There are various approaches to ontology metamodelling, and the notion of biologically inspired modular knowledge representation systems can provide insight in the workings of such phenomena as emergent properties of network structures. What is more relevant from knowledge engineering standpoint, such approach could provide innovation and enhancement of the level of expression as well as overall functionality of modular ontologies. To do so, one needs to find biological structures that would be the basis for modularity on different levels (...) of hierarchy within the artificial system. Network analysis tools as well as systems biology and biocomputing provide a framework for research in this field. (shrink)

Modularity in the human brain remains a controversial issue, with disagreement over the nature of the modules that exist, and why, when, and how they emerge. It is a natural assumption that modularity offers some form of computational advantage, and hence evolution by natural selection has translated those advantages into the kind of modular neural structures familiar to cognitive scientists. However, simulations of the evolution of simplified neural systems have shown that, in many cases, it is actually non-modular (...) architectures that are most efficient. In this paper, the relevant issues are discussed and a series of simulations are presented that reveal crucial dependencies on the details of the learning algorithms and tasks that are being modelled, and the importance of taking into account known physical brain constraints, such as the degree of neural connectivity. A pattern is established which provides one explanation of why modularity should emerge reliably across a range of neural processing tasks. (shrink)

Abstractα/β barrels have an ill‐defined origin. Evidence exists which favours their divergent evolution from a common ancestral barrel and convergent evolution to a stable fold. However, recent sequence and structural information for the flavin oxidase/dehydrogenase family of barrel enzymes indicate that sub‐families of α/β barrels have evolved divergently. The modular fusion of barrel domains with core structures from other gene families has also contributed to the evolution of related but catalytically distinct enzyme molecules within each sub‐family of the flavin oxidases/dehydrogenases. (...) An analysis of the structures and sequences of the flavin oxidases/dehydrogenases has now enabled studies focusing on the evolutionary origins and modular assembly of this important family of proteins to be initiated. (shrink)

What are the elements from which the human mind is composed? What structures make up our _cognitive architecture?_ One of the most recent and intriguing answers to this question comes from the newly emerging interdisciplinary field of evolutionary psychology. Evolutionary psychologists defend a _massively modular_ conception of mental architecture which views the mind –including those parts responsible for such ‘central processes’ as belief revision and reasoning— as composed largely or perhaps even entirely of innate, special-purpose computational mechanisms or ‘modules’ that (...) have been shaped by natural selection to handle the sorts of recurrent information processing problems that confronted our hunter-gatherer forebears (Cosmides and Tooby,192; Sperber, 1994; Samuels, 1998a). (shrink)

Previous neural network models of concept learning were mainly implemented with supervised learning schemes. However, studies of human conceptual memory have shown that concepts may be learned without a teacher who provides the category name to associate with exemplars. A modular neural network architecture that realizes concept acquisition through two functionally distinct operations, categorizing and naming, is proposed as an alternative. An unsupervised algorithm realizes the categorizing module by constructing representations of categories compatible with prototype theory. The naming module associates (...) category names to the output of the categorizing module in a supervised mode. In such a modular architecture, the interface between the modules can be conceived of as an “information relay” that encodes, constrains, and propagates important information. Five experiments were conducted to analyze the relationships among internal conceptual codes and simple conceptual and lexical development. The first two experiments show a prototype effect and illustrate some basic characteristics of the system. The third experiment presents a bottom‐up model of the narrowing down of children's early lexical categories that honors mutual exclusivity. The fourth experiment introduces top‐down constraints on conceptual coding. The fifth experiment exhibits how hierarchical relationships between concepts are learned by the architecture, and also demonstrates how a spectrum of conceptual expertise may gradually emerge as a consequence of experiencing more with certain categories than with others. (shrink)

Can emotions be rational or are they necessarily irrational? Are emotions universally shared states? Or are they socio-cultural constructions? Are emotions perceptions of some kind? Since the publication of Jerry Fodor’s The Modularity of Mind (1983), a new question about the philosophy of emotions has emerged: are emotions modular? A positive answer to this question would mean, minimally, that emotions are cognitive capacities that can be explained in terms of mental components that are functionally dissociable from other parts of (...) the mind. But depending on the kind of modules that are considered, be they Chomskyan, Fodorian, Darwinian, or some other kind, the answer to this question might well be different. The twelve new essays in this volume address the question of whether emotions, or at least some of them, are, in some sense of the word, modules, and explore how this could potentially influence our understanding of emotional phenomena. (shrink)

Previous neural network models of concept learning were mainly implemented with supervised learning schemes. However, studies of human conceptual memory have shown that concepts may be learned without a teacher who provides the category name to associate with exemplars. A modular neural network architecture that realizes concept acquisition through two functionally distinct operations, categorizing and naming, is proposed as an alternative. An unsupervised algorithm realizes the categorizing module by constructing representations of categories compatible with prototype theory. The naming module associates (...) category names to the output of the categorizing module in a supervised mode. In such a modular architecture, the interface between the modules can be conceived of as an “information relay” that encodes, constrains, and propagates important information. Five experiments were conducted to analyze the relationships among internal conceptual codes and simple conceptual and lexical development. The first two experiments show a prototype effect and illustrate some basic characteristics of the system. The third experiment presents a bottom‐up model of the narrowing down of children's early lexical categories that honors mutual exclusivity. The fourth experiment introduces top‐down constraints on conceptual coding. The fifth experiment exhibits how hierarchical relationships between concepts are learned by the architecture, and also demonstrates how a spectrum of conceptual expertise may gradually emerge as a consequence of experiencing more with certain categories than with others. (shrink)

