivers of those signals. Neurons have been the default candidate, with action potentials as the signals. But there are alternatives: synapses fit the action potential picture more cleanly, and glial activities (e.g., in astrocytes) might also be characterized as signaling. Are synapses or nonneuronal cells better candidates to play the (...) class='Hi'>role of functional units? Will informational signaling still be the best model for brain function if we move beyond the neuron doctrine? (shrink)

Interleukin 5 (IL‐5) is a kind of peptide hormone released from T lymphocytes of mammals infected with microorganisms or parasites. It is an acidic glycoprotein with a molecular mass of 40 to 50 kDa that consists of a homodimer of polypeptides. It controls hematopoiesis so that it increases natural immunity. In the mouse, IL‐5 acts on committed B cells to induce differentiation into Ig‐producing cells and on common progenitors for CD5+ pre‐B cells and CD5+ macrophages to support their survival. The (...) antibodies secreted by CD5+ B cells seem to be responsible for the primary protection against the infection with microorganisms or parasites. It also supports the growth and/or differentiation of eosinophil precursor and mature eosinophils, which can be effective for the removal of parasites in combination with the antibodies against them. Murine IL‐5 receptor (IL‐5R) consists of two different polypeptide chains; αL chain and β chain. The IL‐5R α chain is 60 kDa protein that binds IL‐5 with low affinity. The IL‐5R β chain is a 130 kDa protein which does not bind IL‐5 by itself but is necessary to form the high affinity IL‐5R. The β chain was identified by using one of the anti‐IL‐5R mAb and anti‐IL‐3R mAb as the IL‐3R homologue. This β chain is also used as the β chain of GM‐CSF receptor. This fact suggests that there is a common signaling mechanism among these cytokines and efficient cooperation among them. At the same time, these findings may explain the overlapping role of these cytokines in the development of granulocytes. (shrink)