The functional complexity, or the number of functions, of organisms hasfigured prominently in certain theoretical and empirical work inevolutionary biology. Large-scale trends in functional complexity andcorrelations between functional complexity and other variables, such assize, have been proposed. However, the notion of number of functions hasalso been operationally intractable, in that no method has been developedfor counting functions in an organism in a systematic and reliable way.Thus, studies have had to rely on the largely unsupported (...) assumption thatnumber of functions can be measured indirectly, by using number ofmorphological, physiological, and behavioral parts as a proxy. Here, amodel is developed that supports this assumption. Specifically, the modelpredicts that few parts will have many functions overlapping in them, andtherefore the variance in number of functions per part will be low. If so,then number of parts is expected to be well correlated with number offunctions, and we can use part counts as proxies for function counts incomparative studies of organisms, even when part counts are low. Alsodiscussed briefly is a strategy for identifying certain kinds of parts inorganisms in a systematic way. (shrink)

This article sketches the main features of traditional philosophical models of evidence, indicating idealizations in such models that it regards as doing more harm than good. It then proceeds to elaborate on an alternative model of evidence that is functionalist, complex, dynamic, and contextual, a view the author calls dynamic evidential functionalism (DEF). This alternative builds on insights from philosophy of scientific practice, Kuhnian philosophy of science, pragmatist epistemology, philosophy of experimentation, and functionalist philosophy of mind. Along the way, the (...) article raises concerns about the total evidence condition, requirements of certainty or incorrigibility on evidence, and accounts that restrict the type of things that can serve as evidence (to, for example, sense data, facts about particulars). DEF can also help us see the special value of novel predictions and experiments as evidence, as well as help us think about how to critically evaluate the putative evidence to determine whether it is evidence. (shrink)

Recent findings emphasize the complexity, both genetic and functional, of the manifold genes and mutations causing inherited retinal degeneration in humans. Knowledge of the genetic bases of these diseases can contribute to design of rational therapy, as well as elucidating the function of each gene product in normal visual processes.

Functional decomposition is an important goal in the life sciences, and is central to mechanistic explanation and explanatory reduction. A growing literature in philosophy of science, however, has challenged decomposition-based notions of explanation. ‘Holists’ posit that complex systems exhibit context-sensitivity, dynamic interaction, and network dependence, and that these properties undermine decomposition. They then infer from the failure of decomposition to the failure of mechanistic explanation and reduction. I argue that complexity, so construed, is only incompatible with one notion (...) of decomposition, which I call ‘atomism’, and not with decomposition writ large. Atomism posits that function ascriptions must be made to parts with minimal reference to the surrounding system. Complexity does indeed falsify atomism, but I contend that there is a weaker, ‘contextualist’ notion of decomposition that is fully compatible with the properties that holists cite. Contextualism suggests that the function of parts can shift with external context, and that interactions with other parts might help determine their context-appropriate functions. This still admits of functional decomposition within a given context. I will give examples based on the notion of oscillatory multiplexing in systems neuroscience. If contextualism is feasible, then holist inferences are faulty—one cannot infer from the presence of complexity to the failure of decomposition, mechanism, and reductionism. (shrink)

This book explains the relationship between intelligence and environmental complexity, and in so doing links philosophy of mind to more general issues about the relations between organisms and environments, and to the general pattern of 'externalist' explanations. The author provides a biological approach to the investigation of mind and cognition in nature. In particular he explores the idea that the function of cognition is to enable agents to deal with environmental complexity. The history of the idea in the (...) work of Dewey and Spencer is considered, as is the impact of recent evolutionary theory on our understanding of the place of mind in nature. (shrink)

Sad1 and UNC84 (SUN) and Klarsicht, ANC‐1, and Syne homology (KASH) proteins interact at the nuclear periphery to form the linker of nucleoskeleton and cytoskeleton (LINC) complex, spanning the nuclear envelope (NE) and connecting the cytoskeleton with the nuclear interior. It is now well‐documented that several cellular functions depend on LINC complex formation, including cell differentiation and migration. Intriguingly, recent studies suggest that SUN proteins participate in cellular processes where their association with KASH proteins may not be required. Building on (...) this recent research, we elaborate on the hypothesis that SUN proteins may perform LINC‐independent functions and discuss the modalities that may allow SUN proteins to function at the INM when they are not forming LINC complex. (shrink)