In the present paper I analyse the modularity thesis and, more specifically, the thesis of domain-specificity of processing. I argue that this thesis is not trivial only under the assumption of a variety of processes which differ from each other at the implementation level; otherwise, the variety of cognitive processes can only be explained as emergent on the basic mechanism of associative activation in that it operates on domain-specific representations, which is something that no one would deny. But (...) that assumption is untenable: there are no other processes than associative activation (and inhibition) at the implementation level. Any claim to the contrary is the result of a conceptual confusion between two senses of “associative”: a behavioural one, relative to which there are cognitive processes that exceed the ability to code elementary spatio-temporal contingencies, and one that lies instead at the implementation level. Since the assumption of a plurality of processes at the implementation level is untenable, the only viable interpretation of modularism (as far as domain-specificity is concerned) is a trivial one. By this I do not mean that the thesis is devoid of any content. However, its content is scarcely debatable, and far less thrilling than the debate has suggested so far. (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)

Language is at the core of the cognitive revolution that has transformed that discipline over the last forty years or so, and it is also the central paradigm for the most prominent attempt to synthesise psychology and evolutionary theory. A single and distinctively modular view of language has emerged out of both these perspectives, one that encourages a certain idealisation. Linguistic competence is uniform, independent of other cognitive capacities, and with a developmental trajectory that is largely independent of environmental input (...) (Pinker 1994; Pinker 1997). Thus language is seen as a paradigm of John Tooby and Leda Cosmides’ concept of “evoked culture”: linguistic experience serves only to select a specific item from a menu of innately available options (Tooby and Cosmides 1992). In explaining this concept, they appeal to the metaphor of a jukebox. The human genome pre-stores a set of options, and the different experiences provided by different cultures select different elements out of this option set. I think an appropriate evolutionary perspective on language substantially undercuts this idealisation and the evoked culture model of language. Variability between speakers; the sensitivity of linguistic development to environmental input; and the limits of encapsulation are not noise. They are central to the language and its evolution. (shrink)

Currently, there is widespread skepticism that higher cognitive processes, given their apparent flexibility and globality, could be carried out by specialized computational devices, or modules. This skepticism is largely due to Fodor’s influential definition of modularity. From the rather flexible catalogue of possible modular features that Fodor originally proposed has emerged a widely held notion of modules as rigid, informationally encapsulated devices that accept highly local inputs and whose opera- tions are insensitive to context. It is a mistake, however, (...) to equate such features with computational devices in general and therefore to assume, as Fodor does, that higher cognitive processes must be non-computational. Of the many possible non-Fodorean architectures, one is explored here that offers possible solutions to computational problems faced by conventional modular systems: an ‘enzymatic’ architecture. Enzymes are computational devices that use lock-and-key template matching to iden- tify relevant information (substrates), which is then operated upon and returned to a common pool for possible processing by other devices. Highly specialized enzymes can operate together in a common pool of information that is not pre-sorted by information type. Moreover, enzymes can use molecular ‘tags’ to regulate the operations of other devices and to change how particular substrates are construed and operated upon, allowing for highly interactive, context-specific processing. This model shows how specialized, modular processing can occur in an open system, and suggests that skepti- cism about modularity may largely be due to failure to consider alternatives to the standard model. (shrink)

In a recent survey of contemporary philosophy of emotion, Ronald de Sousa states that "in recent years … emotions have once again become the focus of vigorous interest in philosophy, as well as in other branches of cognitive science" (de Sousa 2003, 1). He then goes on to make the important observation that "in view of the proliferation of increasingly fruitful exchanges between researchers of different stripes, it is no longer useful to speak of the philosophy of emotion in isolation (...) from the approaches of other disciplines, particularly psychology, neurology and evolutionary biology" (de Sousa 2003, 1). This last remark is particularly apt in the case of a topic like modularity and emotion, which represents an ideal opportunity for reflecting on the emerging alliance between the philosophy of emotion and emotion science. In addition to being interesting in its own right, the topic also illustrates some of the perils associated with the new alliance, as different academic traditions must adapt to interdisciplinary dialogue... (shrink)

Currently, there is widespread skepticism that higher cognitive processes, given their apparent flexibility and globality, could be carried out by specialized computational devices, or modules. This skepticism is largely due to Fodor's influential definition of modularity. From the rather flexible catalogue of possible modular features that Fodor originally proposed has emerged a widely held notion of modules as rigid, informationally encapsulated devices that accept highly local inputs and whose operations are insensitive to context. It is a mistake, however, to (...) equate such features with computational devices in general and therefore to assume, as Fodor does, that higher cognitive processes must be non‐computational. Of the many possible non‐Fodorean architectures, one is explored here that offers possible solutions to computational problems faced by conventional modular systems: an ‘enzymatic’ architecture. Enzymes are computational devices that use lock‐and‐key template matching to identify relevant information (substrates), which is then operated upon and returned to a common pool for possible processing by other devices. Highly specialized enzymes can operate together in a common pool of information that is not pre‐sorted by information type. Moreover, enzymes can use molecular ‘tags’ to regulate the operations of other devices and to change how particular substrates are construed and operated upon, allowing for highly interactive, context‐specific processing. This model shows how specialized, modular processing can occur in an open system, and suggests that skepticism about modularity may largely be due to failure to consider alternatives to the standard model. (shrink)

