An overview of the following three related papers in this issue presents the Emergence of Highly Complex Systems such as living organisms, man, society and the human mind from the viewpoint of the current Ontological Theory of Levels. The ontology of spacetime structures in the Universe is discussed beginning with the quantum level; then, the striking emergence of the higher levels of reality is examined from a categorical—relational and logical viewpoint. The ontological problems and methodology aspects discussed in the (...) first two papers are followed by a rigorous paper based on Category Theory, Algebraic Topology and Logic that provides a conceptual and mathematical basis for a Categorical Ontology Theory of Levels. The essential links and relationships between the following three papers of this issue are pointed out, and further possible developments are being considered. (shrink)

A novel conceptual framework is introduced for the Complexity Levels Theory in a Categorical Ontology of Space and Time. This conceptual and formal construction is intended for ontological studies of Emergent Biosystems, Super-complex Dynamics, Evolution and Human Consciousness. A claim is defended concerning the universal representation of an item’s essence in categorical terms. As an essential example, relational structures of living organisms are well represented by applying the important categorical concept of natural transformations to biomolecular reactions and relational (...) structures that emerge from the latter in living systems. Thus, several relational theories of living systems can be represented by natural transformations of organismic, relational structures. The ascent of man and other living organisms through adaptation, is viewed in novel categorical terms, such as variable biogroupoid representations of evolving species. Such precise but flexible evolutionary concepts will allow the further development of the unifying theme of local-to-global approaches to highly complex systems in order to represent novel patterns of relations that emerge in super- and ultra-complex systems in terms of compositions of local procedures. Solutions to such local-to-global problems in highly complex systems with ‘broken symmetry’ might be possible to be reached with the help of higher homotopy theorems in algebraic topology such as the generalized van Kampen theorems (HHvKT). Categories of many-valued, Łukasiewicz-Moisil (LM) logic algebras provide useful concepts for representing the intrinsic dynamic ‘asymmetry’ of genetic networks in organismic development and evolution, as well as to derive novel results for (non-commutative) Quantum Logics. Furthermore, as recently pointed out by Baianu and Poli (Theory and applications of ontology, vol 1. Springer, Berlin, in press), LM-logic algebras may also provide the appropriate framework for future developments of the ontological theory of levels with its complex/entangled/intertwined ramifications in psychology, sociology and ecology. As shown in the preceding two papers in this issue, a paradigm shift towards non-commutative, or non-Abelian, theories of highly complex dynamics—which is presently unfolding in physics, mathematics, life and cognitive sciences—may be implemented through realizations of higher dimensional algebras in neurosciences and psychology, as well as in human genomics, bioinformatics and interactomics. (shrink)

A categorical, higher dimensional algebra and generalized topos framework for Łukasiewicz–Moisil Algebraic–Logic models of non-linear dynamics in complex functional genomes and cell interactomes is proposed. Łukasiewicz–Moisil Algebraic–Logic models of neural, genetic and neoplastic cell networks, as well as signaling pathways in cells are formulated in terms of non-linear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable ‘next-state functions’ is extended to a (...) Łukasiewicz–Moisil Topos with an n-valued Łukasiewicz–Moisil Algebraic Logic subobject classifier description that represents non-random and non-linear network activities as well as their transformations in developmental processes and carcinogenesis. The unification of the theories of organismic sets, molecular sets and Robert Rosen’s (M,R)-systems is also considered here in terms of natural transformations of organismal structures which generate higher dimensional algebras based on consistent axioms, thus avoiding well known logical paradoxes occurring with sets. Quantum bionetworks, such as quantum neural nets and quantum genetic networks, are also discussed and their underlying, non-commutative quantum logics are considered in the context of an emerging Quantum Relational Biology. (shrink)

A categorical, higher dimensional algebra and generalized topos framework for Łukasiewicz–Moisil Algebraic–Logic models of non-linear dynamics in complex functional genomes and cell interactomes is proposed. Łukasiewicz–Moisil Algebraic–Logic models of neural, genetic and neoplastic cell networks, as well as signaling pathways in cells are formulated in terms of non-linear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable ‘next-state functions’ is extended to a (...) Łukasiewicz–Moisil Topos with an n-valued Łukasiewicz–Moisil Algebraic Logic subobject classifier description that represents non-random and non-linear network activities as well as their transformations in developmental processes and carcinogenesis. The unification of the theories of organismic sets, molecular sets and Robert Rosen’s (M,R)-systems is also considered here in terms of natural transformations of organismal structures which generate higher dimensional algebras based on consistent axioms, thus avoiding well known logical paradoxes occurring with sets. Quantum bionetworks, such as quantum neural nets and quantum genetic networks, are also discussed and their underlying, non-commutative quantum logics are considered in the context of an emerging Quantum Relational Biology. (shrink)

This paper argues that besides mechanistic explanations, there is a kind of explanation that relies upon “topological” properties of systems in order to derive the explanandum as a consequence, and which does not consider mechanisms or causal processes. I first investigate topological explanations in the case of ecological research on the stability of ecosystems. Then I contrast them with mechanistic explanations, thereby distinguishing the kind of realization they involve from the realization relations entailed by mechanistic explanations, and explain how both (...) kinds of explanations may be articulated in practice. The second section, expanding on the case of ecological stability, considers the phenomenon of robustness at all levels of the biological hierarchy in order to show that topological explanations are indeed pervasive there. Reasons are suggested for this, in which “neutral network” explanations are singled out as a form of topological explanation that spans across many levels. Finally, I appeal to the distinction of explanatory regimes to cast light on a controversy in philosophy of biology, the issue of contingence in evolution, which is shown to essentially involve issues about realization. (shrink)