The past two decades have seen an explosion in the methods and directions of neuroscience research. Along with many others, complexity research has rapidly gained traction as both an independent research field and a valuable subdiscipline in computational neuroscience. In the past decade alone, several studies have suggested that psychiatric disorders affect the spatiotemporal complexity of both global and region-specific brain activity (Liu et al., 2013; Adhikari et al., 2017; Li et al., 2018). However, many of these studies (...) have not accounted for the distributed nature of cognition in either the global or regional complexity estimates, which may lead to erroneous interpretations of both global and region-specific entropy estimates. To alleviate this concern, we propose a novel method for estimating complexity. This method relies upon projecting dynamic functional connectivity into a low-dimensional space which captures the distributed nature of brain activity. Dimension-specific entropy may be estimated within this space, which in turn allows for a rapid estimate of global signal complexity. Testing this method on a recently acquired obsessive-compulsive disorder dataset reveals substantial increases in the complexity of both global and dimension-specific activity versus healthy controls, suggesting that obsessive-compulsive patients may experience increased disorder in cognition. To probe the potential causes of this alteration, we estimate subject-level effective connectivity via a Hopf oscillator-based model dynamic model, the results of which suggest that obsessive-compulsive patients may experience abnormally high connectivity across a broad network in the cortex. These findings are broadly in line with results from previous studies, suggesting that this method is both robust and sensitive to group-level complexity alterations. (shrink)

An analysis of two heuristic strategies for the development of mechanistic models, illustrated with historical examples from the life sciences. In Discovering Complexity, William Bechtel and Robert Richardson examine two heuristics that guided the development of mechanistic models in the life sciences: decomposition and localization. Drawing on historical cases from disciplines including cell biology, cognitive neuroscience, and genetics, they identify a number of "choice points" that life scientists confront in developing mechanistic explanations and show how different choices result in (...) divergent explanatory models. Describing decomposition as the attempt to differentiate functional and structural components of a system and localization as the assignment of responsibility for specific functions to specific structures, Bechtel and Richardson examine the usefulness of these heuristics as well as their fallibility—the sometimes false assumption underlying them that nature is significantly decomposable and hierarchically organized. When Discovering Complexity was originally published in 1993, few philosophers of science perceived the centrality of seeking mechanisms to explain phenomena in biology, relying instead on the model of nomological explanation advanced by the logical positivists (a model Bechtel and Richardson found to be utterly inapplicable to the examples from the life sciences in their study). Since then, mechanism and mechanistic explanation have become widely discussed. In a substantive new introduction to this MIT Press edition of their book, Bechtel and Richardson examine both philosophical and scientific developments in research on mechanistic models since 1993. (shrink)

We explore the relationship between analytic behavior of a computable real valued function and the computability-theoretic complexity of the individual values of its derivative almost-everywhere. Given a computable function f, the values of its derivative \\), where they are defined, are uniformly computable from \, the Turing jump of the input. It is known that when f is \, the values of \\) are actually computable from x. We construct a \ function f so that, almost everywhere, \\ge _T (...) x'\). Although the values \\) at each point x cannot uniformly compute the corresponding jumps \ of the inputs x almost everywhere for any \ function f, we produce an example of a \ function f such that \\ge _T \emptyset '\) uniformly on subsets of arbitrarily large measure, effectively. We also explore analogous questions for weaker smoothness conditions, such as for f differentiable everywhere, and f differentiable almost everywhere. (shrink)

Complex diseases involve both a genetic component and a response to environmental factors or lifestyle changes. Recently, genome-wide association studies (GWAS) have succeeded in identifying hundreds of polymorphisms that are statistically associated with complex diseases. However, the association is usually weak and none of the associated allelic forms is either necessary or sufficient for the disease occurrence. We argue that this promotes a network view, centred on functional redundancy. We adapted reliability theory to the concerned sub-network, modelled as a (...) parallel array of functional modules. In our model, as long as one module remains active, the function correlated with the respective disease is ensured and disease does not occur. Genetic factors reduce the initial number of available modules while environment, contingent surroundings, personal history, epigenetics, and some intrinsic stochasticity influence their persistence time. This model reproduces age-specific incidence curves and explains the influence of environmental changes. It offers a new paradigm, according to which disease occurs due to a lack of functional elements, depending on many idiosyncratic factors. Genetic risk assessed from GWAS is only a statistical notion with no direct interpretation at the individual level. However, genomic profiling could be useful at population level in devising models to guide decisions in health care policy. (shrink)

