Talk of different types of cells is commonplace in the biological sciences. We know a great deal, for example, about human muscle cells by studying the same type of cells in mice. Information about cell type is apparently largely projectible across species boundaries. But what defines cell type? Do cells come pre-packaged into different natural kinds? Philosophical attention to these questions has been extremely limited [see e.g., Wilson (Species: New Interdisciplinary Essays, pp 187–207, 1999; Genes and the (...) Agents of Life, 2005; Wilson et al. Philos Top 35(1/2):189–215, 2007)]. On the face of it, the problems we face in individuating cellular kinds resemble those biologists and philosophers of biology encountered in thinking about species: there are apparently many different (and interconnected) bases on which we might legitimately classify cells. We could, for example, focus on their developmental history (a sort of analogue to a species’ evolutionary history); or we might divide on the basis of certain structural features, functional role, location within larger systems, and so on. In this paper, I sketch an approach to cellular kinds inspired by Boyd’s Homeostatic Property Cluster Theory, applying some lessons from this application back to general questions about the nature of natural kinds. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and (...) applied this method to develop a dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

In computer science, Artificial Intelligence (AI), sometimes called machine intelligence, is intelligence demonstrated by machines, in contrast to the natural intelligence displayed by humans and other animals. Computer science defines AI research as the study of "intelligent agents": any device that perceives its environment and takes actions that maximize its chance of successfully achieving its goals. Deep Learning is a new field of research. One of the branches of Artificial Intelligence Science deals with the creation of theories and algorithms that (...) allow the machine to learn by simulating neurons in the human body. Most in-depth learning research focuses on finding high-level methods. The strippers analyze a large data set using linear and nonlinear transformations. The method of deep learning is used in the detection of several diseases including blood cell diseases and their classification using the radiography of blood cells to help decision makers to know the type of blood cell and its associated diseases and the results will be presented in detail and discussed. This thesis is using python language and deep learning to detect blood cell diseases and their classifications. The proposed deep learning model was trained, validated and the tested. The accuracy of proposed model was 98.00%. (shrink)

Much of the current research in regenerative medicine concentrates on stem-cell therapy that exploits the regenerative capacities of stem cells when injected into different types of human tissues. Although new therapeutic paths have been opened up by induced pluripotent cells and human mesenchymal cells, the rate of success is still low and mainly due to the difficulties of managing cell proliferation and differentiation, giving rise to non-controlled stem cell differentiation that ultimately leads to cancer. Despite being (...) still far from becoming a reality, these studies highlight the role of physical and biological constraints (e.g., cues and morphogenetic fields) placed by tissue microenvironment on stem cell fate. This asks for a clarification of the coupling of stem cells and microenvironmental factors in regenerative medicine. We argue that extracellular matrix and stem cells have a causal reciprocal and asymmetric relationship in that the 3D organization and composition of the extracellular matrix establish a spatial, temporal, and mechanical control over the fate of stem cells, which enable them to interact and control (as well as be controlled by) the cellular components and soluble factors of microenvironment. Such an account clarifies the notions of stemness and stem cell regeneration consistently with that of microenvironment. (shrink)

H.L.A. Hart’s objection to defining a law as a subtype of an unclear type, or one of his objections, suffers from two oversights, which I identify.

Paper type: Conceptual perspective. Background(s): Physics, biology, epistemology Perspectives: Theory of autopoietic systems, Popperian evolutionary epistemology and the biology of cognition. Context: This paper is a contribution to developing the theories of hierarchically complex living systems and the natures of knowledge in such systems. Problem: Dissonance between the literatures of knowledge management and organization theory and my observations of the living organization led to consideration of foundation questions: What does it mean to be alive? What is knowledge? How are life (...) and knowledge related? Method: The approach is synthetic and multidisciplinary. The concept of autopoiesis (as defined by Maturana) as a definition for life, and knowledge as a product of autopoiesis are developed from first principles regarding the behavior of dynamical systems in time. Results: Autopoiesis and the construction of knowledge are inseparable aspects of physical phenomena scalable to many levels of organization (e.g., cells, multicellular organisms, organizations, social systems, etc.). The result unifies theories of epistemology, physical dynamics, life, biological evolution, knowledge and social systems. Implications: Results highlight the importance to understand autopoiesis as first defined by Maturana and Varela – as a complex physical phenomenon persisting over time. Autopoietic “self-observation” is not paradoxical. As dynamic physical processes, any internal/external activities relating to “observations” are displaced in time. The worlds living systems act on are not those observed. “Circularly closed” systems are actually open spirals along the axis of time. (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)

Types are fundamental for conceptual modeling and knowledge representation, being an essential construct in all major modeling languages in these fields. Despite that, from an ontological and cognitive point of view, there has been a lack of theoretical support for precisely defining a consensual view on types. As a consequence, there has been a lack of precise methodological support for users when choosing the best way to model general terms representing types that appear in a domain, (...) and for building sound taxonomic structures involving them. For over a decade now, a community of researchers has contributed to the development of the Unified Foundational Ontology (UFO) - aimed at providing foundations for all major conceptual modeling constructs. At the core of this enterprise, there has been a theory of types specially designed to address these issues. This theory is ontologically well- founded, psychologically informed, and formally characterized. These results have led to the development of a Conceptual Modelling language dubbed OntoUML, reflecting the ontological micro-theories comprising UFO. Over the years, UFO and OntoUML have been successfully employed on conceptual model design in a variety of domains including academic, industrial, and governmental settings. These experiences exposed improvement opportunities for both the OntoUML language and its underlying theory, UFO. In this paper, we revise the theory of types in UFO in response to empirical evidence. The new version of this theory shows that many of OntoUML’s meta-types (e.g. kind, role, phase, mixin) should be considered not as restricted to substantial types but instead should be applied to model endurant types in general, including relator types, quality types, and mode types. We also contribute with a formal characterization of this fragment of the theory, which is then used to advance a new metamodel for OntoUML (termed OntoUML 2). To demonstrate that the benefits of this approach are extended beyond OntoUML, the proposed formal theory is then employed to support the definition of UFO-based lightweight Semantic Web ontologies with ontological constraint checking in OWL. Additionally, we report on empirical evidence from the literature, mainly from cognitive psychology but also from linguistics, supporting some of the key claims made by this theory. Finally, we propose a computational support for this updated metamodel. (shrink)

In times of crisis, when current theories are revealed as inadequate to task, and new physics is thought to be required—physics turns to re-evaluate its principles, and to seek new ones. This paper explores the various types, and roles of principles that feature in the problem of quantum gravity as a current crisis in physics. I illustrate the diversity of the principles being appealed to, and show that principles serve in a variety of roles in all stages of the (...) crisis, including in motivating the need for a new theory, and defining what this theory should be like. In particular, I consider: the generalised correspondence principle, UV-completion, background independence, and the holographic principle. I also explore how the current crisis fits with Friedman’s view on the roles of principles in revolutionary theory-change, finding that while many key aspects of this view are not represented in quantum gravity, the view could potentially offer a useful diagnostic, and prescriptive strategy. This paper is intended to be relatively non-technical, and to bring some of the philosophical issues from the search for quantum gravity to a more general philosophical audience interested in the roles of principles in scientific theory-change. (shrink)