Formal spaces have become commonplace conceptual and computational tools in a large array of scientific disciplines, including both the natural and the social sciences. Morphological spaces are spaces describing and relating organismal phenotypes. They play a central role in morphometrics, the statistical description of biological forms, but also underlie the notion of adaptive landscapes that drives many theoretical considerations in evolutionary biology. We briefly review the topological and geometrical properties of the most common morphospaces in the biological literature. In (...) contemporary geometric morphometrics, the notion of a morphospace is based on the Euclidean tangent space to Kendall’s shape space, which is a Riemannian manifold. Many more classical morphospaces, such as Raup’s space of coiled shells, lack these metric properties, e.g., due to incommensurably scaled variables, so that these morphospaces typically are affine vector spaces. Other notions of a morphospace, like Thomas and Reif’s skeleton space, may not give rise to a quantitative measure of similarity at all. Such spaces can often be characterized in terms of topological or pretopological spaces. (shrink)

Algebraic/topological descriptions of living processes are indispensable to the understanding of both biological and cognitive functions. This paper presents a fundamental algebraic description of living/cognitive processes and exposes its inherent ambiguity. Since ambiguity is forbidden to computation, no computational description can lend insight to inherently ambiguous processes. The impredicativity of these models is not a flaw, but is, rather, their strength. It enables us to reason with ambiguous mathematical representations of ambiguous natural processes. The noncomputability of these structures means computerized (...) simulacra of them are uninformative of their key properties. This leads to the question of how we should reason about them. That question is answered in this paper by presenting an example of such reasoning, the demonstration of a topological strategy for understanding how the fundamental structure can form itself from within itself. (shrink)

I formulate in relational terms the ubiquitous biological interaction of symbiosis. I explicate the topology of the different modes of relational interactions of (M, R)-networks, the entailment diagrams that model the host and the symbiont. These modes all have biological realizations as various categories of symbiotic relationships, ranging from mutualism to parasitism to infection.

A novel conceptual framework is introduced for the Complexity Levels Theory in a Categorical Ontology of Space and Time. This conceptual and formal construction is intended for ontological studies of Emergent Biosystems, Super-complex Dynamics, Evolution and Human Consciousness. A claim is defended concerning the universal representation of an item’s essence in categorical terms. As an essential example, relational structures of living organisms are well represented by applying the important categorical concept of natural transformations to biomolecular reactions and relational (...) structures that emerge from the latter in living systems. Thus, several relational theories of living systems can be represented by natural transformations of organismic, relational structures. The ascent of man and other living organisms through adaptation, is viewed in novel categorical terms, such as variable biogroupoid representations of evolving species. Such precise but flexible evolutionary concepts will allow the further development of the unifying theme of local-to-global approaches to highly complex systems in order to represent novel patterns of relations that emerge in super- and ultra-complex systems in terms of compositions of local procedures. Solutions to such local-to-global problems in highly complex systems with ‘broken symmetry’ might be possible to be reached with the help of higher homotopy theorems in algebraic topology such as the generalized van Kampen theorems (HHvKT). Categories of many-valued, Łukasiewicz-Moisil (LM) logic algebras provide useful concepts for representing the intrinsic dynamic ‘asymmetry’ of genetic networks in organismic development and evolution, as well as to derive novel results for (non-commutative) Quantum Logics. Furthermore, as recently pointed out by Baianu and Poli (Theory and applications of ontology, vol 1. Springer, Berlin, in press), LM-logic algebras may also provide the appropriate framework for future developments of the ontological theory of levels with its complex/entangled/intertwined ramifications in psychology, sociology and ecology. As shown in the preceding two papers in this issue, a paradigm shift towards non-commutative, or non-Abelian, theories of highly complex dynamics—which is presently unfolding in physics, mathematics, life and cognitive sciences—may be implemented through realizations of higher dimensional algebras in neurosciences and psychology, as well as in human genomics, bioinformatics and interactomics. (shrink)

BackgroundEthical and regulatory guidance on the collection and use of human biospecimens for research forms an essential component of national health systems in Sub-Saharan Africa, where rapid advances in genetic- and genomic-based technologies are fueling clinical trials involving HBS and the establishment of large-scale biobanks.MethodsAn extensive multi-level search for publicly available ethics regulatory guidance was conducted for each SSA country. A second review documented active trials listed in the WHO International Clinical Trials Registry Platform as of January 2015 in which (...) HBS collection was specified in the protocol. Findings were combined to determine the extent to which countries that are study sites for HBS-related research are supported by regulatory guidance language on the collection, use, ownership and storage of biospecimens.ResultsOf the 49 SSA countries, 29 had some form of national ethics guidance, yet only 17 provided language relating to HBS-related research, with specific guidance on consent, ownership, reuse, storage, and export/import/transfer. Ten countries accounted for 84 % of the active clinical trials involving the collection of HBS in SSA. All except one of these countries were found to have some national guidance in the form of regulations, codes of ethics, and/or standard operating procedures; however, only seven of the ten offered any language specific to HBS.ConclusionsDespite the fact that the bulk of registered clinical trials in SSA involving HBS, as well as existing and proposed sites for biorepositories under the H3Africa Initiative, are currently situated in countries with the most complete ethics and regulatory guidance, variability in the regulations themselves may create challenges for planned and future pan-African collaborations and may require legislative action at the national level to revise. Countries in SSA that still lack regulatory guidance on HBS will require extensive health system strengthening in ethics governance before they can be full participants in the modern research enterprise. (shrink)