The concept of complexity has become very important in theoretical biology. It is a many faceted concept and too new and ill defined to have a universally accepted meaning. This review examines the development of this concept from the point of view of its usefulness as a criteria for the study of living systems to see what it has to offer as a new approach. In particular, one definition of complexity has been put forth which has the necessary (...) precision and rigor to be considered as a useful categorization of systems, especially as it pertains to those we call living. This definition, due to Robert Rosen, has been developed in a number of works and involves some deep new concepts about the way we view systems. In particular, it focuses on the way we view the world and actually practice science through the use of the modelling relation. This mathematical object models the process by which we assign meaning to the world we perceive. By using the modelling relation, it is possible to identify the subjective nature of our practices and deal with this issue explicitly. By so doing, it becomes clear that our notion of complexity and especially its most popular manifestations, is in large part a product of the historical processes which lead to the present state of scientific epistemology. In particular, it is a reaction to the reductionist/mechanistic view of nature which can be termed the Newtonian Paradigm. This approach to epistemology has dominated for so long that its use as a model has become implicit in most of what we do in and out of science. The alternative to this approach is examined and related to the special definition of complexity given by Rosen. Some historical examples are used to emphasize the dependence of our view of what is complex in a popular sense on the ever changing state of our knowledge. The role of some popular concepts such as chaotic dynamics are examined in this context. The fields of artificial life and related areas are also viewed from the perspective of this rigorous view of complexity and found lacking. The notion that in some way life exists at the edge of chaos is examined from the perspective of the second law of thermodynamics given by Schneider and Kay. Finally, the causal elements in complex systems are explored in relation to complexity. Rosen has shown that a clear difference in causal relations exists between complex and simple systems and that this difference leads to a uniquely useful definition of what we mean by living. Rosen makes it very clear that the class of systems which are complex is a much larger class than those which we call living. For that reason, the focus of this review will be on complexity as a stepping stone towards the deeper question of what makes a system alive. (shrink)

In this paper, we will explore the relation between molecular structure and functions displayed by biochemical molecules in complex physiological processes by using tools from the philosophy of science and the philosophy of scientific practice. We will argue that biochemical functions are weakly emergent from molecular structure by using an account of weak. In order to explore this thesis, we will consider the role of vitamin B12 in contributing to the process of erythropoiesis. The structure of the paper is the (...) following: First, we will consider biochemical functions and why they cannot be easily reduced to their chemical realisers. We will suggest weak emergence as an alternative while also accounting for the relevance of the context, in our case, systemic and organisational. The paper will conclude by considering (1) how the usage of tools from the philosophy of science, such as weak emergence, can aid our understanding of the relations between the components of complex phenomena, such as erythropoiesis, and (2) how the philosophy of scientific practice sheds light on the explanatory role of processes that are dynamically stabilised and the different levels of organisation implied. (shrink)

Let E be a separable Banach space with separable dual. We show that the operation of subdifferentiation and the inverse operation are Borel from the convex functions on E into the monotone operators on E for the Effros–Borel structures.We also prove that the set of derivatives of differentiable convex functions is coanalytic non-Borel, by using the already known fact that the set of differentiable convex functions is itself coanalytic non-Borel, as proved in Bossard et al. 142).At last, we give a (...) new proof of this latter fact, for reflexive E's, by giving a coanalytic rank on those sets and constructing functions of “high ranks”. This approach, based on an ordinal rank which follows from a construction of trees, is quite different — not so general but actually more constructive — from the previous results of this kind, in Bossard et al. 142) and Godefroy et al. , based on reductions of arbitrary coanalytic or difference of analytic sets to the studied sets. (shrink)

The first-order logical theory Th $({\mathbb{N}},x + 1,F(x))$ is proved to be complete for the class ATIME-ALT $(2^{O(n)},O(n))$ when $F(x) = 2^{x}$ , and the same result holds for $F(x) = c^{x}, x^{c} (c \in {\mathbb{N}}, c \ge 2)$ , and F(x) = tower of x powers of two. The difficult part is the upper bound, which is obtained by using a bounded Ehrenfeucht–Fraïssé game.