In this chapter, a new type Hyper groups are defined, corresponding basic properties and examples for new type Hyper groups are given and proved. Moreover, new type Hypergroups groups and are compared to hyper groups and groups. New type Hyper groups are shown to have a more general structure according to Hyper groups and groups. Also, new type SuperHyper groups are defined, corresponding basic properties and examples for new type SuperHyper are given and proved. Furthermore, we defined neutro-new type SuperHyper (...) groups. (shrink)

In the domain of ontology design as well as in Knowledge Representation, modeling universals is a challenging problem.Most approaches that have addressed this problem rely on Description Logics (DLs) but many difficulties remain, due to under-constrained representation which reduces the inferences that can be drawn and further causes problems in expressiveness. In mathematical logic and program checking, type theories have proved to be appealing but, so far they have not been applied in the formalization of ontologies. To bridge this gap, (...) we present in this paper a theory for representing ontologies in a dependently typed framework which relies on strong formal foundations including both a constructive logic and a functional type system. The language of this theory defines in a precise way what ontological primitives such as classes, relations, properties, etc., and thereof roles, are. The first part of the paper details how these primitives are defined and used within the theory. In a second part, we focus on the formalization of the role primitive. A review of significant role properties leads to the specification of a role profile and most of the remaining work details through numerous examples, how the proposed theory is able to fully satisfy this profile. It is demonstrated that dependent types can model several non-trivial aspects of roles including a formal solution for generalization hierarchies, identity criteria for roles and other contributions. A discussion is given on how the theory is able to cope with many of the constraints inherent in a good role representation. (shrink)

In general, a system S (that may be a company, association, institution, society, country, etc.) is formed by sub-systems Si { or P(S), the powerset of S }, and each sub-system Si is formed by sub-sub-systems Sij { or P(P(S)) = P2(S) } and so on. That’s why the n-th PowerSet of a Set S { defined recursively and denoted by Pn(S) = P(Pn-1(S) } was introduced, to better describes the organization of people, beings, objects etc. in our real world. (...) The n-th PowerSet was used in defining the SuperHyperOperation, SuperHyperAxiom, and their corresponding Neutrosophic SuperHyperOperation, Neutrosophic SuperHyperAxiom in order to build the SuperHyperAlgebra and Neutrosophic SuperHyperAlgebra. In general, in any field of knowledge, one in fact encounters SuperHyperStructures. Also, six new types of topologies have been introduced in the last years (2019-2022), such as: Refined Neutrosophic Topology, Refined Neutrosophic Crisp Topology, NeutroTopology, AntiTopology, SuperHyperTopology, and Neutrosophic SuperHyperTopology. (shrink)

The notion of the human embryo is not immutable. Various scientific and technological breakthroughs in reproductive biology have compelled us to revisit the definition of the human embryo during the past 2 decades. Somatic cell nuclear transfer, oocyte haploidisation and, more recently, human stem cell-derived embryo models have challenged this scientific term, which has both ethical and legal repercussions. Here, we offer a legal perspective to identify a universally accepted definition of ‘embryo’ which could help to ease and (...) unify the regulation of such entities in different countries. (shrink)

The purpose of this chapter is twofold. On the one hand, our goal is theoretical, as we aim at providing an instrument for detecting, analyzing, and solving ambiguities based on the reasoning mechanism underlying interpretation. To this purpose, combining the insights from pragmatics and argumentation theory, we represent the background assumptions driving an interpretation as presumptions. Presumptions are then investigated as the backbone of the argumentative reasoning that is used to assess and solve ambiguities and drive (theoretically) interpretive mechanisms. On (...) the other hand, our goal is practical. By analyzing ambiguities as stemming from different presumptions concerning language or, more importantly, expected communicative roles and goals, we can use communicative misunderstandings as the signal of deeper disagreements concerning mutual expectations or cultural differences. This argumentation-based interpretive mechanism will be applied to the analysis of medical interviews in the area of diabetes care, and will be used to bring to light the sources of misunderstanding and the different presumptions that define distinct cultures. We will consequently illustrate the analytical tools by identifying and distinguishing the various types of ambiguity underlying misunderstandings, and we will address them by describing the communicative intentions ascribed to the ambiguous utterances. (shrink)

In this paper we propose a formal theory of partitions (ways of dividing up or sorting or mapping reality) and we show how the theory can be applied in the geospatial domain. We characterize partitions at two levels: as systems of cells (theory A), and in terms of their projective relation to reality (theory B). We lay down conditions of well-formedness for partitions and we define what it means for partitions to project truly onto reality. We continue by classifying well-formed (...) partitions along three axes: (a) degree of correspondence between partition cells and objects in reality; (b) degree to which a partition represents the mereological structure of the domain it is projected onto; and (c) degree of completeness and exhaustiveness with which a partition represents reality. This classification is used to characterize three types of partitions that play an important role in spatial information science: cadastral partitions, categorical coverages, and the partitions involved in folk categorizations of the geospatial domain. (shrink)

In a series of recent publications, orofacial researchers have debated the question of how ‘bruxism’ should be defined for the purposes of accurate diagnosis and reliable clinical research. Following the principles of realism-based ontology, we performed an analysis of the arguments involved. This revealed that the disagreements rested primarily on inconsistent use of terms, so that issues of ontology were thus obfuscated by shortfalls in terminology. In this paper, we demonstrate how bruxism terminology can be improved by paying attention to (...) the relationships between (1) particulars and types, and (2) continuants and occurrents. (shrink)

Although Nietzsche accepted a distant cousin of Brian Leiter’s “Doctrine of Types,” according to which, “Each person has a fixed psycho-physical constitution, which defines him as a particular type of person,” the details of his actual view are quite different from the flat-footed position Leiter attributes to him. Leiter argues that Nietzsche thought that type-facts partially explain the beliefs and actions, including moral beliefs and actions, of the person whom those type-facts characterize. With this much, I agree. However, the (...) Doctrine of Types as formulated by Leiter, is manifestly unsupported both by Nietzsche’s texts and as an empirical hypothesis. Although Leiter has teamed up with Joshua Knobe to shore up the empirical credentials of his version of the Doctrine of Types, and although Knobe is one of the best experimental philosophers currently working in moral psychology, their account of the Doctrine is wrong both textually and empirically. That is to say, Nietzsche did not hold the version of the Doctrine they attribute to him, and it’s a good thing he didn’t, because the version that he actually did hold is better empirically supported than the version that they attribute to him. For Nietzsche – and in reality – types are not immutable or fixed. Although not everyone is endowed with the same type, which type someone belongs to can (though needn’t) evolve over the course of her lifetime. In particular, whereas I agree with Leiter that the neo-Aristotelian account of character development is empirically inadequate, I do so not because I think no character development occurs but because I think that character development occurs in a different way. In addition, for Nietzsche – and in reality – types on their own are not normative. Character, which is normatively evaluable, only arises through the refinement, calibration, and development of temperament. It might seem like I’ve just set myself an ambitious-enough goal, but I want to do more in this paper. The main point I want to argue is that Nietzsche held a person-type-relative unity of virtue thesis, according to which what’s intrinsically good for a particular person is to develop and act from particular character traits that “fit” her type. (shrink)