This rare publication continues an exploratory journey in relational biology, a study of biology in terms of the organization of networked connections in living systems. It builds on the author's two earlier monographs which looked at the epistemology of life and the ontogeny of life. Here the emphasis is on the intangibility of life, that the real nature of living systems is conveyed not by their tangible material basis but by their intangible inherent processes. Relational (...) class='Hi'>biology is the approach that hails 'function dictates structure'; it is mathematics decoded into biological realizations. Therefore, the work begins with a concise introduction to category theory, equiping the reader with the mathematical metalanguage of relation biology. The book is organized around three parts: Part I is a comprehensive study of the most important functor in relational biology, the power set functor. The author lays the set-theoretic foundations of the functorial connections in relational biology, exploring relations, mappings, and set-valued mappings. In Part II, Natural Law receives a new mathematical formulation founded on two axioms: 'Everything is a set.' and 'Every process is a set-valued mapping.' The reader sees how Metabolism-Repair networks, equipped with set-valued processors, expand their role from models of biological entities to generic models of all natural systems. Part III expounds the various shades of invertibility in general, and the inversion of encoding to decoding in particular. A plethora of mathematical and biological examples illustrate the category-theoretic concepts of equivalence and adjunction. This book's algebraic approach to biological models will appeal to researchers and graduate students in mathematics, biology, and the philosophy of science. (shrink)

This essay explores the universal cognitive bases of biological taxonomy and taxonomic inference using cross-cultural experimental work with urbanized Americans and forest-dwelling Maya Indians. A universal, essentialist appreciation of generic species appears as the causal foundation for the taxonomic arrangement of biodiversity, and for inference about the distribution of causally-related properties that underlie biodiversity. Universal folkbiological taxonomy is domain-specific: its structure does not spontaneously or invariably arise in other cognitive domains, like substances, artifacts or persons. It is plausibly an innately-determined (...) evolutionary adaptation to relevant and recurrent aspects of ancestral hominid environments, such as the need to recognize, locate, react to, and profit from many ambient species. Folkbiological concepts are special players in cultural evolution, whose native stability attaches to more variable and difficult-to-learn representational forms, thus enhancing the latter's prospects for regularity and recurrence in transmission within and across cultures. This includes knowledge that cumulatively enriches (folk expertise), overrides (religious belief) or otherwise transcends (science) the commonsense ontology prescribed by folkbiology. Finally, the studies summarized here indicate that results gathered from “standard populations” in regard to biological categorization and reasoning more often than not fail to generalize in straightforward ways to humanity at large. This suggests the need for much more serious attention to cross-cultural research on basic cognitive processes. (shrink)

Contemporary psychiatry faces serious challenges because it has failed to incorporate accumulated knowledge from basic neuroscience, neurophilosophy, and brain–mind relation studies. As a consequence, it has limited explanatory power, and effective treatment options are hard to come by. A new conceptual framework for understanding mental health based on underlying neurobiological spatial-temporal mechanisms of mental disorders (already gained by the experimental studies) is beginning to emerge.

A three-variable biochemical prototype involving two enzymes with autocatalytic regulation proposed by Decroly and Goldbeter (1987) is analyzed using a topological approach. A two-branched manifold, a so-called template, is thus identified. For certain control parameter values, this template is a horseshoe template with a global torsion of two half-turns. This implies that the bifurcation diagram can be described using the usual sequences associated with a unimodal map with a differentiable maximum as well as exemplified by the logistic map. Moreover, (...) a type-I intermittency associated with a saddle-node bifurcation is exhibited. The dynamics from a single time series are also investigated to determine whether it is possible to investigate the dynamics of this biochemical model from the measure of a single concentration. (shrink)

Three issues related to Feldman and Levin's treatment of biological variability are discussed. We question the usefulness of the indirect component of δλ. We suggest that trade-offs between speed and accuracy in aimed movements support identification of δλ, rather than λ, as a control variable. We take issue with the authors' proposal for resolving redundancy in multi-joint movements, given recent data.

: Models that fail to satisfy the Markov condition are unstable in the sense that changes in state variable values may cause changes in the values of background variables, and these changes in background lead to predictive error. This sort of error arises exactly from the failure of non-Markovian models to track the set of causal relations upon which the values of response variables depend. The result has implications for discussions of the level of selection: under certain plausible conditions (...) the models of selection presented in such debates will not satisfy the Markov condition when fit to data from real populations. Since this is true both for group and individual level models, models of neither sort correctly represent the causal structure generating, nor correctly explain, the phenomena of interest. (shrink)

In the last 20 years or so, since the publication of a seminal paper by Watts and Strogatz :440–442, 1998), an interest in topological explanations has spread like a wild fire over many areas of science, e.g. ecology, evolutionary biology, medicine, and cognitive neuroscience. The topological approach is still very young by all standards, and even within special sciences it still doesn’t have a single methodological programme that is applicable across all areas of science. That is why this special (...) issue is important as a first systematic philosophical study of topological explanations and their relation to a well understood and widespread explanatory strategy, such as mechanistic one. (shrink)

The extent to which machine metaphors are used in synthetic biology is striking. These metaphors contain a specific perspective on organisms as well as on scientific and technological progress. Expressions such as “genetically engineered machine”, “genetic circuit”, and “platform organism”, taken from the realms of electronic engineering, car manufacturing, and information technology, highlight specific aspects of the functioning of living beings while at the same time hiding others, such as evolutionary change and interdependencies in ecosystems. Since these latter aspects (...) are relevant for, for example, risk evaluation of uncontained uses of synthetic organisms, it is ethically imperative to resist the thrust of machine metaphors in this respect. In addition, from the perspective of the machine metaphor viewing an entity as a moral agent or patient becomes dubious. If one were to regard living beings, including humans, as machines, it becomes difficult to justify ascriptions of moral status. Finally, the machine metaphor reinforces beliefs in the potential of synthetic biology to play a decisive role in solving societal problems, and downplays the role of alternative technological, and social and political measures. (shrink)