This chapter develops a subtle model that integrates environmental and internal factors. It describes the phylogenetic distribution of multicellular organisms in general and complex multicellular life in particular, clarifying the important distinction between the two. This chapter shows that the long apparent lag between the appearance of simple multicellularity in eukaryotes and the radiation of groups with complex multicellular organization has an environmental component that can be associated back to the consequences of life with interior and exterior cells. It suggests (...) that the evolutionary transition from unicells to complex multicellular organisms has several steps. (shrink)

Religion as a social and spiritual phenomenon in its functional manifestation responds to various human needs, while satisfying, above all, those spiritual needs that can not satisfy any other social phenomenon. Religion, however, appears as a certain qualitative certainty characterizing the ability and ability to satisfy the vital needs of man, religious communities and society, and helping a believer in comprehending the inner essence of the world in his transcendental co-ordinates, posing a "normative and content quintessence of experience", inherent (...) in this social phenomenon. overcoming suffering, life problems, and also contributes to the awareness of the meaning and significance of earthly life as a believer in the perspective of "the last reality". (shrink)

The length of resolution proofs is investigated, relative to the model-theoretic measure of Herband complexity. A concept of resolution deduction is introduced which is somewhat more general than the classical concepts. It is shown that proof complexity is exponential in terms of Herband complexity and that this bound is tight. The concept of R-deduction is extended to FR-deduction, where, besides resolution, a function introduction rule is allowed. As an example, consider the clause P Q: conclude P) Q, (...) where a, f are new function symbols extending Herbrand's universe. P ()Q from Q) and Skolemization). By modification of a construction of Statman it is shown that FR-deductions may be nonelementarily shorter than R-deductions . Finally it is proved that FR-deduction has weaker effects only if clausal logic is restricted to Horn logic. (shrink)

We develop a category theoretical scheme for the comprehension of the information structure associated with a complex system, in terms of families of partial or local information carriers. The scheme is based on the existence of a categorical adjunction, that provides a theoretical platform for the descriptive analysis of the complex system as a process of functorial information communication.

Complex systems are pervasive in the world around us. Making sense of a complex system should require that a person construct a network of concepts and principles about some domain that represents key (often dynamic) phenomena and their interrelationships. This raises the question of how expert understanding of complex systems differs from novice understanding. In this study we examined individuals' representations of an aquatic system from the perspective of structural (elements of a system), behavioral (mechanisms), and functional aspects of (...) a system. Structure–Behavior–Function (SBF) theory was used as a framework for analysis. The study included participants from middle school children to preservice teachers to aquarium experts. Individual interviews were conducted to elicit participants' mental models of aquaria. Their verbal responses and pictorial representations were analyzed using an SBF‐based coding scheme. The results indicated that representations ranged from focusing on structures with minimal understanding of behaviors and functions to representations that included behaviors and functions. Novices' representations focused on perceptually available, static components of the system, whereas experts integrated structural, functional, and behavioral elements. This study suggests that the SBF framework can be one useful formalism for understanding complex systems. (shrink)

Hox complex genes are key developmental regulators highly conserved throughout evolution. The encoded proteins share a 60‐amino‐acid DNA‐binding motif, the homeodomain, and function as transcription factors to control axial patterning. An important question concerns the nature and function of genes acting downstream of Hox proteins. This review focuses on Drosophila, as little is known about this question in other organisms. The noticeable progress gained in the field during the past few years has significantly improved our current understanding of how Hox (...) genes control diversified morphogenesis. Here we summarise the strategies deployed to identify Hox target genes and discuss how their function contributes to pattern formation and morphogenesis. The regulation of target genes is also considered with special emphasis on the mechanisms underlying the specificity of action of Hox proteins in the whole animal. (shrink)

The history of research on pseudoalleles, closely linked genes that have similar functions, is rich and complex. Because pseudoalleles’ proximity on the chromosome makes their distinction by the complementation tests traditionally used by geneticists difficult, and because they have similar functions, they were initially often considered as allelic forms of the same gene, hence their name. The Hox cluster is an emblematic example of a pseudoallelic gene complex. The first observations of pseudoalleles were made very early but remained puzzling until (...) a simple model explaining their formation and characteristics emerged in the middle of the 1930s. This model suggested that pseudoalleles originated by gene.. (shrink)