An analysis of the classical-quantum correspondence shows that it needs to identify a preferred class of coordinate systems, which defines a torsionless connection. One such class is that of the locally-geodesic systems, corresponding to the Levi-Civita connection. Another class, thus another connection, emerges if a preferred reference frame is available. From the classical Hamiltonian that rules geodesic motion, the correspondence yields two distinct Klein-Gordon equations and two distinct Dirac-type equations in a general metric, depending on the connection used. Each of (...) these two equations is generally-covariant, transforms the wave function as a four-vector, and differs from the Fock-Weyl gravitational Dirac equation (DFW equation). One obeys the equivalence principle in an often-accepted sense, whereas the DFW equation obeys that principle only in an extended sense. (shrink)

Generation of clean energy is one of the main challenges of the 21st century. Solar energy is the most abundantly available renewable energy source which would be supplying more than 50 of the global electricity demand in 2100. Solar cells are used to convert light energy into electrical energy directly with an appeal that it does not generate any harmful bi products, like greenhouse gasses. The manufacturing of solar cells is actually based on the types of semiconducting or non (...) semiconducting materials used and commercial maturity. From the very beginning of the terrestrial use of Solar Cells, efficiency and costs are the main focusing areas of research. The definition of so called emerging technologies sometimes described as including any technology capable of overcoming the Shockley-Queisser limit of power conversion efficiency 33.7 percent for a single junction device. In this paper, few promising materials for solar cells are discussed including their structural morphology, electrical and optical properties. The excellent state of the art technology, advantages and potential research issues yet to be explored are also pointed out. Md. Samiul Islam Sadek | Dr. M Junaebur Rashid | Dr. Zahid Hasan Mahmood "Emerging Next Generation Solar Cells: Route to High Efficiency and Low Cost" Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-1 | Issue-4 , June 2017 . (shrink)

Logical and philosophical literature provides different classifications of reasoning. In the Polish literature on the subject, for instance, there are three popular ones accepted by representatives of the Lvov-Warsaw School: Jan Łukasiewicz, Tadeusz Czeżowski and Kazimierz Ajdukiewicz (Ajdukiewicz in Logika pragmatyczna [Pragmatic Logic]. PWN, Warsaw (1965, 2nd ed. 1974). Translated as: Pragmatic Logic. Reidel & PWN, Dordrecht, 1975). The author of this paper, having modified those classifications, distinguished the following types of reasoning: (1) deductive and (2) non-deductive, and additionally (...) two types of them in each of the two, depending on the manner of combining their premises with the conclusion through the relation of classical logical entailment. Consequently, the four types of reasoning: unilateral deductive (incl. its sub-types: deductive inference and proof), bilateral deductive (incl. complete induction), and reductive (incl. the sub-types: explanation and verification), logically nonvaluable (incl. inference by analogy, statistic inference), correspond to four operators of derivability. They are defined formally on the ground of Tarski’s axiomatic theory of deductive systems, by means of the consequence operation _Cn_ (Tarski in Monatshefte Math Phys 37:361–404, 1930a, C R Soc Sci Lett Vars 23:22–29, 1930b). Also, certain metalogical properties of these operators are given, as well as their relations with Tarski’s consequence operations \(Cn^+\) ( \(Cn^+ = Cn\) ) and dual consequences \(Cn^{-1}\) (Słupecki in Zeszyty Naukowe Uniwersytetu Wrocławskiego Seria B Nr 3:33–40, 1959, Słupecki et al. in Stud Log 29:76–123, 1971, Wybraniec-Skardowska, in: Wybraniec-Skardowska, Bryll (eds) Z badań nad teorią zdań odrzuconych [Studies in the Theory of Rejected Propositions], Series B, Studia i Monografie, Zeszyty Naukowe Wyższej Szkoły Pedagogicznej w Opolu, Opole, 1969), and \(Cn^-\) (Wójcicki in Bull Sect Log 2(2):54–57, 1973)). (shrink)

This essay examines the concept of leadership as it is commonly understood within the field of leadership studies today. The inquiry is framed by an analysis of three generally accepted definitions of leadership. I look at the selected definitions from four angles, which I call the four dimensions of leadership: the behavioral (what the leader does, or ought to do, that makes it leadership), the asymmetrical (in what sense a leader is different from the others in the group), the social (...) (what it is that the leader is leading), and the teleological (what the direction is). By doing this, I find that these definitions can be problematic, if instructively so. I identify two underlying concerns. The first problem is the tendency to fuse informal and formal leadership into a single concept. I argue that informal and formal leadership can be more helpfully understood, rather, as two separate, if sometimes overlapping, concepts, each needing its own definition and analysis. This is because formal leadership is a functional concept, while informal leadership is not; this entails not only that each type of leader is leading a different type of entity, but also that each is judged by different standards. The second problem is, paradoxically, a bias against leadership. To put this less polemically: scholars who recognize that organizational success can be hindered by excessive emphasis upon hierarchy, and who thus study the dynamics of egalitarian collaboration, can inadvertently generate confusion by allowing the honorific of “leadership” to be applied also to that work. So, I propose definitions of the two key concepts, formal and informal leadership, with the suggestion that this provides a helpful method of sorting leadership scholarship into three categories: formal leadership; informal leadership; and egalitarianism. (shrink)

A long-standing puzzle for moral philosophers and psychologists alike is the concept of psychopathy, a personality disorder marked by tendencies to defy moral norms despite cognitive knowledge about right and wrong. Previously, discussions of the moral deficits of psychopathy have focused on willingness to harm and cheat others as well as reasoning about rule-based transgressions. Yet recent research in moral psychology has begun to more clearly define the domains of morality, en- compassing issues of harm, fairness, loyalty, authority, and spiritual (...) purity. Clinical descriptions and theories of psychopathy suggest that deficits may exist primarily in the areas of harm and fairness, although quantitative evidence is scarce. Within a broad sample of participants, we found that scores on a measure of psychopathy predicted sharply lower scores on the harm and fairness subscales of a measure of moral concern, but showed no relationship with authority, and very small relationships with ingroup and purity. On a measure of willingness to violate moral standards for money, psychopathy scores predicted greater willingness to violate moral concerns of any type. Results are further explored via potential mediators and analyses of the two factors of psychopathy. (shrink)