The formal framework of Kauffman (1991) depicts the constraints of self-organization on the evolution of complex systems and the relation of self-organization to selection. We discuss his treatment of 'generic constraints' as sources of order (section 2) and the relation between adaptation and organization (section 3). We then raise a number of issues, including the role of adaptation in explaining order (section 4) and the limitations of formal approaches in explaining the distinctively biological (section 5). The principal question we pose (...) is the relation of generic constraints on evolution to more specific local constraints, imposed, for example, by the characteristic materials out of which organisms are constructed, the accidental features characteristic of the Bauplan of a lineage, and the local vicissitudes of adaptation. We offer no answer to this large question. (shrink)

I explain the difficulty of making various concepts of and relating to probability precise, rigorous and physically significant when attempting to apply them in reasoning about objects living in infinite-dimensional spaces, working through many examples from cosmology. I focus on the relation of topological to measure-theoretic notions of and relating to probability, how they diverge in unpleasant ways in the infinite-dimensional case, and are even difficult to work with on their own. Even in cases where an appropriate family of spacetimes (...) is finite-dimensional, and so admits a measure of the relevant sort, however, it is always the case that the family is not a compact topological space, and so does not admit a physically significant, well behaved probability measure. Problems of a different but still deeply troubling sort plague arguments about likelihood in that context, which I also discuss. I conclude that most standard forms of argument used in cosmology to estimate the likelihood of the occurrence of various properties or behaviors of spacetimes have serious mathematical, physical and conceptual problems. (shrink)

Besides mechanistic explanations of phenomena, which have been seriously investigated in the last decade, biology and ecology also include explanations that pinpoint specific mathematical properties as explanatory of the explanandum under focus. Among these structural explanations, one finds topological explanations, and recent science pervasively relies on them. This reliance is especially due to the necessity to model large sets of data with no practical possibility to track the proper activities of all the numerous entities. The paper first defines topological (...) explanations and then explains why topological explanations and mechanisms are different in principle. Then it shows that they are pervasive both in the study of networks—whose importance has been increasingly acknowledged at each level of the biological hierarchy—and in contexts where the notion of selective neutrality is crucial; this allows me to capture the difference between mechanisms and topological explanations in terms of practical modelling practices. The rest of the paper investigates how in practice mechanisms and topologies are combined. They may be articulated in theoretical structures and explanatory strategies, first through a relation of constraint, second in interlevel theories, or they may condition each other. Finally, I explore how a particular model can integrate mechanistic informations, by focusing on the recent practice of merging networks in ecology and its consequences upon multiscale modelling. (shrink)

BackgroundDepression is a prevalent condition that has a significant impact on psychosocial functioning and quality of life. The onset and persistence of depression have been linked to a variety of biological and psychosocial variables. Many of these variables are associated with specific lifestyle characteristics, such as physical activity, diet, and sleep patterns. Some psychosocial determinants have an impact on people’ health-related behavior change. These include personal factors such as sense of coherence, patient activation, health literacy, self-efficacy, and procrastination. This study (...) aims to analyze the association between the severity of depression, lifestyle patterns, and personal factors related to health behavior. It also aims to analyze whether personal factors moderate the relationship between lifestyles and depression.MethodsThis study is a secondary data analysis of baseline data collected at the start of a randomized controlled trial. A sample of 226 patients with subclinical, mild, or moderate depression from primary healthcare centers in two sites in Spain was used, and descriptive, bivariate, multivariate, and moderation analyses were performed. Depression was the primary outcome, measured by Beck II Self-Applied Depression Inventory. Lifestyle variables such as physical exercise, adherence to Mediterranean diet and sleep quality, social support, and personal factors such as self-efficacy, patient activation in their own health, sense of coherence, health literacy, and procrastination were considered secondary outcomes.ResultsLow sense of coherence, poor sleep quality, low patient activation, and sedentarism are predictors of having more depressive symptoms. Moderation analyses were not significant.DiscussionLifestyle and personal factors are related to depressive symptomatology. Our findings reveal that sense of coherence, patient’s activation level, sedentarism, and sleep quality are associated with depression. Further research is needed regarding adherence to Mediterranean diet, minutes walking per week and the interrelationship between lifestyles, personal factors, and depression. (shrink)