The use of modular construction technology has emerged as a promising solution to the challenges of the construction industry all over the world. This paper examines the new horizons and opportunities that modular construction technology offers not only in the Albanian context but also in some European countries. The paper provides an overview of the status of Albania's construction market and emphasizes the advantages of modular construction technology, including quicker construction, lower costs, and better quality control. Unfortunately, prefabricated constructions are (...) not very present Albanian construction industry, and it is not given the proper attention due to lack of infrastructure, organizational purposes, and lack of proper experience. The paper also examines the challenges associated with the implementation of modular construction technology in Albania, exploring the history of prefabricated constructions, also including regulatory barriers, lack of awareness, and the need for skilled labor. Finally, the paper concludes by suggesting strategies to overcome these challenges and promote the adoption of modular construction technology in Albania, such as targeted government policies, education and training programs, and partnerships between industry stakeholders. (shrink)

Members of a human group are bound with one another by multiple flows of information. (Here we use “information” in a broad sense that includes not only the content of people’s knowledge, but also that of their beliefs, assumptions, fictions, rules, norms, skills, maps, images, and so on.) This information is materially realized in the mental representations of the people, and in their public productions, that is, their cognitively guided behaviors and the enduring material traces of these behaviors. Mentally represented (...) information is transmitted from individuals to individuals through public productions. Public representations such as speech, gestures, writing, or pictures are a special type of public productions, the function of which is to communicate a content. Public representations play a major role in information transmission. Much information, however, is communicated implicitly, that is, without being publicly represented. Information can also be transmitted without being properly speaking communicated, not even implicitly, as when one individual acquires a skill by observing and imitating the behavior of others. Most information transmitted among humans is about local and transient circumstances, and is not transmitted beyond these. Some information of more general relevance, however, is repeatedly transmitted, and propagates throughout the group. Talk of “culture” (whatever the preferred definition or theory of culture) is about this widely distributed information and about its material realizations inside people’s mind and in their common environment (see Sperber 1996). One can study cultural phenomena in two main ways. One can interpret them, that is, try and make their contents intelligible to people of another culture, or more intelligible to members of the culture in which these phenomena occurs, as do anthropologists and historians. One may also try and explain causally how these cultural phenomena emerge, stabilize and evolve.. (shrink)

The processes of constructing meaning in digital database environments entail a paradigm shift from previous models of audio-visual communication. Media emerging from the Electro-mechanical era (film/TV/video) present fixed spatio-temporal linearity and material conditions which objectify and render passive viewer and process. The problematic aspects of cinematic communication were addressed by Latin American filmmakers of the “Third Cinema” movement. Their concerns and approach presaged and assisted an understanding of the radical redefinition of audio-visual communication possible with digital databases. The conceptual and (...) aesthetic aspirations of “Third Cinema” artists such as Julio Garcia Espinosa and Fernando Solanas were ultimately contradictory to linear media and find their fitting medium in digital modular construction. The materiality of database expression lacks an intrinsic temporal or spatial state and permits a more dynamic and multidirectional set of power relationships between author/s, piece, viewer/s. Other important referents for contextualising database art are modern art practitioners that rejected linear representational space and fractured the centrality of authorship. The author's own work, “...two, three, many Guevaras,” an exploratory database environment, embraces the redefinition of process as artistic expression, the empowerment of interacting generative forces, and serves to illustrate the revolutionary potential of the new media. (shrink)

Disabled‐2 (Dab2) is a multimodular scaffold protein with signaling roles in the domains of cell growth, trafficking, differentiation, and homeostasis. Emerging evidences place Dab2 as a novel modulator of cell–cell interaction; however, its mode of action has remained largely elusive. In this review, we highlight the relevance of Dab2 function in cell signaling and development and provide the most recent and comprehensive analysis of Dab2's action as a mediator of homotypical and heterotypical interactions. Accordingly, Dab‐2 controls the extent of platelet (...) aggregation through various motifs within its N‐terminus. Dab2 interacts with the cytosolic tail of the integrin receptor blocking inside‐out signaling, whereas extracellular Dab2 competes with fibrinogen for integrin αIIbβ3 receptor binding and, thus, modulates outside‐in signaling. An additional level of regulation results from Dab2's association with cell surface lipids, an event that defines the extent of cell–cell interactions. As a multifaceted regulator, Dab2 acts as a mediator of endocytosis through its association with the [FY]xNPx[YF] motifs of internalized cell surface receptors, phosphoinositides, and clathrin. Other emerging roles of Dab2 include its participation in developmental mechanisms required for tissue formation and in modulation of immune responses. This review highlights the various novel mechanisms by which Dab2 mediates an array of signaling events with vast physiological consequences. (shrink)

Embryonic development and ontogeny occupy whatis often depicted as the black box betweengenes – the genotype – and the features(structures, functions, behaviors) of organisms– the phenotype; the phenotype is not merelya one-to-one readout of the genotype. Thegenes home, context, and locus of operation isthe cell. Initially, in ontogeny, that cell isthe single-celled zygote. As developmentensues, multicellular assemblages of like cells(modules) progressively organized as germlayers, embryonic fields, anlage,condensations, or blastemata, enable genes toplay their roles in development and evolution.As modules, condensations are (...) fundamentaldevelopmental and selectable units ofmorphology (morphogenetic units) that mediateinteractions between genotype and phenotype viaevolutionary developmental mechanisms. In ahierarchy of emergent processes, gene networksand gene cascades (genetic modules) link thegenotype with morphogenetic units such ascondensations, while epigenetic processes suchas embryonic inductions, tissue interactionsand functional integration, link morphogeneticunits to the phenotype. To support theseconclusions I distinguish units of heredityfrom units of transmission and discussepigenetic inheritance by tracing the historyof relationship between embryology andevolution, especially the role(s) assigned tocells or to cellular components in generatingtheories of morphological change in evolution.The concept of cells as modular morphogeneticunits is modeled and illustrated using themammalian dentary bone. (shrink)