This quantitative study explores the acceptability of Online Learning Action Cell (LAC) practice as a school-based professional development strategy for Tagumpay National High School (TNHS) teachers. The research was motivated by the Department of Education (DepEd) Order No. 35 s. 2016 which prompts public schools to comply with the implementation of LAC sessions because it has a positive impact on teachers’ beliefs and practices resulting in education reforms for learners’ benefit. However, in compliance with DepEd’s policy on maximizing Time-On-Task (...) (DepEd Order No. 9 s. 2005) and the teacher’s conflict of schedule and other ancillary and coordination functions, absences or non-participation in classroom LAC was noted. The viability of offering Online LAC sessions using appropriate media and technologies to provide more options and flexibility for the study is suggested and tested utilizing a conceptual framework drawn from DepEd Order No. 35 s. 2016, Simonson’s Equivalency Theory and Anderson’s Community of Inquiry (COI). A descriptive survey method was used in this study with purposive sampling identifying ten Technology and Livelihood Education (TLE) teachers to pilot the Online LAC based on the memorandum issued by the school head. The subjects went through a week of experience in a LAC session using Facebook (FB) as Learning Management System (LMS) while a researcher-designed survey tool in the form of a Likert-type scale questionnaire was administered via Google forms before and after the online session to measure teacher’s acceptability of Online LAC Session practice. In the analysis, a descriptive statistic shows that pre-post survey results on Online LAC session planning is from ‘moderately acceptable’ to ‘very highly acceptable’; implementation is from ‘acceptable’ to ‘very highly acceptable’, and evaluation is from ‘moderately acceptable’ to ‘very highly acceptable’. TNHS teachers' acceptability of Online LAC session practice increases after their participation in a fully-online learning environment. Limitations, recommendations, future research directions, and conclusions are also included in the study. -/- . (shrink)

The introductory personal remarks refer to my motivations for choosing research projects, and for moving from physics to molecular biology and then to development, with Hydra as a model system. Historically, Trembley’s discovery of Hydra regeneration in 1744 was the begin¬ning of developmental biology as we understand it, with passionate debates about preformation versus de novo generation, mechanisms versus organisms. In fact, seemingly conflicting bottom-up and top-down concepts are both required in combination to understand development. In modern terms, this means (...) analysing the molecules involved, as well as searching for physical principles underlying development within systems of molecules, cells and tissues. During the last decade, molecular biology has provided surprising and impressive evidence that the same types of mol¬ecules and molecular systems are involved in pattern formation in a wide range of organisms, including coelenterates like Hydra, and thus appear to have been “invented” early in evolution. Likewise, the features of certain systems, especially those of developmental regulation, are found in many different organisms. This includes the generation of spatial structures by the interplay of self-enhancing activation and “lateral” inhibitory effects of wider range, which is a main topic of my essay. Hydra regeneration is a particularly clear model for the formation of defined patterns within initially near-uniform tissues. In conclusion, this essay emphasizes the analysis of development in terms of physical laws, including the application of mathematics, and insists that Hydra was, and will continue to be, a rewarding model for understanding general features of embryogenesis and regeneration. -/- -/- . (shrink)

In this paper we challenge the notion of ‘normativity’ used by some enactive approaches to cognition. We define some varieties of enactivism and their assumptions and make explicit the reasoning behind the co-emergence of individuality and normativity. Then we argue that appealing to dispositions for explaining some living processes can be more illuminating than claiming that all such processes are normative. For this purpose, we will present some considerations, inspired by Wittgenstein, regarding norm-establishing and norm-following and show that attributions of (...) normativity to non-social agents are deeply paradoxical. The main conclusions of our discussion are: (1) circular and internal explanations centred on the stability of living systems are insufficient to account for processes where the environment plays an important role, such as adaptation. Enactivism is not an explanatory alternative to evolutionary biology but needs it as a complement to accounts focused on the internal self-assembly of organisms; (2) though we share enactivism’s anti-representational spirit, we argue that ecological psychology can offer a better account of perception. (shrink)

Let us start by some general definitions of the concept of complexity. We take a complex system to be one composed by a large number of parts, and whose properties are not fully explained by an understanding of its components parts. Studies of complex systems recognized the importance of “wholeness”, defined as problems of organization (and of regulation), phenomena non resolvable into local events, dynamics interactions in the difference of behaviour of parts when isolated or in higher configuration, etc., in (...) short, systems of various orders (or levels) not understandable by investigation of their respective parts in isolation. In a complex system it is essential to distinguish between ‘global’ and ‘local’ properties. Theoretical physicists in the last two decades have discovered that the collective behaviour of a macro-system, i.e. a system composed of many objects, does not change qualitatively when the behaviour of single components are modified slightly. Conversely, it has been also found that the behaviour of single components does change when the overall behaviour of the system is modified. There are many universal classes which describe the collective behaviour of the system, and each class has its own characteristics; the universal classes do not change when we perturb the system. The most interesting and rewarding work consists in finding these universal classes and in spelling out their properties. This conception has been followed in studies done in the last twenty years on second order phase transitions. The objective, which has been mostly achieved, was to classify all possible types of phase transitions in different universality classes and to compute the parameters that control the behaviour of the system near the transition (or critical or bifurcation) point as a function of the universality class. This point of view is not very different from the one expressed by Thom in the introduction of Structural Stability and Morphogenesis (1975). It differs from Thom’s program because there is no a priori idea of the mathematical framework which should be used. Indeed Thom considers only a restricted class of models (ordinary differential equations in low dimensional spaces) while we do not have any prejudice regarding which models should be accepted. One of the most interesting and surprising results obtained by studying complex systems is the possibility of classifying the configurations of the system taxonomically. It is well-known that a well founded taxonomy is possible only if the objects we want to classify have some unique properties, i.e. species may be introduced in an objective way only if it is impossible to go continuously from one specie to another; in a more mathematical language, we say that objects must have the property of ultrametricity. More precisely, it was discovered that there are conditions under which a class of complex systems may only exist in configurations that have the ultrametricity property and consequently they can be classified in a hierarchical way. Indeed, it has been found that only this ultrametricity property is shared by the near-optimal solutions of many optimization problems of complex functions, i.e. corrugated landscapes in Kauffman’s language. These results are derived from the study of spin glass model, but they have wider implications. It is possible that the kind of structures that arise in these cases is present in many other apparently unrelated problems. Before to go on with our considerations, we have to pick in mind two main complementary ideas about complexity. (i) According to the prevalent and usual point of view, the essence of complex systems lies in the emergence of complex structures from the non-linear interaction of many simple elements that obey simple rules. Typically, these rules consist of 0–1 alternatives selected in response to the input received, as in many prototypes like cellular automata, Boolean networks, spin systems, etc. Quite intricate patterns and structures can occur in such systems. However, what can be also said is that these are toy systems, and the systems occurring in reality rather consist of elements that individually are quite complex themselves. (ii) So, this bring a new aspect that seems essential and indispensable to the emergence and functioning of complex systems, namely the coordination of individual agents or elements that themselves are complex at their own scale of operation. This coordination dramatically reduces the degree of freedom of those participating agents. Even the constituents of molecules, i.e. the atoms, are rather complicated conglomerations of subatomic particles, perhaps ultimately excitations of patterns of superstrings. Genes, the elementary biochemical coding units, are very complex macromolecular strings, as are the metabolic units, the proteins. Neurons, the basic elements of cognitive networks, themselves are cells. In those mentioned and in other complex systems, it is an important feature that the potential complexity of the behaviour of the individual agents gets dramatically simplified through the global interactions within the system. The individual degrees of freedom are drastically reduced, or, in a more formal terminology, the factual space of the system is much smaller than the product of the state space of the individual elements. That is one key aspect. The other one is that on this basis, that is utilizing the coordination between the activities of its members, the system then becomes able to develop and express a coherent structure at a higher level, that is, an emergent behaviour (and emergent properties) that transcends what each element is individually capable of. (shrink)