This work is mainly concerned with the notion of hierarchical modularity and its use in explaining structure and dynamical behavior of complex systems by means of hierarchical modular models, as well as with a concept of my proposal, antimodularity, tied to the possibility of the algorithmic detection of hierarchical modularity. Specifically, I highlight the pragmatic bearing of hierarchical modularity on the possibility of scientific explanation of complex systems, that is, systems which, according to a chosen basic description, can be considered (...) as composed of elementary, discrete, interrelated parts. I stress that hierarchical modularity is also required by the experimentation aimed to discover the structure of such systems. Algorithmic detection of hierarchical modularity turns out to be a task plagued by the demonstrated computational intractability of the search for the best hierarchical modular description, and by the high computational expensiveness of even approximated detection methods. Antimodularity consists in the lack of a modular description fitting the needs of the observer, a lack due either to absence of modularity in the system’s chosen basic description, or to the impossibility, due to the excessive size of the system under assessment in relation to the computational cost of algorithmic methods, to algorithmically produce a valid hierarchical description. I stress that modularity and antimodularity depend on the pragmatic choice of a given basic description of the system, a choice made by the observer based on explanatory goals. I show how antimodularity hinders the possibility of applying at least three well-known types of explanation: mechanistic, deductive-nomological and computational. A fourth type, topological explanation, remains unaffected. I then assess the presence of modularity in biological systems, and evaluate the possible consequences, and the likelihood, of incurring in antimodularity in biology and other sciences, concluding that this eventuality is quite likely, at least in systems biology. I finally indulge in some metaphysical and historical speculations: metaphysically, antimodularity seems to suggest a possible position according to which natural kinds are detected modules, and as such, due to the computational hardness of the detection of the best hierarchical modular description, they are unlikely to be the best possible way to describe the world, because the modularity of natural kinds quite probably does not reflect the best possible modularity of the world. From an historical point of view, the growing use of computational methods for modularity detection or simulation of complex systems, especially in certain areas of scientific research, hints at the envisioning of a multiplicity of emerging scientific disciplines guided by a self- sustained, growing production of possibly human-unintelligible explanations. This, I suggest, would constitute an historical change in science, which, if has not already occurred, could well be on the verge of happening. (shrink)

I explicate the crucial role played by efficient cause in Robert Rosen’s characterization of life, by elaborating on the topic of Aristotelian causality, and exploring the many alternate descriptions of causal and inferential entailments. In particular, I discuss the concepts of functional entailment and immanent causation, and examine how they fit into Robert Rosen’s relational-biology universe of living, anticipatory, and complex systems.

We argue that living systems process information such that functionality emerges in them on a continuous basis. We then provide a framework that can explain and model the normativity of biological functionality. In addition we offer an explanation of the anticipatory nature of functionality within our overall approach. We adopt a Peircean approach to Biosemiotics, and a dynamical approach to Digital-Analog relations and to the interplay between different levels of functionality in autonomous systems, taking an integrative approach. We then apply (...) the underlying biosemiotic logic to a particular biological system, giving a model of the B-Cell Receptor signaling system, in order to demonstrate how biosemiotic concepts can be used to build an account of biological information and functionality. Next we show how this framework can be used to explain and model more complex aspects of biological normativity, for example, how cross-talk between different signaling pathways can be avoided. Overall, we describe an integrated theoretical framework for the emergence of normative functions and, consequently, for the way information is transduced across several interconnected organizational levels in an autonomous system, and we demonstrate how this can be applied in real biological phenomena. Our aim is to open the way towards realistic tools for the modeling of information and normativity in autonomous biological agents. (shrink)

We are used to regarding actions and other events, such as Brutus’ stabbing of Caesar or the sinking of the Titanic, as occupying intervals of some underlying linearly ordered temporal dimension. This attitude is so natural and compelling that one is tempted to disregard the obvious difference between time periods and actual happenings in favor of the former: events become mere “intervals cum description”.1 On the other hand, in ordinary circumstances the point of talking about time is to talk about (...) what actually happens or might happen at some time or another. We talk about ‘now’ and ‘then’ in an effort to put some order in our description of what goes on. And since different events seem to overlap in so many different ways, a full account of their temporal relations seems to run afoul of a reductionist strategy. This raises two philosophical questions. The first is whether we can actually go beyond time, as it were, i.e., whether we can take events as bona fide entities and deal with them directly, just as we can deal with spatial entities such as physical bodies or masses without confining ourselves to their spatial representations. This is a controversial issue (though probably not as controversial as it used to be), and ties in with a number of unsettled problems concerning, e.g., the structure of causality or the definition of adequate identity and individuation criteria for events. 2 The second question is whether we can perhaps do without time, i.e., whether we can dispense with time points or intervals as an independent ontological category and focus only on actual or potential happenings, in opposition to the form of reductionism mentioned above—in short, whether we can account for the temporal dimension in terms of suitable relations among events. This is also a highly controversial issue, and relates to the classical dispute concerning relational vs. absolutist conceptions of (space and) time.3 It is this second question that we intend to focus on here.. (shrink)

Consistent findings about the inverse association of social network level with coronary heart disease mortality and morbidity suggest the importance of investigating biological pathways of association. Differences in plasma fibrinogen level were investigated among middle-aged men with weak and strong structural and functional social network ties. Men with low scores in the adequacy of social participation variable (structural) had higher mean values of plasma fibrinogen than those with high scores. The difference remained after adjustment for age, smoking and cardiovascular (...) health status and after possible modifying factors were taken into account, but did not remain significant after allowing for physical fitness. Men with high scores in overall support (functional) had higher plasma fibrinogen levels compared to the men with low scores. This difference persisted after age and cardiovascular health status were taken into account but was explained by smoking. The data suggest that smoking and cardiorespiratory fitness are important mediating or modifying factors between structural and functional aspects of social network ties and plasma fibrinogen. (shrink)

Relational complexity theory has important virtues, but the present model omits key aspects and evidence. In contrast, skill theory specifies (1) a detailed series of developmental changes in relational complexity from birth to age 30, (2) processes of interaction of content and structure that produce variability in complexity, (3) the role of cortical development, and (4) empirical criteria for complexity levels, including developmental discontinuities. Many findings support these specifications.