In the period running roughly from 1810 to 1860, French brain research remained split into two large provinces, each of which provided its own epistemological principles, methodological rules, and theoretical aims for the study of man’s mind. The controversies resulting from this split concerned issues as diverse as the intelligibility of mental processes, the unitary or the modular structure of cerebral activities, the relations holding between organic matter and mental function, the relevance and evidential weight of clinical and of experimental—i.e., (...) physiological—data for the explanation of the brain’s workings, and other similarly troublesome conceptual, ontological, and metaphysical riddles pertaining to something that had not yet been baptized ‘the mind-body problem’. (shrink)

The proteasome family of proteases comprises oligomeric assemblies of very different symmetry. In different sizes, it features ring‐like oligomers with dihedral symmetry that allow the stacking of further rings of regulatory subunits as observed in the modular proteasome system, but also less symmetric helical assemblies. Comprehensive sequence and structural analyses of proteasome homologs reveal a parsimonious scenario of how symmetry may have emerged from a monomeric ancestral precursor and how it may have evolved throughout the proteasome family. The four characterized (...) representatives—ancestral β subunit (Anbu), HslV, betaproteobacterial proteasome homolog (BPH), and the 20S proteasome—are outlasting cornerstones in the family's evolutionary history, each marking a transition in symmetry. This article contextualizes the evolutionary and functional key aspects of these symmetry transitions, explaining how they facilitated the diversification and concurrent evolution of independent proteolytic systems side by side, each with its customized network of auxiliary interactors. -/- . (shrink)

With the fast development of web 2.0, information generation and propagation among online users become deeply interweaved. How to effectively and immediately discover the new emerging topic and further how to uncover its evolution law are still wide open and urgently needed by both research and practical fields. This paper proposed a novel early emerging topic detection and its evolution law identification framework based on dynamic community detection method on time-evolving and scalable heterogeneous social networks. The framework is composed of (...) three major steps. Firstly, a time-evolving and scalable complex network denoted as KeyGraph is built up by deeply analyzing the text features of all kinds of data crawled from heterogeneous online social network platforms; secondly, a novel dynamic community detection method is proposed by which the new emerging topic is detected on the modeled time-evolving and scalable KeyGraph network; thirdly, a unified directional topic propagation network modeled by a great number of short texts including microblogs and news titles is set up, and the topic evolution law of the previously detected early emerging topic is identified by fully utilizing local network variations and modularity optimization of the “time-evolving” and directional topic propagation network. Our method is proved to yield preferable results on both a huge amount of computer-generated test data and a great amount of real online network data crawled from mainstream heterogeneous social networks. (shrink)

Achieving food system sustainability is one of the more pressing challenges of this century. Over the last decades, experts from diverse disciplines and intellectual traditions have worked to document the critical threats to food system sustainability and to define an appropriate agenda for action. Nevertheless, these efforts have tended to focus selectively on only a few components of the food system or have tended to be framed in particular discourses. Depending on the point of departure, what aspects of the food (...) system are considered threatened, and what must be sustained, can differ greatly between perspectives. In this article, we draw from systems-thinking and social-ecological systems concepts to focus on the underlying process-related attributes that could support a more sustainable food system. We then examine the support for specific system attributes in six different knowledge domains addressing sustainable agriculture and food. From this review, we identify five system attributes—diversity, modularity, transparency, innovation and congruence—that are repeatedly featured in the different knowledge domains as critical aspects of food system sustainability. We argue that in the face of considerable complexity and high uncertainty, these attributes can serve as a guide to conceptualizing food system choices adaptively and iteratively. (shrink)

Achieving food system sustainability is one of the more pressing challenges of this century. Over the last decades, experts from diverse disciplines and intellectual traditions have worked to document the critical threats to food system sustainability and to define an appropriate agenda for action. Nevertheless, these efforts have tended to focus selectively on only a few components of the food system or have tended to be framed in particular discourses. Depending on the point of departure, what aspects of the food (...) system are considered threatened, and what must be sustained, can differ greatly between perspectives. In this article, we draw from systems-thinking and social-ecological systems concepts to focus on the underlying process-related attributes that could support a more sustainable food system. We then examine the support for specific system attributes in six different knowledge domains addressing sustainable agriculture and food. From this review, we identify five system attributes—diversity, modularity, transparency, innovation and congruence—that are repeatedly featured in the different knowledge domains as critical aspects of food system sustainability. We argue that in the face of considerable complexity and high uncertainty, these attributes can serve as a guide to conceptualizing food system choices adaptively and iteratively. (shrink)

Given that the world as we perceive it appears to be predominantly classical, how can we stabilize quantum effects? Given the fundamental description of our world is quantum mechanical, how do classical phenomena emerge? Answers can be found from the analysis of the scaling properties of modular quantum systems with respect to a given level of description. It is argued that, depending on design, such partitioned quantum systems may support various functions. Despite their local appearance these functions are emergent (...) properties of the system as a whole. With respect to the separation of subject and object such functions of interest are control, simulation, and observation. They are interpreted in close analogy with more basic physical behavior. (shrink)