Barbour shows that time does not exist in the physical world, and similar conclusions are reached by others such as Deutsch, Davies and Woodward. Every possible configuration of a physical environment simply exists in the universe. The system is objectively static. Observation, however, is an inherently transtemporal phenomenon, involving actual or effective change of the configuration, collapse. Since, in a static environment, all possible configurations exist, transtemporal reality is of the logical type of a movie. The frame of a movie (...) film is of one logical type, an element of a set of frames, the movie, itself of a second logical type. In a static no-collapse universe, the configurations are of the first logical type, transtemporal reality of the second. To run, the movie requires iteration, a third logical type. Phenomenal consciousness is subjectively experienced as of this third logical type with regard to physical configurations. Everett's formulation clearly describes the transtemporal reality of an observer, which follows the physical in the linear dynamics, but departs from it on observation, giving rise to the the appearance of collapse, and the alternation of dynamics defined in the standard von Neumann-Dirac formulation. Since there is no physical collapse, his formulation is disputed. Given an iterator of the third logical type, the appearance of collapse is simply evidence of iteration. Chalmers demonstrates that phenomenal consciousness is of this logical type, an emergent property of the unitary system as a whole. Given an iterative function of this nature, one contextual to the physical configurations, paradoxes of time are resolved. Subjectively, meaning from the perspective of the iterative process, time passes in an objectively static universe, and the appearance of collapse is effected. (shrink)

Metaphors allow us to come to terms with abstract and complex information, by comparing it to something which is structured, familiar and concrete. Although modern science is “iconoclastic”, as Gaston Bachelard phrases it, scientists are at the same time prolific producers of metaphoric images themselves. Synthetic biology is an outstanding example of a technoscientific discourse replete with metaphors, including textual metaphors such as the “Morse code” of life, the “barcode” of life and the “book” of life. This paper focuses on (...) a different type of metaphor, however, namely on the archetypal metaphor of the mandala as a symbol of restored unity and wholeness. Notably, mandala images emerge in textual materials related to one of the new “frontiers” of contemporary technoscience, namely the building of a synthetic cell: a laboratory artefact that functions like a cell and is even able to replicate itself. The mandala symbol suggests that, after living systems have been successfully reduced to the elementary building blocks and barcodes of life, the time has now come to put these fragments together again. We can only claim to understand life, synthetic cell experts argue, if we are able to technically reproduce a fully functioning cell. This holistic turn towards the cell as a meaningful whole also requires convergence at the “subject pole”: the building of a synthetic cell as a practice of the self, representing a turn towards integration, of multiple perspectives and various forms of expertise. (shrink)

• Aggregates of previously isolated cells of Hydra are capable, under suitable solvant conditions, of regeneration forming complete animals. In a first stage, ecto- and endodermal cells sort out, producing the bilayered hollow structure characteristic of Hydra tissue; thereafter, heads are formed (even if the original cell preparation contained no head cells), eventually leading to the separation of normal animals with head, body column and foot. Hydra appears to be the highest type of organism that allows for regeneration of (...) the entire structure from random cell aggregates. The system is particularly useful for studying cell interactions, tissue polarity, pattern formation, and cell differentiation. (shrink)

(English, then french abstract) : -/- Fantasy, Discourse, Ideology – Transmission Beyond Propaganda. -/- Propaganda is everywhere, not only in commercials or politics. It is aimed at faraway strangers as well as nearby friends and relations. Propaganda in fact relies on a certain type of psychic structure, one that is tuned to receive it and disseminate it. This structure is a result of an unconscious subjective identification which is therefore not open to change through either cognition, argumentation or reasoning. Propaganda’s (...) form and content are best explained by an unconscious subjectivity rather than by Pavlov’s theory. The social dimension of this subjectivity may be defined by what we refer to as our ‘Analysis of Subjective Logics’ (a legacy of Lacan’s theory of the Four Discourses, which is deficient in some respects). We will first explore the various facets of the ‘Fantasy to Propagate’ by means of a word by word analysis, and will then go on to describe the connexions between Fantasy, Discourse and Ideology. We will show how a clever manipulator triggers an echo in the psyche of his victims, knitting together different and sometimes even contradictory fantasies in an unsteady synthesis he manages to maintain through patient repetition. As for psychoanalysis, it is not only possible but also highly desirable to practise it in the absence of all propaganda : among analysts, on condition that the precept of authority be outwitted, and within each analysis, by undoing the analysand’s sensitivity to suggestion. Psychoanalysis indeed does not only address the individual’s symptoms and their unravelling, but also, more ambitiously, aims to heal civilization of its discontents. This would entitle us to speak in terms of a genuine form of ‘propaganda prevention.’ -/- ---------------------- -/- Fantasme, Discours, Idéologie - D’une transmission qui ne serait pas propagande -/- La propagande se rencontre partout, pas seulement en publicité ou en politique. Avant d’être verticale et adressée aux lointains inconnus, elle est horizontale et s’adresse aux connaissances proches. C’est qu’elle repose en fait sur une structure psychique apte à la recevoir et à la répercuter, structure qui résulte de l’identification subjective, inconsciente donc non modifiable par la cognition, l’argumentation, la raison. Plutôt que par Pavlov, la forme et le contenu de la propagande s’expliquent par la subjectivité inconsciente. Celle-ci se laisse décrire dans le champ social par notre « Analyse des Logiques Subjectives » (héritière critique de la théorie des Quatre Discours de Lacan, insuffisante à maints égards). Nous passerons de l’analyse des facettes du « fantasme de propager » (par le détail des expressions qui en constituent les réalisations) à la description des rapports entre Fantasme, Discours et Idéologie : comment les habiles suscitent un écho dans le psychisme de leurs victimes en fédérant des fantasmes divers –voire opposés– dans une synthèse instable, mais que sa patiente répétition a pour effet de maintenir. En psychanalyse, transmettre sans propagande est non seulement possible mais souhaitable : horizontalement chez les analystes, à condition d’y déjouer l’argument d’autorité, et verticalement dans chaque analyse, en défaisant chez l’analysant les réseaux de suggestibilité. Car la psychanalyse, loin de se borner à la simple disparition des symptômes individuels, a pour vocation plus ambitieuse de contribuer à déconstruire le « malaise dans la civilisation ». On serait alors en droit de parler d’un authentique « prévention de la propagande ». (shrink)