It is widely assumed that functional and dispositional properties are not identical to their physical base, but that there is some kind of asymmetrical ontological dependence between them. In this regard, a popular idea is that the former are realized by the latter, which, under the non-identity assumption, is generally understood to be a non-causal, constitutive relation. In this paper we examine two of the most widely accepted approaches to realization, the so-called ‘flat view’ and the ‘dimensioned view’, and we (...) analyze their explanatory relevance in the light of a number of examples from the life sciences, paying special attention to developmental phenomena. Our conclusion is that the emphasis placed by modern-day biology on such properties as variability, evolvability, and a whole collection of phenomena like modularity, robustness, and developmental constraint or developmental bias requires the adoption of a much more dynamic perspective than traditional realization frameworks are able to capture. (shrink)

A. H. Louie's More Than Life Itself is an exploratory journey in relational biology, a study of life in terms of the organization of entailment relations in living systems. This book represents a synergy of the mathematical theories of categories, lattices, and modelling, and the result is a synthetic biology that provides a characterization of life. Biology extends physics. Life is not a specialization of mechanism, but an expansive generalization of it. Organisms and machines share some (...) common features, but organisms are not machines. Life is defined by a relational closure that places it beyond the reach of physicochemical and mechanistic dogma, outside the reductionistic universe, and into the realm of impredicativity. Function dictates structure. Complexity brings forth living beings. (shrink)

As the accompanying articles in the Special Issue on Semiotic Scaffolding will attest, my colleagues in biosemiotics have done an exemplary job in showing us how to think about the critically generative role that semiotic scaffolding plays “vertically” – i.e., in evolutionary and developmental terms – by “allowing access to the upper floors” of biological complexity, cognition and evolution.In addition to such diachronic considerations of semiotic scaffolding, I wish to offer here a consideration of semiotic scaffolding’s synchronic power, as well (...) – and in particular the ability that it can afford its users to access new and other sign relations “horizontally” as a function of the way that multiple semiotically scaffolded relations intertwine to result in a “definite semantic topology that determines the ways that symbols modify each other’s referential functions in different combinations”.Taking up, in turn, Terrence Deacon’s later challenge that what the sciences of cognition – and biology more generally – needs to “come to grips with [is] the process of semiosis; the dynamic of interpretive activity by which semiotic relationships emerge from other semiotic relationships [as] intrinsically dynamic phases in a generative process”, I attempt here to show how Deacon’s own Peirce-inspired matrix of referential sign relations as presented in The Symbolic Species, when viewed as a semiotic scaffold of interactional constraints and possibility biases, provides the key to understanding the essentially thirdness-manifesting nature of symbol reference, formation and growth. (shrink)

The classical theories of the genetic code claimed that its coding rules were determined by chemistry—either by stereochemical affinities or by metabolic reactions—but the experimental evidence has revealed a totally different reality: it has shown that any codon can be associated with any amino acid, thus proving that there is no necessary link between them. The rules of the genetic code, in other words, obey the laws of physics and chemistry but are not determined by them. They are arbitrary, or (...) conventional, rules. The result is that the genetic code is not a metaphorical entity, as implied by the classical theories, but a real code, because it is precisely the presence of arbitrary rules that divides a code from all other natural processes. In the past 20 years, furthermore, various independent discoveries have shown that many other organic codes exist in living systems, which means that the genetic code has not been an isolated case in the history of life. These experimental facts have one outstanding theoretical implication: they imply that in addition to the concept of information we must introduce in biology the concept of meaning, because we cannot have codes without meaning or meaning without codes. The problem is that at present we have two different theoretical frameworks for that purpose: one is Code Biology, where meaning is the result of coding, and the other is Peircean biosemiotics, where meaning is the result of interpretation. Recently, however, a third party has entered the scene, and it has been proposed that Robert Rosen’s relational biology can provide a bridge between Code Biology and Peircean biosemiotics. (shrink)

This collection of essays by Robert Brandon spans two decades and most of the important problems in the philosophy of biology. Four of his five most important contributions to the philosophy of biology can be found here: the concept of relative adaptedness and its role in the propensity interpretation of fitness; the principle of natural selection; the use of the screening-off relation in defense of organismic selection; and the distinction between units of selection and levels of selection. The (...) fifth major contribution, an analysis of the concept of "environment," mentioned briefly in an essay on the co-evolution of organisms and environment, is given an extended treatment in his 1990 book, Adaptation and Environment. (shrink)

Open peer commentary on the article “Homeostats for the 21st Century? Simulating Ashby Simulating the Brain” by Stefano Franchi. Upshot: The target article proposes that Ashby’s investigations of the homeostat and ultrastability lead to a view of living systems as heteronomous, passive “sleeping” machines and thus are in fundamental conflict with concepts of autonomy developed by Jonas, Varela and others. I disagree, arguing that (1) the maintenance of essential variables within viability limits is not a passive process for living systems (...) and (2) the purpose of Ashby’s investigations of the homeostat was to investigate adaptivity, a subject that is related to, but clearly distinct from, autonomy. As such, I find Ashby’s work on adaptivity to be neither in opposition to nor in direct support of modern concepts of biological autonomy and suggest that a productive way forward involves the investigation of the intersection between these two fundamental properties of living systems. (shrink)

Stuart Kauffman’s forthcoming book, The Origins of Order: Self Organization and Selection in Evolution (1991), is a large and ambitious attempt to bring about a major reorientation in theoretical biology and to provide a fundamental reinterpretation of the place of selection in evolutionary theory. Kauffman offers a formal framework which allows one to pose precise and well-defined questions about the constraints that self-organization imposes on the evolution of complex systems, and the relation of self-organization and selection. He says at (...) the outset that he wants to “delineate the spontaneous sources of order, the self organized properties of simple and complex systems” and to understand how they “permit, enable and limit the efficacy of natural selection” (Introduction, p. 2).2 As he says somewhat later, the central theme running through his book is that “the order in organisms may largely reflect spontaneous order in complex systems” (ch. 6, p. 224). (shrink)