This paper investigates a stochastic two-patch predator-prey model with ratio-dependent functional responses. First, the existence of a unique global positive solution is proved via the stochastic comparison theorem. Then, two different methods are used to discuss the long-time properties of the solutions pathwise. Next, sufficient conditions for extinction and persistence in mean are obtained. Moreover, stochastic persistence of the model is discussed. Furthermore, sufficient conditions for the existence of an ergodic stationary distribution are derived by a suitable Lyapunov function. (...) Next, we apply the main results in some special models. Finally, some numerical simulations are introduced to support the main results obtained. The results in this paper generalize and improve the previous related results. (shrink)

The gastrointestinal tract is normally investigated using reductionism methods in human studies, where the focus is on each segment of the gastrointestinal system and the specific links between various parts of it. This helps researchers and clinicians to produce a simple relationship between the elements of the gastrointestinal tract based on clinical diagnosis and treatment. However, there is evidence indicating that the gastrointestinal tract has properties that are beyond function of the simple systems, such as, multiplicity of elements, network communication, (...) emergence, self-organization, sudden transition, nonlinearity, and adaptation, all of which are attributes of complex systems. It seems that the gastrointestinal tract is an appropriate candidate for complexity research. If the gastrointestinal tract is assumed as a complex system, then it would be more fitting to study the tract using holistic methods through interdisciplinary perspective. In the present paper, the features of the gastrointestinal that correlate to complex systems have been explained using physiological examples from studies done on human subjects. (shrink)

The reliability of previous findings on two crucial aspects of counterfactual thinking, namely the content of counterfactual modifications and their impact on future performance, has been questioned for the frequent use of tasks characterised by simple causal domains, that restrict participants’ possibility to consider a broad range of modifications. To overcome this limitation, we utilised a new experimental task featuring a complex causal domain to investigate such key aspects. The results indicated that participants tend to generate counterfactuals about elements outside (...) their control, especially when presented with a challenging version of the task (Study 1a) and, to a lesser extent, when they receive negative feedback on their performance (Study 1b). Moreover, despite occasional implementations of actions mentioned in controllable counterfactuals, being engaged in counterfactual thinking did not lead to subsequent performance improvements (Study 2). The implications of these findings for the debate on the function of counterfactual thinking are discussed. (shrink)

(1984). Reading Accuracy as a Function of Teaching Strategy, Personality and Word Complexity in Seven‐year‐old Children. Educational Studies: Vol. 10, No. 3, pp. 263-272.

Kolmogorov complexity was originally defined for finitely-representable objects. Later, the definition was extended to real numbers based on the asymptotic behaviour of the sequence of the Kolmogorov complexities of the finitely-representable objects—such as rational numbers—used to approximate them.This idea will be taken further here by extending the definition to continuous functions over real numbers, based on the fact that every continuous real function can be represented as the limit of a sequence of finitely-representable enclosures, such as polynomials with rational (...) coefficients.Based on this definition, we will prove that for any growth rate imaginable, there are real functions whose Kolmogorov complexities have higher growth rates. In fact, using the concept of prevalence, we will prove that ‘almost every’ continuous real function has such a high-growth Kolmogorov complexity. An asymptotic bound on the Kolmogorov complexities of total single-valued computable real functions will be presented as well. (shrink)

Large protein assemblies are usually the effectors of major cellular processes. The intricate cell homeostasis network is divided into numerous interconnected pathways, each controlled by a set of protein machines. One of these master regulators is the CCR4‐NOT complex, which ultimately controls protein expression levels. This multisubunit complex assembles around a scaffold platform, which enables a wide variety of well‐studied functions from mRNA synthesis to transcript decay, as well as other tasks still being identified. Solving the structure of the entire (...) CCR4‐NOT complex will help to define the distribution of its functions. The recently published three‐dimensional reconstruction of the complex, in combination with the known crystal structures of some of the components, has begun to address this. Methodological improvements in structural biology, especially in cryoelectron microscopy, encourage further structural and protein‐protein interaction studies, which will advance our comprehension of the gene expression machinery. (shrink)