Stephen Palmquist is Professor of Religion and Philosophy at Hong Kong Baptist University. We invited him to answer the question "What norms or values define excellent philosophy of religion? as part of our "Philosophers of Religion on Philosophy of Religion" series. If we regard this as a philosophical (not a scientific) question, then the first step to answering it is to determine what norms or values define excellent philosophy, in general. Once that is established, we can inquire whether the nature (...) of religion brings with it any special features that make the task of doing excellent philosophy of religion unique. Unlike scientific explanations, excellent philosophical explanations must be multi-perspectival. A question that has only one right answer is not philosophical; instead, it is likely to be about facts. While we philosophers should care (deeply!) about any facts relevant to our inquiries, our peculiar way of interpreting facts means that answering a philosophical question cannot be done in one absolutely "right" way. This does not mean there are no right answers to philosophical questions; rather, there are many. But this does not make any answer equally good; for there would then be no such thing as excellent philosophy. The essentially perspectival nature of all genuinely philosophical questions means that the correctness of each purportedly "right" answer must be assessed in terms of its aptness for the perspective the questioner adopts when posing the question. A single question, such as "Does God exist?" can have many good answers, depending on whether the questioner assumes science, morality, aesthetics, or something else as the context. Each different type of inquiry has different boundary-conditions, so a good answer within each context is bound to differ from those in other contexts. Bad philosophy typically lacks depth: like a cyclops, its approach to answering questions is mono-perspectival. But if good philosophy acknowledges perspectives, what makes philosophy excellent? Good philosophy achieves excellence when it approaches a completeness whereby we begin to understand the range of relevant perspectives from which a given question can be asked, and the distinct boundary-conditions for answering it properly from each relevant perspective. Before applying this definition of excellent philosophy to the specific case at hand, we must pause to consider whether anything distinctive characterizes the range of philosophical topics and questions that typically come under the umbrella of philosophy of religion. In particular, does religion have features that make it especially difficult (or for that matter, easy) to think about philosophically, compared to other philosophical topics? Yes and no. (shrink)

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

In this paper we define intensional models for the classical theory of types, thus arriving at an intensional type logic ITL. Intensional models generalize Henkin's general models and have a natural definition. As a class they do not validate the axiom of Extensionality. We give a cut-free sequent calculus for type theory and show completeness of this calculus with respect to the class of intensional models via a model existence theorem. After this we turn our attention to applications. Firstly, (...) it is argued that, since ITL is truly intensional, it can be used to model ascriptions of propositional attitude without predicting logical omniscience. In order to illustrate this a small fragment of English is defined and provided with an ITL semantics. Secondly, it is shown that ITL models contain certain objects that can be identified with possible worlds. Essential elements of modal logic become available within classical type theory once the axiom of Extensionality is given up. (shrink)

While seeking novel food sources to feed the increasing population of the globe, several alternatives have been discussed, including algae, fungi or in vitro meat. The increasingly propagated usage of farmed insects for human nutrition raises issues regarding food safety, consumer information and animal protection. In line with law, insects like any other animals must not be reared or manipulated in a way that inflicts unnecessary pain, distress or harm on them. Currently, there is a great need for research in (...) the area of insect welfare, especially regarding species-specific needs, health, farming systems and humane methods of killing. Recent results from neurophysiological, neuroanatomical and behavioral sciences prompt caution when denying consciousness and therefore the likelihood of presence of pain and suffering or something closely related to it to insects. From an animal protection point of view, these issues should be satisfyingly solved before propagating and establishing intensive husbandry systems for insects as a new type of mini-livestock factory farming. (shrink)

To construct a synthetic cell we need to understand the rules that permit life. A central idea in modern biology is that in addition to the four entities making reality, matter, energy, space and time, a fifth one, information, plays a central role. As a consequence of this central importance of the management of information, the bacterial cell is organised as a Turing machine, where the machine, with its compartments defining an inside and an outside and its (...) metabolism, reads and expresses the genetic program carried by the genome. This highly abstract organisation is implemented using concrete objects and dynamics, and this is at the cost of repeated incompatibilities (frustration), which need to be sorted out by appropriate «patches». After describing the organisation of the genome into the paleome (sustaining and propagating life) and the cenome (permitting life in context), we describe some chemical hurdles that the cell as to cope with, ending with the specific case of the methionine salvage pathway. (shrink)

Modern computing is generally taken to consist primarily of symbol manipulation. But symbols are abstract, and computers are physical. How can a physical device manipulate abstract symbols? Neither Church nor Turing considered this question. My answer is that the bit, as a hardware-implemented abstract data type, serves as a bridge between materiality and abstraction. Computing also relies on three other primitive—but more straightforward—abstractions: Sequentiality, State, and Transition. These physically-implemented abstractions define the borderline between hardware and software and between physicality and (...) abstraction. At a deeper level, asking how a physical device can interact with abstract symbols is the wrong question. The relationship between symbols and physical devices begins with the realization that human beings already know what it means to manipulate symbols. We build and program computers to do what we understand to be symbol manipulation. To understand what that means, consider a light switch. A light switch doesn’t turn a light on or off. Those are abstractions. Light switches don’t operate with abstractions. We build light switches, so that when flipped, the world is changed in such a way that we understand the light to be on or off. Similarly, we build computers to perform operations that we understand as manipulating symbols. (shrink)

The key to the measurement problem is the entity at the heart of Everett's formulation, the state of the memory, defined as the record of observations. In humans, the integrated synthesis defines the perceptual reality, a projective, three-dimensional representation of the world. This 'world hologram' is the conscious point of view, the mind in Lockwood's interpretation, the 'phenomenal perspective'. As Everett demonstrates, the collapse dynamics operates only judged by the state of the memory; the physical observer remains in a superposed (...) state. An operational mind-body property dualism is defined. This field of information is multiply instantiated in the many worlds of the unitary wave function. As these are superposed and coincident, the net result is a single world hologram. The physical frame of reference on this view is the superposition of the class of instantiating worlds, a second-logical-type phenomenon. By definition determinate only where defined by observations, this is the physical ontology of Everett's relative state. Collapse on observation is inherent. The evidence is the retrodiction of the holographic universe. This is the cosmology of the relative state. As it is determinate solely where defined by the world hologram that delineates the outer boundary, entropy is defined solely by this surface. The quasi-classical world is the cosmology in the absolute state. The incompatible dynamics of quantum mechanics operate in these two different types of physical frames of reference. The linear dynamics is the time evolution of the quasi-classical worlds. On observation, judged by the state of the world hologram, the class of instantiating worlds is redefined, becoming the class of worlds in which the observed outcome occurred. Collapse effectively operates. The holographic universe of the mind updates. The dynamics operate at different levels of logical type. The measurement problem is a category error. (shrink)