An emerging class of theories concerning the functional structure of the brain takes the reuse of neural circuitry for various cognitive purposes to be a central organizational principle. According to these theories, it is quite common for neural circuits established for one purpose to be exapted (exploited, recycled, redeployed) during evolution or normal development, and be put to different uses, often without losing their original functions. Neural reuse theories thus differ from the usual understanding of the role of neural plasticity (...) (which is, after all, a kind of reuse) in brain organization along the following lines: According to neural reuse, circuits can continue to acquire new uses after an initial or original function is established; the acquisition of new uses need not involve unusual circumstances such as injury or loss of established function; and the acquisition of a new use need not involve (much) local change to circuit structure (e.g., it might involve only the establishment of functional connections to new neural partners). Thus, neural reuse theories offer a distinct perspective on several topics of general interest, such as: the evolution and development of the brain, including (for instance) the evolutionary-developmental pathway supporting primate tool use and human language; the degree of modularity in brain organization; the degree of localization of cognitive function; and the cortical parcellation problem and the prospects (and proper methods to employ) for function to structure mapping. The idea also has some practical implications in the areas of rehabilitative medicine and machine interface design. (shrink)

Synthetic biology emerged around 2000 as a new biological discipline. It shares with systems biology the same modular vision of organisms, but is more concerned with applications than with a better understanding of the functioning of organisms. A herald of this new discipline is Craig Venter who aims to create an artificial microorganism with the minimal genome compatible with life and to implement into it different 'functional modules' to generate new micro-organisms adapted to specific tasks. Synthetic biology is based on (...) the possibilities raised by genetic engineering, but it aims to engineer organisms, and not simply to modify them, mimicking the practice of computer engineers. Three points will be discussed: In what regard does synthetic biology represent a new epistemology of the life sciences? What are the relations between synthetic biology and evolutionary biology? What is the raison d'être of synthetic biology as a discipline independent of nanotechnologies? (shrink)

An influential view of the nature of the language system is that of an evolved biological system in which a set of rules is combined with a lexicon that contains the words of the language together with a representation of their context. Alternative views, usually based on connectionist modeling, attempt to explain the structure of language on the basis of complex associative processes. Here, I put forward a third view that stresses experience-dependent structural development of the brain circuits supporting language (...) as a core principle of the organization of the language system. In this view, embodied in a recent neuroconstructivist neural network of past tense development and processing, initial domain-general predispositions enable the development of functionally specialized brain structures through interactions between experience-dependent brain development and statistical learning in a structured environment. Together, these processes shape a biological adult language system that appears to separate into distinct mechanism for processing rules and exceptions, whereas in reality those subsystems co-develop and interact closely. This view puts experience-dependent brain development in response to a specific language environment at the heart of understanding not only language development but adult language processing as well. (shrink)

The concept of scaffolding has wide resonance in several scientific fields. Here we attempt to adopt it for the study of development. In this perspective, the embryo is conceived as an integral whole, comprised of several hierarchical modules as in a recurrent circularity of emerging patterns. Within the developmental hierarchy, each module yields an inter-level relationship that makes it possible for the scaffolding to mediate the production of selectable variations. A wide range of genetic, cellular and morphological mechanisms allows the (...) scaffolding to integrate these modular variations into a functionally coordinate unit. A genetic scaffolding accounts for the inherited invariance of pattern formation during the embryo’s growth. At higher level, cells behave as agents endowed with the capacity to interpret any scaffolding variation as signs. The full hierarchy of a multi-level scaffolding is eventually attained when the embryo acquires the capacity to impose a number of developmental constraints on its constituting parts in a top-down direction. The acquisition of this capacity allows a semiotic threshold to emerge between the living cellular world and the underlying non-living molecular world. As this boundary is gradually defined during development, cells enter into new functional relationships, while, at the same time, are relieved from their physical determinism. The resulting constraints can thus become the driving forces that upgrade embryonic scaffolding from the simple molecular signalling to the complexity of sign recognition proper of a cellular community. In this semiotic perspective, the apparent goal directness of any developmental strategy should no longer be accounted for by a predetermined genetic program, but by the gradual definition of the relationships selected amongst the ones historically explored. (shrink)

The emerging discipline of evolutionary developmental biology has opened up many new lines of investigation into morphological evolution. Here I explore how two of the core theoretical concepts in ‘evo-devo’ – modularity and homology – apply to evolutionary psychology. I distinguish three sorts of module – developmental, functional and mental modules and argue that mental modules need only be ‘virtual’ functional modules. Evolutionary psychologists have argued that separate mental modules are solutions to separate evolutionary problems. I argue that the (...) structure of developmental modules in an organism helps determine what counts as a separate evolutionary problem for that organism. I suggest that homology as an organizing principle for research in evolutionary psychology, has been severely neglected in favor of analogy (adaptive function). I consider some arguments suggesting that determining homology is less epistemically demanding than determining adaptive function and argue that psychological categories defined by homology are, in fact, more suitable objects of psychological – and particularly neuropsychological – investigation than categories defined by analogy. (shrink)