Living systems employ several mechanisms and behaviors to achieve robustness and maintain themselves under changing internal and external conditions. Regulation stands out from them as a specific form of higher-order control, exerted over the basic regime responsible for the production and maintenance of the organism, and provides the system with the capacity to act on its own constitutive dynamics. It consists in the capability to selectively shift between different available regimes of self-production and self-maintenance in response to specific signals and (...) perturbations, due to the action of a dedicated subsystem which is operationally distinct from the regulated ones. The role of regulation, however, is not exhausted by its contribution to maintain a living system’s viability. While enhancing robustness, regulatory mechanisms play a fundamental role in the realization of an autonomous biological organization. Specifically, they are at the basis of the remarkable integration of biological systems, insofar as they coordinate and modulate the activity of distinct functional subsystems. Moreover, by implementing complex and hierarchically organized control architectures, they allow for an increase in structural and organizational complexity while minimizing fragility. Finally, they endow living systems, from their most basic unicellular instances, with the capability to control their own internal dynamics to adaptively respond to specific features of their interaction with the environment, thus providing the basis for the emergence of minimal forms of cognition. (shrink)

The purpose of this article is to retrieve the work presented in on the transcendent function and complexes as well as an ontological interpretation of Jung’s work on the Rosarium Philosophorum to project a new meaning of the phenomenology and ontology of the transcendent function. This article enables complexes and the Rosarium Philosophorum to be understood in connection to the ontology of the transcendent function that was presented in. This article can hermeneutically retrieve the transcendent function because when complexes and (...) the Rosarium Philosophorum are explained ontologically they unconceal new possibilities that were not available in. By retrieving the transcendent function in this way, this article will explain more detail of the phenomenological and ontological meaning of the transcendent function which will include complexes and the Rosarium Philosophorum. (shrink)

A transcription and translation of Hermann Hankel's 1867 Vorlesungen über die complexen Zahlen und ihre Functionen, I. Theil: Theorie der Complexen Zahlensysteme, a textbook on complex analysis that played an important role in the transition to modern mathematics in nineteenth century Germany.

The double membrane of the nuclear envelope is a formidable barrier separating the nucleus and cytoplasm of eukaryotic cells. However, movement of specific macromolecules across the nuclear envelope is critical for embryonic development, cell growth and differentiation. Transfer of molecules between the nucleus and cytoplasm occurs through the aqueous channel formed by the nuclear pore complex (NPC)Abbreviations: NPC, nuclear pore complex; GlcNac, N‐acetylglucosamine; WGA, wheat germ agglutinin. Although small molecules may simply diffuse across the NPC, transport of large proteins and (...) RNA requires specific transport signals and is energy dependent. A family of pore glycoproteins modified by O‐linked N‐acetylglucosamine moieties are essential for transport through the NPC. Recent evidence suggests that the regulation of nuclear transport may also involve the inteaction of RNA and nuclear proteins with specific binding proteins that recognize these transport signals. Are these nuclear pore glycoproteins and signal binding proteins the ‘gatekeepers’ that control access to the genetic material? Recent evidence obtained from a combination of biochemical and genetic approaches suggests – perhaps. (shrink)

Even the simplest cell exhibits a high degree of functional differentiation (FD) realized through several mechanisms and devices contributing differently to its maintenance. Searching for the origin of FD, we briefly argue that the emergence of the respective organizational complexity cannot be the result of either natural selection (NS) or solely of the dynamics of simple self-maintaining (SM) systems. Accordingly, a highly gradual and cumulative process should have been necessary for the transition from either simple self-assembled or self-maintaining (...) systems of functionless structural components to systems with FD. We follow results of recent in vitro experiments with respect to competition among protocells, where a primitive type of selection begins to operate among them accompanied by a parallel evolution of their functional domain. We argue that minimal forms of FD should be established within the evolution of SM processes in protocells as they undergo a simpler selection process for stability and persistence in a prebiotic environment. We then suggest the concept of closure of constraints (CoC) as a way to identify and describe minimal FD in a far-from-equilibrium SM organization. We show in detail how the concept of CoC together with the conditions for its fulfillment can be applied in the case of a simple protocellular system that begins to couple internal chemical reactions with the formation of its membrane components. Finally, we discuss how such SM systems can evolve towards significantly higher levels of FD, suggesting this is mainly the result of functional recombination (formation of mechanisms) in the context of a modular SM organization. (shrink)