The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...) to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

The plurality of definitions of life is often perceived as an unsatisfying situation stemming from still incomplete knowledge about ‘what it is to live’ as well as from the existence of a variety of methods for reaching a definition. For many, such plurality is to be remedied and the search for a unique and fully satisfactory definition of life pursued. In this contribution on the contrary, it is argued that the existence of such a variety of definitions of life undermines (...) the very feasibility of ever reaching a unique unambiguous definition. It is argued that focusing on the definitions of specific types of ‘living systems’ – somehow in the same way that one can define specific types of ‘flying systems’ – could be more fruitful from a heuristic point of view than looking for ‘the’ right definition of life, and probably more accurate in terms of carving Nature at its joints. (shrink)

Located within the ascending reticular activating system are nuclei which release neurotransmitters such as acetylcholine, serotonin, dopamine, and norepinephrine. These nuclei have widespread projections that extend into the limbic system and throughout cortex. Activation of these neurotransmitters during awake states leads to arousal, while inhibition leads to the loss of consciousness experienced during slow-wave sleep. Previously, we proposed a mechanism in which cardiorespiratory synchronization may underlie the widespread hyperpolarization that occurs throughout the brain during slow-wave sleep. We further propose that (...) a similar homeostatic mechanism may be involved in sleep-wake transitions and maintaining various arousal states including rapid eye movement sleep, waking, and anxiety. Widespread depolarization associated with more rapid, shallow breathing and desynchronized cardiorespiratory oscillatory activity may underlie waking, anxiety, and rapid eye movement sleep states. The exact voltage values of these widespread membrane potential changes remain unknown and possibly highly variable between different neural areas and cell types. Here, we place these consciousness states on a spectrum of approximated widespread membrane potential values with anxiety states being the most depolarized, followed by waking states, and rapid eye movement sleep. We propose that although these widespread membrane potential changes are minor, they may underlie transitions between and maintenance of varying levels of arousal. Further research on these mechanisms could provide insights into how the brain functions. This homeodynamic arousal mechanism involves the established feed-forward and feedback signaling between the ascending reticular activating system and the hypothalamus, as well as the modulation by cardiorespiratory oscillatory feedback from the body. Understanding the basic mechanisms responsible for the states of sleep, waking, and anxiety could lead to better treatment options in health and disease. (shrink)

Molecular developmental biology has expanded our conceptions of gene actions, underpinning that embryonic development is not only governed by a set of specific genes, but as much by space–time conditions of its developing modules. Typically, formation of cellular spheres, their transformation into planar epithelia, followed by tube formations and laminations are modular steps leading to the development of nervous tissues. Thereby, actions of organising centres, morphogenetic movements, inductive events between epithelia, tissue polarity reversal, widening of epithelia, and all these occurring (...) orderly in space and time, are driving forces of emergent laminar neural tissues, e.g. the vertebrate retina. Analyses of self-organisational formation of retina-like 3D structures from dispersed cells under defined cell culture conditions demonstrate that not only particular genetic networks, but—at least as important—the applied culture conditions define phenotypes of emergent tissues. Such in vitro approaches allow assigning emerging tissue formation to ground-laying genetic networks separately from contributions by conditional constraints. (shrink)

The book is a collection of papers and aims to unify the questions of syntax and semantics of language, which are included in logic, philosophy and ontology of language. The leading motif of the presented selection of works is the differentiation between linguistic tokens (material, concrete objects) and linguistic types (ideal, abstract objects) following two philosophical trends: nominalism (concretism) and Platonizing version of realism. The opening article under the title “The Dual Ontological Nature of Language Signs and the Problem (...) of Their Mutual Relations” provides a broad introduction into the problem area connected with this differentiation, while the logic-formal characteristics of the distinction are framed in the work entitled “On the Type-Token Relationships” (Chapter 1). The basic part of the book deals with issues relating to syntax (Chapters 2-4) and semantics of language (Chapters 5-6), as well as pertaining to syntactic-semantic pragmatic questions (Chapters 7-13). Throughout the book, language, categorial language, is characterized syntactically as generated by classical categorial grammar (Chapter 2) and formalized on two opposing levels: as language of expression-tokens (level of tokens) and language of expression-types (level of types). The author’s considerations contained in Chapters 2 and 4 lead to the important philosophical conclusion that in formal-logical syntactic studies on language the assumption that expression-types constitute the primary language layer while expression-tokens make the secondary one, can be neglected; thus, this speaks in favour of the opposing standpoint—the concretistic one—in the ontology of language syntax. In the works “Meaning and Interpretations”, Parts I and II (Chapters 5 and 6), it is underlined, however, that such semantic concepts as: meaning, denotation and interpretation are defined on the types level, yet their formal definitions require making use of notions of the tokens level. The semantic notions introduced in the above-mentioned articles are also used in the following works of the present selection, under the titles: “Three Principles of Compositionality” and “On Metaknowledge and Truth” (Chapters 7 and 8). They formalize two principles of compositionality that are well known in the literature on the subject, deriving from Frege, i.e. those of meaning and of denotation; they are related to the syntactic principle of compositionality which was introduced by the author. All the three principles are, at the same time, three conditions of homomorphism of categorial language algebra into three kinds of non-standard models of language (one syntactic and two semantic ones: intensional and extensional), which allows introducing three definitions of truthfulness into these models. The next two works in the collection, entitled: “On Language Adequacy” and “What is the Sense in Logic and Philosophy of Language” (Chapters 9 and 10) concern adequacy of categorial language syntax along with its dual semantics: intensional and extensional, and categorial compatibility of any of its syntactic categories with two corresponding semantic categories: intensional and extensional, based on the compatibility the syntactic category of each language expression with the ontological category assigned to its denotatum. The well-known problem of categorial compatibility for first-order quantifiers finds its solution in the paper “Categories of First-Order Quantifiers” (Chapter 11). In the work “Logic and Ontology of Language” (Chapter 12), being in a sense a summary of the considerations presented in the preceding chapters of the book, language is treated as an ontological being, characterized in compliance with the logical conception of language proposed by Ajdukiewicz. Application—like throughout the book—of tools of classical logic and set theory has resulted in emergence of a general formal logical theory of syntax, semantics and pragmatics of language, which takes into account duality in the understanding of linguistic expressions as tokens (concretes) and types (abstract objects). In terms that take into account a functional approach to language itself, there comes out an ontological neutrality of logic with respect to existential assumptions relating to the ontological nature of linguistic expressions and their extra-linguistic ontological counterparts. The issues connected with applying logic while explaining the manner of using linguistic tokens and linguistic types to determine notions of language communication are raised and illustrated in the last chapter of the work, bearing the title “A Logical Conceptualization of Knowledge on the Notion of Language Communication”. (shrink)