We are sometimes led to a different picture of things when something unexpected occurs which needs explaining. The aim of this thesis is to examine a series of related issues in the philosophy of mind in the light of the unusual condition known to psychologists as ‘synaesthesia’. Although the emphasis will be on the philosophical issues a view of synaesthesia itself will also emerge. Synaesthesia is a distinct type of cross-modal association: stimulation of one sensory modality automatically triggers an additional (...) phenomenal character of experience associated with a second sensory modality in the absence of any direct stimulation of the second modality. Chapter 1 introduces synaesthesia to a philosophical audience by outlining the early history of synaesthesia studies, by summarising contemporary research and by indicating areas of philosophical interest to be considered in the rest of the thesis. Chapter 2 uses synaesthesia to examine one important philosophical model of the mind, Fodor’s modularity hypothesis, and, in turn, investigates the nature of synaesthesia in the light of that model. Fodor claims that cognitive modules can be thought of as belonging to a psychological natural kind in virtue of their possession of most or all of nine specified properties. The most common form of synaesthesia possesses Fodor’s nine specified properties of modularity, and hence it should be understood in terms of an extra cognitive module, and thus as belonging to the abovementioned psychological natural kind. Many psychologists believe that synaesthesia involves a breakdown in modularity. A breakdown in modularity would also explain the apparent presence of the nine specified properties in synaesthesia. I discuss the two concepts of function which underlie the respective theories, defending the breakdown thesis, arguing, in any case, that properties deriving from evolutionary history should also be used to decide between the two theses and thus ultimately membership of a psychological natural kind such as Fodor suggests. The argument is then used to respond to two challenges to the notion of a psychological natural kind. Chapter 3 focuses on the phenomenal character of synaesthetic experience. Externalists about the phenomenal character of experience tend to argue that the character of perceptual experience is to be explained either by the properties objects present to percipients, or by the properties objects are represented by percipients as having. Some internalists argue that there is a need to postulate hrther properties of the individual - in other words, qualia - to account for the individuation of the character of perceptual experience. The existence of additional phenomenal characters of experience in synaesthesia, which cannot directly be explained by reference to features of objects, suggests the existence of extra qualia and thus the presence of qualia in normal perception. The aim of this chapter is to meet the challenge presented by synaesthesia and the extra quaZia argument, and contrariwise, use synaesthesia as a way of fbrther clarifjmg the merits of the respective externalist positions. In the previous chapters the locution of ‘coloured hearing’ will have been adopted. Occasionally the process underlying synaesthesia is described as one of ‘hearing colours’. Chapter 4 rejects the latter usage. In so doing it focuses on the place of synaesthesia vis-a-vis normal perceptual processes. Considerations from previous chapters are further developed in order to shed light both on the metaphysical individuation of perceptual modalities and on how we know the distinctive perceptual modalities. Given the actual content of our concepts of perceptual modalities, it is argued that the actual world is one in which even synaesthetes are unable to hear colours. Consideration is given as to whether there is a possible world in which people could hear colours. The justification of the usage of ‘coloured-hearing’ then leads to a discussion of the relative importance of the individuating conditions of modes of perception. The thesis focuses largely on coloured hearing. What merits the preceding considerations have might be supported if they can be generalised. Chapter 5 goes a small way in that direction. (shrink)

Descartes argued that productivity, namely our ability to generate an unlimited number of new thoughts or ideas from previous ones, derives from a single undividable source in the human soul. Cognitive scientists, in contrast, have viewed productivity as a modular phenomenon. According to this latter view, syntactic, semantic, musical or visual productivity emerges each from their own generative engines in the human brain. Recent evidence has, however, led some authors to revitalize the Cartesian theory. According to this view, a single (...) source or a single mechanism in the human brain produces productivity in every cognitive domain, whether in the domain of music, semantics or syntax. In this article, we will address recent evidence concerning the single source hypothesis from brain-imaging studies, linguistics, cognitive theories of music perception, biology of cognition and cognitive development, along with several objections that have been presented against this hypothesis. We formulate two versions of the Cartesian theory which combine the more recent computational theory of cognition with Descartes' view on productivity. (shrink)

Evolutionary psychology tends to be associated with a massively modular cognitive architecture. On this framework of human cognition, an assembly of specialized information processors called modules developed under selection pressures encountered throughout the phylogenic history of hominids. The coordinated activity of domain-specific modules carries out all the processes of belief fixation, abstract reasoning, and other facets of central cognition. Against the massive modularity thesis, I defend an account of systemic functional adaptedness, according to which non-modular systems emerged because of (...) adaptive problems imposed by the intrinsic physiology of the evolving human brain. The proposed reformulation of evolutionary theorizing draws from neural network models and Cummins’ (1975) account of systemic functions to identify selection pressures that gave rise to non-modular, domain-general mechanisms in cognitive architecture. (shrink)

Construction of the eukaryotic ribosome is a complex process in which a nascent ribosomal RNA (rRNA) emerging from RNA Polymerase I hierarchically folds into a native three‐dimensional structure. Modular assembly of individual RNA domains through interactions with ribosomal proteins and a myriad of assembly factors permit efficient disentanglement of the error‐prone RNA folding process. Following these dynamic events, long‐range tertiary interactions are orchestrated to compact rRNA. A combination of genetic, biochemical, and structural studies is now providing clues into how a (...) nascent rRNA is transformed into a functional ribosome with high precision. With this essay, we aim to draw attention to the poorly understood process of establishing correct RNA tertiary contacts during ribosome formation. (shrink)

This paper explores the issue of performative spaces in the medieval Latin Church, examining the mindsets of the time and the ways practitioners adopted the Platonic notion of world harmony. We then look at the Palatine Chapel of Aachen in the light of the Plato’s doctrine. At the heart of this analysis will be the cosmological drama at the creation of the world, described by Ambrose as a chorus of the constitutive elements. It is from this image that the proto-model (...) of the Christian Church as ‘moving waters’ was derived, a vision shared by both the Eastern and the Western world. To this day, the Palatine chapel of Aquisgranum conveys the appearance of the Ambrosian vision of the primordial waters, with its renewed marble revetments imitating the cosmic waters. The church is designed according to propria dispositione, i. e. modularity. Augustine’s concept of modularity and his psychology of sound, space, movement, and time will be explored in the hypothetical inquiry into the dramatization of space at Aachen. Here, we find that the Chapel has two choreographies which unfold in the space like-stage set up as a synthesis of the arts shaped according to numbers. Relevant concepts to our topic will emerge in the analysis, such as concord, consonance and agreement, measure and movement – metaphors of the idea of a ‘dance’ that exceeds the character of a mere performance. (shrink)