Observability is a modelling property that describes the possibility of inferring the internal state of a system from observations of its output. A related property, structural identifiability, refers to the theoretical possibility of determining the parameter values from the output. In fact, structural identifiability becomes a particular case of observability if the parameters are considered as constant state variables. It is possible to simultaneously analyse the observability and structural identifiability of a model using the conceptual tools of differential geometry. Many (...) complex biological processes can be described by systems of nonlinear ordinary differential equations and can therefore be analysed with this approach. The purpose of this review article is threefold: to serve as a tutorial on observability and structural identifiability of nonlinear systems, using the differential geometry approach for their analysis; to review recent advances in the field; and to identify open problems and suggest new avenues for research in this area. (shrink)

Research on electroencephalogram (EEG) characteristics associated with major depressive disorder (MDD) has accumulated diverse neurophysiologic findings related to the content, topography, neurochemistry, and functions of EEG oscillations. Significant progress has been made since the first landmark EEG study on affective disorders by Davidson 35 years ago. A systematic account of these data is important and necessary for building a consistent neuropsychophysiologic model of MDD and other affective disorders. Given the extensive data on frequency-dependent functional significance of EEG oscillations, a frequency (...) domain approach may reveal the types of brain functions involved and disturbed in MDD. In this review, we systematize and integrate diverse and often unconnected observations on the content, topography, neurochemistry, and functions of EEG oscillations involved in MDD within the general concept of an EEG oscillatory pattern. (shrink)

The concept of rhetorical predicates reveals significant information about Anggor semantic structure. Still greater generality comes from introducing the theoretical concept of a topologically based time index. This topological handling of time provides a tool for studying universal aspects of the cognition of time. Time indexing provides an adequate means of indicating temporal relations in semantic structure without being compelled to consider particular surface manifestations of temporal relations as basic, and also provides a means of relating intralinguistic and extralinguistic temporal (...) reference. Time indexing appears to go more appropriately with propositions than with variables. (shrink)

Advances in science and technology has led to the rise of different issues in relation to human life and security as well as the environment. These issues also paved the way for the field of Bioethics with its principles aiming to uphold moral standards on these issues. This study aimed to test and modify the theoretical models of the factors influencing the conviction schemas of BS Biology Bioethics students of a state university toward bioethical issues. One hundred ten (110) (...) undergraduate students were pre-tested and post-tested for comprehension of Bioethics principles, moral disengagement, and convictions toward bioethical issues. Identified personal factors were also retrieved for testing. Results showed that the Bioethics course has increased the participants’ comprehension of Bioethics principles, moral disengagement, and convictions. Stepwise multiple regression results revealed that anxiety, extraversion, exposure to media, and moral disengagement can predict pre-convictions. On the other hand, only moral disengagement was found to predict post-convictions. Furthermore, moral disengagement can be predicted by convictions before the course while anxiety, openness to change, and convictions were the predictors after the course. The proposed theoretical model was for tested goodness of fit using Structural Equation Modeling (SEM) and acceptance was based on the model fit criteria. Since the proposed model was not found to fit the data, this was revised based on the results of multiple regression and correlation among exogenous variables. Three models were constructed and found to fit the data adequately. These models show the direct and indirect effects of personal factors and moral disengagement on convictions. The mediating effects of moral disengagement and convictions to each other were also shown. Findings further imply that the ability to understand the principles does not influence convictions, but rather moral disengagement has a greater influence on the said factor. Improving moral education by integrating Bioethics to the curriculum is recommended to further strengthen the moral judgement and reasoning of students. (shrink)

Reconstructability analysis (RA) decomposes wholes, namely data in the form either of set theoretic relations or multivariate probability distributions, into parts, namely relations or distributions involving subsets of variables. Data is modeled and compressed by variable-based decomposition, by more general state-based decomposition, or by the use of latent variables. Models, which specify the interdependencies among the variables, are selected to minimize error and complexity.

In this paper, I argue that the newly developed network approach in neuroscience and biology provides a basis for formulating a unique type of realization, which I call topological realization. Some of its features and its relation to one of the dominant paradigms of realization and explanation in sciences, i.e. the mechanistic one, are already being discussed in the literature. But the detailed features of topological realization, its explanatory power and its relation to another prominent view of realization, namely (...) the semantic one, have not yet been discussed. I argue that topological realization is distinct from mechanistic and semantic ones because the realization base in this framework is not based on local realisers, regardless of the scale but on global realizers. In mechanistic approach, the realization base is always at the local level, in both ontic and epistemic accounts. The explanatory power of realization relation in mechanistic approach comes directly from the realization relation-either by showing how a model is mapped onto a mechanism, or by describing some ontic relations that are explanatory in themselves. Similarly, the semantic approach requires that concepts at different scales logically satisfy microphysical descriptions, which are at the local level. In topological framework the realization base can be found at different scales, but whatever the scale the realization base is global, within that scale, and not local. Furthermore, topological realization enables us to answer the “why” questions, which according to Polger 2010 make it explanatory. The explanatoriness of topological realization stems from understanding mathematical consequences of different topologies, not from the mere fact that a system realizes them. (shrink)