Systems biologists often distance themselves from reductionist approaches and formulate their aim as understanding living systems “as a whole.” Yet, it is often unclear what kind of reductionism they have in mind, and in what sense their methodologies would offer a superior approach. To address these questions, we distinguish between two types of reductionism which we call “modular reductionism” and “bottom-up reductionism.” Much knowledge in molecular biology has been gained by decomposing living systems into functional modules or through detailed (...) studies of molecular processes. We ask whether systems biology provides novel ways to recompose these findings in the context of the system as a whole via computational simulations. As an example of computational integration of modules, we analyze the first whole-cell model of the bacterium M. genitalium. Secondly, we examine the attempt to recompose processes across different spatial scales via multi-scale cardiac models. Although these models rely on a number of idealizations and simplifying assumptions as well, we argue that they provide insight into the limitations of reductionist approaches. Whole-cell models can be used to discover properties arising at the interfaces of dynamically coupled processes within a biological system, thereby making more apparent what is lost through decomposition. Similarly, multi-scale modeling highlights the relevance of macroscale parameters and models and challenges the view that living systems can be understood “bottom-up.” Specifically, we point out that system-level properties constrain lower-scale processes. Thus, large-scale modeling reveals how living systems at the same time are more and less than the sum of the parts. (shrink)

Research ethics committees must sometimes deliberate about objects that do not fit nicely into any existing category. This is currently the case with the “gastruloid,” which is a self-assembling blob of cells that resembles a human embryo. The resemblance makes it tempting to group it with other members of that kind, and thus to ask whether gastruloids really are embryos. But fitting an ambiguous object into an existing category with well-worn pathways in research ethics, like the embryo, is only a (...) temporary fix. The bigger problem is that we no longer know what an embryo is. We haven’t had a non-absurd definition of ‘embryo’ for several decades and without a well-defined comparison class, asking whether gastruloids belong to the morally relevant class of things we call embryos is to ask a question without an answer. What’s the alternative? A better approach needs to avoid what I’ll refer to as “the potentiality trap” and, instead, rely on the emergence of morally salient facts about gastruloids and other synthetic embryos. (shrink)

Mark Schroeder has argued that all reasonable forms of inconsistency of attitude consist of having the same attitude type towards a pair of inconsistent contents (A-type inconsistency). We suggest that he is mistaken in this, offering a number of intuitive examples of pairs of distinct attitudes types with consistent contents which are intuitively inconsistent (B-type inconsistency). We further argue that, despite the virtues of Schroeder's elegant A-type expressivist semantics, B-type inconsistency is in many ways the more natural choice in (...) developing an expressivist account of moral discourse. We close by showing how to adapt ordinary formality-based accounts of logicality to define a B-type account of logical inconsistency and distinguish it from both semantic and pragmatic inconsistency. In sum, we provide a roadmap of how to develop a successful B-type expressivism. (shrink)

Autism has been defined as a disorder of social cognition, interaction and communication where ritualistic, repetitive behaviors are commonly observed. But how should we understand the behavioral and cognitive differences that have been the main focus of so much autism research? Can high-level cognitive processes and behaviors be identified as the core issues people with autism face, or do these characteristics perhaps often rather reflect individual attempts to cope with underlying physiological issues? Much research presented in this volume will point (...) to the latter possibility, i.e. that people on the autism spectrum cope with issues at much lower physiological levels pertaining not only to Central Nervous Systems (CNS) function, but also to peripheral and autonomic systems (PNS, ANS) (Torres, Brincker, et al. 2013). The question that we pursue in this chapter is what might be fruitful ways of gaining objective measures of the large-scale systemic and heterogeneous effects of early atypical neurodevelopment; how to track their evolution over time and how to identify critical changes along the continuum of human development and aging. We suggest that the study of movement variability—very broadly conceived as including all minute fluctuations in bodily rhythms and their rates of change over time (coined micro-movements (Figure 1A-B) (Torres, Brincker, et al. 2013))—offers a uniquely valuable and entirely objectively quantifiable lens to better assess, understand and track not only autism but cognitive development and degeneration in general. This chapter presents the rationale firstly behind this focus on micro-movements and secondly behind the choice of specific kinds of data collection and statistical metrics as tools of analysis (Figure 1C). In brief the proposal is that the micro-movements (defined in Part I – Chapter 1), obtained using various time scales applied to different physiological data-types (Figure 1), contain information about layered influences and temporal adaptations, transformations and integrations across anatomically semi-independent subsystems that crosstalk and interact. Further, the notion of sensorimotor re-afference is used to highlight the fact that these layered micro-motions are sensed and that this sensory feedback plays a crucial role in the generation and control of movements in the first place. In other words, the measurements of various motoric and rhythmic variations provide an access point not only to the “motor systems”, but also access to much broader central and peripheral sensorimotor and regulatory systems. Lastly, we posit that this new lens can also be used to capture influences from systems of multiple entry points or collaborative control and regulation, such as those that emerge during dyadic social interactions. (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)

A remarkable event occurred at the December 3, 2004, meeting of the U. S. President’s Council on Bioethics. Council member William Hurlbut, a physician and Consulting Professor in the Program in Human Biology at Stanford University, formally unveiled a proposal that he claimed would solve the ethical problems surrounding the extraction of stem cells from human embryos. The proposal would involve the creation of genetically defective embryos that “never rise to the level of integrated organismal existence essential to be designated (...) human life with potential,” and therefore could be used as morally acceptable sources of stem cells for research and therapy. The aim of this essay is to show that Hurlbut’s proposal does not solve the ethical problems associated with human embryonic stem cell research. Two major reasons are presented. First, the proposal, which involves modification of a somatic cell nucleus, suffers from an ethical problem that is common to all types of human genetic engineering: since the procedure is not foolproof, there will be failures. In the case of the procedure Hurlbut proposes, some normal (albeit cloned) embryos will be produced. Second, the embryo engineered in the manner described is, at least in the early stages of its development, fully human despite its genetic defect. This essay also will show how a reasonable person might mistakenly view the proposal as legitimate if he or she makes the error of conflating genetic determinism with Aristotelian teleology. Finally, it will argue that ethical clarity can be achieved by seeing the embryo as a holistic entity possessing emergent properties that cannot simply be spelled out by genes. (shrink)