A theme that emerged at the Sheffield Conference with particular force, to my way of thinking, was a new way of recognizing, and then avoiding, a seductive bad idea. One of its many guises is what I have called the Cartesian Theater, but it also appears in the roles of Central Processing, or Central Executive, or Norman and Shallice's SAS, or Fodor's non-modular central arena of belief fixation. What is wrong with this idea is not (just) that it (apparently) postulates (...) an _anatomically_ discernible central region of the brain--maximally non-peripheral, one might say--but that it supposes that there is a functionally identifiable _subsystem_ (however located or even distributed in the brain) that has some all too remarkable competences achieved by some all too remarkable means. There are many routes to it. Here is one that starts off in an excellent direction but then veers off. The mistaken fork is not explicitly endorsed by anybody that I can think of, but I daresay it has covertly influenced a lot of thinking on the topic. (shrink)

Synthetic biology, an emerging field of science and technology, intends to make of the natural world a substrate for engineering practice. Drawing inspiration from conventional engineering disciplines, practitioners of synthetic biology hope to make biological systems standardized, calculable, modular, and predictably functional. This essay develops a Heideggerian reading of synthetic biology as a useful perspective with which to identify and explore key facets of this field, its knowledge, its practices, and its products. After overviews of synthetic biology and Heidegger’s account (...) of technology, I discuss calculability, utility, function, setting-upon, and ordering, with the aim of discussing the manner in which synthetic biology works to render the biological world intelligible as something to be used, rather than something that is in and of itself. Having developed this Heideggerian reading, I proffer a number of corrections to his account that enable a more accurate, nuanced understanding of synthetic biology. Specifically, I discuss the notion of Ge-stell and submit that multiple systems of “enframing” may help to make Heidegger’s argument more robust. I suggest that synthetic biology may work to reveal the natural world as a standing-reserve of function. (shrink)

In this important book, Susan Hurley sheds new light on consciousness by examining its relationships to action from various angles. She assesses the role of agency in the unity of a conscious perspective, and argues that perception and action are more deeply interdependent than we usually assume. A standard view conceives perception as input from world to mind and action as output from mind to world, with the serious business of thought in between. Hurley criticizes this picture, and considers how (...) the interdependence of perceptual experience and agency at the personal level (of mental contents and norms) may emerge from the subpersonal level (of underlying causal processes and complex dynamic feedback systems). Her two-level view has wide implications, for topics that include self-consciousness, the modularity of mind, and the relations of mind to world. The self no longer lurks hidden somewhere between perceptual input and behavioral output, but reappears out in the open, embodied and embedded in its environment. Hurley traces these themes from Kantian and Wittgensteinian arguments through to intriguing recent work in neuropsychology and in dynamic systems approaches to the mind, providing a bridge from mainstream philosophy to work in other disciplines. Consciousness in Action is unique in the range of philosophical and scientific work it draws on, and in the deep criticism it offers of centuries-old habits of thought. (shrink)

This bold and brilliant book asks the ultimate question of the life sciences: How did the human mind acquire its incomparable power? In seeking the answer, Merlin Donald traces the evolution of human culture and cognition from primitive apes to the era of artificial intelligence, and presents an original theory of how the human mind evolved from its presymbolic form. In the emergence of modern human culture, Donald proposes, there were three radical transitions. During the first, our bipedal but still (...) apelike ancestors acquired "mimetic" skill—the ability to represent knowledge through voluntary motor acts—which made Homo erectus successful for over a million years. The second transition—to "mythic" culture —coincided with the development of spoken language. Speech allowed the large-brained Homo sapiens to evolve a complex preliterate culture that survives in many parts of the world today. In the third transition, when humans constructed elaborate symbolic systems ranging from cuneiforms, hieroglyphics, and ideograms to alphabetic languages and mathematics, human biological memory became an inadequate vehicle for storing and processing our collective knowledge. The modern mind is thus a hybrid structure built from vestiges of earlier biological stages as well as new external symbolic memory devices that have radically altered its organization. According to Donald, we are symbol-using creatures, more complex than any that went before us, and we may have not yet witnessed the final modular arrangement of the human mind. (shrink)

Predictive processing approaches to the mind are increasingly popular in the cognitive sciences. This surge of interest is accompanied by a proliferation of philosophical arguments, which seek to either extend or oppose various aspects of the emerging framework. In particular, the question of how to position predictive processing with respect to enactive and embodied cognition has become a topic of intense debate. While these arguments are certainly of valuable scientific and philosophical merit, they risk underestimating the variety of approaches gathered (...) under the predictive label. Here, we first present a basic review of neuroscientific, cognitive, and philosophical approaches to PP, to illustrate how these range from solidly cognitivist applications—with a firm commitment to modular, internalistic mental representation—to more moderate views emphasizing the importance of ‘body-representations’, and finally to those which fit comfortably with radically enactive, embodied, and dynamic theories of mind. Any nascent predictive processing theory must take into account this continuum of views, and associated theoretical commitments. As a final point, we illustrate how the Free Energy Principle attempts to dissolve tension between internalist and externalist accounts of cognition, by providing a formal synthetic account of how internal ‘representations’ arise from autopoietic self-organization. The FEP thus furnishes empirically productive process theories by which to guide discovery through the formal modelling of the embodied mind. (shrink)