We propose a logic for reasoning about metric spaces with the induced topologies. It combines the ‘qualitative’ interior and closure operators with ‘quantitative’ operators ‘somewhere in the sphere of radiusr’ including or excluding the boundary. We supply the logic with both the intended metric space semantics and a natural relational semantics, and show that the latter (i) provides finite partial representations of (in general) infinite metric models and (ii) reduces the standard ‘ε-definitions’ of closure and interior to simple constraints (...) on relations. These features of the relational semantics suggest a finite axiomatisation of the logic and provide means to prove its EXPTIME-completeness (even if the rational numerical parameters are coded in binary). An extension with metric variables satisfying linear rational (in)equalities is proved to be decidable as well. Our logic can be regarded as a ‘well-behaved’ common denominator of logical systems constructed in temporal, spatial, and similarity-based quantitative and qualitative representation and reasoning. Interpreted on the real line (with its Euclidean metric), it is a natural fragment of decidable temporal logics for specification and verification of real-time systems. On the real plane, it is closely related to quantitative and qualitative formalisms for spatial representation and reasoning, but this time the logic becomes undecidable. (shrink)

As a sort of intellectual provocation and as a lateral thinking strategy for creativity, this chapter seeks to determine what the study of the dynamics of biodiversity can offer linguists. In recent years, the analogical equation "language = biological species" has become more widespread as a metaphorical source for conceptual renovation, and, at the same time, as a justification for the defense of language diversity. Language diversity would be protected in a way similar to the mobilization that has taken place (...) to protect endangered species. Nevertheless, one must be careful when uncritically transferring conceptualizations and theoretical frameworks from one field to another, since obviously, these two phenomena are quite different in the real world. The dialogue with bioecologists starts by asking about the formation of diversity, i.e., about specialization. Here, one can observe the similarity between the processes of linguistic and genetic fragmentation, in the sense that both phenomena have a (socio)geographical basis for dispersion and consequently, for the loss of their original compact nature and their intercommunication. The self-organizing and creative properties of human beings favor the development of specific varieties for each subset, varieties that continue to evolve constantly, through the unceasing "languaging" of humanity. Regarding the continuity of species or languages, one can also observe the decisive role of intragroup relations. The staying power of linguistic varieties will increase in direct proportion to the intensity of the relationship among the components of the subset. On the other hand, if exotic elements are introduced, especially if these elements are aggressive in nature, the alteration of the ecological niche may turn out to be fatal for the continuity of the previously existing forms. This suggests to us the need to make an in-depth study of what the minimal contextual conditions would be so that a set linguistic group could be assured a sustainable continuity within a framework of linguistic contact. What type of minimum (socio-)ecological niche would a language have to have if we wished to ensure its habitual reproduction? A proposal is made here to explore the ideas of "exclusive functions" and "non-hierarchical functional distribution" for codes in situations where there is high contact and a danger of disuse. As regards change, this phenomenon is seen as an inherent element in the tendency of life to create new developments, which may or not be accompanied by an adaptation to changing environmental conditions. It is pointed out that, similar to what happens in biology, much of linguistic innovation stems from a systemically reorganized mixture of solutions from different codes. An important research question would be, however, to determine why some of these innovations disappear and others survive and extend throughout the community. The big question mark, as Mufwene points out, is, then how to manage to understand how "the evolution of language proceeds by naturally selecting from among the competing alternatives available through the idiolects of individual speakers". Extinction, whether it be of languages or of species, is caused in most cases "by a combination of demographic processes and environmental changes", as Brown points out. Thus, the environment plays a fundamental role in the direction of evolution, since the "the survival of the fittest is, in actuality, the survival of those who fit into the context (Allen and Hoekstra)". This allows us to see the great degree of importance of political-economic contexts in the case of languages. In the same way, migratory movements are also one of the major variables determining the extinction of biodiversity and language diversity. Species and habitat form the basic unit of existence, and this is the major point of departure for understanding the problem of the preservation and recovery of species or languages. Given the increase in the degree of linguistic contact, the continuity of language diversity depends on determining, as exactly as possible, as Prigogine, the physicist, would say, what precise conditions of imbalance may prove to be stable. The great challenge is not so much avoiding contact but managing it. And "restorative ecology" can also be of help to us here. Being able to reach sustainable solutions for language diversity implies a profound knowledge of the dynamics for determining the ways in which language is used in contact situations. The general conclusion is that linguistics is still terminologically and conceptually ill prepared to deal with the dynamic character of human languages. The world and our objects must be conceived of as elements in a state of flux, as changing systems in an unstable equilibrium. With respect to language policy, it would be necessary to make an effort to manage to establish some general principles regarding the linguistic organization of the human species that would make it possible for local linguistic diversity and communication on a planetary scale, which must necessarily take place, to be compatible with each other. To succeed, it will be necessary to continue promoting an autonomous socio-ecological perspective devoted to the comprehension of language phenomena. Such a perspective would be based on a paradigm of complexity, and would, at the same time, place human beings at the center of its theoretical underpinnings. (shrink)

Symmetries play a major role in physics, in particular since the work by E. Noether and H. Weyl in the first half of last century. Herein, we briefly review their role by recalling how symmetry changes allow to conceptually move from classical to relativistic and quantum physics. We then introduce our ongoing theoretical analysis in biology and show that symmetries play a radically different role in this discipline, when compared to those in current physics. By this comparison, we stress (...) that symmetries must be understood in relation to conservation and stability properties, as represented in the theories. We posit that the dynamics of biological organisms, in their various levels of organization, are not just processes, but permanent (extended, in our terminology) critical transitions and, thus, symmetry changes. Within the limits of a relative structural stability (or interval of viability), variability is at the core of these transitions. (shrink)