The principle of self-organization has acquired a fundamental significance in the newly emerging field of computational philosophy. Self-organizing systems have been described in various domains in science and philosophy including physics, neuroscience, biology and medicine, ecology, and sociology. While system architecture and their general purpose may depend on domain-specific concepts and definitions, there are (at least) seven key properties of self-organization clearly identified in brain systems: 1) modular connectivity, 2) unsupervised learning, 3) adaptive ability, 4) functional resiliency, 5) functional plasticity, (...) 6) from-local-to-global functional organization, and 7) dynamic system growth. These are defined here in the light of insight from neurobiology, cognitive neuroscience and Adaptive Resonance Theory (ART), and physics to show that self-organization achieves stability and functional plasticity while minimizing structural system complexity. A specific example informed by empirical research is discussed to illustrate how modularity, adaptive learning, and dynamic network growth enable stable yet plastic somatosensory representation for human grip force control. Implications for the design of “strong” artificial intelligence in robotics are brought forward. (shrink)

In a now classic paper published in 1991, Alberch introduced the concept of genotype–phenotype (G!P) mapping to provide a framework for a more sophisticated discussion of the integration between genetics and developmental biology that was then available. The advent of evo-devo first and of the genomic era later would seem to have superseded talk of transitions in phenotypic space and the like, central to Alberch’s approach. On the contrary, this paper shows that recent empirical and theoretical advances have only sharpened (...) the need for a different conceptual treat- ment of how phenotypes are produced. Old-fashioned metaphors like genetic blueprint and genetic programme are not only woefully inadequate but positively misleading about the nature of G!P, and are being replaced by an algorithmic approach emerging from the study of a variety of actual G!P maps. These include RNA folding, protein function and the study of evolvable soft- ware. Some generalities are emerging from these disparate fields of analysis, and I suggest that the concept of ‘developmental encoding’ (as opposed to the classical one of genetic encoding) provides a promising computational–theoretical underpinning to coherently integrate ideas on evolvability, modularity and robustness and foster a fruitful framing of the G!P mapping problem. (shrink)

Evolutionary developmental biology (evo-devo) is considered a ‘mechanistic science,’ in that it causally explains morphological evolution in terms of changes in developmental mechanisms. Evo-devo is also an interdisciplinary and integrative approach, as its explanations use contributions from many fields and pertain to different levels of organismal organization. Philosophical accounts of mechanistic explanation are currently highly prominent, and have been particularly able to capture the integrative nature of multifield and multilevel explanations. However, I argue that evo-devo demonstrates the need for a (...) broadened philosophical conception of mechanisms and mechanistic explanation. Mechanistic explanation (in terms of the qualitative interactions of the structural parts of a whole) has been developed as an alternative to the traditional idea of explanation as derivation from laws or quantitative principles. Against the picture promoted by Carl Craver, that mathematical models describe but usually do not explain, my discussion of cases from the strand of evo-devo which is concerned with developmental processes points to qualitative phenomena where quantitative mathematical models are an indispensable part of the explanation. While philosophical accounts have focused on the actual organization and operation of mechanisms, properties of developmental mechanisms that are about how a mechanism reacts to modifications are of major evolutionary significance, including robustness, phenotypic plasticity, and modularity. A philosophical conception of mechanisms is needed that takes into account quantitative changes, transient entities and the generation of novel types of entities, feedback loops and complex interaction networks, emergent properties, and, in particular, functional-dynamical aspects of mechanisms, including functional (as opposed to structural) organization and distributed, system-wide phenomena. I conclude with general remarks on philosophical accounts of explanation. (shrink)

This article presents six ideas about the construction of emotion: (a) Emotions are more readily distinguished by the situations they signify than by patterns of bodily responses; (b) emotions emerge from, rather than cause, emotional thoughts, feelings, and expressions; (c) the impact of emotions is constrained by the nature of the situations they represent; (d) in the OCC account (the model proposed by Ortony, Clore, and Collins in 1988), appraisals are psychological aspects of situations that distinguish one emotion from another, (...) rather than triggers that elicit emotions; (e) analyses of the affective lexicon indicate that emotion words refer to internal mental states focused on affect; (f) the modularity of emotion, long sought in biology and behavior, exists as mental schemas for interpreting human experience in story, song, drama, and conversation. (shrink)

One sceptical rejoinder to those who claim that sensory perception is cognitively penetrable is to appeal to the involvement of attention. So, while a phenomenon might initially look like one where, say, a perceiver’s beliefs are influencing her visual experience, another interpretation is that because the perceiver believes and desires as she does, she consequently shifts her spatial attention so as to change what she senses visually. But, the sceptic will urge, this is an entirely familiar phenomenon, and it hardly (...) involves some special or theoretically important cognitive effect on sensory perception. Even supposing that the sceptic is correct about cases that are accurately described in this way, the rejoinder oversimplifies the possible roles that attention may play in mediating cognition and perception. This paper aims to identify these different roles, and by emphasis on empirical research on feature-based and object-based attention. What emerges is a plausible and well- evidenced mental schema that describes attention -mediated cognitive penetration. At the very least, the burden of proof is shifted to the sceptic, as he then must show that there are no mental phenomena involving attention in the more nuanced ways described here. One additional benefit of this analysis is that it illuminates various features of attention and its relation to both cognition and phenomenal consciousness. Therefore the analysis should be of interest to a broad range of theorists of the mind, and not just those invested in the cognitive penetration debate. (shrink)